@article {pmid36167684,
year = {2022},
author = {Seong, HJ and Roux, S and Hwang, CY and Sul, WJ},
title = {Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {157},
pmid = {36167684},
issn = {2049-2618},
support = {NRF-2014R1A1A2A16055779//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.

RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.

CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.},
}

@article {pmid36166154,
year = {2022},
author = {Duarte, IO and Hissa, DC and Quintela, BCSF and Rabelo, MC and Oliveira, FADS and Lima, NCB and Melo, VMM},
title = {Genomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {36166154},
issn = {1559-0291},
support = {312462/2017-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.},
}

@article {pmid36166070,
year = {2022},
author = {Alcantara, DMC and Ikeda, P and Souza, CS and de Mello, VVC and Torres, JM and Lourenço, EC and Bassini-Silva, R and Herrera, HM and Machado, RZ and Barros-Battesti, DM and Graciolli, G and André, MR},
title = {Multilayer Networks Assisting to Untangle Direct and Indirect Pathogen Transmission in Bats.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36166070},
issn = {1432-184X},
support = {2018/02753-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/14124-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 59/300.187/2016//Fundação de Apoio ao Desenvolvimento do Ensino, Ciência e Tecnologia do Estado de Mato Grosso do Sul/ ; 302420/2017-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303802/2021-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 308768/2017-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; E-26/202.158/2015//Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; RED-00253-16//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
abstract = {The importance of species that connect the different types of interactions is becoming increasingly recognized, and this role may be related to specific attributes of these species. Multilayer networks have two or more layers, which represent different types of interactions, for example, between different parasites and hosts that are nonetheless connected. The understanding of the ecological relationship between bats, ectoparasites, and vector-borne bacteria could shed some light on the complex transmission cycles of these pathogens. In this study, we investigated a multilayer network in Brazil formed by interactions between bat-bacteria, bat-ectoparasite, and ectoparasite-bacteria, and asked how these interactions overlap considering different groups and transmission modes. The multilayer network was composed of 31 nodes (12 bat species, 14 ectoparasite species, and five bacteria genera) and 334 links, distributed over three layers. The multilayer network has low modularity and shows a core-periphery organization, that is, composed of a few generalist species with many interactions and many specialist species participating in few interactions in the multilayer network. The three layers were needed to accurately describe the multilayer structure, while aggregation leads to loss of information. Our findings also demonstrated that the multilayer network is influenced by a specific set of species that can easily be connected to the behavior, life cycle, and type of existing interactions of these species. Four bat species (Artibeus lituratus, A. planirostris, Phyllostomus discolor, and Platyrrhinus lineatus), one ectoparasite species (Steatonyssus) and three bacteria genera (Ehrlichia, hemotropic Mycoplasma and Neorickettsia) are the most important species for the multilayer network structure. Finally, our study brings an ecological perspective under a multilayer network approach on the interactions between bats, ectoparasites, and pathogens. By using a multilayer approach (different types of interactions), it was possible to better understand these different ecological interactions and how they affect each other, advancing our knowledge on the role of bats and ectoparasites as potential pathogen vectors and reservoirs, as well as the modes of transmission of these pathogens.},
}

@article {pmid36164984,
year = {2022},
author = {Li, HB and Xu, ML and Xu, XD and Tang, YY and Jiang, HL and Li, L and Xia, WJ and Cui, N and Bai, J and Dai, ZM and Han, B and Li, Y and Peng, B and Dong, YY and Aryal, S and Manandhar, I and Eladawi, MA and Shukla, R and Kang, YM and Joe, B and Yang, T},
title = {Faecalibacterium Prausnitzii Attenuates CKD via Butyrate-Renal GPR43 Axis.},
journal = {Circulation research},
volume = {},
number = {},
pages = {101161CIRCRESAHA122320184},
doi = {10.1161/CIRCRESAHA.122.320184},
pmid = {36164984},
issn = {1524-4571},
abstract = {BACKGROUND: Despite available clinical management strategies, chronic kidney disease (CKD) is associated with severe morbidity and mortality worldwide, which beckons new solutions. Host-microbial interactions with a depletion of Faecalibacterium prausnitzii in CKD are reported. However, the mechanisms about if and how F prausnitzii can be used as a probiotic to treat CKD remains unknown.

METHODS: We evaluated the microbial compositions in 2 independent CKD populations for any potential probiotic. Next, we investigated if supplementation of such probiotic in a mouse CKD model can restore gut-renal homeostasis as monitored by its effects on suppression on renal inflammation, improvement in gut permeability and renal function. Last, we investigated the molecular mechanisms underlying the probiotic-induced beneficial outcomes.

RESULTS: We observed significant depletion of Faecalibacterium in the patients with CKD in both Western (n=283) and Eastern populations (n=75). Supplementation of F prausnitzii to CKD mice reduced renal dysfunction, renal inflammation, and lowered the serum levels of various uremic toxins. These are coupled with improved gut microbial ecology and intestinal integrity. Moreover, we demonstrated that the beneficial effects in kidney induced by F prausnitzii-derived butyrate were through the GPR (G protein-coupled receptor)-43.

CONCLUSIONS: Using a mouse CKD model, we uncovered a novel beneficial role of F prausnitzii in the restoration of renal function in CKD, which is, at least in part, attributed to the butyrate-mediated GPR-43 signaling in the kidney. Our study provides the necessary foundation to harness the therapeutic potential of F prausnitzii for ameliorating CKD.},
}

@article {pmid36163700,
year = {2022},
author = {Orsi, WD},
title = {Quantitative microbial ecology: Future challenges and opportunities.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16204},
pmid = {36163700},
issn = {1462-2920},
support = {OR 417/7-1//Deutsche Forschungsgemeinschaft/ ; },
}

@article {pmid36160374,
year = {2020},
author = {Wang, X and Aulenta, F and Puig, S and Esteve-Núñez, A and He, Y and Mu, Y and Rabaey, K},
title = {Microbial electrochemistry for bioremediation.},
journal = {Environmental science and ecotechnology},
volume = {1},
number = {},
pages = {100013},
pmid = {36160374},
issn = {2666-4984},
abstract = {Lack of suitable electron donors or acceptors is in many cases the key reason for pollutants to persist in the environment. Externally supplementation of electron donors or acceptors is often difficult to control and/or involves chemical additions with limited lifespan, residue formation or other adverse side effects. Microbial electrochemistry has evolved very fast in the past years - this field relates to the study of electrochemical interactions between microorganisms and solid-state electron donors or acceptors. Current can be supplied in such so-called bioelectrochemical systems (BESs) at low voltage to provide or extract electrons in a very precise manner. A plethora of metabolisms can be linked to electrical current now, from metals reductions to denitrification and dechlorination. In this perspective, we provide an overview of the emerging applications of BES and derived technologies towards the bioremediation field and outline how this approach can be game changing.},
}

@article {pmid36159604,
year = {2020},
author = {Uria, N and Fiset, E and Pellitero, MA and Muñoz, FX and Rabaey, K and Campo, FJD},
title = {Immobilisation of electrochemically active bacteria on screen-printed electrodes for rapid in situ toxicity biosensing.},
journal = {Environmental science and ecotechnology},
volume = {3},
number = {},
pages = {100053},
pmid = {36159604},
issn = {2666-4984},
abstract = {Microbial biosensors can be an excellent alternative to classical methods for toxicity monitoring, which are time-consuming and not sensitive enough. However, bacteria typically connect to electrodes through biofilm formation, leading to problems due to lack of uniformity or long device production times. A suitable immobilisation technique can overcome these challenges. Still, they may respond more slowly than biofilm-based electrodes because bacteria gradually adapt to electron transfer during biofilm formation. In this study, we propose a controlled and reproducible way to fabricate bacteria-modified electrodes. The method consists of an immobilisation step using a cellulose matrix, followed by an electrode polarization in the presence of ferricyanide and glucose. Our process is short, reproducible and led us to obtain ready-to-use electrodes featuring a high-current response. An excellent shelf-life of the immobilised electrochemically active bacteria was demonstrated for up to one year. After an initial 50% activity loss in the first month, no further declines have been observed over the following 11 months. We implemented our bacteria-modified electrodes to fabricate a lateral flow platform for toxicity monitoring using formaldehyde (3%). Its addition led to a 59% current decrease approximately 20 min after the toxic input. The methods presented here offer the ability to develop a high sensitivity, easy to produce, and long shelf life bacteria-based toxicity detectors.},
}

@article {pmid36159602,
year = {2020},
author = {De Vrieze, J},
title = {The next frontier of the anaerobic digestion microbiome: From ecology to process control.},
journal = {Environmental science and ecotechnology},
volume = {3},
number = {},
pages = {100032},
pmid = {36159602},
issn = {2666-4984},
abstract = {The anaerobic digestion process has been one of the key processes for renewable energy recovery from organic waste streams for over a century. The anaerobic digestion microbiome is, through the continuous development of novel techniques, evolving from a black box to a well-defined consortium, but we are not there yet. In this perspective, I provide my view on the current status and challenges of the anaerobic digestion microbiome, as well as the opportunities and solutions to exploit it. I consider identification and fingerprinting of the anaerobic digestion microbiome as complementary tools to monitor the anaerobic digestion microbiome. However, data availability, method-inherent biases and correct taxa identification hamper the accuracy and reproducibility of anaerobic digestion microbiome characterization. Standardisation of microbiome research in anaerobic digestion and other engineered systems will be essential in the coming decades, for which I proposed some targeted solutions. These will bring anaerobic digestion from a single-purpose energy-recovery technology to a versatile process for integrated resource recovery. It is my opinion that the exploitation of the microbiome will be a driver of innovation, and that it has a key role to play in the bio-based economy of the decades to come.},
}

@article {pmid36157708,
year = {2020},
author = {Wang, M and Cernava, T},
title = {Overhauling the assessment of agrochemical-driven interferences with microbial communities for improved global ecosystem integrity.},
journal = {Environmental science and ecotechnology},
volume = {4},
number = {},
pages = {100061},
pmid = {36157708},
issn = {2666-4984},
abstract = {Recent studies have shown that various agrochemicals can substantially affect microbial communities; especially those that are associated with cultivated plants. Under certain circumstances, up to 50% of the naturally occurring microorganisms can be negatively affected by common agricultural practices such as seed coating with fungicide-based matrices. Nevertheless, the off-target effects of commonly applied agrochemicals are still understudied in terms of their interferences with microbial communities. At the same time, agrochemical inputs are steadily increasing due to the intensification of agriculture and the increasing pathogen pressure that is currently observed worldwide. In this article, we briefly reflect on the current knowledge related to pesticide interference with microbial communities and discuss negative implications for the plant holobiont as well as such that are spanning beyond local system borders. Cumulative effects of pesticide inputs that cause alterations in microbial functioning likely have unforeseen implications on geochemical cycles that should be addressed with a high priority in ongoing research. A holistic assessment of such implications will allow us to objectively select the most suitable means for food production under the scenario of a growing global population and aggravating climatic conditions. We present three hypothetical solutions that might facilitate a more sustainable and less damaging application of pesticides in the future.},
}

@article {pmid36153325,
year = {2022},
author = {Zhu, H and Xu, L and Luan, G and Zhan, T and Kang, Z and Li, C and Lu, X and Zhang, X and Zhu, Z and Zhang, Y and Li, Y},
title = {A miniaturized bionic ocean-battery mimicking the structure of marine microbial ecosystems.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5608},
pmid = {36153325},
issn = {2041-1723},
support = {BX20220333//China Postdoctoral Science Foundation/ ; 2022M710161//China Postdoctoral Science Foundation/ ; 22072180//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Bioelectric Energy Sources ; Bionics ; Hydrogels ; *Microbiota ; Oceans and Seas ; },
abstract = {Marine microbial ecosystems can be viewed as a huge ocean-battery charged by solar energy. It provides a model for fabricating bio-solar cell, a bioelectrochemical system that converts light into electricity. Here, we fabricate a bio-solar cell consisting of a four-species microbial community by mimicking the ecological structure of marine microbial ecosystems. We demonstrate such ecological structure consisting of primary producer, primary degrader, and ultimate consumers is essential for achieving high power density and stability. Furthermore, the four-species microbial community is assembled into a spatial-temporally compacted cell using conductive hydrogel as a sediment-like anaerobic matrix, forming a miniaturized bionic ocean-battery. This battery directly converts light into electricity with a maximum power of 380 μW and stably operates for over one month. Reproducing the photoelectric conversion function of marine microbial ecosystems in this bionic battery overcomes the sluggish and network-like electron transfer, showing the biotechnological potential of synthetic microbial ecology.},
}

*Bioelectric Energy Sources
Bionics
Hydrogels
*Microbiota
Oceans and Seas

@article {pmid36161873,
year = {2022},
author = {Orner, KD and Deleu, E and Rabaey, K and Nelson, KL},
title = {Accelerating Urea Hydrolysis in Fresh Urine by Modifying Operating Conditions of a Sequencing Batch Reactor.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-33},
doi = {10.1080/09593330.2022.2129456},
pmid = {36161873},
issn = {1479-487X},
abstract = {AbstractA number of existing and emerging technologies can recover nitrogen from urine. A preliminary step in many nitrogen recovery processes is hydrolyzing urea to ammonium, a biologically-mediated process that can take days to weeks without intervention. The ability to achieve urea hydrolysis quickly and reliably would increase the feasibility of decentralized nitrogen recovery, especially where space and treatment time are constrained. The goal of this research was to determine whether urea hydrolysis could be accelerated by providing an inoculum containing microorganisms likely to have urease activity (feces or soil), providing a carrier to support attached growth (plastic carriers, granular activated carbon, or no carrier), and modifying the hydraulic retention time (HRT; 1.3, 2, and 4 days) and feeding frequency (Δt = 4 h, 24 h). Inoculated reactors achieved significantly more urea hydrolysis, and reactors inoculated with soil were able to sustain higher urea hydrolysis rates over time than those inoculated with feces. The mean zero-order rate constants (mM/hr) for reactors with a soil inoculum (15.1) were about three times higher than that of reactors with an inoculum of feces (4.9). A reactor with GAC and an inoculum of soil fed daily with fresh urine achieved greater than 90% hydrolysis with an HRT of 2 days; results suggest the HRT could be reduced to 16 h without reducing performance. No significant benefit was provided by increasing the frequency of feedings for the same HRT, likely because urease enzymes were saturated and operating at maximum hydrolysis rates during most of the reaction period.},
}

@article {pmid36161499,
year = {2022},
author = {Alonso-Reyes, DG and Galván, FS and Irazoqui, JM and Amadio, A and Tschoeke, D and Thompson, F and Albarracín, VH and Farias, ME},
title = {Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36161499},
issn = {1432-184X},
support = {2019-03216//PICT RAICES/ ; G603//PIUNT/ ; },
abstract = {Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.},
}

@article {pmid36160194,
year = {2022},
author = {Guajardo-Leiva, S and Alarcón, J and Gutzwiller, F and Gallardo-Cerda, J and Acuña-Rodríguez, IS and Molina-Montenegro, M and Crandall, KA and Pérez-Losada, M and Castro-Nallar, E},
title = {Source and acquisition of rhizosphere microbes in Antarctic vascular plants.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {916210},
pmid = {36160194},
issn = {1664-302X},
abstract = {Rhizosphere microbial communities exert critical roles in plant health, nutrient cycling, and soil fertility. Despite the essential functions conferred by microbes, the source and acquisition of the rhizosphere are not entirely clear. Therefore, we investigated microbial community diversity and potential source using the only two native Antarctic plants, Deschampsia antarctica (Da) and Colobanthus quitensis (Cq), as models. We interrogated rhizosphere and bulk soil microbiomes at six locations in the Byers Peninsula, Livingston Island, Antarctica, both individual plant species and their association (Da.Cq). Our results show that host plant species influenced the richness and diversity of bacterial communities in the rhizosphere. Here, the Da rhizosphere showed the lowest richness and diversity of bacteria compared to Cq and Da.Cq rhizospheres. In contrast, for rhizosphere fungal communities, plant species only influenced diversity, whereas the rhizosphere of Da exhibited higher fungal diversity than the Cq rhizosphere. Also, we found that environmental geographic pressures (i.e., sampling site, latitude, and altitude) and, to a lesser extent, biotic factors (i.e., plant species) determined the species turnover between microbial communities. Moreover, our analysis shows that the sources of the bacterial communities in the rhizosphere were local soils that contributed to homogenizing the community composition of the different plant species growing in the same sampling site. In contrast, the sources of rhizosphere fungi were local (for Da and Da.Cq) and distant soils (for Cq). Here, the host plant species have a specific effect in acquiring fungal communities to the rhizosphere. However, the contribution of unknown sources to the fungal rhizosphere (especially in Da and Da.Cq) indicates the existence of relevant stochastic processes in acquiring these microbes. Our study shows that rhizosphere microbial communities differ in their composition and diversity. These differences are explained mainly by the microbial composition of the soils that harbor them, acting together with plant species-specific effects. Both plant species acquire bacteria from local soils to form part of their rhizosphere. Seemingly, the acquisition process is more complex for fungi. We identified a significant contribution from unknown fungal sources due to stochastic processes and known sources from soils across the Byers Peninsula.},
}

@article {pmid36159733,
year = {2022},
author = {Van de Walle, A and Torfs, E and Gaublomme, D and Rabaey, K},
title = {In silico assessment of household level closed water cycles: Towards extreme decentralization.},
journal = {Environmental science and ecotechnology},
volume = {10},
number = {},
pages = {100148},
pmid = {36159733},
issn = {2666-4984},
abstract = {Water management in most of the developed world is currently practiced in a highly centralized manner, leading to major infrastructure and energy costs to transport water. To decrease the impacts of water scarcity and climate change, the decentralization of water can increase local robustness. In extremis, decentralization can involve building or house level water supply and treatment. Here, we constructed a MATLAB/Simulink model for two decentralized water management configurations at the household level, assuming the socio-environmental setting of Flanders, Belgium. Independence from the potable water grid and sewer system was pursued through rainwater harvesting, reuse of wastewater streams fit-for-purpose, and discharge via infiltration. The mass balance for water was calculated over the system boundaries showing high potential for independence from the grid with a reasonable treatment train and storage options. Next, the risk of contaminant accumulation within the circular system was assessed, showing a key limitation on decentralized system performance necessitating a system purge. Up to 59% of system rainwater usage was due to the replacement of this purge. Employing treatment units with high (95%) contaminant rejection efficiencies eliminated contaminant accumulation issues. The raw model output was quantitatively assessed by constructing four newly proposed key performance indicators (KPIs), quantifying system independence, circularity, drought tolerance and local water body recharge, which allowed for facilitated system comparison and communication to stakeholders. A sensitivity analysis was performed in which the effect of input parameter variability and uncertainty on system performance was quantified. The sensitivity analysis showed the importance of water recovery and contaminant removal efficiencies of the applied treatment technologies on system performance when contaminant accumulation in the system forms an issue. In systems not severely affected by pollutant accumulation, parameters such as inhabitant number and roof surface had the largest effect. As a whole, this work shows the potential of extreme decentralization of water systems and addresses the obstacle towards implementation formed by the accumulation of contaminants due to system circularity. Additionally, this study provides a framework for operational and technological decision support of decentralized household-scale water systems and, by extension, for future water policy-making.},
}

@article {pmid36158753,
year = {2022},
author = {Ostermeyer, P and Van Landuyt, J and Bonin, L and Folens, K and Williamson, A and Hennebel, T and Rabaey, K},
title = {High rate production of concentrated sulfides from metal bearing wastewater in an expanded bed hydrogenotrophic sulfate reducing bioreactor.},
journal = {Environmental science and ecotechnology},
volume = {11},
number = {},
pages = {100173},
pmid = {36158753},
issn = {2666-4984},
abstract = {Metallurgical wastewaters contain high concentrations of sulfate, up to 15 g L-1. Sulfate-reducing bioreactors are employed to treat these wastewaters, reducing sulfates to sulfides which subsequently co-precipitate metals. Sulfate loading and reduction rates are typically restricted by the total H2S concentration. Sulfide stripping, sulfide precipitation and dilution are the main strategies employed to minimize inhibition by H2S, but can be adversely compromised by suboptimal sulfate reduction, clogging and additional energy costs. Here, metallurgical wastewater was treated for over 250 days using two hydrogenotrophic granular activated carbon expanded bed bioreactors without additional removal of sulfides. H2S toxicity was minimized by operating at pH 8 ± 0.15, resulting in an average sulfate removal of 7.08 ± 0.08 g L-1, sulfide concentrations of 2.1 ± 0.2 g L-1 and peaks up to 2.3 ± 0.2 g L-1. A sulfate reduction rate of 20.6 ± 0.9 g L-1 d-1 was achieved, with maxima up to 27.2 g L-1 d-1, which is among the highest reported considering a literature review of 39 studies. The rates reported here are 6-8 times higher than those reported for other reactors without active sulfide removal and the only reported for expanded bed sulfate-reducing bioreactors using H2. By increasing the influent sulfate concentration and maintaining high sulfide concentrations, sulfate reducers were promoted while fermenters and methanogens were suppressed. Industrial wastewater containing 4.4 g L-1 sulfate, 0.036 g L-1 nitrate and various metals (As, Fe, Tl, Zn, Ni, Sb, Co and Cd) was successfully treated with all metal(loid)s, nitrates and sulfates removed below discharge limits.},
}

@article {pmid36154441,
year = {2022},
author = {Zhang, S and Yang, Q and Defoirdt, T},
title = {Halogenated Indoles Decrease the Virulence of Vibrio campbellii in a Gnotobiotic Brine Shrimp Model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0268922},
doi = {10.1128/spectrum.02689-22},
pmid = {36154441},
issn = {2165-0497},
abstract = {Indole signaling is viewed as a potential target for antivirulence therapy against antibiotic-resistant pathogens because of its link with the production of virulence factors. This study examined the antimicrobial and antivirulence properties of 44 indoles toward Vibrio campbellii. Based on the results, 17 halogenated indole analogues were selected, as they significantly improved the survival of brine shrimp larvae challenged with V. campbellii. Specifically, 6-bromoindole, 7-bromoindole, 4-fluoroindole, 5-iodoindole, and 7-iodoindole showed a high protective effect, improving the survival of brine shrimp to over 80% even at a low concentration of 10 μM. To explore the impact of selected indole analogues on bacterial virulence phenotypes, swimming motility, biofilm formation, protease activity, and hemolytic activity of V. campbellii were determined. The results showed that all of the 17 selected indole analogues decreased swimming motility at both 10 μM and 100 μM. Most of the indole analogues decreased biofilm formation at a concentration of 100 μM. In contrast, only a slightly decreased protease activity and no effect on hemolytic activity were observed at both concentrations. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system, and the results demonstrate the potential of these compounds in applications aiming at the protection of shrimp from vibriosis, a major disease in aquaculture. IMPORTANCE Bacterial diseases are a major problem in the aquaculture industry. In order to counter this problem, farmers have been using antibiotics, and this has led to the evolution and spread of antibiotic resistance. In order for the aquaculture industry to further grow in a sustainable way, novel and sustainable methods to control diseases are needed. We previously reported that indole signaling is a valid target for the development of novel therapies to control disease caused by Vibrio campbellii and related bacteria, which are among the major bacterial pathogens in aquaculture. In the present study, we identified indole analogues that are more potent in protecting brine shrimp (a model organism for shrimp) from V. campbellii. To our knowledge, this is the first study of the structure-activity relation of halogenated indole analogues with respect to virulence inhibition of a pathogenic bacterium in an in vivo host model system.},
}

@article {pmid36152855,
year = {2022},
author = {Zhang, X and Shen, M and Wang, C and Gao, M and Wang, L and Jin, Z and Xia, X},
title = {Impact of aluminum exposure on oxidative stress, intestinal changes and immune responses in red swamp crayfish (Procambarus clarkii).},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {158902},
doi = {10.1016/j.scitotenv.2022.158902},
pmid = {36152855},
issn = {1879-1026},
abstract = {Aluminum (Al) is an abundant metal that has been classified as a threatening pollutant due to indiscriminate use and anthropogenic activities. This study aimed to evaluate the impacts of Al on crayfish (Procambarus clarkii), including biochemical change, histological alteration, gut microbial community diversification, and immune changes. The bioaccumulation of Al was detected in the hemolymph and intestine of crayfish after Al exposure at different time points. Results showed that Al exposure significantly induced oxidative stress and caused pathohistological changes on intestinal barrier structures in crayfish. It was found that the intestinal microbiota was affected by retained Al and the intestinal community diversity was changed after Al treated in the crayfish. Furthermore, Al exposure affected the immunity in crayfish, by altering the expression of a set of immune-related genes, as well as reducing the phenoloxidase and lysozyme activities. Moreover, Al exposure promoted hemocytes apoptosis and impaired hemophagocytic capacity against Vibro parahamolyticus, resulting in higher mortality of crayfish upon bacterial infection. Taken these results together, we conclude that excessive Al exposure caused adverse effects on multiple biological processes of crayfish and Al pollution is a potential threat to crayfish culture.},
}

@article {pmid36152034,
year = {2022},
author = {Weingarten, EA and Jackson, CR},
title = {Microbial Composition of Freshwater Marsh Sediment Responds more Strongly to Microcosm Seawater Addition than Simulated Nitrate or Phosphate Eutrophication.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36152034},
issn = {1432-184X},
abstract = {As sea level rise impacts coastal wetlands, saltmarsh will overtake coastal freshwater marsh in many areas, but changes in the sediment microbiome in response to saltwater intrusion are difficult to predict. Coastal freshwater marsh sediment was exposed to ambient, brackish, and saline conditions as well as to elevated nitrate and phosphate to model the combined stresses of saltwater intrusion and coastal eutrophication. Initially, sediment prokaryotic composition was similar to prior studies of freshwater marsh but diverged over time, reflecting the magnitude of increase in saltwater. There was no observed effect of nutrient amendment, potentially ranking seawater intrusion as a higher-importance compositional driver. Although the previously described loss of methanogenic populations and promotion of sulfate reducers in response to saltwater exposure was observed, taxonomic distribution was not similar to typical meso-polyhaline wetlands. Without colonization by marine taxa, such a community may be short-lived naturally, ultimately equilibrating with more common saltmarsh species. However, the recapitulation of salinity concentration by freshwater sediment microbial composition demonstrates the overwhelming nature of saltwater intrusion relative to other drivers like eutrophication.},
}

@article {pmid36151709,
year = {2022},
author = {Prosser, JI},
title = {How and why in microbial ecology: an appeal for scientific aims, questions, hypotheses and theories.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16221},
pmid = {36151709},
issn = {1462-2920},
abstract = {This article precedes a series of articles on the important questions, hypotheses and theories in microbial ecology. It considers why, as scientists, we ask questions and propose hypotheses and what makes them important, good or significant. Emphasis is placed on 'scientific' questions, the need for scientific aims and on possible reasons for, and inadequacy of aim-less studies and question-free. Current global issues surrounding the climate crisis, pandemics and antibiotic resistance focus attention on science and scientists. They exemplify the urgent need for greater understanding of the interactions between microbes and their biological and physicochemical environments, i.e. of microbial ecology. They also provide examples of reaction against science and scientists and highlight why we must be clear what defines (good) science, its power and limitations, and ensure that this is communicated to stakeholders and the general public. This article is protected by copyright. All rights reserved.},
}

@article {pmid36151339,
year = {2022},
author = {Zhou, X and Lee, J and Yun, J and Kim, J and Yang, Y and Kang, H},
title = {Distinct Nitrification Rates and Nitrifiers in Needleleaf and Evergreen Broadleaf Forest Soils.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36151339},
issn = {1432-184X},
abstract = {Research on niche specialization in the microbial communities of ammonia oxidizers is important for assessing the consequences of vegetation shift on nitrogen (N) cycling. In this study, soils were sampled from three tree stands (needleleaf, mixed, and evergreen broadleaf) from the Hannam experimental forest in South Korea in spring (May 2019), summer (August 2019), autumn (November 2019), and winter (January 2020). Quantitative polymerase chain reaction (qPCR) and high-throughput sequencing were used to measure the abundance and community structure of various nitrifiers: ammonia-oxidizing archaea and bacteria (AOA and AOB, respectively) as well as complete ammonia oxidizers (comammox). Nitrification rates and total ammonia oxidizer abundance were significantly higher in needleleaf forest soil than those in other forest stands, and they were lowest in evergreen broadleaf forest soil. Comammox clade B was most abundant in needleleaf and evergreen broadleaf forest soils, while AOA were significantly more abundant in mixed forest soil. The abundances of comammox clade B and AOA were negatively correlated with dissolved organic carbon. Phylogenetic analysis showed that NT-alpha and NS-gamma-2.3.2 were the most abundant AOA lineages in all the samples. The seasonal of AOA, AOB, and comammox varied with the sites, suggesting the need to examine the combinations of environmental factors when considering the effects of seasonal changes in the environment. Overall, the results suggest that potential vegetation shifts in forest ecosystems might affect nitrification activities by regulating the abundance and community structure of ammonia oxidizers.},
}

@article {pmid36150718,
year = {2022},
author = {Kritzberg, E and Bååth, E},
title = {Seasonal variation in temperature sensitivity of bacterial growth in a temperate soil and lake.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiac111},
pmid = {36150718},
issn = {1574-6941},
abstract = {Faster bacterial biomass turnover is expected in water compared to soil, which would result in more rapid community adaption to changing environmental conditions, including temperature. Bacterial community adaptation for growth is thus predicted to have larger seasonal amplitudes in lakes than in soil. To test this prediction, we compared the seasonal variation in temperature adaptation of bacterial community growth in a soil and lake in Southern Sweden (Tin situ 0-20 °C, mean 10 °C) during 1.5 yrs, based on monthly samplings including two winters and summers. An indicator of community adaptation, minimum temperature for growth (Tmin), was calculated from bacterial growth measurements (Leu incorporation) using the Ratkowsky model. The seasonal variation in Tmin (sinusoidal function, R2 = 0.71) was most pronounced for the lake bacterial community, with an amplitude for Tmin of 3.0 °C (-4.5 to -10.5 °C) compared to 0.6 °C (-7 to -8 °C) for the soil. Tmin in water thus increased by 0.32 °C/degree change of Tin situ. Similar differences were also found when comparing four lakes and soils in the winter and summer (amplitudes 2.9 °C and 0.9 °C for lakes and soils, respectively). Thus, seasonal variation in temperature adaptation has to be taken into account in lakes, while for soils a constant Tmin can be used.},
}

@article {pmid36150364,
year = {2022},
author = {Mitrović, M and Kostešić, E and Marković, T and Selak, L and Hausmann, B and Pjevac, P and Orlić, S},
title = {Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia.},
journal = {Systematic and applied microbiology},
volume = {45},
number = {6},
pages = {126359},
doi = {10.1016/j.syapm.2022.126359},
pmid = {36150364},
issn = {1618-0984},
abstract = {In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by Hydrogenophilus, Sulfuricurvum, Sulfurovum, Thiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.},
}

@article {pmid36145836,
year = {2022},
author = {Vidal, C and González, F and Santander, C and Pérez, R and Gallardo, V and Santos, C and Aponte, H and Ruiz, A and Cornejo, P},
title = {Management of Rhizosphere Microbiota and Plant Production under Drought Stress: A Comprehensive Review.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {18},
pages = {},
doi = {10.3390/plants11182437},
pmid = {36145836},
issn = {2223-7747},
support = {ANID/FONDECYT/1210964//Agencia Nacional de Investigación y Desarrollo/ ; ANID/FONDAP/15130015//Agencia Nacional de Investigación y Desarrollo/ ; InES19-FRO19001//Ministry of Education/ ; FONDECYT1210964//Agencia Nacional de Investigación y Desarrollo/ ; ANID/FONDAP/15130015//Agencia Nacional de Investigación y Desarrollo/ ; InES19.FRO19001//Ministry of Education/ ; },
abstract = {Drought generates a complex scenario worldwide in which agriculture should urgently be reframed from an integrative point of view. It includes the search for new water resources and the use of tolerant crops and genotypes, improved irrigation systems, and other less explored alternatives that are very important, such as biotechnological tools that may increase the water use efficiency. Currently, a large body of evidence highlights the role of specific strains in the main microbial rhizosphere groups (arbuscular mycorrhizal fungi, yeasts, and bacteria) on increasing the drought tolerance of their host plants through diverse plant growth-promoting (PGP) characteristics. With this background, it is possible to suggest that the joint use of distinct PGP microbes could produce positive interactions or additive beneficial effects on their host plants if their co-inoculation does not generate antagonistic responses. To date, such effects have only been partially analyzed by using single omics tools, such as genomics, metabolomics, or proteomics. However, there is a gap of information in the use of multi-omics approaches to detect interactions between PGP and host plants. This approach must be the next scale-jump in the study of the interaction of soil-plant-microorganism. In this review, we analyzed the constraints posed by drought in the framework of an increasing global demand for plant production, integrating the important role played by the rhizosphere biota as a PGP agent. Using multi-omics approaches to understand in depth the processes that occur in plants in the presence of microorganisms can allow us to modulate their combined use and drive it to increase crop yields, improving production processes to attend the growing global demand for food.},
}

@article {pmid36145178,
year = {2022},
author = {Overbeeke, A and Lang, M and Hausmann, B and Watzka, M and Nikolov, G and Schwarz, J and Kohl, G and De Paepe, K and Eislmayr, K and Decker, T and Richter, A and Berry, D},
title = {Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.},
journal = {Nutrients},
volume = {14},
number = {18},
pages = {},
doi = {10.3390/nu14183802},
pmid = {36145178},
issn = {2072-6643},
support = {741623/ERC_/European Research Council/International ; P27831-B28//FWF Austrian Science Fund/ ; LS18-053//Vienna Science and Technology Fund/ ; MAINTAIN DOC 69//FWF Austrian Science Fund/ ; },
abstract = {The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.},
}

@article {pmid36144291,
year = {2022},
author = {Kuzyk, SB and Ma, X and Yurkov, V},
title = {Seasonal Dynamics of Lake Winnipeg's Microbial Communities Reveal Aerobic Anoxygenic Phototrophic Populations Coincide with Sunlight Availability.},
journal = {Microorganisms},
volume = {10},
number = {9},
pages = {},
doi = {10.3390/microorganisms10091690},
pmid = {36144291},
issn = {2076-2607},
support = {5492-2018//Natural Sciences and Engineering Research Council/ ; },
abstract = {In this first comprehensive study of Lake Winnipeg's microbial communities, limnetic and littoral euphotic zones were examined during each season from 2016 through 2020. Classical cultivation and modern high-throughput sequencing techniques provided quantification and identification of key phototrophic populations, including aerobic anoxygenic phototrophs (AAP). Annual dynamics found total heterotrophs reached 4.23 × 106 CFU/g in littoral sands, and 7.69 × 104 CFU/mL in summer littoral waters on oligotrophic media, higher counts than for copiotrophic compositions. Limnetic numbers inversely dipped to 4.34 × 103 CFU/mL midsummer. Cultured AAP did not follow heterotrophic trends, instead peaking during the spring in both littoral and limnetic waters as 19.1 and 4.7% of total copiotrophs, or 3.9 and 4.9% of oligotrophs, decreasing till autumn each year. Complementary observations came from environmental 16S V4 rRNA gene analysis, as AAP made up 1.49 and 1.02% of the littoral and limnetic sequenced communities in the spring, declining with seasonal progression. Spatial and temporal fluctuations of microbes compared to environmental factors exposed photosynthetic populations to independently and regularly fluctuate in the ecosystem. Oxygenic phototrophic numbers expectantly matched the midsummer peak of Chl a and b, oxygenic photosynthesis related carbon fixation, and water temperature. Independently, AAP particularly colonized spring littoral areas more than limnetic, and directly corresponded to habitat conditions that specifically promoted growth: the requirement of light and organic material.},
}

@article {pmid36143410,
year = {2022},
author = {Johnston-Monje, D and Gutiérrez, JP and Becerra Lopez-Lavalle, LA},
title = {Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/life12091372},
pmid = {36143410},
issn = {2075-1729},
abstract = {A plant's health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant-microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production.},
}

@article {pmid36139115,
year = {2022},
author = {Qing, J and Zheng, F and Zhi, H and Yaigoub, H and Tirichen, H and Li, Y and Zhao, J and Qiang, Y and Li, Y},
title = {Identification of Unique Genetic Biomarkers of Various Subtypes of Glomerulonephritis Using Machine Learning and Deep Learning.},
journal = {Biomolecules},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/biom12091276},
pmid = {36139115},
issn = {2218-273X},
support = {82170716//The National Natural Science Foundation of China/ ; 2020-183//Research Project Supported by Shanxi Scholarship Council of China/ ; },
abstract = {(1) Objective: Identification of potential genetic biomarkers for various glomerulonephritis (GN) subtypes and discovering the molecular mechanisms of GN. (2) Methods: four microarray datasets of GN were downloaded from Gene Expression Omnibus (GEO) database and merged to obtain the gene expression profiles of eight GN subtypes. Then, differentially expressed immune-related genes (DIRGs) were identified to explore the molecular mechanisms of GN, and single-sample gene set enrichment analysis (ssGSEA) was performed to discover the abnormal inflammation in GN. In addition, a nomogram model was generated using the R package "glmnet", and the calibration curve was plotted to evaluate the predictive power of the nomogram model. Finally, deep learning (DL) based on a multilayer perceptron (MLP) network was performed to explore the characteristic genes for GN. (3) Results: we screened out 274 common up-regulated or down-regulated DIRGs in the glomeruli and tubulointerstitium. These DIRGs are mainly involved in T-cell differentiation, the RAS signaling pathway, and the MAPK signaling pathway. ssGSEA indicates that there is a significant increase in DC (dendritic cells) and macrophages, and a significant decrease in neutrophils and NKT cells in glomeruli, while monocytes and NK cells are increased in tubulointerstitium. A nomogram model was constructed to predict GN based on 7 DIRGs, and 20 DIRGs of each subtype of GN in glomeruli and tubulointerstitium were selected as characteristic genes. (4) Conclusions: this study reveals that the DIRGs are closely related to the pathogenesis of GN and could serve as genetic biomarkers in GN. DL further identified the characteristic genes that are essential to define the pathogenesis of GN and develop targeted therapies for eight GN subtypes.},
}

@article {pmid36138209,
year = {2022},
author = {Liu, Q and Zhang, H and Huang, X},
title = {Strong Linkage Between Symbiotic Bacterial Community and Host Age and Morph in a Hemipteran Social Insect.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36138209},
issn = {1432-184X},
support = {31970446//National Natural Science Foundation of China/ ; },
abstract = {The relationships between symbionts and insects are complex, and symbionts usually have diverse ecological and evolutionary effects on their hosts. The phloem sap-sucking aphids are good models to study the interactions between insects and symbiotic microorganisms. Although aphids usually exhibit remarkable life cycle complexity, most previous studies on symbiotic diversity sampled only apterous viviparous adult females or very few morphs. In this study, high-throughput 16S rDNA amplicon sequencing was used to assess the symbiotic bacterial communities of eleven morphs or developmental stages of the social aphid Pseudoregma bambucicola. We found there were significant differences in bacterial composition in response to different morphs and developmental stages, and for the first time, we revealed male aphids hosted very different symbiotic composition featured with low abundance of dominant symbionts but high diversity of total symbionts. The relative abundance of Pectobacterium showed relatively stable across different types of samples, while that of Wolbachia fluctuated greatly, indicating the former may have a consistent function in this species and the latter may provide specific function for certain morphs or developmental stages. Our study presents new evidence of complexity of symbiotic associations and indicates strong linkage between symbiotic bacterial community and host age and morph.},
}

@article {pmid36138151,
year = {2022},
author = {Simpson, RC and Shanahan, ER and Batten, M and Reijers, ILM and Read, M and Silva, IP and Versluis, JM and Ribeiro, R and Angelatos, AS and Tan, J and Adhikari, C and Menzies, AM and Saw, RPM and Gonzalez, M and Shannon, KF and Spillane, AJ and Velickovic, R and Lazar, AJ and Damania, AV and Mishra, AK and Chelvanambi, M and Banerjee, A and Ajami, NJ and Wargo, JA and Macia, L and Holmes, AJ and Wilmott, JS and Blank, CU and Scolyer, RA and Long, GV},
title = {Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {36138151},
issn = {1546-170X},
abstract = {The gut microbiota shapes the response to immune checkpoint inhibitors (ICIs) in cancer, however dietary and geographic influences have not been well-studied in prospective trials. To address this, we prospectively profiled baseline gut (fecal) microbiota signatures and dietary patterns of 103 trial patients from Australia and the Netherlands treated with neoadjuvant ICIs for high risk resectable metastatic melanoma and performed an integrated analysis with data from 115 patients with melanoma treated with ICIs in the United States. We observed geographically distinct microbial signatures of response and immune-related adverse events (irAEs). Overall, response rates were higher in Ruminococcaceae-dominated microbiomes than in Bacteroidaceae-dominated microbiomes. Poor response was associated with lower fiber and omega 3 fatty acid consumption and elevated levels of C-reactive protein in the peripheral circulation at baseline. Together, these data provide insight into the relevance of native gut microbiota signatures, dietary intake and systemic inflammation in shaping the response to and toxicity from ICIs, prompting the need for further studies in this area.},
}

@article {pmid36135386,
year = {2022},
author = {Mason, AR and McKee-Zech, HS and Hoeland, KM and Davis, MC and Campagna, SR and Steadman, DW and DeBruyn, JM},
title = {Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0032522},
doi = {10.1128/msphere.00325-22},
pmid = {36135386},
issn = {2379-5042},
abstract = {Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.},
}

@article {pmid36133177,
year = {2022},
author = {Villegas-Plazas, M and Villamil, L and Martínez-Silva, MA and González-Jiménez, T and Salazar, M and Güiza, L and Mendoza, M and Junca, H},
title = {Microbiome composition and autochthonous probiotics from contrasting probiosis/dysbiosis states in cobia (Rachycentron canadum) fish epitheliocystis.},
journal = {Access microbiology},
volume = {4},
number = {8},
pages = {acmi000405},
doi = {10.1099/acmi.0.000405},
pmid = {36133177},
issn = {2516-8290},
abstract = {Microbiome components and bacterial isolates related to healthy and epitheliocystis states in aquaculture cycles of cobia fish were studied. We detected well-defined 16S rRNA amplicon gene sequence variants showing differential abundance in healthy or diseased cycles. Isolation trials were performed, and experimental tests were used to determine probiotic potential of the bacterial strains obtained from water, tissues or live food used in this aquaculture model. The taxonomic affiliation of these strains was cross-compared against microbiome components, finding that some of them had close or identical affiliation to the abundant types found in healthy cycles. Strains belonging to the groups already identified as predominant by culture-independent means were screened as potential probiotics based on desirable activities such as antagonism and antibiosis against marine pathogenic bacteria, quorum quenching, bile acid resistance, antibiotic sensitivity and enzymatic activities for improved nutrient digestion. We have also found that in the tracking of microbiome composition across different developmental stages of cobia, healthy cycles exhibited a consistent high relative abundance of a Mesobacillus sp., while in the diseased cycle the emergence of a Vibrio sp. was observed. Our study suggests that epithelocystis in cobia is associated with a displacement of a symbiotic microbiome community linked to the increase frequency of Vibrio species.},
}

@article {pmid36133174,
year = {2022},
author = {Beirne, C and McCann, E and McDowell, A and Miliotis, G},
title = {Genetic determinants of antimicrobial resistance in three multi-drug resistant strains of Cutibacterium acnes isolated from patients with acne: a predictive in silico study.},
journal = {Access microbiology},
volume = {4},
number = {8},
pages = {acmi000404},
doi = {10.1099/acmi.0.000404},
pmid = {36133174},
issn = {2516-8290},
abstract = {Objectives: Using available whole genome data, the objective of this in silico study was to identify genetic mechanisms that could explain the antimicrobial resistance profile of three multi-drug resistant (MDR) strains (CA17, CA51, CA39) of the skin bacterium Cutibacterium acnes previously recovered from patients with acne. In particular, we were interested in detecting novel genetic determinants associated with resistance to fluoroquinolone and macrolide antibiotics that could then be confirmed experimentally.

Methods: A range of open source bioinformatics tools were used to 'mine' genetic determinants of antimicrobial resistance and plasmid borne contigs, and to characterise the phylogenetic diversity of the MDR strains.

Results: As probable mechanisms of resistance to fluoroquinolones, we identified a previously described resistance associated allelic variant of the gyrA gene with a 'deleterious' S101L mutation in type IA1 strains CA51 (ST1) and CA39 (ST1), as well as a novel E761R 'deleterious' mutation in the type II strain CA17 (ST153). A distinct genomic sequence of the efflux protein YfmO which is potentially associated with resistance to MLSB antibiotics was also present in CA17; homologues in CA51, CA39, and other strains of Cutibacterium acnes , were also found but differed in amino acid content. Strikingly, in CA17 we also identified a circular 2.7 kb non-conjugative plasmid (designated pCA17) that closely resembled a 4.8 kb plasmid (pYU39) from the MDR Salmonella enterica strain YU39.

Conclusions: This study has provided a detailed explanation of potential genetic determinants for MDR in the Cutibacterium acnes strains CA17, CA39 and CA51. Further laboratory investigations will be required to validate these in silico results, especially in relation to pCA17.},
}

@article {pmid36132223,
year = {2022},
author = {Yanez-Montalvo, A and Aguila, B and Gómez-Acata, ES and Guerrero-Jacinto, M and Oseguera, LA and Falcón, LI and Alcocer, J},
title = {Shifts in water column microbial composition associated to lakes with different trophic conditions: "Lagunas de Montebello" National Park, Chiapas, México.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13999},
doi = {10.7717/peerj.13999},
pmid = {36132223},
issn = {2167-8359},
abstract = {Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the "Lagunas de Montebello" National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.},
}

@article {pmid36131874,
year = {2021},
author = {Legin, AA and Schintlmeister, A and Sommerfeld, NS and Eckhard, M and Theiner, S and Reipert, S and Strohhofer, D and Jakupec, MA and Galanski, MS and Wagner, M and Keppler, BK},
title = {Nano-scale imaging of dual stable isotope labeled oxaliplatin in human colon cancer cells reveals the nucleolus as a putative node for therapeutic effect.},
journal = {Nanoscale advances},
volume = {3},
number = {1},
pages = {249-262},
doi = {10.1039/d0na00685h},
pmid = {36131874},
issn = {2516-0230},
abstract = {Oxaliplatin shows a superior clinical activity in colorectal cancer compared to cisplatin. Nevertheless, the knowledge about its cellular distribution and the mechanisms responsible for the different range of oxaliplatin-responsive tumors is far from complete. In this study, we combined highly sensitive element specific and isotope selective imaging by nanometer-scale secondary ion mass spectrometry (NanoSIMS) with transmission electron microscopy to investigate the subcellular accumulation of oxaliplatin in three human colon cancer cell lines (SW480, HCT116 wt, HCT116 OxR). Oxaliplatin bearing dual stable isotope labeled moieties, i.e. 2H-labeled diaminocyclohexane (DACH) and 13C-labeled oxalate, were applied for comparative analysis of the subcellular distribution patterns of the central metal and the ligands. In all the investigated cell lines, oxaliplatin was found to have a pronounced tendency for cytoplasmic aggregation in single membrane bound organelles, presumably related to various stages of the endocytic pathway. Moreover, nuclear structures, heterochromatin and in particular nucleoli, were affected by platinum-drug exposure. In order to explore the consequences of oxaliplatin resistance, subcellular drug distribution patterns were investigated in a pair of isogenic malignant cell lines with distinct levels of drug sensitivity (HCT116 wt and HCT116 OxR, the latter with acquired resistance to oxaliplatin). The subcellular platinum distribution was found to be similar in both cell lines, with only slightly higher accumulation in the sensitive HCT116 wt cells which is inconsistent with the resistance factor of more than 20-fold. Instead, the isotopic analysis revealed a disproportionally high accumulation of the oxalate ligand in the resistant cell line.},
}

@article {pmid22611351,
year = {2012},
author = {Tong, J and Trapido-Rosenthal, H and Wang, J and Wang, Y and Li, QX and Lu, Y},
title = {Antiviral activities and putative identification of compounds in microbial extracts from the Hawaiian coastal waters.},
journal = {Marine drugs},
volume = {10},
number = {3},
pages = {521-538},
pmid = {22611351},
issn = {1660-3397},
support = {P50 ES012740/ES/NIEHS NIH HHS/United States ; P50ES012740/ES/NIEHS NIH HHS/United States ; P20 MD006084/MD/NIMHD NIH HHS/United States ; G12RR003061/RR/NCRR NIH HHS/United States ; G12 RR003061/RR/NCRR NIH HHS/United States ; },
mesh = {Analysis of Variance ; Animals ; Antiviral Agents/chemistry/*pharmacology ; Aquatic Organisms ; Bacteria/chemistry ; Cell Survival/drug effects ; Chlorocebus aethiops ; Chromatography, Gas ; Hawaii ; Herpesvirus 1, Human/drug effects ; Humans ; Mass Spectrometry ; Pacific Ocean ; Porifera/chemistry ; Seawater/*microbiology ; Vero Cells ; Viral Plaque Assay ; Virus Replication/drug effects ; },
abstract = {Marine environments are a rich source of significant bioactive compounds. The Hawaiian archipelago, located in the middle of the Pacific Ocean, hosts diverse microorganisms, including many endemic species. Thirty-eight microbial extracts from Hawaiian coastal waters were evaluated for their antiviral activity against four mammalian viruses including herpes simplex virus type one (HSV-1), vesicular stomatitis virus (VSV), vaccinia virus and poliovirus type one (poliovirus-1) using in vitro cell culture assay. Nine of the 38 microbial crude extracts showed antiviral potencies and three of these nine microbial extracts exhibited significant activity against the enveloped viruses. A secosteroid, 5α(H),17α(H),(20R)-beta-acetoxyergost-8(14)-ene was putatively identified and confirmed to be the active compound in these marine microbial extracts. These results warrant future in-depth tests on the isolation of these active elements in order to explore and validate their antiviral potential as important therapeutic remedies.},
}

Analysis of Variance
Animals
Antiviral Agents/chemistry/*pharmacology
Aquatic Organisms
Bacteria/chemistry
Cell Survival/drug effects
Chlorocebus aethiops
Chromatography, Gas
Hawaii
Herpesvirus 1, Human/drug effects
Humans
Mass Spectrometry
Pacific Ocean
Porifera/chemistry
Seawater/*microbiology
Vero Cells
Viral Plaque Assay
Virus Replication/drug effects

@article {pmid36128567,
year = {2022},
author = {El Amrani, B},
title = {Aspects of the rhizospheric microbiota and their interactions with the soil ecosystem.},
journal = {Vavilovskii zhurnal genetiki i selektsii},
volume = {26},
number = {5},
pages = {442-448},
doi = {10.18699/VJGB-22-54},
pmid = {36128567},
issn = {2500-0462},
abstract = {Soil microbial communities play a key role in the evolution of the rhizosphere. In addition, proper exploration of these microbial resources represents a promising strategy that guarantees the health and sustainability of all ecosystems connected to the ground. Under the inf luence of environmental conditions, microbial communities can change compositions in terms of abundance and diversity. Beyond the descriptive level, the current orientation of microbial ecology is to link these structures to the functioning of ecosystems; specif ically, to understand the effect of environmental factors on the functional structure of microbial communities in ecosystems. This review focuses on the main interactions between the indigenous soil microf lora and the major constituents of the rhizosphere to understand, on the one hand, how microbial biodiversity can improve plant growth and maintain homeostasis of the rhizospheric ecosystem, on the other hand, how the maintenance and enrichment of plant biodiversity can contribute to the conservation of soil microbial diversity; knowing that these microorganisms are also controlled by the abiotic properties of the soil. Overall, understanding the dynamics of the rhizosphere microbiome is essential for developing innovative strategies in the f ield of protecting and maintaining the proper functioning of the soil ecosystem.},
}

@article {pmid36128049,
year = {2022},
author = {Külekci, B and Schwarz, S and Brait, N and Perkmann-Nagele, N and Jaksch, P and Hoetzenecker, K and Puchhammer-Stöckl, E and Goerzer, I},
title = {Human cytomegalovirus strain diversity and dynamics reveal the donor lung as a major contributor after transplantation.},
journal = {Virus evolution},
volume = {8},
number = {2},
pages = {veac076},
doi = {10.1093/ve/veac076},
pmid = {36128049},
issn = {2057-1577},
abstract = {Mixed human cytomegalovirus (HCMV) strain infections are frequent in lung transplant recipients (LTRs). To date, the influence of the donor (D) and recipient (R) HCMV serostatus on intra-host HCMV strain composition and viral population dynamics after transplantation is only poorly understood. Here, we investigated ten pre-transplant lungs from HCMV-seropositive donors and 163 sequential HCMV-DNA-positive plasma and bronchoalveolar lavage samples from fifty LTRs with multiviremic episodes post-transplantation. The study cohort included D+R+ (38 per cent), D+R- (36 per cent), and D-R+ (26 per cent) patients. All samples were subjected to quantitative genotyping by short amplicon deep sequencing, and twenty-four of them were additionally PacBio long-read sequenced for genotype linkages. We find that D+R+ patients show a significantly elevated intra-host strain diversity compared to D+R- and D-R+ patients (P = 0.0089). Both D+ patient groups display significantly higher viral population dynamics than D- patients (P = 0.0061). Five out of ten pre-transplant donor lungs were HCMV DNA positive, whereof three multiple HCMV strains were detected, indicating that multi-strain transmission via lung transplantation is likely. Using long reads, we show that intra-host haplotypes can share distinctly linked genotypes, which limits overall intra-host diversity in mixed infections. Together, our findings demonstrate donor-derived strains as the main source of increased HCMV strain diversity and dynamics post-transplantation. These results foster strategies to mitigate the potential transmission of the donor strain reservoir to the allograft, such as ex vivo delivery of HCMV-selective immunotoxins prior to transplantation to reduce latent HCMV.},
}

@article {pmid36126627,
year = {2022},
author = {Xu, G and He, J},
title = {Resilience of organohalide-detoxifying microbial community to oxygen stress in sewage sludge.},
journal = {Water research},
volume = {224},
number = {},
pages = {119055},
doi = {10.1016/j.watres.2022.119055},
pmid = {36126627},
issn = {1879-2448},
abstract = {Organohalide pollutants are prevalent in the environment, causing harms to wildlife and human. Organohalide-respiring bacteria (OHRB) could detoxify these pollutants in anaerobic environments, but the most competent OHRB (i.e., Dehalococcoides) is susceptible to oxygen. This study reports exceptional resistance and resilience of sewage sludge microbial communities to oxygen stress for attenuation of structurally distinct organohalide pollutants, including tetrachloroethene, tetrabromobisphenol A, and polybrominated diphenyl ethers. The dehalogenation rate constant of these organohalide pollutants in oxygen-exposed sludge microcosms was maintained as 74-120% as that in the control without oxygen exposure. Subsequent top-down experiments clarified that sludge flocs and non-OHRB contributed to alleviating oxygen stress on OHRB. In the dehalogenating microcosms, multiple OHRB (Dehahlococcoides, Dehalogenimonas, and Sulfurospirillum) harboring distinct reductive dehalogenase genes (pceA, pteA, tceA, vcrA, and bdeA) collaborated to detoxify organohalide pollutants but responded differentially to oxygen stress. Comprehensive microbial community analyses (taxonomy, diversity, and structure) demonstrated certain resilience of the sludge-derived dehalogenating microbial communities to oxygen stress. Additionally, microbial co-occurrence networks were intensified by oxygen stress in most microcosms, as a possible stress mitigation strategy. Altogether the mechanistic and ecological findings in this study contribute to remediation of organohalide-contaminated sites encountering oxygen disturbance.},
}

@article {pmid36123806,
year = {2022},
author = {Zhang, Y and Yang, X and Van de Peer, Y and Chen, J and Marchal, K and Shi, T},
title = {Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.},
journal = {The Plant journal : for cell and molecular biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/tpj.15984},
pmid = {36123806},
issn = {1365-313X},
abstract = {Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contribution of the two key mechanisms to the evolution of gene function is largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea, N. nucifera, and the outgroup Arabidopsis thaliana, for both single-copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs, and that the origin of lineage-specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single-copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue-dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms from local, small-scale duplicated, isoforms of whole-genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contribute to creating the diversity of gene function during the evolution of lotus.},
}

@article {pmid36123554,
year = {2022},
author = {Xu, MP and Zhi, RC and Jian, JN and Feng, YZ and Han, XH and Zhang, W},
title = {Changes in Soil Organic C Fractions and C Pool Stability Are Mediated by C-Degrading Enzymes in Litter Decomposition of Robinia pseudoacacia Plantations.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36123554},
issn = {1432-184X},
abstract = {Litter decomposition is the main source of soil organic carbon (SOC) pool, regarding as an important part of terrestrial ecosystem C dynamics. The turnover of SOC is mainly regulated by extracellular enzymes secreted by microorganisms. However, the response mechanism of soil C-degrading enzymes and SOC in litter decomposition remains unclear. To clarify how SOC fraction dynamics respond to C-degrading enzymes in litter decomposition, we used field experiments to collect leaf litter and SOC fractions from the underlying layer in Robinia pseudoacacia plantations on the Loess Plateau. Our results showed that SOC, easily oxidizable organic C, dissolved organic C, and microbial biomass C increased significantly during the decomposition process. Litter decomposition significantly decreased soil hydrolase activity, but slightly increased oxidase activity. Correlation analysis results showed that SOC fractions were significantly positively correlated with the litter mass, lignin, soil moisture, and oxidase activity, but significantly negatively correlated with cellulose content and soil pH. Partial least squares path models revealed that soil C-degrading enzymes can directly or indirectly affect the changes of soil C fractions. The most direct factors affecting the SOC fractions of topsoil during litter decomposition were litter lignin and cellulose degradation, soil pH, and C-degrading enzymes. Furthermore, regression analysis showed that the decrease of SOC stability in litter decomposition was closely related to the decrease of soil hydrolase to oxidase ratio. These results highlighted that litter degradation-induced changes in C-degrading enzyme activity significantly affected SOC fractions. Furthermore, the distribution of soil hydrolases and oxidases affected the stability of SOC during litter decomposition. These findings provided a theoretical framework for a more comprehensive understanding of C turnover and stabilization mechanisms between plant and soil.},
}

@article {pmid36123442,
year = {2022},
author = {Hedlund, BP and Chuvochina, M and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, IC and Venter, SN and Whitman, WB},
title = {SeqCode: a nomenclatural code for prokaryotes described from sequence data.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {36123442},
issn = {2058-5276},
abstract = {Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.},
}

@article {pmid36122204,
year = {2022},
author = {Peng, R and Xu, Y and Tian, S and Unver, T and Liu, Z and Zhou, Z and Cai, X and Wang, K and Wei, Y and Liu, Y and Wang, H and Hu, G and Zhang, Z and Grover, CE and Hou, Y and Wang, Y and Li, P and Wang, T and Lu, Q and Wang, Y and Conover, JL and Ghazal, H and Wang, Q and Zhang, B and Van Montagu, M and Van de Peer, Y and Wendel, JF and Liu, F},
title = {Evolutionary divergence of duplicated genomes in newly described allotetraploid cottons.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {39},
pages = {e2208496119},
doi = {10.1073/pnas.2208496119},
pmid = {36122204},
issn = {1091-6490},
abstract = {Allotetraploid cotton (Gossypium) species represents a model system for the study of plant polyploidy, molecular evolution, and domestication. Here, chromosome-scale genome sequences were obtained and assembled for two recently described wild species of tetraploid cotton, Gossypium ekmanianum [(AD)6, Ge] and Gossypium stephensii [(AD)7, Gs], and one early form of domesticated Gossypium hirsutum, race punctatum [(AD)1, Ghp]. Based on phylogenomic analysis, we provide a dated whole-genome level perspective for the evolution of the tetraploid Gossypium clade and resolved the evolutionary relationships of Gs, Ge, and domesticated G. hirsutum. We describe genomic structural variation that arose during Gossypium evolution and describe its correlates-including phenotypic differentiation, genetic isolation, and genetic convergence-that contributed to cotton biodiversity and cotton domestication. Presence/absence variation is prominent in causing cotton genomic structural variations. A presence/absence variation-derived gene encoding a phosphopeptide-binding protein is implicated in increasing fiber length during cotton domestication. The relatively unimproved Ghp offers the potential for gene discovery related to adaptation to environmental challenges. Expanded gene families enoyl-CoA δ isomerase 3 and RAP2-7 may have contributed to abiotic stress tolerance, possibly by targeting plant hormone-associated biochemical pathways. Our results generate a genomic context for a better understanding of cotton evolution and for agriculture.},
}

@article {pmid36118848,
year = {2022},
author = {Rabapane, KJ and Ijoma, GN and Matambo, TS},
title = {Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {946449},
pmid = {36118848},
issn = {1664-8021},
abstract = {Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.},
}

@article {pmid36113308,
year = {2022},
author = {Alves, KJ and Pylro, VS and Nakayama, CR and Vital, VG and Taketani, RG and Santos, DG and Rodrigues, JLM and Tsai, SM and Andreote, FD},
title = {Methanogenic communities and methane emissions from enrichments of Brazilian Amazonia soils under land-use change.},
journal = {Microbiological research},
volume = {265},
number = {},
pages = {127178},
doi = {10.1016/j.micres.2022.127178},
pmid = {36113308},
issn = {1618-0623},
abstract = {Amazonian forest conversion into agricultural and livestock areas is considered one of the activities that contribute most to the emission of greenhouse gases, including methane. Biogenic methane production is mainly performed by methanogenic Archaea, which underscores the importance of understanding the drivers shaping microbial communities involved in the methane cycling and changes in methane metabolism. Here, we aimed to investigate the composition and structure of bacterial and archaeal communities in tropical soils in response to land-use changes, emphasizing the methanogenic communities. We collected soil samples from primary forest, pasture, and secondary forest of the Amazonian region and used a strategy based on the enrichment of the methanogenic community with three different methanogenic substrates followed by measurements of methane emission, quantification of mcrA gene copies by qPCR, and total 16 S rRNA gene sequencing (metataxonomics). We observed variations in the structure of bacterial and archaeal communities of soils under different uses. The richness of methanogenic communities was higher in pasture than forest soils and this richness remained during the incubation period, and as a consequence, the enrichment induced earlier methane emission in pastures-derived samples. Furthermore, pastures enrichments exhibited methanogenic archaea networks more complex than primary and secondary forests. In conclusion, pastures harbor a richer and more responsive methanogenic community than forest samples, suggesting that conversion of forest areas to pasture may boost methane emission.},
}

@article {pmid36112603,
year = {2022},
author = {Miller, JC and Babu, AKS and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Babu, PVA},
title = {Gut Microbes are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e2200112},
doi = {10.1002/mnfr.202200112},
pmid = {36112603},
issn = {1613-4133},
abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. We investigated whether strawberry consumption reduces vascular complications in an animal model of MetS and identified whether this effect is associated with changes in the composition of gut microbes.

METHODS AND RESULTS: Seven-week-old male mice consumed diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups were fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to ∼160 g of strawberry. After 12 weeks treatment, vascular inflammation was enhanced in HF vs C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppressed vascular inflammation in HF+SB vs. HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe was decreased in HF+SB. Importantly, circulating chemokines were positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).

CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS. This article is protected by copyright. All rights reserved.},
}

@article {pmid36112501,
year = {2022},
author = {Abdel-Rahman, LIH and Morgan, XC},
title = {Searching for a Consensus Among Inflammatory Bowel Disease Studies: A Systematic Meta-Analysis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izac194},
pmid = {36112501},
issn = {1536-4844},
support = {//Department of Microbiology and Immunology at the University of Otago/ ; },
abstract = {BACKGROUND: Numerous studies have examined the gut microbial ecology of patients with Crohn's disease (CD) and ulcerative colitis, but inflammatory bowel disease-associated taxa and ecological effect sizes are not consistent between studies.

METHODS: We systematically searched PubMed and Google Scholar and performed a meta-analysis of 13 studies to analyze how variables such as sample type (stool, biopsy, and lavage) affect results in inflammatory bowel disease gut microbiome studies, using uniform bioinformatic methods for all primary data.

RESULTS: Reduced alpha diversity was a consistent feature of both CD and ulcerative colitis but was more pronounced in CD. Disease contributed significantly variation in beta diversity in most studies, but effect size varied, and the effect of sample type was greater than the effect of disease. Fusobacterium was the genus most consistently associated with CD, but disease-associated genera were mostly inconsistent between studies. Stool studies had lower heterogeneity than biopsy studies, especially for CD.

CONCLUSIONS: Our results indicate that sample type variation is an important contributor to study variability that should be carefully considered during study design, and stool is likely superior to biopsy for CD studies due to its lower heterogeneity.},
}

@article {pmid36112189,
year = {2022},
author = {Peralta-Maraver, I and Rutere, C and Horn, MA and Reche, I and Behrends, V and Reiss, J and Robertson, AL},
title = {Intermediate Levels of Predation and Nutrient Enrichment Enhance the Activity of Ibuprofen-Degrading Bacteria.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36112189},
issn = {1432-184X},
support = {641939//Horizon 2020 Framework Programme/ ; },
abstract = {Water is the most indispensable natural resource; yet, organic pollution of freshwater sources is widespread. In recent years, there has been increasing concern over the vast array of emerging organic contaminants (EOCs) in the effluent of wastewater treatment plants (WWTPs). Several of these EOCs are degraded within the pore space of riverbeds by active microbial consortia. However, the mechanisms behind this ecosystem service are largely unknown. Here, we report how phosphate concentration and predator-prey interactions drive the capacity of bacteria to process a model EOC (ibuprofen). The presence of phosphate had a significant positive effect on the population growth rate of an ibuprofen-degrading strain. Thus, when phosphate was present, ibuprofen removal efficiency increased. Moreover, low and medium levels of predation, by a ciliated protozoan, stimulated bacterial population growth. This unimodal effect of predation was lost under high phosphate concentration, resulting in the flattening of the relationships between predator density and population growth of ibuprofen degraders. Our results suggest that moderate nutrient and predation levels promote the growth rate of bacterial degraders and, consequently, the self-purifying capability of the system. These findings enhance our understanding of the mechanisms by which riverbed communities drive the processing of EOCs.},
}

@article {pmid36111808,
year = {2022},
author = {Marzorati, M and Bubeck, S and Bayne, T and Krishnan, K and Giusto, M},
title = {Effects of combined prebiotic, probiotic, IgG and amino acid supplementation on the gut microbiome of patients with inflammatory bowel disease.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {},
doi = {10.2217/fmb-2022-0066},
pmid = {36111808},
issn = {1746-0921},
support = {//Microbiome Labs/ ; },
abstract = {Background: The effects of the Total Gut Restoration (TGR) system supplementation on the gut microbiome were evaluated. Materials & methods: A mucosal in vitro simulation of the human gastrointestinal tract (M-SHIME®) system was inoculated with fecal samples from patients with inflammatory bowel disease. Chambers were supplemented for 5 days with the TGR system (five probiotic Bacillus strains, prebiotic mixture, immunoglobulin concentrate, amino acids and prebiotic flavonoids). Results: Compared with unsupplemented controls, supplementation was associated with a significant increase in short-chain fatty acid production, and changes to the microbiome were observed. Supernatants from supplemented chambers improved intestinal barrier function, increased IL-6 and IL-10 production and decreased MCP1 production versus control in Caco-2/THP1 coculture. Conclusion: Daily TGR supplementation facilitated changes to the gut microbiome of patients with inflammatory bowel disease.},
}

@article {pmid36110415,
year = {2022},
author = {Song, W and Gong, H and Wang, Q and Zhang, L and Qiu, L and Hu, X and Han, H and Li, Y and Li, R and Li, Y},
title = {Using Bayesian networks with Max-Min Hill-Climbing algorithm to detect factors related to multimorbidity.},
journal = {Frontiers in cardiovascular medicine},
volume = {9},
number = {},
pages = {984883},
pmid = {36110415},
issn = {2297-055X},
abstract = {Objectives: Multimorbidity (MMD) is a medical condition that is linked with high prevalence and closely related to many adverse health outcomes and expensive medical costs. The present study aimed to construct Bayesian networks (BNs) with Max-Min Hill-Climbing algorithm (MMHC) algorithm to explore the network relationship between MMD and its related factors. We also aimed to compare the performance of BNs with traditional multivariate logistic regression model.

Methods: The data was downloaded from the Online Open Database of CHARLS 2018, a population-based longitudinal survey. In this study, we included 10 variables from data on demographic background, health status and functioning, and lifestyle. Missing value imputation was first performed using Random Forest. Afterward, the variables were included into logistic regression model construction and BNs model construction. The structural learning of BNs was achieved using MMHC algorithm and the parameter learning was conducted using maximum likelihood estimation.

Results: Among 19,752 individuals (9,313 men and 10,439 women) aged 64.73 ± 10.32 years, there are 9,129 ones without MMD (46.2%) and 10,623 ones with MMD (53.8%). Logistic regression model suggests that physical activity, sex, age, sleep duration, nap, smoking, and alcohol consumption are associated with MMD (P < 0.05). BNs, by establishing a complicated network relationship, reveals that age, sleep duration, and physical activity have a direct connection with MMD. It also shows that education levels are indirectly connected to MMD through sleep duration and residence is indirectly linked to MMD through sleep duration.

Conclusion: BNs could graphically reveal the complex network relationship between MMD and its related factors, outperforming traditional logistic regression model. Besides, BNs allows for risk reasoning for MMD through Bayesian reasoning, which is more consistent with clinical practice and thus holds some application prospects.},
}

@article {pmid36108399,
year = {2022},
author = {Sun, H and Xia, J and Wu, B and Ren, H and Zhang, X and Ye, L},
title = {Aerobic starvation treatment of activated sludge enhances the degradation efficiency of refractory organic compounds.},
journal = {Water research},
volume = {224},
number = {},
pages = {119069},
doi = {10.1016/j.watres.2022.119069},
pmid = {36108399},
issn = {1879-2448},
abstract = {Many refractory organic compounds (ROCs) in wastewater are toxic to human and aquatic organisms. Here, we reported an aerobic starvation approach to improve the degradation efficiencies of ROCs in activated sludge systems. The highest degradation rates of bisphenol AF (BPAF) (11.4 mg/g VSS · h) and gabapentin (GBP) (8.9 mg/g VSS · h) were achieved on the second day of the starvation process. While, the degradation rate of bisphenol A (BPA) on the 43rd day reached the maximum value of 0.8 mg/g VSS ·h, which was significantly higher than that of the seeding sludge (0.01 mg/g VSS · h). To investigate the mechanisms of this finding, we applied magnetic-nanoparticle mediated isolation, 16S rRNA gene sequencing, metagenomic sequencing and metatranscriptomic sequencing to analyze the microbial community structures and functions during the starvation process. The results showed that the increase of the BPA degradation ability was caused by the increase of the relative abundance of BPA degrading bacteria (Sphingomonas, Achromobacter, etc.), while, the enhancement of BPAF and GBP degradation was attributed to the increase of the expression of ROC degrading genes. Overall, these results improve our understanding of the microbial ecology of starved activated sludge and provide useful information for the future development of ROC removal technologies.},
}

@article {pmid36106503,
year = {2022},
author = {Law, CKY and Bolea-Fernandez, E and Liu, T and Bonin, L and Wallaert, E and Verbeken, K and De Gusseme, B and Vanhaecke, F and Boon, N},
title = {The influence of H2 partial pressure on biogenic palladium nanoparticle production assessed by single-cell ICP-mass spectrometry.},
journal = {Microbial biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-7915.14140},
pmid = {36106503},
issn = {1751-7915},
support = {12ZA320N//Fonds Wetenschappelijk Onderzoek/ ; 826244//European Union's Horizon 2020 research and innovation program/ ; },
abstract = {The production of biogenic palladium nanoparticles (bio-Pd NPs) is widely studied due to their high catalytic activity, which depends on the size of nanoparticles (NPs). Smaller NPs (here defined as <100 nm) are more efficient due to their higher surface/volume ratio. In this work, inductively coupled plasma-mass spectrometry (ICP-MS), flow cytometry (FCM) and transmission electron microscopy (TEM) were combined to obtain insight into the formation of these bio-Pd NPs. The precipitation of bio-Pd NPs was evaluated on a cell-per-cell basis using single-cell ICP-MS (SC-ICP-MS) combined with TEM images to assess how homogenously the particles were distributed over the cells. The results provided by SC-ICP-MS were consistent with those provided by "bulk" ICP-MS analysis and FCM. It was observed that heterogeneity in the distribution of palladium over an entire cell population is strongly dependent on the Pd2+ concentration, biomass and partial H2 pressure. The latter three parameters affected the particle size, ranging from 15.6 to 560 nm, and exerted a significant impact on the production of the bio-Pd NPs. The TEM combined with SC-ICP-MS revealed that the mass distribution for bacteria with high Pd content (144 fg Pd cell-1) indicated the presence of a large number of very small NPs (D50 = 15.6 nm). These results were obtained at high cell density (1 × 105 ± 3 × 104 cells μl-1) and H2 partial pressure (180 ml H2). In contrast, very large particles (D50 = 560 nm) were observed at low cell density (3 × 104 ± 10 × 102 cells μl-1) and H2 partial pressure (10-100 ml H2). The influence of the H2 partial pressure on the nanoparticle size and the possibility of size-tuned nanoparticles are presented.},
}

@article {pmid36106339,
year = {2022},
author = {Van Wyk, JC and Sewell, BT and Danson, MJ and Tsekoa, TL and Sayed, MF and Cowan, DA},
title = {Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.},
journal = {Current research in structural biology},
volume = {4},
number = {},
pages = {256-270},
pmid = {36106339},
issn = {2665-928X},
abstract = {Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4-7.6 ​kJ/mol increase in the activation energy of thermal inactivation at 63 ​°C. High resolution X-ray crystal structures (1.15-1.80 ​Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 ​Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.},
}

@article {pmid36102128,
year = {2022},
author = {Sampson, MM and Polk, CM and Fairman, RT and DeWitt, ME and Leonard, MK and Davidson, L and McCurdy, L and Passaretti, CL},
title = {Monkeypox testing delays: The need for drastic expansion of education and testing for monkeypox virus.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-2},
doi = {10.1017/ice.2022.237},
pmid = {36102128},
issn = {1559-6834},
}

@article {pmid36100598,
year = {2022},
author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H},
title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {565},
pmid = {36100598},
issn = {2052-4463},
mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; },
abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.},
}

Bacteria/genetics
Databases, Genetic
High-Throughput Nucleotide Sequencing
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
South America
Water Microbiology

@article {pmid36100325,
year = {2022},
author = {Xu, Q and Vandenkoornhuyse, P and Li, L and Guo, J and Zhu, C and Guo, S and Ling, N and Shen, Q},
title = {Microbial generalists and specialists differently contribute to the community diversity in farmland soils.},
journal = {Journal of advanced research},
volume = {40},
number = {},
pages = {17-27},
pmid = {36100325},
issn = {2090-1224},
mesh = {Bacteria ; *Ecosystem ; Farms ; *Soil ; Soil Microbiology ; },
abstract = {INTRODUCTION: Microbial generalists and specialists are thought to have distinct impacts on community dynamics, while there have been limited efforts to estimate their contribution to microbial diversity.

OBJECTIVES: We aimed to resolve this research gap in microbial ecology to strengthen our understanding of the biogeography of microbial diversity, with implications for global-scale biodiversity mapping.

METHODS: Herein, we identified the ecological characteristics of microbial generalists and specialists across over 3,000 farmland soil samples from eleven countries that encompassed seven climate types.

RESULTS: Considering the distinct distributions of generalists and specialists in degree of connexions, betweenness and as key species in network topology, both generalists and specialists contributed to species interactions, though through different modalities. A stronger signature of deterministic processes in specialists indicated their lower tolerance to environment fluctuations. Generalists, in contrast, were more characterized by stochastic processes with higher diversification and transition rates that suggested more important roles in maintaining community stability when exposed to environmental disturbances. The relationship between latitude and diversity combining with distance-decay effects showed that generalists dampened microbial biogeographical patterns, with contrasting impacts by specialists.

CONCLUSION: By demonstrating the ecological characteristics of microbial generalists and specialists, this study deepens our understanding of microbial diversity and highlights the need to impart systematic distinctions among different categories of species when modelling and predicting the fate of ecosystems in the face of global climate change, rather than assuming that species are functionally equivalent.},
}

Bacteria
*Ecosystem
Farms
*Soil
Soil Microbiology

@article {pmid36098749,
year = {2022},
author = {Angelella, G and Nalam, V and Nachappa, P and White, J and Kaplan, I},
title = {Correction to: Endosymbionts Differentially Alter Exploratory Probing Behavior of a Nonpersistent Plant Virus Vector.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-022-02107-4},
pmid = {36098749},
issn = {1432-184X},
}

@article {pmid36094300,
year = {2022},
author = {Brugiroux, S and Berry, D and Ring, D and Barnich, N and Daims, H and Stecher, B},
title = {Specific Localization and Quantification of the Oligo-Mouse-Microbiota (OMM12) by Fluorescence In Situ Hybridization (FISH).},
journal = {Current protocols},
volume = {2},
number = {9},
pages = {e548},
doi = {10.1002/cpz1.548},
pmid = {36094300},
issn = {2691-1299},
mesh = {Animals ; In Situ Hybridization, Fluorescence/methods ; Mice ; *Microbiota ; Oligonucleotide Probes ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The oligo-mouse-microbiota (OMM12) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM12 strains on intestinal tissue cross sections. 16S rRNA-specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Localization and quantification of OMM12 single strains in mouse cecum cross section Support Protocol: Establishment of specific FISH probe set for OMM12 syncom.},
}

Animals
In Situ Hybridization, Fluorescence/methods
Mice
*Microbiota
Oligonucleotide Probes
RNA, Ribosomal, 16S/genetics

@article {pmid36087683,
year = {2022},
author = {Yaigoub, H and Fath, N and Tirichen, H and Wu, C and Li, R and Li, Y},
title = {Bidirectional crosstalk between dysbiotic gut microbiota and systemic lupus erythematosus: What is new in therapeutic approaches?.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {244},
number = {},
pages = {109109},
doi = {10.1016/j.clim.2022.109109},
pmid = {36087683},
issn = {1521-7035},
abstract = {Systemic lupus erythematosus is an autoimmune disease characterized by chronic inflammation and multiple organs damage. Its pathogenesis is complex and involves multiple factors including gut microbiota. Accumulating evidence indicates the interaction of microbial communities with the host immune system to maintain a state of homeostasis. Imbalances within the gut microbial composition and function may contribute to the development of many autoimmune diseases including SLE. In this review, we aim to highlight the dysregulation of commensal bacteria and their metabolites in the gastrointestinal tract and the resulting autoimmune responses in lupus and to decrypt the cross-link between the altered gut microbiota and the immune system in the SLE condition. We also provide new insights into targeting gut microbiota as a promising therapeutic approach to treat and manage SLE.},
}

@article {pmid36084824,
year = {2022},
author = {Van Winckel, T and Ngo, N and Sturm, B and Al-Omari, A and Wett, B and Bott, C and Vlaeminck, SE and De Clippeleir, H},
title = {Enhancing bioflocculation in high-rate activated sludge improves effluent quality yet increases sensitivity to surface overflow rate.},
journal = {Chemosphere},
volume = {308},
number = {Pt 2},
pages = {136294},
doi = {10.1016/j.chemosphere.2022.136294},
pmid = {36084824},
issn = {1879-1298},
abstract = {High-rate activated sludge (HRAS) relies on good bioflocculation and subsequent solid-liquid separation to maximize the capture of organics. However, full-scale applications often suffer from poor and unpredictable effluent suspended solids (ESS). While the biological aspects of bioflocculation are thoroughly investigated, the effects of fines (settling velocity < 0.6 m3/m2/h), shear and surface overflow rate (SOR) are unclear. This work tackled the impact of fines, shear, and SOR on the ESS in absence of settleable influent solids. This was assessed on a full-scale HRAS step-feed (SF) and pilot-scale HRAS contact-stabilization (CS) configuration using batch settling tests, controlled clarifier experiments, and continuous operation of reactors. Fines contributed up to 25% of the ESS in the full-scale SF configuration. ESS decreased up to 30 mg TSS/L when bioflocculation was enhanced with the CS configuration. The feast-famine regime applied in CS promoted the production of high-quality extracellular polymeric substances (EPS). However, this resulted in a narrow and unfavorable settling velocity distribution, with 50% ± 5% of the sludge mass settling between 0.6 and 1.5 m3/m2/h, thus increasing sensitivity towards SOR changes. A low shear environment (20 s-1) before the clarifier for at least one min was enough to ensure the best possible settling velocity distribution, regardless of prior shear conditions. Overall, this paper provides a more complete view on the drivers of ESS in HRAS systems, creating the foundation for the design of effective HRAS clarifiers. Tangible recommendations are given on how to manage fines and establish the optimal settling velocity of the sludge.},
}

@article {pmid36083443,
year = {2022},
author = {Fournier, GP and Parsons, CW and Cutts, EM and Tamre, E},
title = {Standard Candles for Dating Microbial Lineages.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2569},
number = {},
pages = {41-74},
pmid = {36083443},
issn = {1940-6029},
mesh = {Animals ; Bayes Theorem ; *Biological Evolution ; Eukaryotic Cells ; Evolution, Molecular ; *Fossils ; Phylogeny ; Plants/genetics ; },
abstract = {Molecular clock analyses are challenging for microbial phylogenies, due to a lack of fossil calibrations that can reliably provide absolute time constraints. An alternative source of temporal constraints for microbial groups is provided by the inheritance of proteins that are specific for the utilization of eukaryote-derived substrates, which have often been dispersed across the Tree of Life via horizontal gene transfer. In particular, animal, algal, and plant-derived substrates are often produced by groups with more precisely known divergence times, providing an older-bound on their availability within microbial environments. Therefore, these ages can serve as "standard candles" for dating microbial groups across the Tree of Life, expanding the reach of informative molecular clock investigations. Here, we formally develop the concept of substrate standard candles and describe how they can be propagated and applied using both microbial species trees and individual gene family phylogenies. We also provide detailed evaluations of several candidate standard candles and discuss their suitability in light of their often complex evolutionary and metabolic histories.},
}

Animals
Bayes Theorem
*Biological Evolution
Eukaryotic Cells
Evolution, Molecular
*Fossils
Phylogeny
Plants/genetics

@article {pmid36081452,
year = {2022},
author = {Duan, Q and Tian, L and Feng, J and Ping, X and Li, L and Yaigoub, H and Li, R and Li, Y},
title = {Trametenolic Acid Ameliorates the Progression of Diabetic Nephropathy in db/db Mice via Nrf2/HO-1 and NF-κB-Mediated Pathways.},
journal = {Journal of immunology research},
volume = {2022},
number = {},
pages = {6151847},
pmid = {36081452},
issn = {2314-7156},
mesh = {Albumins/metabolism ; Animals ; Antioxidants/metabolism ; Body Weight ; *Diabetes Mellitus ; *Diabetic Nephropathies/drug therapy ; Glutathione/metabolism ; Heme Oxygenase-1/metabolism ; Interleukin-6/metabolism ; Mice ; NF-E2-Related Factor 2/metabolism ; NF-kappa B/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism ; *Triterpenes/therapeutic use ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Diabetic nephropathy (DN) is a fatal complication of diabetes and the main cause of end-stage renal disease. Due to the suboptimal effects of current treatments, there is an urgent need to develop new therapeutic strategies for DN. Trametenolic acid (TA), a lanostane-type tetracyclic triterpenoid, is one of the main active ingredients extracted from the natural product Inonotus obliquus. Our study was aimed at clarifying the potential protective effects of TA on DN and its underlying mechanism. In this research, C57BLKS/db (db/db) mice were used as the spontaneous DN model, and TA (10 mg/kg/d) was intraperitoneally injected for 4 consecutive weeks. Ratio of right kidney weight/body weight was calculated, and the contents of serum creatinine (Scr), blood urea nitrogen (BUN), and urine albumin were detected. The activities of superoxide dismutase (SOD) and catalase (CAT) and the contents of reductive glutathione (GSH) and malondialdehyde (MDA) were measured. The histopathological changes of renal tissues were observed by hematoxylin and eosin (HE), periodic acid-Schiff (PAS), and Masson staining. The protein expressions of nuclear factor erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), NAD(P)H:quinone oxidoreductase-1 (NQO-1), nuclear factor kappa B (NF-κB), proinflammation cytokine tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-1β (IL-1β), Nephrin, and Podocin were detected by western blot assay. Immunohistochemistry was utilized to detect expressions of collagen III (COL-III) and fibronectin (FN). Our results showed that TA administration significantly reduced the ratio of right kidney weight/body weight, BUN, Scr, and urine albumin levels and alleviated the histopathological changes of DN mice. Moreover, TA administration remarkably increased GSH content and SOD and CAT activities and decreased MDA content. Western blot assay demonstrated that TA activated Nrf2 signaling and increased the expression of downstream antioxidant enzymes HO-1 and NQO-1. Further studies illustrated that NF-κB signaling was inhibited, and downstream proinflammation cytokine expressions of TNF-α, IL-6, and IL-1β were also downregulated. In addition, we also found that TA administration significantly increased the expression of nephrin and podocin proteins and reduced the protein expression of COL-III and FN. These findings suggested that TA exhibited a renoprotective effect by ameliorating oxidative stress and inflammation via Nrf2/HO-1 and NF-κB signaling pathways.},
}

Albumins/metabolism
Animals
Antioxidants/metabolism
Body Weight
*Diabetes Mellitus
*Diabetic Nephropathies/drug therapy
Glutathione/metabolism
Heme Oxygenase-1/metabolism
Interleukin-6/metabolism
Mice
NF-E2-Related Factor 2/metabolism
NF-kappa B/metabolism
Oxidative Stress
Superoxide Dismutase/metabolism
*Triterpenes/therapeutic use
Tumor Necrosis Factor-alpha/metabolism

@article {pmid36078654,
year = {2022},
author = {Zou, J and Yang, J and He, H and Wang, X and Mei, R and Cai, L and Li, J},
title = {Effect of Seed Sludge Type on Aerobic Granulation, Pollutant Removal and Microbial Community in a Sequencing Batch Reactor Treating Real Textile Wastewater.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {17},
pages = {},
doi = {10.3390/ijerph191710940},
pmid = {36078654},
issn = {1660-4601},
support = {2020C03080//Key Research and Development Program of Zhejiang Province/ ; LY21E080014//Basic public Welfare Research Program of Zhejiang Province/ ; 51708500//National Natural Science Foundation of China/ ; },
mesh = {Aerobiosis ; Bioreactors/microbiology ; *Environmental Pollutants ; *Microbiota ; Nitrogen ; Sewage/microbiology ; Textiles ; Waste Disposal, Fluid/methods ; Waste Water ; },
abstract = {The aerobic granulation, pollutant removal, and microbial community in real textile wastewater (TWW) treatment were compared using conventional activated sludge (CAS) and preformed aerobic granular sludge (AGS) in synthetic wastewater as seed in two reactors, reactor-1 (R1) and reactor-2 (R2), respectively. The results showed that complete granulation was achieved in R1 (sludge volume index at 5 min (SVI5) and 30 min (SVI30): 19.4 mL/g; granule size: 210 μm) within 65 days, while it only required 28 days in R2 (SVI5 and SVI30: 27.3 mL/g; granule size: 496 μm). The removal of COD, NH4+-N and TN in R1 (49.8%, 98.8%, and 41.6%) and R2 (53.6%, 96.9%, and 40.8%) were comparable in 100% real TWW treatment, but stable performance was achieved much faster in R2. The real TWW had an inhibitory effect on heterotrophic bacteria activity, but it had no inhibition on ammonia-oxidizing bacteria activity. AGS with a larger particle size had a higher microbial tolerance to real TWW. Furthermore, filamentous Thiothrix in the AGS in R2 disappeared when treating real TWW, leading to the improvement of sludge settleability. Thus, seeding preformed AGS is suggested as a rapid start-up method for a robust AGS system in treating real TWW.},
}

Aerobiosis
Bioreactors/microbiology
*Environmental Pollutants
*Microbiota
Nitrogen
Sewage/microbiology
Textiles
Waste Disposal, Fluid/methods
Waste Water

@article {pmid36077481,
year = {2022},
author = {Villalba, LA and Kasada, M and Zoccarato, L and Wollrab, S and Grossart, HP},
title = {Differing Escape Responses of the Marine Bacterium Marinobacter adhaerens in the Presence of Planktonic vs. Surface-Associated Protist Grazers.},
journal = {International journal of molecular sciences},
volume = {23},
number = {17},
pages = {},
pmid = {36077481},
issn = {1422-0067},
support = {not asigned yet//Leibniz Association/ ; },
mesh = {Bacteria ; Ecosystem ; Humans ; Marinobacter ; *Plankton ; *Stramenopiles ; Water ; },
abstract = {Protist grazing pressure plays a major role in controlling aquatic bacterial populations, affecting energy flow through the microbial loop and biogeochemical cycles. Predator-escape mechanisms might play a crucial role in energy flow through the microbial loop, but are yet understudied. For example, some bacteria can use planktonic as well as surface-associated habitats, providing a potential escape mechanism to habitat-specific grazers. We investigated the escape response of the marine bacterium Marinobacter adhaerens in the presence of either planktonic (nanoflagellate: Cafeteria roenbergensis) or surface-associated (amoeba: Vannella anglica) protist predators, following population dynamics over time. In the presence of V. anglica, M. adhaerens cell density increased in the water, but decreased on solid surfaces, indicating an escape response towards the planktonic habitat. In contrast, the planktonic predator C. roenbergensis induced bacterial escape to the surface habitat. While C. roenbergensis cell numbers dropped substantially after a sharp initial increase, V. anglica exhibited a slow, but constant growth throughout the entire experiment. In the presence of C. roenbergensis, M. adhaerens rapidly formed cell clumps in the water habitat, which likely prevented consumption of the planktonic M. adhaerens by the flagellate, resulting in a strong decline in the predator population. Our results indicate an active escape of M. adhaerens via phenotypic plasticity (i.e., behavioral and morphological changes) against predator ingestion. This study highlights the potentially important role of behavioral escape mechanisms for community composition and energy flow in pelagic environments, especially with globally rising particle loads in aquatic systems through human activities and extreme weather events.},
}

Bacteria
Ecosystem
Humans
Marinobacter
*Plankton
*Stramenopiles
Water

@article {pmid36076760,
year = {2022},
author = {Mutalub, YB and Abdulwahab, M and Mohammed, A and Yahkub, AM and Al-Mhanna, SB and Yusof, W and Tang, SP and Rasool, AHG and Mokhtar, SS},
title = {Gut Microbiota Modulation as a Novel Therapeutic Strategy in Cardiometabolic Diseases.},
journal = {Foods (Basel, Switzerland)},
volume = {11},
number = {17},
pages = {},
pmid = {36076760},
issn = {2304-8158},
support = {1001/PPSP/8012346//Universiti Sains Malaysia/ ; },
abstract = {The human gut harbors microbial ecology that is in a symbiotic relationship with its host and has a vital function in keeping host homeostasis. Inimical alterations in the composition of gut microbiota, known as gut dysbiosis, have been associated with cardiometabolic diseases. Studies have revealed the variation in gut microbiota composition in healthy individuals as compared to the composition of those with cardiometabolic diseases. Perturbation of host-microbial interaction attenuates physiological processes and may incite several cardiometabolic disease pathways. This imbalance contributes to cardiometabolic diseases via metabolism-independent and metabolite-dependent pathways. The aim of this review was to elucidate studies that have demonstrated the complex relationship between the intestinal microbiota as well as their metabolites and the development/progression of cardiometabolic diseases. Furthermore, we systematically itemized the potential therapeutic approaches for cardiometabolic diseases that target gut microbiota and/or their metabolites by following the pathophysiological pathways of disease development. These approaches include the use of diet, prebiotics, and probiotics. With the exposition of the link between gut microbiota and cardiometabolic diseases, the human gut microbiota therefore becomes a potential therapeutic target in the development of novel cardiometabolic agents.},
}

@article {pmid36076344,
year = {2022},
author = {Xu, H and Qian, Y and Jia, S and Shi, Z and Zhong, Q},
title = {Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.14373},
pmid = {36076344},
issn = {1601-0825},
abstract = {In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes of the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.},
}

@article {pmid36075785,
year = {2022},
author = {Martín-Rodríguez, AJ},
title = {Respiration-induced biofilm formation as a driver for bacterial niche colonization.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2022.08.007},
pmid = {36075785},
issn = {1878-4380},
abstract = {Depending on their physiology and metabolism, bacteria can carry out diverse redox processes for energy acquisition, which facilitates adaptation to environmental or host-associated niches. Of these processes, respiration, using oxygen or alternative terminal electron acceptors, is energetically the most favorable in heterotrophic bacteria. The biofilm lifestyle, a coordinated multicellular behavior, is ubiquitous in bacteria and is regulated by a variety of intrinsic and extrinsic cues. Respiration of distinct electron acceptors has been shown to induce biofilm formation or dispersal. The notion of biofilm formation regulation by electron acceptor availability and respiration has often been considered species-specific. However, recent evidence suggests that this phenomenon can be strain-specific, even in strains sharing the same functional respiratory pathways, thereby implying subtle regulatory mechanisms. On this basis, I argue that induction of biofilm formation by sensing and respiration of electron acceptors might direct subgroups of redox-specialized strains to occupy certain niches. A palette of respiration and electron-transfer-mediated microbial social interactions within biofilms may broaden ecological opportunities. The strain specificity of this phenomenon represents an important opportunity to identify key molecular mechanisms and their ecophysiological significance, which in turn may lay the ground for applications in areas ranging from biotechnology to the prevention of antimicrobial resistance.},
}

@article {pmid36075698,
year = {2022},
author = {Van Holm, W and Verspecht, T and Carvalho, R and Bernaerts, K and Boon, N and Zayed, N and Teughels, W},
title = {Glycerol strengthens probiotic effect of Limosilactobacillus reuteri in oral biofilms: a synergistic synbiotic approach.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12386},
pmid = {36075698},
issn = {2041-1014},
abstract = {Both in vitro and in vivo studies have shown that the probiotic Limosilactobacillus reuteri can improve oral health. L. reuteri species are known to produce the antimicrobial 'reuterin' from glycerol. In order to further increase its antimicrobial activity, this study evaluated the effect of the combined use of glycerol and Limosilactobacillus reuteri (ATCC PTA 5289) in view of using a synergistic synbiotic over a probiotic. An antagonistic agar growth and a multispecies biofilm model showed that the antimicrobial potential of the probiotic was significantly enhanced against periodontal pathobionts and anaerobic commensals when supplemented with glycerol. Synbiotic biofilms also showed a significant reduction in inflammatory expression of human oral keratinocytes (HOK-18A), but only when the keratinocytes were preincubated with the probiotic. Probiotic preincubation of keratinocytes or probiotic- and synbiotic treatment of biofilms alone were insufficient to significantly reduce inflammatory expression. Overall, this study shows that combining glycerol with the probiotic L. reuteri into a synergistic synbiotic can greatly improve the effectiveness of the latter. One sentence summary: The use of a synbiotic formulation of Limosilactobacillus reuteri with glycerol over the probiotic improves antimicrobial effects and reduced inflammatory response to oral biofilms. This article is protected by copyright. All rights reserved.},
}

@article {pmid36073497,
year = {2022},
author = {Lammers, A and Nazipi, S and Zweers, H and Bilde, T and Schramm, A and Garbeva, P and Lalk, M},
title = {Antimicrobial Volatiles emitted by Members of the Nest Microbiome of Social Spiders.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnac088},
pmid = {36073497},
issn = {1574-6968},
abstract = {Microbes produce and respond to a range of structurally and functionally diverse volatiles. Many microbial volatiles have antimicrobial properties. Since volatiles can diffuse through complex three-dimensional systems like spider nests they are promising pathogen protection for social arthropods. Here, we analyzed the volatilomes of five nest microbiome members of the Namibian, social spider Stegodyphus dumicola, namely the bacteria Massilia sp. IC2-278, Massilia sp. IC2-477, Sphingomonas sp. IC-11, Streptomyces sp. IC-207, and the fungus Aureobasidium sp. CE_32, and tested their antimicrobial activity against two putative spider pathogens, namely Bacillus thuringiensis and Purpureocillium lilacinum. Most nest microbiome members released volatilomes with antibacterial and/or antifungal activities under in vitro conditions. The analysis of their volatilomes using GC/Q-TOF revealed that they include numerous antimicrobial volatiles. We tested the antimicrobial activity of five pure volatile compounds found in the volatilomes and revealed that all of them were antibacterial and/or antifungal. We could not identify the same antimicrobial volatiles as in a previous in situ study, but our results indicate that social spider-associated microorganisms as a source of antimicrobial volatiles are important for pathogen inhibition. Additionally, we showed the influence of the volatilomes on the antibiotic sensitivity of B. thuringiensis offering novel approaches to counter antibiotic resistance.},
}

@article {pmid36073311,
year = {2022},
author = {McLean, AR and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Welch, JLM},
title = {Site-tropism of streptococci in the oral microbiome.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.12387},
pmid = {36073311},
issn = {2041-1014},
abstract = {A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provides species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content. This article is protected by copyright. All rights reserved.},
}

@article {pmid36069784,
year = {2022},
author = {Hahn, MW and Pitt, A and Schmidt, J and Koll, U and Wolf, J and Whitman, WB and Bodelier, PLE and Neumann-Schaal, M},
title = {Zwartia hollandica gen. nov., sp. nov., Jezberella montanilacus gen. nov., sp. nov. and Sheuella amnicola gen. nov., comb. nov., representing the environmental GKS98 (betIII) cluster.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {72},
number = {9},
pages = {},
doi = {10.1099/ijsem.0.005513},
pmid = {36069784},
issn = {1466-5034},
mesh = {*Alcaligenaceae/genetics ; Animals ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Gastropoda ; Lakes ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; },
abstract = {We present two strains affiliated with the GKS98 cluster. This phylogenetically defined cluster is representing abundant, mainly uncultured freshwater bacteria, which were observed by many cultivation-independent studies on the diversity of bacteria in various freshwater lakes and streams. Bacteria affiliated with the GKS98 cluster were detected by cultivation-independent methods in freshwater systems located in Europe, Asia, Africa and the Americas. The two strains, LF4-65T (=CCUG 56422T=DSM 107630T) and MWH-P2sevCIIIbT (=CCUG 56420T=DSM 107629T), are aerobic chemoorganotrophs, both with genome sizes of 3.2 Mbp and G+C values of 52.4 and 51.0 mol%, respectively. Phylogenomic analyses based on concatenated amino acid sequences of 120 proteins suggest an affiliation of the two strains with the family Alcaligenaceae and revealed Orrella amnicola and Orrella marina (= Algicoccus marinus) as being the closest related, previously described species. However, the calculated phylogenomic trees clearly suggest that the current genus Orrella represents a polyphyletic taxon. Based on the branching order in the phylogenomic trees, as well as the revealed phylogenetic distances and chemotaxonomic traits, we propose to establish the new genus Zwartia gen. nov. and the new species Z. hollandica sp. nov. to harbour strain LF4-65T and the new genus Jezberella gen. nov. and the new species J. montanilacus sp. nov. to harbour strain MWH-P2sevCIIIbT. Furthermore, we propose the reclassification of the species Orrella amnicola in the new genus Sheuella gen. nov. The new genera Zwartia, Jezberella and Sheuella together represent taxonomically the GKS98 cluster.},
}

*Alcaligenaceae/genetics
Animals
Bacteria/genetics
Bacterial Typing Techniques
Base Composition
DNA, Bacterial/genetics
Fatty Acids/chemistry
*Gastropoda
Lakes
Phylogeny
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA

@article {pmid36069437,
year = {2022},
author = {Eddie, BJ and Bird, LJ and Pelikan, C and Mussmann, M and Martínez-Pérez, C and Pinamang, P and Malanoski, AP and Glaven, SM},
title = {Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0022322},
doi = {10.1128/msphere.00223-22},
pmid = {36069437},
issn = {2379-5042},
abstract = {Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.},
}

@article {pmid36068360,
year = {2022},
author = {Xie, Z and Xu, G and Miao, F and Kong, H and Hu, M and Wang, Y},
title = {Predator Presence Alters Intestinal Microbiota in Mussel.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36068360},
issn = {1432-184X},
support = {31872587//National Natural Science Foundation of China/ ; },
abstract = {Intestinal microbes are essential participants in host vital activities. The composition of the microbiota is closely related to the environmental factors. Predator presence may impact on intestinal microbiota of prey. In the present study, stone crab Charybdis japonica was used as potential predator, an external stress on mussel Mytilus coruscus, to investigate the intestinal microbiota alteration in M. coruscus. We set up two forms of predator presence including free crab and trapped crab, with a blank treatment without crab. The composition of intestinal microbiota in mussels among different treatments showed significant differences by 16S rRNA techniques. The biodiversity increased with trapped crab presence, but decreased with free crab presence. Neisseria, the most abundant genus, fell with the presence of crabs. Besides, the Arcobacter, a kind of pathogenic bacteria, increased with free crab presence. Regarding PICRUTs analysis, Environmental Information Processing, Genetic Information Processing and Metabolism showed differences in crab presence treatments compared with the blank, with a bit higher in the presence of free crab than trapped crab. In conclusion, trapped crab effects activated the metabolism and immunity of the intestinal flora, but free crabs made mussels more susceptible to disease and mortality, corresponding to the decreased biodiversity and the increased Arcobacter in their intestine.},
}

@article {pmid36067300,
year = {2022},
author = {Saunders, JK and McIlvin, MR and Dupont, CL and Kaul, D and Moran, DM and Horner, T and Laperriere, SM and Webb, EA and Bosak, T and Santoro, AE and Saito, MA},
title = {Microbial functional diversity across biogeochemical provinces in the central Pacific Ocean.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {37},
pages = {e2200014119},
pmid = {36067300},
issn = {1091-6490},
support = {NPP Postdoctoral Fellowship//NASA | NASA Astrobiology Institute (NAI)/ ; OCE-1850719//National Science Foundation (NSF)/ ; GM135709-01A1//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01 GM135709/GM/NIGMS NIH HHS/United States ; Simons Early Career Investigator Fellowship//Simons Foundation (SF)/ ; OCE-1736599//National Science Foundation (NSF)/ ; OCE-1259994//National Science Foundation (NSF)/ ; OCE-1437310//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//Joint Genome Institute (JGI)/ ; 3782//Gordon and Betty Moore Foundation (GBMF)/ ; OCE-1031271//National Science Foundation (NSF)/ ; 8453//Gordon and Betty Moore Foundation (GBMF)/ ; Sloan Research Fellowship//Alfred P. Sloan Foundation (APSF)/ ; OCE-1924554//National Science Foundation (NSF)/ ; OCE-1657766//National Science Foundation (NSF)/ ; },
mesh = {Archaea/classification/enzymology ; *Archaeal Proteins/analysis ; Bacteria/classification/enzymology ; *Bacterial Proteins/analysis ; Biodiversity ; *Microbiota ; *Nitrification ; Nitrite Reductases/metabolism ; Pacific Ocean ; Proteomics/methods ; *Seawater/microbiology ; },
abstract = {Enzymes catalyze key reactions within Earth's life-sustaining biogeochemical cycles. Here, we use metaproteomics to examine the enzymatic capabilities of the microbial community (0.2 to 3 µm) along a 5,000-km-long, 1-km-deep transect in the central Pacific Ocean. Eighty-five percent of total protein abundance was of bacterial origin, with Archaea contributing 1.6%. Over 2,000 functional KEGG Ontology (KO) groups were identified, yet only 25 KO groups contributed over half of the protein abundance, simultaneously indicating abundant key functions and a long tail of diverse functions. Vertical attenuation of individual proteins displayed stratification of nutrient transport, carbon utilization, and environmental stress. The microbial community also varied along horizontal scales, shaped by environmental features specific to the oligotrophic North Pacific Subtropical Gyre, the oxygen-depleted Eastern Tropical North Pacific, and nutrient-rich equatorial upwelling. Some of the most abundant proteins were associated with nitrification and C1 metabolisms, with observed interactions between these pathways. The oxidoreductases nitrite oxidoreductase (NxrAB), nitrite reductase (NirK), ammonia monooxygenase (AmoABC), manganese oxidase (MnxG), formate dehydrogenase (FdoGH and FDH), and carbon monoxide dehydrogenase (CoxLM) displayed distributions indicative of biogeochemical status such as oxidative or nutritional stress, with the potential to be more sensitive than chemical sensors. Enzymes that mediate transformations of atmospheric gases like CO, CO2, NO, methanethiol, and methylamines were most abundant in the upwelling region. We identified hot spots of biochemical transformation in the central Pacific Ocean, highlighted previously understudied metabolic pathways in the environment, and provided rich empirical data for biogeochemical models critical for forecasting ecosystem response to climate change.},
}

Archaea/classification/enzymology
*Archaeal Proteins/analysis
Bacteria/classification/enzymology
*Bacterial Proteins/analysis
Biodiversity
*Microbiota
*Nitrification
Nitrite Reductases/metabolism
Pacific Ocean
Proteomics/methods
*Seawater/microbiology

@article {pmid36067150,
year = {2022},
author = {Wilberts, L and Vuts, J and Caulfield, JC and Thomas, G and Birkett, MA and Herrera-Malaver, B and Verstrepen, KJ and Sobhy, IS and Jacquemyn, H and Lievens, B},
title = {Impact of endophytic colonization by entomopathogenic fungi on the behavior and life history of the tobacco peach aphid Myzus persicae var. nicotianae.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0273791},
pmid = {36067150},
issn = {1932-6203},
mesh = {Animals ; *Aphids/physiology ; *Beauveria/physiology ; *Capsicum ; Insecta ; Tobacco ; },
abstract = {Entomopathogenic fungi can adopt an endophytic lifestyle and provide protection against insect herbivores and plant pathogens. So far, most studies have focused on Beauveria bassiana to increase plant resistance against abiotic and biotic stresses, while only little is known for other entomopathogenic fungi. In this study, we investigated whether root inoculation of sweet pepper (Capsicum annuum L.) by the entomopathogenic fungi Akanthomyces muscarius ARSEF 5128 and B. bassiana ARSEF 3097 can improve resistance against the tobacco peach aphid Myzus persicae var. nicotianae. First, dual-choice experiments were performed to test the hypothesis that the fungi deter aphids via modifying plant volatile profiles. Next, we tested the hypothesis that endophytic colonization negatively affects aphid life history traits, such as fecundity, development and mortality rate. Aphids were significantly attracted to the odor of plants inoculated with A. muscarius over non-inoculated plants. Plants inoculated with A. muscarius emitted significantly higher amounts of β-pinene than non-inoculated plants, and significantly higher amounts of indole than B. bassiana-inoculated and non-inoculated plants. Inoculation with the fungal strains also caused significantly higher emission of terpinolene. Further, both aphid longevity and fecundity were significantly reduced by 18% and 10%, respectively, when feeding on plants inoculated with A. muscarius, although intrinsic rate of population increase did not differ between inoculated and non-inoculated plants. Sweet pepper plants inoculated with B. bassiana ARSEF 3097 did not elicit a significant behavioral response nor affected the investigated life history traits. We conclude that endophytic colonization by entomopathogenic fungi has the potential to alter olfactory behavior and performance of M. persicae var. nicotianae, but effects are small and depend on the fungal strain used.},
}

Animals
*Aphids/physiology
*Beauveria/physiology
*Capsicum
Insecta
Tobacco

@article {pmid36065063,
year = {2022},
author = {Nottingham, AT and Scott, JJ and Saltonstall, K and Broders, K and Montero-Sanchez, M and Püspök, J and Bååth, E and Meir, P},
title = {Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {36065063},
issn = {2058-5276},
support = {NE/T012226//RCUK | Natural Environment Research Council (NERC)/ ; NE/K01627X/1//RCUK | Natural Environment Research Council (NERC)/ ; FP7-2012-329360//EC | EC Seventh Framework Programm | FP7 Ideas: European Research Council (FP7-IDEAS-ERC - Specific Programme: "Ideas" Implementing the Seventh Framework Programme of the European Community for Research, Technological Development and Demonstration Activities (2007 to 2013))/ ; },
abstract = {Perturbation of soil microbial communities by rising temperatures could have important consequences for biodiversity and future climate, particularly in tropical forests where high biological diversity coincides with a vast store of soil carbon. We carried out a 2-year in situ soil warming experiment in a tropical forest in Panama and found large changes in the soil microbial community and its growth sensitivity, which did not fully explain observed large increases in CO2 emission. Microbial diversity, especially of bacteria, declined markedly with 3 to 8 °C warming, demonstrating a breakdown in the positive temperature-diversity relationship observed elsewhere. The microbial community composition shifted with warming, with many taxa no longer detected and others enriched, including thermophilic taxa. This community shift resulted in community adaptation of growth to warmer temperatures, which we used to predict changes in soil CO2 emissions. However, the in situ CO2 emissions exceeded our model predictions threefold, potentially driven by abiotic acceleration of enzymatic activity. Our results suggest that warming of tropical forests will have rapid, detrimental consequences both for soil microbial biodiversity and future climate.},
}

@article {pmid36064650,
year = {2022},
author = {Morillo-Lopez, V and Sjaarda, A and Islam, I and Borisy, GG and Mark Welch, JL},
title = {Corncob structures in dental plaque reveal microhabitat taxon specificity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {145},
pmid = {36064650},
issn = {2049-2618},
support = {DE027958/NH/NIH HHS/United States ; DE022586/NH/NIH HHS/United States ; },
mesh = {Bacteria/genetics ; Biofilms ; *Dental Plaque ; Humans ; In Situ Hybridization, Fluorescence/methods ; Mouth/microbiology ; Streptococcus ; *Zea mays ; },
abstract = {BACKGROUND: The human mouth is a natural laboratory for studying how bacterial communities differ across habitats. Different bacteria colonize different surfaces in the mouth-teeth, tongue dorsum, and keratinized and non-keratinized epithelia-despite the short physical distance between these habitats and their connection through saliva. We sought to determine whether more tightly defined microhabitats might have more tightly defined sets of resident bacteria. A microhabitat may be characterized, for example, as the space adjacent to a particular species of bacterium. Corncob structures of dental plaque, consisting of coccoid bacteria bound to filaments of Corynebacterium cells, present an opportunity to analyze the community structure of one such well-defined microhabitat within a complex natural biofilm. Here, we investigate by fluorescence in situ hybridization and spectral imaging the composition of the cocci decorating the filaments.

RESULTS: The range of taxa observed in corncobs was limited to a small subset of the taxa present in dental plaque. Among four major groups of dental plaque streptococci, two were the major constituents of corncobs, including one that was the most abundant Streptococcus species in corncobs despite being relatively rare in dental plaque overall. Images showed both Streptococcus types in corncobs in all individual donors, suggesting that the taxa have different ecological roles or that mechanisms exist for stabilizing the persistence of functionally redundant taxa in the population. Direct taxon-taxon interactions were observed not only between the Streptococcus cells and the central corncob filament but also between Streptococcus cells and the limited subset of other plaque bacteria detected in the corncobs, indicating species ensembles involving these taxa as well.

CONCLUSIONS: The spatial organization we observed in corncobs suggests that each of the microbial participants can interact with multiple, albeit limited, potential partners, a feature that may encourage the long-term stability of the community. Additionally, our results suggest the general principle that a precisely defined microhabitat will be inhabited by a small and well-defined set of microbial taxa. Thus, our results are important for understanding the structure and organizing principles of natural biofilms and lay the groundwork for future work to modulate and control biofilms for human health. Video Abstract.},
}

Bacteria/genetics
Biofilms
*Dental Plaque
Humans
In Situ Hybridization, Fluorescence/methods
Mouth/microbiology
Streptococcus
*Zea mays

@article {pmid36063938,
year = {2022},
author = {Navarrete, AA and Aburto, F and González-Rocha, G and Guzmán, CM and Schmidt, R and Scow, K},
title = {Anthropogenic degradation alter surface soil biogeochemical pools and microbial communities in an Andean temperate forest.},
journal = {The Science of the total environment},
volume = {854},
number = {},
pages = {158508},
doi = {10.1016/j.scitotenv.2022.158508},
pmid = {36063938},
issn = {1879-1026},
abstract = {Soil microbial communities regulate a myriad of critical biogeochemical functions in forest ecosystems. Anthropogenic disturbances in natural forests could drive major shifts in plant and microbial communities resulting in substantial biogeochemical alterations. We evaluated the effect of anthropogenic disturbances in the soils of Andean temperate forests with different levels of degradation: i) mature forest (MF), ii) secondary forest (SF), iii) degraded forest (DF), and iv) deforested site converted into a prairie (DP). We quantified total soil carbon, nitrogen and phosphorous (TC, TN, and TP), and available nutrient stocks. The soil microbial community structure (i.e., composition, diversity, and abundance) was assessed under each condition from amplicon sequence variants (ASVs) obtained via NGS-Illumina sequencing and subsequent microbiome analysis. There were no significant differences in TC, TN, and TP across the forested states (MF, SF, DF). The deforested site condition presented significantly higher soil TC, TN, and TP and the lowest C:N, C:P, and N:P ratios. The DP soil microbiome was significantly more diverse in bacteria (D' = 0.47 ± 0.04); and fungi (H' = 5.11 ± 0.33). The bacterial microbiome was dominated by Proteobacteria (45.35 ± 0.89 %), Acidobacteria (20.73 ± 1.48 %), Actinobacteria (12.59 ± 0.34 %), and Bacteroidetes (7.32 ± 0.36 %) phyla in all sites. The soil fungal community was dominated by the phyla Ascomycota (42.11 ± 0.95 %), Mortierellomycota (28.74 ± 2.25 %), Basidiomycota (24.61 ± 0.52), and Mucoromycota (2.06 ± 0.43 %). Yet, there were significant differences at the genus level across conditions. Forest to prairie conversion facilitated the introduction of exotic bacterial and fungal taxa associated with agricultural activities and livestock grazing (∼50 % of DP core microbiome composed of unique ASVs). For example, the ammonia-oxidizing bacteria community emerged as a dominant group in the DP soils, along with a reduction in the ectomycorrhizal fungi community. The surface soil microbial community was surprisingly resistant to forest degradation and did not show a clear succession along the degradation gradient, but it was strongly altered after deforestation.},
}

@article {pmid36063436,
year = {2022},
author = {Li, YQ and Bletsa, M and Zisi, Z and Boonen, I and Gryseels, S and Kafetzopoulou, LE and Webster, JP and Catalano, S and Pybus, OG and Van de Perre, F and Li, HT and Li, YY and Li, YC and Abramov, A and Lymberakis, P and Lemey, P and Lequime, S},
title = {Endogenous viral elements in shrew genomes provide insights into Pestivirus ancient history.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msac190},
pmid = {36063436},
issn = {1537-1719},
abstract = {As viral genomic imprints in host genomes, endogenous viral elements (EVEs) shed light on the deep evolutionary history of viruses, ancestral host ranges, and ancient viral-host interactions. In addition, they may provide crucial information for calibrating viral evolutionary timescales. In this study, we conducted a comprehensive in silico screening of a large dataset of available mammalian genomes for EVEs deriving from members of the viral family Flaviviridae, an important group of viruses including well-known human pathogens, such as Zika, dengue, or hepatitis C viruses. We identified two novel pestivirus-like EVEs in the reference genome of the Indochinese shrew (Crocidura indochinensis). Homologs of these novel EVEs were subsequently detected in vivo by molecular detection and sequencing in 27 shrew species, including 26 species representing a wide distribution within the Crocidurinae subfamily and one in the Soricinae subfamily on different continents. Based on this wide distribution, we estimate that the integration event occurred before the last common ancestor of the subfamily, about 10.8 million years ago, attesting to an ancient origin of pestiviruses and Flaviviridae in general. Moreover, we provide the first description of Flaviviridae-derived EVEs in mammals even though the family encompasses numerous mammal-infecting members. This also suggests that shrews were past and perhaps also current natural reservoirs of pestiviruses. Taken together, our results expand the current known Pestivirus host range and provide novel insight into the ancient evolutionary history of pestiviruses and the Flaviviridae family in general.},
}

@article {pmid36061686,
year = {2022},
author = {Liu, B and Chen, J and Li, Y},
title = {Keystone Microorganisms Regulate the Methanogenic Potential in Coals with Different Coal Ranks.},
journal = {ACS omega},
volume = {7},
number = {34},
pages = {29901-29908},
pmid = {36061686},
issn = {2470-1343},
abstract = {Microorganisms are the core drivers of coal biogeochemistry and are closely related to the formation of coalbed methane. However, it remains poorly understood about the network relationship and stability of microbial communities in coals with different ranks. In this study, a high-throughput sequencing data set was analyzed to understand the microbial co-occurrence network in coals with different ranks including anthracite, medium-volatile bituminous, and high-volatile bituminous. The results showed similar topological properties for the microbial networks among coals with different ranks, but a great difference was found in the microbial composition in different large modules among coals with different ranks, and these three networks had three, four, and four large modules with seven, nine, and nine phyla, respectively. Among these networks, a total of 46 keystone taxa were identified in large modules, and these keystone taxa were different in coals with different ranks. Bacteria dominated the keystone taxa in the microbial network, and these bacterial keystone taxa mainly belonged to phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Besides, the removal of the key microbial data could reduce the community stability of microbial communities in bituminous coals. A partial least-squares path model further showed that these bacterial keystone taxa indirectly affected methanogenic potential by maintaining the microbial community stability and bacterial diversity. In summary, these results showed that keystone taxa played an important role in determining the community diversity, maintaining the microbial community stability, and controlling the methanogenic potential, which is of great significance for understanding the microbial ecology and the geochemical cycle of coal seams.},
}

@article {pmid36061525,
year = {2022},
author = {von Hoermann, C and Weithmann, S and Sikorski, J and Nevo, O and Szpila, K and Grzywacz, A and Grunwald, JE and Reckel, F and Overmann, J and Steiger, S and Ayasse, M},
title = {Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles.},
journal = {Royal Society open science},
volume = {9},
number = {8},
pages = {220555},
pmid = {36061525},
issn = {2054-5703},
abstract = {Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.},
}

@article {pmid36061322,
year = {2022},
author = {Jones, PA and Frischer, D and Mueller, S and Le, T and Schwanes, A and Govindaraju, A and Shalvarjian, K and Leducq, JB and Marx, CJ and Martinez-Gomez, NC and Lee, JA},
title = {Methylothon: a Versatile Course-Based High School Research Experience in Microbiology and Bioinformatics with Pink Bacteria.},
journal = {Journal of microbiology & biology education},
volume = {23},
number = {2},
pages = {},
pmid = {36061322},
issn = {1935-7877},
abstract = {Methylothon is an inquiry-based high school learning module in microbial ecology, molecular biology, and bioinformatics that centers around pink-pigmented plant-associated methylotrophic bacteria. Here, we present an overview of the module's learning goals, describe course resources (available for public use at http://methylothon.com), and relate lessons learned from adapting Methylothon for remote learning during the pandemic in spring of 2021. This curriculum description is intended not only for instructors but also for microbial ecology researchers with an interest in conducting K-12 outreach. The original in-person version of the module allows students to isolate their own strains of methylotrophic bacteria from plants they sample from the environment, to identify these using PCR, sequencing, and phylogenetic analysis, and to contribute their strains to original research in a university lab. The adapted version strengthens the focus on bioinformatics and increases its flexibility and accessibility by making the lab portion optional and adopting free web-based tools. Student feedback and graded assignments from spring 2021 revealed that the lesson was especially effective at introducing the concepts of BLAST and phylogenetic trees and that students valued and felt inspired by the opportunity to conduct hands-on work and to participate in community science.},
}

@article {pmid36059518,
year = {2022},
author = {Qing, J and Hu, X and Li, C and Song, W and Tirichen, H and Yaigoub, H and Li, Y},
title = {Fucose as a potential therapeutic molecule against the immune-mediated inflammation in IgA nepharopathy: An unrevealed link.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {929138},
pmid = {36059518},
issn = {1664-3224},
mesh = {Fucose ; *Gene Expression Profiling ; *Glomerulonephritis, IGA/drug therapy/genetics/metabolism ; Humans ; Immunoglobulin A/genetics ; Inflammation/genetics ; },
abstract = {Background: IgA nephropathy (IgAN) is an autoimmune disease that affects people of any age and is an important cause of end-stage renal disease. However, the pathogenesis and pathophysiology of IgAN is not clear. This article aimed to explore the immune-mediated inflammation and genetic mechanisms in IgAN.

Methods: The transcriptome sequencing data of IgAN glomeruli in the Gene Expression Omnibus database were downloaded. Single-sample gene set enrichment analysis was used to estimate the immune microenvironment of the merged microarray data and GSE141295. IgAN samples were divided into two clusters by cluster analysis. "limma" and "DEseq2" package in R were used to identify differentially expressed genes (DEGs). The weighted gene co-expression network analysis (WGCNA) was used to identify the co-expression modules related to inflammation in IgAN. R software package "clusterProfiler" was used for enrichment analysis, whereas Short Time-Series Expression Miner (STEM) analysis was used to identify the trend of gene expression. Machine-learn (ML) was performed using the shiny app. Finally, Drug Signatures Database (DSigDB) was used to identify potential molecules for treating IgAN.

Results: The infiltration of macrophages in IgAN glomeruli was increased, whereas CD4+ T cells, especially inducedregulatory T cells (iTregs) were decreased. A total of 1,104 common DEGs were identified from the merged data and GSE141295. Brown module was identified to have the highest inflammatory correlation with IgAN using WGCNA, and 15 hub genes were screened from this module. Among these 15 hub genes, 14 increased with the severity of IgAN inflammation based on STEM analysis. Neural network (nnet) is considered as the best model to predict the severity of IgAN. Fucose identified from DSigDB has a potential biological activity to treat IgAN.

Conclusion: The increase of macrophages and the decrease of iTregs in glomeruli represent the immune-mediated inflammation of IgAN, and fucose may be a potential therapeutic molecule against IgAN because it affects genes involved in the severe inflammation of IgAN.},
}

Fucose
*Gene Expression Profiling
*Glomerulonephritis, IGA/drug therapy/genetics/metabolism
Humans
Immunoglobulin A/genetics
Inflammation/genetics

@article {pmid36056428,
year = {2022},
author = {Ma, X and Wang, T and Shi, Z and Chiariello, NR and Docherty, K and Field, CB and Gutknecht, J and Gao, Q and Gu, Y and Guo, X and Hungate, BA and Lei, J and Niboyet, A and Le Roux, X and Yuan, M and Yuan, T and Zhou, J and Yang, Y},
title = {Correction: Long-term nitrogen deposition enhances microbial capacities in soil carbon stabilization but reduces network complexity.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {144},
pmid = {36056428},
issn = {2049-2618},
}

@article {pmid36056039,
year = {2022},
author = {Arandia-Gorostidi, N and Berthelot, H and Calabrese, F and Stryhanyuk, H and Klawonn, I and Iversen, M and Nahar, N and Grossart, HP and Ploug, H and Musat, N},
title = {Efficient carbon and nitrogen transfer from marine diatom aggregates to colonizing bacterial groups.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {14949},
pmid = {36056039},
issn = {2045-2322},
mesh = {Bacteria/metabolism ; Biomass ; Carbon/metabolism ; *Diatoms/metabolism ; Nitrogen/metabolism ; },
abstract = {Bacterial degradation of sinking diatom aggregates is key for the availability of organic matter in the deep-ocean. Yet, little is known about the impact of aggregate colonization by different bacterial taxa on organic carbon and nutrient cycling within aggregates. Here, we tracked the carbon (C) and nitrogen (N) transfer from the diatom Leptocylindrus danicus to different environmental bacterial groups using a combination of 13C and 15N isotope incubation (incubated for 72 h), CARD-FISH and nanoSIMS single-cell analysis. Pseudoalteromonas bacterial group was the first colonizing diatom-aggregates, succeeded by the Alteromonas group. Within aggregates, diatom-attached bacteria were considerably more enriched in 13C and 15N than non-attached bacteria. Isotopic mass balance budget indicates that both groups showed comparable levels of diatom C in their biomass, accounting for 19 ± 7% and 15 ± 11%, respectively. In contrast to C, bacteria of the Alteromonas groups showed significantly higher levels of N derived from diatoms (77 ± 28%) than Pseudoalteromonas (47 ± 17%), suggesting a competitive advantage for Alteromonas in the N-limiting environments of the deep-sea. Our results imply that bacterial succession within diatom aggregates may largely impact taxa-specific C and N uptake, which may have important consequences for the quantity and quality of organic matter exported to the deep ocean.},
}

Bacteria/metabolism
Biomass
Carbon/metabolism
*Diatoms/metabolism
Nitrogen/metabolism

@article {pmid36054689,
year = {2022},
author = {Calvo-Martin, E and Teira, E and Álvarez-Salgado, XA and Rocha, C and Jiang, S and Justel-Díez, M and Ibánhez, JSP},
title = {On the hidden diversity and niche specialization of the microbial realm of subterranean estuaries.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16160},
pmid = {36054689},
issn = {1462-2920},
support = {CTM2017-83362-R//Agencia Estatal de Investigación (Spain)/ ; IN606A-2021/022//Agencia Estatal de Investigación (Spain)/ ; INTERESproject//Agencia Estatal de Investigación (Spain)/ ; 713279//H2020 Marie Skłodowska-Curie Actions, Irish Research Council/ ; CLNE/2017/210//H2020 Marie Skłodowska-Curie Actions, Irish Research Council/ ; FPU PhD grant number FPU20/04707//Spanish Government/ ; IN606A-2021/022//Axencia Galega de Innovación/ ; },
abstract = {Subterranean estuaries (STEs) modulate the chemical composition of continental groundwater before it reaches the coast, but their microbial community is poorly known. Here, we explored the microbial ecology of two neighbouring, yet contrasting STEs (Panxón and Ladeira STEs; Ría de Vigo, NW Iberian Peninsula). We investigated microbial composition (16S rRNA gene sequencing), abundance, heterotrophic production and their geochemical drivers. A total of 10,150 OTUs and 59 phyla were retrieved from porewater sampled during four surveys covering each STE seepage face. In both STEs, we find a very diverse microbial community composed by abundant cosmopolitans and locally restricted rare taxa. Porewater oxygen and dissolved organic matter are the main environmental predictors of microbial community composition. More importantly, the high variety of benthic microbiota links to biogeochemical processes of different elements in STEs. The oxygen-rich Panxón beach showed strong associations of the ammonium oxidizing archaea Nitrosopumilales with the heterotrophic community, thus acting as a net source of nitrogen to the coast. On the other hand, the prevailing anoxic conditions of Ladeira beach promoted the dominance of anaerobic heterotrophs related to the degradation of complex and aromatic compounds, such as Dehalococcoidia and Desulfatiglans, and the co-occurrence of methane oxidizers and methanogens.},
}

@article {pmid36054683,
year = {2022},
author = {Fan, L and Chen, J and Pan, L and Xin, X and Geng, B and Yang, L and Wang, Q and Ma, W and Lou, Y and Bian, J and Cui, X and Li, J and Wang, L and Chen, Z and Wang, W and Cui, C and Li, S and Gao, Q and Song, Q and Deng, Y and Fan, J and Yu, J and Zhang, H and Li, Y and Cai, J},
title = {Alterations of gut microbiome, metabolome and lipidome in Takayasu arteritis.},
journal = {Arthritis & rheumatology (Hoboken, N.J.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/art.42331},
pmid = {36054683},
issn = {2326-5205},
abstract = {OBJECTIVE: Mounting evidences have linked microbiome and metabolome to systemic autoimmunity and cardiovascular diseases (CVDs). A rare disease sharing features of immune-related inflammatory diseases and CVDs, Takayasu arteritis (TA), has limited relative information. This study aimed to characterize gut microbial dysbiosis, and its crosstalk with phenotypes in TA.

METHODS: To address the discriminatory signatures, we performed shotgun sequencing of fecal metagenome across discovery cohort (n=97) and independent validation cohort (n=75) encompassing TA patients, healthy and Bechet's disease (BD) controls. Interrogation of untargeted metabolomics and lipidomics profiling of plasma and fecal samples was also employed to refine features mediating associations between microorganisms and TA phenotypes.

RESULTS: A combined model of bacterial species encompassing unclassified Escherichia, Veillonella parvula, Streptococcus parasanguinis, Dorea formicigenerans, Bifidobacterium adolescentis, Lachnospiraceae bacterium 7 1 58FAA, Escherichia coli, Streptococcus salivarius, Klebsiella pneumoniae, Bifidobacterium longum and Lachnospiraceae Bacterium 5 1 63FAA, discriminated TA from controls with area under curves (AUCs) of 87.8%, 85.9%, 81.1%, and 71.1% in training, test, validation sets including healthy or BD controls, respectively. Diagnostic species were directly or indirectly via metabolites or lipids correlated with TA phenotypes of vascular involvement, inflammation, discharge medication, and prognosis. External validation against publicly metagenomic studies (n=184) on hypertension, atrial fibrillation and healthy controls, confirmed the TA-diagnostic accuracy of the model.

CONCLUSION: This study firstly identifies the discriminatory gut microbes in TA. Dysbiotic microbes also link to TA phenotypes directly or indirectly via metabolic and lipid modules. Further explorations on microbiome-metagenome interface in TA subtype prediction and pathogenesis are indicated.},
}

@article {pmid36053304,
year = {2022},
author = {Trumhová, K and Klimešová, V and Pichrtová, M},
title = {Seasonal Dynamics of Zygnema (Zygnematophyceae) Mats from the Austrian Alps.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36053304},
issn = {1432-184X},
support = {980518//Univerzita Karlova v Praze/ ; 204069//Univerzita Karlova v Praze/ ; },
abstract = {Filamentous green algae of the genus Zygnema are an essential part of hydro-terrestrial ecosystems. Despite several studies on their resistance to natural stresses, little is known about the composition of their assemblages and the changes they undergo over time. Two sites at altitudes above 2200 m a.s.l. in the Austrian Alps were selected for a 2-year observation period and sampled five times. Molecular phylogenetic analysis of the 152 isolated strains of Zygnema sp. was performed based on the rbcL and trnG sequences. Seven genotypes were found at these sites during the samplings, but their proportion varied throughout the seasons. The site with a more stable water regime also had a more stable representation of genotypes, in contrast to the site with fluctuating water availability. The mats formed resistant pre-akinetes at the end of the season with reduced photosynthetic activity. Contrary to expectations, the mats were not exposed to extremely cold temperatures in winter due to snow cover. Some genotypes have been previously observed at this site, indicating that the population composition is stable. This work highlights the importance of resistant pre-akinetes in surviving winter conditions, the ability of algae to re-establish mats, and the need to address the hidden diversity of the genus Zygnema.},
}

@article {pmid36050462,
year = {2021},
author = {Fang, Y and Qin, X and Liao, Q and Du, R and Luo, X and Zhou, Q and Li, Z and Chen, H and Jin, W and Yuan, Y and Sun, P and Zhang, R and Zhang, J and Wang, L and Cheng, S and Yang, X and Yan, Y and Zhang, X and Zhang, Z and Bai, S and Van de Peer, Y and Lucas, WJ and Huang, S and Yan, J},
title = {The genome of homosporous maidenhair fern sheds light on the euphyllophyte evolution and defences.},
journal = {Nature plants},
volume = {8},
number = {9},
pages = {1024-1037},
pmid = {36050462},
issn = {2055-0278},
mesh = {*Adiantum/genetics ; *Ferns/genetics ; Genome, Plant ; Phylogeny ; },
abstract = {Euphyllophytes encompass almost all extant plants, including two sister clades, ferns and seed plants. Decoding genomes of ferns is the key to deep insight into the origin of euphyllophytes and the evolution of seed plants. Here we report a chromosome-level genome assembly of Adiantum capillus-veneris L., a model homosporous fern. This fern genome comprises 30 pseudochromosomes with a size of 4.8-gigabase and a contig N50 length of 16.22 Mb. Gene co-expression network analysis uncovered that homospore development in ferns has relatively high genetic similarities with that of the pollen in seed plants. Analysing fern defence response expands understanding of evolution and diversity in endogenous bioactive jasmonates in plants. Moreover, comparing fern genomes with those of other land plants reveals changes in gene families important for the evolutionary novelties within the euphyllophyte clade. These results lay a foundation for studies on fern genome evolution and function, as well as the origin and evolution of euphyllophytes.},
}

*Adiantum/genetics
*Ferns/genetics
Genome, Plant
Phylogeny

@article {pmid36049255,
year = {2022},
author = {Whitman, WB and Chuvochina, M and Hedlund, BP and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, I and Venter, SN},
title = {Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type.},
journal = {Systematic and applied microbiology},
volume = {45},
number = {5},
pages = {126305},
doi = {10.1016/j.syapm.2022.126305},
pmid = {36049255},
issn = {1618-0984},
support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; },
abstract = {Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.},
}

@article {pmid36048618,
year = {2022},
author = {Li, G and Wu, C and Wang, D and Srinivasan, V and Kaeli, DR and Dy, JG and Gu, AZ},
title = {Machine Learning-Based Determination of Sampling Depth for Complex Environmental Systems: Case Study with Single-Cell Raman Spectroscopy Data in EBPR Systems.},
journal = {Environmental science & technology},
volume = {56},
number = {18},
pages = {13473-13484},
doi = {10.1021/acs.est.1c08768},
pmid = {36048618},
issn = {1520-5851},
abstract = {Rapid progress in various advanced analytical methods, such as single-cell technologies, enable unprecedented and deeper understanding of microbial ecology beyond the resolution of conventional approaches. A major application challenge exists in the determination of sufficient sample size without sufficient prior knowledge of the community complexity and, the need to balance between statistical power and limited time or resources. This hinders the desired standardization and wider application of these technologies. Here, we proposed, tested and validated a computational sampling size assessment protocol taking advantage of a metric, named kernel divergence. This metric has two advantages: First, it directly compares data set-wise distributional differences with no requirements on human intervention or prior knowledge-based preclassification. Second, minimal assumptions in distribution and sample space are made in data processing to enhance its application domain. This enables test-verified appropriate handling of data sets with both linear and nonlinear relationships. The model was then validated in a case study with Single-cell Raman Spectroscopy (SCRS) phenotyping data sets from eight different enhanced biological phosphorus removal (EBPR) activated sludge communities located across North America. The model allows the determination of sufficient sampling size for any targeted or customized information capture capacity or resolution level. Promised by its flexibility and minimal restriction of input data types, the proposed method is expected to be a standardized approach for sampling size optimization, enabling more comparable and reproducible experiments and analysis on complex environmental samples. Finally, these advantages enable the extension of the capability to other single-cell technologies or environmental applications with data sets exhibiting continuous features.},
}

@article {pmid36048179,
year = {2022},
author = {Cook, K and Taylor, AD and Sharma, J and Taylor, DL},
title = {Inter-annual Persistence of Canopy Fungi Driven by Abundance Despite High Spatial Turnover.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36048179},
issn = {1432-184X},
support = {DEB-1355155//National Science Foundation/ ; },
abstract = {While it is now well established that fungal community composition varies spatially at a variety of scales, temporal turnover of fungi is less well understood. Here we studied inter-annual community compositional changes of fungi in a rainforest tree canopy environment. We tracked fungal community shifts over 3 years in three substrate types (live bryophytes, dead bryophytes, and host tree bark) and compared these changes to amounts of community turnover seen at small spatial scales in the same system. The effect of substrate type on fungal community composition was stronger than that of sampling year, which was very small but significant. Although levels of temporal turnover varied among substrates, with greater turnover in live bryophytes than other substrates, the amount of turnover from year to year was comparable to what is seen at spatial distances between 5 and 9 cm for the same substrate. Stability of communities was largely driven by a few fungi with high relative abundances. A majority of fungal occurrences were at low relative abundances (≤ 0.1%). These fungi tended to be short lived and persisted to following years ≤ 50% of the time, depending on substrate. Their presence and persistence are likely impacted by stochastic processes like dispersal limitation and disturbance. Most samples contained only one or a few fungi at high relative abundance (≥ 10%) that persisted half or more of the time. These more abundant and persistent fungi are expected to have sustained functional interactions within the canopy ecosystem.},
}

@article {pmid36047700,
year = {2022},
author = {Versluis, DM and Schoemaker, R and Looijesteijn, E and Muysken, D and Jeurink, PV and Paques, M and Geurts, JMW and Merks, RMH},
title = {A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0044622},
doi = {10.1128/msystems.00446-22},
pmid = {36047700},
issn = {2379-5077},
abstract = {The human intestinal microbiota starts to form immediately after birth and is important for the health of the host. During the first days, facultatively anaerobic bacterial species generally dominate, such as Enterobacteriaceae. These are succeeded by strictly anaerobic species, particularly Bifidobacterium species. An early transition to Bifidobacterium species is associated with health benefits; for example, Bifidobacterium species repress growth of pathogenic competitors and modulate the immune response. Succession to Bifidobacterium is thought to be due to consumption of intracolonic oxygen present in newborns by facultative anaerobes, including Enterobacteriaceae. To study if oxygen depletion suffices for the transition to Bifidobacterium species, here we introduced a multiscale mathematical model that considers metabolism, spatial bacterial population dynamics, and cross-feeding. Using publicly available metabolic network data from the AGORA collection, the model simulates ab initio the competition of strictly and facultatively anaerobic species in a gut-like environment under the influence of lactose and oxygen. The model predicts that individual differences in intracolonic oxygen in newborn infants can explain the observed individual variation in succession to anaerobic species, in particular Bifidobacterium species. Bifidobacterium species became dominant in the model by their use of the bifid shunt, which allows Bifidobacterium to switch to suboptimal yield metabolism with fast growth at high lactose concentrations, as predicted here using flux balance analysis. The computational model thus allows us to test the internal plausibility of hypotheses for bacterial colonization and succession in the infant colon. IMPORTANCE The composition of the infant microbiota has a great impact on infant health, but its controlling factors are still incompletely understood. The frequently dominant anaerobic Bifidobacterium species benefit health, e.g., they can keep harmful competitors under control and modulate the intestinal immune response. Controlling factors could include nutritional composition and intestinal mucus composition, as well as environmental factors, such as antibiotics. We introduce a modeling framework of a metabolically realistic intestinal microbial ecology in which hypothetical scenarios can be tested and compared. We present simulations that suggest that greater levels of intraintestinal oxygenation more strongly delay the dominance of Bifidobacterium species, explaining the observed variety of microbial composition and demonstrating the use of the model for hypothesis generation. The framework allowed us to test a variety of controlling factors, including intestinal mixing and transit time. Future versions will also include detailed modeling of oligosaccharide and mucin metabolism.},
}

@article {pmid36044056,
year = {2022},
author = {Li, W and Xie, L and Zhao, C and Hu, X and Yin, C},
title = {Nitrogen Fertilization Increases Soil Microbial Biomass and Alters Microbial Composition Especially Under Low Soil Water Availability.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
pmid = {36044056},
issn = {1432-184X},
abstract = {Soil microbial biomass and composition are affected by resource supply and water availability. However, the response of soil microbial communities to nitrogen fertilization under different water availability conditions is unclear. Therefore, this study conducted a 6-year pot experiment comprising five watering regimes (40%, 50%, 60%, 80%, and 100% of field capacity (FC)) and three nitrogen fertilization levels (NH4NO3 solution; 0 [N0], 20 [N1], and 40 [N2] g N m-2 year-1) to investigate soil microbial biomass, composition, and properties. The results indicated that soil microbial biomass and composition were more strongly affected by nitrogen fertilization compared with water regime. Nitrogen fertilization increased soil microbial biomass and altered soil microbial community composition, especially under low soil water availability. Soil microbial biomass was positively linearly associated with soil water regimes under N0, whereas it responded polynomially to soil water regimes under N1 and N2. The maximal soil microbial biomass was observed at FC80 for N1 and FC60 for N2. Furthermore, the biomass of soil microbial groups with high nitrogen and carbon acquisition ability as well as the enzyme activities of carbon and nitrogen cycling (β-1,4-glucosidase and β-1,4-N-acetyl-glucosaminidase, respectively) were stimulated by nitrogen fertilization. Soil microbial biomass was affected directly by nitrogen fertilization and indirectly by nitrogen and water regimes, via altering soil pH, dissolved inorganic nitrogen (NH4+-N and NO3--N) concentration, and soil organic carbon concentration. This study provides new insights into the effect of interaction between soil nitrogen and water availabilities on soil microbial biomass, composition, and its underlying mechanism.},
}

@article {pmid36041615,
year = {2022},
author = {Leistenschneider, C and Le Bohec, C and Eisen, O and Houstin, A and Neff, S and Primpke, S and Zitterbart, DP and Burkhardt-Holm, P and Gerdts, G},
title = {No evidence of microplastic ingestion in emperor penguin chicks (Aptenodytes forsteri) from the Atka Bay colony (Dronning Maud Land, Antarctica).},
journal = {The Science of the total environment},
volume = {851},
number = {Pt 2},
pages = {158314},
doi = {10.1016/j.scitotenv.2022.158314},
pmid = {36041615},
issn = {1879-1026},
abstract = {Microplastic (<5 mm; MP) pollution has been an emerging threat for marine ecosystems around the globe with increasing evidence that even the world's most remote areas, including Antarctica, are no longer unaffected. Few studies however, have examined MP in Antarctic biota, and especially those from Antarctic regions with low human activity, meaning little is known about the extent to which biota are affected. The aim of this study was to investigate, for the first time, the occurrence of MP in the emperor penguin (Aptenodytes forsteri), the only penguin species breeding around Antarctica during the austral winter, and an endemic apex predator in the Southern Ocean. To assess MP ingestion, the gizzards of 41 emperor penguin chicks from Atka Bay colony (Dronning Maud Land, Antarctica), were dissected and analyzed for MP >500 μm using Attenuated Total Reflection Fourier-transform Infrared (ATR-FTIR) spectroscopy. A total of 85 putative particles, mostly in the shape of fibers (65.9 %), were sorted. However, none of the particles were identified as MP applying state-of-the-art methodology. Sorted fibers were further evidenced to originate from contamination during sample processing and analyses. We find that MP concentrations in the local food web of the Weddell Sea and Dronning Maud Land coastal and marginal sea-ice regions; the feeding grounds to chick-rearing emperor penguin adults, are currently at such low levels that no detectable biomagnification is occurring via trophic transfer. Being in contrast to MP studies on other Antarctic and sub-Antarctic penguin species, our comparative discussion including these studies, highlights the importance for standardized procedures for sampling, sample processing and analyses to obtain comparable results. We further discuss other stomach contents and their potential role for MP detection, as well as providing a baseline for the long-term monitoring of MP in apex predator species from this region.},
}

@article {pmid36040152,
year = {2022},
author = {He, J and Shen, X and Zhang, N and Sun, C and Shao, Y},
title = {Smartphones as an Ecological Niche of Microorganisms: Microbial Activities, Assembly, and Opportunistic Pathogens.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0150822},
doi = {10.1128/spectrum.01508-22},
pmid = {36040152},
issn = {2165-0497},
abstract = {Smartphone usage and contact frequency are unprecedentedly high in this era, and they affect humans mentally and physically. However, the characteristics of the microorganisms associated with smartphones and smartphone hygiene habits remain unclear. In this study, using various culture-independent techniques, including high-throughput sequencing, real-time quantitative PCR (RT-qPCR), the ATP bioluminescence system, and electron microscopy, we investigated the structure, assembly, quantity, and dynamic metabolic activity of the bacterial community on smartphone surfaces and the user's dominant and nondominant hands. We found that smartphone microbiotas are more similar to the nondominant hand microbiotas than the dominant hand microbiotas and show significantly decreased phylogenetic diversity and stronger deterministic processes than the hand microbiota. Significant interindividual microbiota differences were observed, contributing to an average owner identification accuracy of 70.6% using smartphone microbiota. Furthermore, it is estimated that approximately 1.75 × 106 bacteria (2.24 × 104/cm2) exist on the touchscreen of a single smartphone, and microbial activities remain stable for at least 48 h. Scanning electron microscopy detected large fragments harboring microorganisms, suggesting that smartphone microbiotas live on the secreta or other substances, e.g., human cell debris and food debris. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. Taken together, our results demonstrate that smartphone surfaces not only are a reservoir of microbes but also provide an ecological niche in which microbiotas, particularly opportunistic pathogens, can survive, be active, and even grow. IMPORTANCE Currently, people spend an average of 4.2 h per day on their smartphones. Due to the COVID-19 pandemic, this figure may still be increasing. The high frequency of smartphone usage may allow microbes, particularly pathogens, to attach to-and even survive on-phone surfaces, potentially causing adverse effects on humans. We employed various culture-independent techniques in this study to evaluate the microbiological features and hygiene of smartphones, including community assembly, bacterial load, and activity. Our data showed that deterministic processes drive smartphone microbiota assembly and that approximately 1.75 × 106 bacteria exist on a single smartphone touchscreen, with activities being stable for at least 48 h. Fortunately, simple smartphone cleaning/hygiene could significantly reduce the bacterial load. This work expands our understanding of the microbial ecology of smartphone surfaces and might facilitate the development of electronic device cleaning/hygiene guidelines to support public health.},
}

@article {pmid36037277,
year = {2022},
author = {Carregosa, D and Pinto, C and Ávila-Gálvez, MÁ and Bastos, P and Berry, D and Santos, CN},
title = {A look beyond dietary (poly)phenols: The low molecular weight phenolic metabolites and their concentrations in human circulation.},
journal = {Comprehensive reviews in food science and food safety},
volume = {},
number = {},
pages = {},
doi = {10.1111/1541-4337.13006},
pmid = {36037277},
issn = {1541-4337},
abstract = {A large number of epidemiological studies have shown that consumption of fruits, vegetables, and beverages rich in (poly)phenols promote numerous health benefits from cardiovascular to neurological diseases. Evidence on (poly)phenols has been applied mainly to flavonoids, yet the role of phenolic acids has been largely overlooked. Such phenolics present in food combine with those resulting from gut microbiota catabolism of flavonoids and chlorogenic acids and those produced by endogenous pathways, resulting in large concentrations of low molecular weight phenolic metabolites in human circulation. Independently of the origin, in human intervention studies using diets rich in (poly)phenols, a total of 137 low molecular weight phenolic metabolites have been detected and quantified in human circulation with largely unknown biological function. In this review, we will pinpoint two main aspects of the low molecular weight phenolic metabolites: (i) the microbiota responsible for their generation, and (ii) the analysis (quali- and quantitative) in human circulation and their respective pharmacokinetics. In doing so, we aim to drive scientific advances regarding the ubiquitous roles of low molecular weight phenolic metabolites using physiologically relevant concentrations and under (patho)physiologically relevant conditions in humans.},
}

@article {pmid36034889,
year = {2022},
author = {He, KJ and Dong, JH and Ouyang, XM and Huo, YN and Cheng, XS and Lin, Y and Li, Y and Gong, G and Liu, J and Ren, JL and Guleng, B},
title = {Glycerol monolaurate ameliorates DSS-induced acute colitis by inhibiting infiltration of Th17, neutrophils, macrophages and altering the gut microbiota.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {911315},
pmid = {36034889},
issn = {2296-861X},
abstract = {Background and aims: Inflammatory bowel disease (IBD) places a heavy medical burden on countries and families due to repeated and prolonged attacks, and the incidence and prevalence of IBD are increasing worldwide. Therefore, finding an effective treatment is a matter of great urgency. Glycerol monolaurate (GML), which has a twelve-carbon chain, is a compound naturally found in human breast milk. Some studies have shown that GML has antibacterial and anti-inflammatory effects. However, the specific mechanism of action remains unclear.

Methods: Acute colitis was established in mice using 3% DSS, and glycerol monolaurate (500 mg·kg-1) was administered for two weeks. QPCR and western blotting were performed to examine the inflammatory status. Mice described were subjected to flow cytometry analysis for immune cell activation.

Results: GML treated alleviated macroscopic symptoms such as shortened colons, increased spleen weight, and caused weight loss in mice with DSS-induced colitis. In addition, GML decreased the expression of pro-inflammatory factors (NF-α, IL-1β and IL-1α) and increased the expression of anti-inflammatory factors (IL-10 and TGF-β). GML inhibited the activation of the MAPK and NF-κB signalling pathways, improved tissue damage, and increased the expression of intestinal tight junction proteins. In addition, LPMCs extracted from intestinal tissue via flow cytometry showed that GML treatment led to a decrease of Th17 cells, Neutrophils and Macrophages. 16S rDNA sequencing showed that GML increased the abundance of commensal bacterium such as Akkermansia and Lactobacillus murinus.

Conclusions: We showed that oral administration of GML ameliorated DSS-induced colitis by inhibiting infiltration of Th17 cells, Neutrophils, and Macrophages, protecting the intestinal mucosal barrier and altered the abundance of commensal bacterium. This study provides new insights into the biological function and therapeutic potential of GML in the treatment of IBD.},
}

@article {pmid36030743,
year = {2022},
author = {Chen, W and Wei, J and Su, Z and Wu, L and Liu, M and Huang, X and Yao, P and Wen, D},
title = {Deterministic mechanisms drive bacterial communities assembly in industrial wastewater treatment system.},
journal = {Environment international},
volume = {168},
number = {},
pages = {107486},
doi = {10.1016/j.envint.2022.107486},
pmid = {36030743},
issn = {1873-6750},
abstract = {Microbial communities are responsible for biological treatment of many industrial wastewater, but our knowledge of their diversity, assembly patterns, and function is still poor. Here, we analyzed the bacterial communities of wastewater and activated sludge samples taken from 11 full-scale industrial wastewater treatment plants (IWWTPs) characterized by the same process design but different wastewater types and WWTP compartments. We found significantly different diversity and compositions of bacterial assemblages among distinct wastewater types and IWWTPs compartments. IWWTPs bacterial communities exhibited a clear species abundance distribution. The dispersal-driven process was weak in shaping IWWTP communities. Meanwhile, environmental and operating conditions were important factors in regulating the structure of the activated sludge community and pollutants removal, indicating that bacterial community was largely driven by deterministic mechanisms. The core microbial community in IWWTPs was different from that in municipal wastewater treatment plants (MWWTPs), and many taxa (e.g. the genus Citreitalea) rarely were detected before, indicating IWWTPs harbored unique core bacterial communities. Furthermore, we found that bacterial community compositions were strongly linked to activated sludge function. These findings are important to both microbial ecologists and environmental engineers, who may optimize the operation strategies jointly for maintaining biodiversity, which in turn may promote a more stable performance of the IWWTP. Overall, our study enhances the mechanistic understanding of the IWWTP microbial community diversity, assembly patterns, and function, and provides important implications for microbial ecology and wastewater treatment processes.},
}

@article {pmid36030426,
year = {2022},
author = {Barman, D and Dkhar, MS},
title = {Characterization and purification of esterase from Cellulomonas fimi DB19 isolated from Zanthoxylum armatum with its possible role in diesel biodegradation.},
journal = {Archives of microbiology},
volume = {204},
number = {9},
pages = {580},
pmid = {36030426},
issn = {1432-072X},
mesh = {Azo Compounds ; Cellulomonas ; Enzyme Stability ; *Esterases ; Hydrogen Peroxide ; Hydrogen-Ion Concentration ; Temperature ; *Zanthoxylum ; },
abstract = {Endophytic bacteria inhabit all or part of their life cycle within the tissues of healthy plants, without causing any apparent symptoms of disease. They are treasure trove of several hydrolytic enzymes with distinct characteristics. Esterase is one of such enzymes and this study aims to characterize esterase produced by endophytic actinobacteria Cellulomonas fimi DB19 isolated from Zanthoxylum armatum with its capacity to degrade diesel oil. The enzyme was purified with purification fold 8.22 and specific activity 124.72 U/mg with 16.43% recovery. The purified enzyme showed a single protein band on SDS-PAGE having molecular mass of approximately 39 kDa. The Km and Vmax value for p-nitrophenyl acetate were 2.23 mM and 22.04 U/mL, respectively. The enzyme was stable in the pH range 6-9 with its optimal activity at pH 8.0. The enzyme was stable at 40 °C and retained more than 80% activity after incubation for two h. The enzyme activity was positively influenced in the presence of Na+, Ba2+, Ca2+, and negatively by Mn2+, and Mg2+. The EDTA and PMSF inhibited the enzyme activity and retained its activity in the presence of SDS, H2O2, β-mercaptoethanol, and organic solvents. Application of the isolate in degradation of diesel showed that its growth and degradation capacity enhanced in media supplemented with 0.2-4% of diesel oil with maximum at 3% of diesel oil. Furthermore, esterase activity was greater in media containing diesel than control which is suggesting the plausible role of esterase produced by Cellulomonas fimi DB19 in the degradation of diesel oil.},
}

Azo Compounds
Cellulomonas
Enzyme Stability
*Esterases
Hydrogen Peroxide
Hydrogen-Ion Concentration
Temperature
*Zanthoxylum

@article {pmid36029817,
year = {2022},
author = {Wang, P and Cao, J and Mao, L and Zhu, L and Zhang, Y and Zhang, L and Jiang, H and Zheng, Y and Liu, X},
title = {Effect of H3PO4-modified biochar on the fate of atrazine and remediation of bacterial community in atrazine-contaminated soil.},
journal = {The Science of the total environment},
volume = {851},
number = {Pt 2},
pages = {158278},
doi = {10.1016/j.scitotenv.2022.158278},
pmid = {36029817},
issn = {1879-1026},
abstract = {The application of chemically modified biochar is a promising strategy for the remediation of contaminated (e.g., pesticides) soil. In this study, H3PO4 was used to modify peanut shell to improve the remediation performance of biochar. Surface area (980.19 m2/g), pore volume (0.12 cm3/g), and the functional groups (OH, CO, and phosphorus-containing groups) on the biochar were increased by H3PO4 treatment. The sorption experimental data were well fitted by Freundlich model, while the sorption affinity (Kf) of H3PO4 modified biochar (PBC) for atrazine was 128 times greater than that of the untreated biochar (BC) in the aquatic systems. The Kf values of PBC-amended soil to atrazine were increased by 13.57 times than that of single soil. The strong sorption of PBC on atrazine delayed the degradation of atrazine in soil, and the residual percentage of atrazine in soil and soil-PBC mixture were 4.90% and 71.44% at the end of 60-day incubation, with the degradation half-life increased from 13.3 to 121.6 d. The analysis of high-throughput sequencing results showed that atrazine reduced the diversity of soil microbial community, but the abundance of microorganisms with degradation function increased and became dominant species. The addition of PBC in soil accelerated the microbial remediation of atrazine stress, which may promote the soil nitrogen cycle. Therefore, amendment of atrazine contaminated soil with PBC can reduce the environmental risk of atrazine and benefit the soil microbial ecology.},
}