@article {pmid38036897,
year = {2023},
author = {Hernández-Pelegrín, L and Ros, VID and Herrero, S and Crava, CM},
title = {Non-retroviral Endogenous Viral Elements in Tephritid Fruit Flies Reveal Former Viral Infections Not Related to Known Circulating Viruses.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {7},
pmid = {38036897},
issn = {1432-184X},
abstract = {A wide variety of insect-specific non-retroviral RNA viruses specifically infect insects. During viral infection, fragments of viral sequences can integrate into the host genomes creating non-retroviral endogenous viral elements (nrEVEs). Although the exact function of nrEVEs is so far unknown, some studies suggest that nrEVEs may interfere with virus replication by producing PIWI-interacting RNAs (piRNAs) that recognize and degrade viral RNAs through sequence complementarity. In this article, we identified the nrEVEs repertoire of ten species within the dipteran family Tephritidae (true fruit flies), which are considered a major threat to agriculture worldwide. Our results suggest that each of these species contains nrEVEs, although in limited numbers, and that nrEVE integration may have occurred both before and after speciation. Furthermore, the majority of nrEVEs originated from viruses with negative single-stranded RNA genomes and represent structural viral functions. Notably, these nrEVEs exhibit low similarity to currently known circulating viruses. To explore the potential role of nrEVEs, we investigated their transcription pattern and the production of piRNAs in different tissues of Ceratitis capitata. We successfully identified piRNAs that are complementary to the sequence of one nrEVE in C. capitata, thereby highlighting a potential link between nrEVEs and the piRNA pathway. Overall, our results provide valuable insights into the comparative landscape of nrEVEs in true fruit flies, contributing to the understanding of the intimate relation between fruit flies and their past and present viral pathogens.},
}

@article {pmid38033596,
year = {2023},
author = {Zhang, M and Kong, Z and Fu, H and Shu, X and Xue, Q and Lai, H and Guo, Q},
title = {Rhizosphere microbial ecological characteristics of strawberry root rot.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1286740},
pmid = {38033596},
issn = {1664-302X},
abstract = {INTRODUCTION: Strawberry (Fragaria × ananassa Duch.) holds a preeminent position among small fruits globally due to its delectable fruits and significant economic value. However, strawberry cultivation is hampered by various plant diseases, hindering the sustainable development of the strawberry industry. The occurrence of plant diseases is closely linked to imbalance in rhizosphere microbial community structure.

METHODS: In the present study, a systematic analysis of the differences and correlations among non-culturable microorganisms, cultivable microbial communities, and soil nutrients in rhizosphere soil, root surface soil, and non-rhizosphere soil of healthy and diseased strawberry plants affected by root rot was conducted. The goal was to explore the relationship between strawberry root rot occurrence and rhizosphere microbial community structure.

RESULTS: According to the results, strawberry root rot altered microbial community diversity, influenced fungal community composition in strawberry roots, reduced microbial interaction network stability, and enriched more endophytic-phytopathogenic bacteria and saprophytic bacteria. In addition, the number of bacteria isolated from the root surface soil of diseased plants was significantly higher than that of healthy plants.

DISCUSSION: In summary, the diseased strawberry plants changed microbial community diversity, fungal species composition, and enriched functional microorganisms significantly, in addition to reshaping the microbial co-occurrence network. The results provide a theoretical basis for revealing the microecological mechanism of strawberry root rot and the ecological prevention and control of strawberry root rot from a microbial ecology perspective.},
}

@article {pmid38033562,
year = {2023},
author = {Farmer, M and Rajasabhai, R and Tarpeh, W and Tyo, K and Wells, G},
title = {Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1287491},
pmid = {38033562},
issn = {1664-302X},
abstract = {Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.},
}

@article {pmid38030916,
year = {2023},
author = {Mlewski, EC and Saona, LA and Boidi, FJ and Chiappero, MF and Vaieretti, MV and Soria, M and Farías, ME and Izquierdo, AE},
title = {Exploring Soil Bacterial Diversity in Relation to Edaphic Physicochemical Properties of High-altitude Wetlands from Argentine Puna.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {6},
pmid = {38030916},
issn = {1432-184X},
support = {PICT 2018-4129//Agencia Nacional de Promoción Científica y Tecnológica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoción Científica y Tecnológica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoción Científica y Tecnológica FONCYT/ ; PICT2018-04228//Agencia Nacional de Promoción Científica y Tecnológica FONCYT/ ; },
abstract = {High Andean wetlands, particularly those known as vegas or bofedales, are essential conservation ecosystems due to their significant contribution to ecosystem services. The soil microbial communities in these ecosystems play a crucial role in fundamental processes such as decomposition and nutrient cycling, sustaining life in the region. However, at present, these microbial communities are poorly understood. In order to contribute to this knowledge, we aimed to characterize and compare the microbial communities from soils of seven Argentine Puna vegas and to analyze their association with soil physicochemical characteristics. Proteobacteria (Gamma and Alphaproteobacteria) was the dominant phylum across all vegas, followed in abundance by Actinobacteriota, Desulfobacterota, and Chloroflexi. Furthermore, the abundance of specific bacterial families and genera varied significantly between the vegas; some of them can be associated with plant growth-promoting bacteria such as Rhodomicrobium in La Quebradita and Quebrada del Diablo, Bacillus in Antofalla and Las Quinuas. Laguna Negra showed no shared ASVs with abundance in genera such as Sphingomonas and Pseudonocardia. The studied vegas also differed in their soil physicochemical properties; however, associations between the composition of microbial communities with the edaphic parameters measured were not found. These results suggest that other environmental factors (e.g., geographic, climatic, and plant communities' characteristics) could determine soil microbial diversity patterns. Further investigations are needed to be focused on understanding the composition and function of microorganisms in the soil associated with specific vegetation types in these high-altitude wetlands, which will provide valuable insights into the ecological dynamics of these ecosystems for conservation strategies.},
}

@article {pmid38030815,
year = {2023},
author = {Zhang, N and Zhu, W and Zhang, S and Liu, T and Gong, L and Wang, Z and Zhang, W and Cui, Y and Wu, Q and Li, J and Yu, H and El-Omar, EM and Hao, J and Lu, W},
title = {A Novel Bifidobacterium/Klebsiella Ratio in Characterization Analysis of the Gut and Bile Microbiota of CCA Patients.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {5},
pmid = {38030815},
issn = {1432-184X},
abstract = {Cholangiocarcinoma (CCA) is a serious health problem worldwide. The gut and bile microbiota have not been clearly characterized in patients with CCA, and better noninvasive diagnostic approaches for CCA need to be established. The aim of this study was to investigate the characteristics of the gut and bile microbiota in CCA patients. Forty-two CCA patients and 16 healthy normal controls (HNCs) were enrolled. DNA was extracted from fecal and bile samples and subjected to 16S rRNA gene analysis. We found that there were significant differences in the species diversity, structure, and composition of the microbial communities between the CCA group and the HNC grouAt the phylum level, compared with that in the HNC group, the relative abundance of Firmicutes and Actinobacteriota was significantly decreased in the CCA group, whereas Proteobacteria and Bacteroidota were significantly enriched. The Firmicutes/Bacteroidota (F/B) ratio significantly decreased in the CCA group compared to the HNC grouThe relative abundance of Klebsiella in the CCA group was significantly higher than that in the HNC group, while the relative abundance of Bifidobacterium was significantly decreased. The Bifidobacterium/Klebsiella (B/K) ratio was established as a novel biomarker and was found to be significantly decreased in the CCA group compared with the HNC grouOur findings provide evidence supporting the use of Klebsiella and Bifidobacterium as noninvasive intestinal microbiomarkers for improving the diagnosis of CCA.},
}

@article {pmid38029116,
year = {2023},
author = {Ouamba, AJK and Gagnon, M and Varin, T and Chouinard, PY and LaPointe, G and Roy, D},
title = {Phylogenetic variation in raw cow milk microbiota and the impact of forage combinations and use of silage inoculants.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1175663},
pmid = {38029116},
issn = {1664-302X},
abstract = {INTRODUCTION: The microbiota of bulk tank raw milk is known to be closely related to that of microbial niches of the on-farm environment. Preserved forage types are partof this ecosystem and previous studies have shown variations in their microbial ecology. However, little is known of the microbiota of forage ration combinations and the transfer rates of associated species to milk.

METHODS: We identified raw milk bacteria that may originate from forage rations encompassing either hay (H) or grass/legume silage uninoculated (GL) as the only forage type, or a combination of GL and corn silage uninoculated (GLC), or grass/legume and corn silage both inoculated (GLICI). Forage and milk samples collected in the fall and spring from 24 dairy farms were analyzed using 16S rRNA gene high-throughput sequencing following a treatment with propidium monoazide to account for viable cells.

RESULTS AND DISCUSSION: Three community types separating H, GL, and GLICI forage were identified. While the H community was co-dominated by Enterobacteriaceae, Microbacteriaceae, Beijerinckiaceae, and Sphingomonadaceae, the GL and GLICI communities showed high proportions of Leuconostocaceae and Acetobacteraceae, respectively. Most of the GLC and GLICI rations were similar, suggesting that in the mixed forage rations involving grass/legume and corn silage, the addition of inoculant in one or both types of feed does not considerably change the microbiota. Raw milk samples were not grouped in the same way, as the GLC milk was phylogenetically different from that of GLICI across sampling periods. Raw milk communities, including the GLICI group for which cows were fed inoculated forage, were differentiated by Enterobacteriaceae and other Proteobacteria, instead of by lactic acid bacteria. Of the 113 amplicon sequence variants (ASVs) shared between forage rations and corresponding raw milk, bacterial transfer rates were estimated at 18 to 31%. Silage-based forage rations, particularly those including corn, share more ASVs with raw milk produced on corresponding farms compared to that observed in the milk from cows fed hay. These results show the relevance of cow forage rations as sources of bacteria that contaminate milk and serve to advance our knowledge of on-farm raw milk contamination.},
}

@article {pmid38029109,
year = {2023},
author = {Crosby, KC and Rojas, M and Sharma, P and Johnson, MA and Mazloom, R and Kvitko, BH and Smits, THM and Venter, SN and Coutinho, TA and Heath, LS and Palmer, M and Vinatzer, BA},
title = {Genomic delineation and description of species and within-species lineages in the genus Pantoea.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1254999},
pmid = {38029109},
issn = {1664-302X},
abstract = {As the name of the genus Pantoea ("of all sorts and sources") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.},
}

@article {pmid38029094,
year = {2023},
author = {Semenov, M and Li, H and Luo, Y and Deng, Y and Kuzyakov, Y},
title = {Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1295624},
doi = {10.3389/fmicb.2023.1295624},
pmid = {38029094},
issn = {1664-302X},
}

@article {pmid38029079,
year = {2023},
author = {Koepper, S and Clark, KF and McClure, JT and Revie, CW and Stryhn, H and Thakur, KK},
title = {Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1245818},
doi = {10.3389/fmicb.2023.1245818},
pmid = {38029079},
issn = {1664-302X},
abstract = {The shell microbial community of lobsters-a key factor in the development of epizootic shell disease (ESD)-is still insufficiently researched in Atlantic Canada and many knowledge gaps remain. This study aimed to establish a baseline description and analysis of the shell microbiome of apparently healthy lobsters from four locations in the region. More than 180 lobster shell swab samples were collected from New Brunswick, Nova Scotia and Prince Edward Island (PEI). PacBio long-read 16S rDNA sequencing and bioinformatic analyses in QIIME2 identified the shell-associated bacteria. The shell microbiome of healthy lobsters consisted mainly of the bacterial classes Gammaproteobacteria, Saprospiria, Verrucomicrobiae, Alphaproteobacteria, Flavobacteriia, Acidimicrobiia and Planctomycetia. The microbial composition differed regionally and seasonally, with some classes showing decreased or increased relative abundances in the PEI samples as well as in the winter and spring samples in Nova Scotia. The core shell microbiome included potentially pathogenic as well as beneficial bacterial taxa, of which some were present only in certain regions. Bacterial taxa that have previously been associated with ESD were present on healthy lobsters in Atlantic Canada, but their frequency differed by location, sampling time, and moult stage. This study indicated that geographical and seasonal factors influenced the shell microbiome of apparently healthy lobsters more than host factors such as sex, size, and moult stage. Our results provide valuable reference microbial data from lobsters in a disease-free state.},
}

@article {pmid38026034,
year = {2023},
author = {Gjini, E and Madec, S},
title = {Towards a mathematical understanding of invasion resistance in multispecies communities.},
journal = {Royal Society open science},
volume = {10},
number = {11},
pages = {231034},
doi = {10.1098/rsos.231034},
pmid = {38026034},
issn = {2054-5703},
abstract = {Multispecies community composition and dynamics are key to health and disease across biological systems, a prominent example being microbial ecosystems. Explaining the forces that govern diversity and resilience in the microbial consortia making up our body's defences remains a challenge. In this, theoretical models are crucial, to bridge the gap between species dynamics and underlying mechanisms and to develop analytic insight. Here we propose a replicator equation framework to model multispecies dynamics where an explicit notion of invasion resistance of a system emerges and can be studied explicitly. For illustration, we derive the conceptual link between such replicator equation and N microbial species' growth and interaction traits, stemming from micro-scale environmental modification. Within this replicator framework, mean invasion fitness arises, evolves dynamically, and may undergo critical predictable shifts with global environmental changes. This mathematical approach clarifies the key role of this resident system trait for invader success, and highlights interaction principles among N species that optimize their collective resistance to invasion. We propose this model based on the replicator equation as a powerful new avenue to study, test and validate mechanisms of invasion resistance and colonization in multispecies microbial ecosystems and beyond.},
}

@article {pmid38026022,
year = {2023},
author = {Tarnowski, MJ and Varliero, G and Scown, J and Phelps, E and Gorochowski, TE},
title = {Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting.},
journal = {Royal Society open science},
volume = {10},
number = {11},
pages = {230963},
doi = {10.1098/rsos.230963},
pmid = {38026022},
issn = {2054-5703},
abstract = {The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.},
}

@article {pmid38023904,
year = {2023},
author = {Fu, X and Huang, Y and Fu, Q and Qiu, Y and Zhao, J and Li, J and Wu, X and Yang, Y and Liu, H and Yang, X and Chen, H},
title = {Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1252821},
doi = {10.3389/fpls.2023.1252821},
pmid = {38023904},
issn = {1664-462X},
abstract = {Over the years, microbial community composition in the rhizosphere has been extensively studied as the most fascinating topic in microbial ecology. In general, plants affect soil microbiota through rhizodeposits and changes in abiotic conditions. However, a consensus on the response of microbiota traits to the rhizosphere and bulk soils in various ecosystems worldwide regarding community diversity and structure has not been reached yet. Here, we conducted a meta-analysis of 101 studies to investigate the microbial community changes between the rhizosphere and bulk soils across various plant species (maize, rice, vegetables, other crops, herbaceous, and woody plants). Our results showed that across all plant species, plant rhizosphere effects tended to reduce the rhizosphere soil pH, especially in neutral or slightly alkaline soils. Beta-diversity of bacterial community was significantly separated between into rhizosphere and bulk soils. Moreover, r-strategists and copiotrophs (e.g. Proteobacteria and Bacteroidetes) enriched by 24-27% in the rhizosphere across all plant species, while K-strategists and oligotrophic (e.g. Acidobacteria, Gemmatimonadete, Nitrospirae, and Planctomycetes) decreased by 15-42% in the rhizosphere. Actinobacteria, Firmicutes, and Chloroflexi are also depleted by in the plant rhizosphere compared with the bulk soil by 7-14%. The Actinobacteria exhibited consistently negative effect sizes across all plant species, except for maize and vegetables. In Firmicutes, both herbaceous and woody plants showed negative responses to rhizosphere effects, but those in maize and rice were contrarily enriched in the rhizosphere. With regards to Chloroflexi, apart from herbaceous plants showing a positive effect size, the plant rhizosphere effects were consistently negative across all other plant types. Verrucomicrobia exhibited a significantly positive effect size in maize, whereas herbaceous plants displayed a negative effect size in the rhizosphere. Overall, our meta-analysis exhibited significant changes in microbial community structure and diversity responding to the plant rhizosphere effects depending on plant species, further suggesting the importance of plant rhizosphere to environmental changes influencing plants and subsequently their controls over the rhizosphere microbiota related to nutrient cycling and soil health.},
}

@article {pmid38016221,
year = {2023},
author = {Zhang, X and Wang, Y and Jiao, P and Zhang, M and Deng, Y and Jiang, C and Liu, XW and Lou, L and Li, Y and Zhang, XX and Ma, L},
title = {Microbiome-functionality in anaerobic digesters: A critical review.},
journal = {Water research},
volume = {249},
number = {},
pages = {120891},
doi = {10.1016/j.watres.2023.120891},
pmid = {38016221},
issn = {1879-2448},
abstract = {Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.},
}

@article {pmid38015286,
year = {2023},
author = {Liu, D and Wei, L},
title = {Epigenetic Regulation in Response to CO2 Fluctuation in Marine Microalga Nannochloropsis oceanica.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {4},
pmid = {38015286},
issn = {1432-184X},
mesh = {*Carbon Dioxide ; Epigenesis, Genetic ; Histones/genetics ; *Microalgae/genetics ; Adaptation, Physiological ; Carbon ; },
abstract = {Microalgae often undergo different CO2 experiment in their habitat. To adapt to low CO2, carbon concentrating mechanism (CCM) could be launched in majority of microalgae and CCM are regulated at RNA level are well known. However, epigenetic modifications and their potential regulation of the transcription of masked genes at the genome level in response to CO2 fluctuation remain unclear. Here epigenetic regulation in response to CO2 fluctuation and epigenome-association with phenotypic plasticity of CCM are firstly uncovered in marine microalga Nannochloropsis oceanica IMET1. The result showed that lysine butyrylation (Kbu) and histone H3K9m2 modifications were present in N. oceanica IMET1. Moreover, Kbu modification positively regulated gene expression. In response to CO2 fluctuation, there were 5,438 and 1,106 genes regulated by Kbu and H3K9m2 in Nannochloropsis, respectively. Gained or lost histone methylations were closely associated with activating or repressing gene expressions. Differential modifications were mainly enriched in carbon fixation, photorespiration, photosynthesis, and lipid metabolism etc. Massive genome-wide epigenetic reprogramming was observed after N. oceanica cells shifted from high CO2 to low CO2. Particularly, we firstly noted that the transcription of the key low CO2 responsive carbonic anhydrase (CA5), a key component involved in CCM stress signaling, was potentially regulated by bivalent Kbu-H3K9m2 modifications in microalgae. This study provides novel insights into the relationship between gene transcription and epigenetic modification in Nannochloropsis, which will lay foundation on genetic improvement of CCM at epigenetic level.},
}

*Carbon Dioxide
Epigenesis, Genetic
Histones/genetics
*Microalgae/genetics
Adaptation, Physiological
Carbon

@article {pmid38008827,
year = {2023},
author = {Zhu, YL and Huang, YJ and Nuerhamanti, N and Bai, XY and Wang, HN and Zhu, XY and Zhang, W},
title = {The Composition and Diversity of the Rhizosphere Bacterial Community of Ammodendron bifolium Growing in the Takeermohuer Desert Are Different from Those in the Nonrhizosphere.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {2},
pmid = {38008827},
issn = {1432-184X},
support = {32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 32160309//National Science Foundation of China/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 2022D01A94//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
mesh = {*Ecosystem ; Rhizosphere ; Bacteria/genetics ; Proteobacteria ; Acidobacteria ; *Fabaceae ; Soil/chemistry ; Plants ; Nitrogen ; Soil Microbiology ; },
abstract = {Soil microorganisms play important roles in vegetation establishment and soil biogeochemical cycling. Ammodendron bifolium is a dominant sand-fixing (i.e., stabilizing sand dunes) and endangered plant in the Takeermohuer Desert, and the bacterial community associated with this plant rhizosphere is still unclear. In this study, we investigated the composition and diversity of the bacterial community from the A. bifolium rhizosphere and bulk soil at different soil depths (i.e., 0-40 cm, 40-80 cm, 80-120 cm) using culture and high-throughput sequencing methods. We preliminarily analyzed the edaphic factors influencing the structure of bacterial communities. The results showed that the high-salinity Takeermohuer Desert has an oligotrophic environment, while the A. bifolium rhizosphere exhibited a relatively nutrient-rich environment due to higher contents of soil organic matter (SOM) and soil alkaline nitrogen (SAN) than bulk soil. The dominant bacterial groups in the desert were Actinobacteria (39.8%), Proteobacteria (17.4%), Acidobacteria (10.2%), Bacteroidetes (6.3%), Firmicutes (6.3%), Chloroflexi (5.6%), and Planctomycetes (5.0%) at the phylum level. However, the relative abundances of Proteobacteria (20.2%) and Planctomycetes (6.1%) were higher in the rhizosphere, and those of Firmicutes (9.8%) and Chloroflexi (6.9%) were relatively higher in barren bulk soil. A large number of Actinobacteria were detected in all soil samples, of which the most abundant genera were Streptomyces (5.4%) and Actinomadura (8.2%) in the bulk soil and rhizosphere, respectively. The Chao1 and PD_whole_tree indices in the rhizosphere soil were significantly higher than those in the bulk soil at the same soil depth and tended to decrease with increasing soil depth. Co-occurrence network analyses showed that the keystone species in the Takeermohuer Desert were the phyla Actinobacteria, Acidobacteria, Proteobacteria, and Chloroflexi. Furthermore, the major edaphic factors affecting the rhizosphere bacterial community were electrical conductivity (EC), SOM, soil total nitrogen (STN), SAN, and soil available potassium (SAK), while the major edaphic factors affecting the bacterial community in bulk soil were distance and ratio of carbon to nitrogen (C/N). We concluded that the A. bifolium rhizosphere bacterial community is different from that of the nonrhizosphere in composition, structure, diversity, and driving factors, which may improve our understanding of the relationship between plant and bacterial communities and lay a theoretical foundation for A. bifolium species conservation in desert ecosystems.},
}

*Ecosystem
Rhizosphere
Bacteria/genetics
Proteobacteria
Acidobacteria
*Fabaceae
Soil/chemistry
Plants
Nitrogen
Soil Microbiology

@article {pmid38008821,
year = {2023},
author = {Fuster, M and Ruiz, T and Lamarque, A and Coulon, M and Legrand, B and Sabart, M and Latour, D and Mallet, C},
title = {Cyanosphere Dynamic During Dolichospermum Bloom: Potential Roles in Cyanobacterial Proliferation.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {3},
pmid = {38008821},
issn = {1432-184X},
mesh = {*Cyanobacteria/genetics ; *Microcystis ; *Microbiota ; Cell Proliferation ; Lakes ; Eutrophication ; },
abstract = {Under the effect of global change, management of cyanobacterial proliferation becomes increasingly pressing. Given the importance of interactions within microbial communities in aquatic ecosystems, a handful of studies explored the potential relations between cyanobacteria and their associated bacterial community (i.e., cyanosphere). Yet, most of them specifically focused on the ubiquitous cyanobacteria Microcystis, overlooking other genera. Here, based on 16s rDNA metabarcoding analysis, we confirmed the presence of cyanosphere representing up to 30% of the total bacterial community diversity, during bloom episode of another preponderant cyanobacterial genus, Dolichospermum. Moreover, we highlighted a temporal dynamic of this cyanosphere. A sPLS-DA model permits to discriminate three important dates and 220 OTUs. With their affiliations, we were able to show how these variations potentially imply a turnover in ecological functions depending on bloom phases. Although more studies are necessary to quantify the impacts of these variations, we argue that cyanosphere can have an important, yet underestimated, role in the modulation of cyanobacterial blooms.},
}

*Cyanobacteria/genetics
*Microcystis
*Microbiota
Cell Proliferation
Lakes
Eutrophication

@article {pmid38006200,
year = {2023},
author = {Houldcroft, CJ and Underdown, S},
title = {Infectious disease in the Pleistocene: Old friends or old foes?.},
journal = {American journal of biological anthropology},
volume = {182},
number = {4},
pages = {513-531},
doi = {10.1002/ajpa.24737},
pmid = {38006200},
issn = {2692-7691},
support = {//Oxford Brookes University/ ; },
mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; },
abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.},
}

Animals
Humans
Friends
*Hominidae
*Communicable Diseases/epidemiology
Genome
DNA

@article {pmid38004650,
year = {2023},
author = {Aponte, H and Sulbaran-Bracho, Y and Mondaca, P and Vidal, C and Pérez, R and Meier, S and Cornejo, P and Rojas, C},
title = {Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing.},
journal = {Microorganisms},
volume = {11},
number = {11},
pages = {},
pmid = {38004650},
issn = {2076-2607},
support = {3210752//FONDECYT/ ; InES19-FRO19101//MINEDUC/ ; },
abstract = {The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroResp[TM] system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.},
}

@article {pmid38001901,
year = {2023},
author = {Macedo-Viñas, M and Lucas, A},
title = {Evolution of Microbial Flora Colonizing Burn Wounds during Hospitalization in Uruguay.},
journal = {Biomedicines},
volume = {11},
number = {11},
pages = {},
doi = {10.3390/biomedicines11112900},
pmid = {38001901},
issn = {2227-9059},
abstract = {(1) Background: Infections are a main cause of morbidity and mortality among burn patients. The spectrum of microorganisms depends on the epidemiological context and treatment practices. We aimed to describe the evolution of microbial flora colonizing burn wounds among patients hospitalized during 15 or more days at the National Burn Center in 2015. (2) Methods: Demographic data, length of stay, total body surface area burn, and status at discharge were collected from electronic records and culture results from the laboratory database. (3) Results: Among 98 included patients, 87 were colonized. The mean length of stay was 39 days overall and 16 days in the ICU. Acinetobacter spp., Enterococcus spp., and Staphylococcus aureus predominated. Fifty-six patients harbored multidrug-resistant bacteria and had a significantly greater TBSA. The mean time to colonization was 6 days overall and 14 days for multidrug-resistant bacteria; it was significantly longer for methicillin-resistant S. aureus than for methicillin-susceptible S. aureus. (4) Conclusions: This is the first report describing the dynamics of microbial colonization of burn wounds in Uruguay. Similarities were found with reports elsewhere, but early colonization with yeasts and the absence of Streptococcus pyogenes were unique. Each burn center needs to monitor its microbial ecology to tailor their antimicrobial strategies effectively.},
}

@article {pmid38000643,
year = {2023},
author = {Jiang, M and Khunjar, W and Li, A and Chandran, K},
title = {Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130069},
doi = {10.1016/j.biortech.2023.130069},
pmid = {38000643},
issn = {1873-2976},
abstract = {In this study, two arrested anaerobic digestion bioreactors, fed with food waste, operated under different hydraulic retention times (HRTs) exhibited similar total volatile fatty acid (VFA) yields (p = 0.09). 16S rRNA gene sequencing revealed distinct microbial structure (p = 0.02) at the two HRTs. However, between the two HRTs, there were no differences in potential (DNA) and extant (mRNA) functionality for the production of acetic (AA)-, propionic (PA)-, butyric (BA)- and valeric-acid (VA), as indicated by the metagenome and metatranscriptome data, respectively. The highest potential and extant functionality for PA production in the reactor microbiomes mirrored the highest abundance of PA in the reactor effluents. Meta-omics analysis of BA production indicated possible metabolite exchange across different community members. Notably, the basis for similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community-level structure alone.},
}

@article {pmid38000642,
year = {2023},
author = {Wu, K and Leliveld, T and Zweers, H and Rijnaarts, H and Langenhoff, A and Fernandes, TV},
title = {Impact of mixed microalgal and bacterial species on organic micropollutants removal in photobioreactors under natural light.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130083},
doi = {10.1016/j.biortech.2023.130083},
pmid = {38000642},
issn = {1873-2976},
abstract = {Single microalgae species are effective at the removal of various organic micropollutants (OMPs), however increased species diversity might enhance this removal. Sixteen OMPs were added to 2 continuous photobioreactors, one inoculated with Chlorella sorokiniana and the other with a microalgal-bacterial community, for 112 d under natural light. Three media were sequentially used in 3 Periods: I) synthetic sewage (d 0-28), II) 10x diluted anaerobically digested black water (AnBW) (d 28-94) and III) 5x diluted AnBW (d 94-112). Twelve OMPs were removed > 30 %, while 4 were < 10 % removed. Removal efficiencies were similar for 9 OMPs, yet the mixed community showed a 2-3 times higher removal capacity (µg OMP/g dry weight) than C. sorokiniana during Period II pseudo steady state. The removal decreased drastically in Period III due to overgrowth of filamentous green algae. This study shows for the first time how microbial community composition and abundance are key for OMPs removal.},
}

@article {pmid37999395,
year = {2023},
author = {Hernanz-Torrijos, M and Ortega, MJ and Úbeda, B and Bartual, A},
title = {Polyunsaturated Aldehydes Profile in the Diatom Cyclotella cryptica Is Sensitive to Changes in Its Phycosphere Bacterial Assemblages.},
journal = {Marine drugs},
volume = {21},
number = {11},
pages = {},
pmid = {37999395},
issn = {1660-3397},
support = {RTI2018-101272-B-I00//Ministerio de Ciencia e Innovación/ ; Plan Propio UCA 2022-2023//University of Cádiz/ ; },
abstract = {Diatoms are responsible for the fixation of ca. 20% of the global CO2 and live associated with bacteria that utilize the organic substances produced by them. Current research trends in marine microbial ecology show which diatom and bacteria interact mediated through the production and exchange of infochemicals. Polyunsaturated aldehydes (PUA) are organic molecules released by diatoms that are considered to have infochemical properties. In this work, we investigated the possible role of PUA as a mediator in diatom-bacteria interactions. To this end, we compare the PUA profile of a newly isolated oceanic PUA producer diatom, Cyclotella cryptica, co-cultured with and without associated bacteria at two phosphate availability conditions. We found that the PUA profile of C. cryptica cultured axenically was different than its profile when it was co-cultured with autochthonous (naturally associated) and non-autochthonous bacteria (unnaturally inoculated). We also observed that bacterial presence significantly enhanced diatom growth and that C. cryptica modulated the percentage of released PUA in response to the presence of bacteria, also depending on the consortium type. Based on our results, we propose that this diatom could use released PUA as a specific organic matter sign to attract beneficial bacteria for constructing its own phycosphere, for more beneficial growth.},
}

@article {pmid37997641,
year = {2023},
author = {Tájmel, D and Cruz-Paredes, C and Rousk, J},
title = {Heat wave-induced microbial thermal trait adaptation and its reversal in the Subarctic.},
journal = {Global change biology},
volume = {},
number = {},
pages = {e17032},
doi = {10.1111/gcb.17032},
pmid = {37997641},
issn = {1365-2486},
support = {9036-00004B//Danmarks Frie Forskningsfond/ ; KAW 2022.0175//Knut och Alice Wallenbergs Stiftelse/ ; 2020-04083//Vetenskapsrådet/ ; 4.3-2021-00164//Vetenskapsrådet/ ; },
abstract = {Climate change predictions suggest that arctic and subarctic ecosystems will be particularly affected by rising temperatures and extreme weather events, including severe heat waves. Temperature is one of the most important environmental factors controlling and regulating microbial decomposition in soils; therefore, it is critical to understand its impact on soil microorganisms and their feedback to climate warming. We conducted a warming experiment in a subarctic birch forest in North Sweden to test the effects of summer heat waves on the thermal trait distributions that define the temperature dependences for microbial growth and respiration. We also determined the microbial temperature dependences 10 and 12 months after the heat wave simulation had ended to investigate the persistence of the thermal trait shifts. As a result of warming, the bacterial growth temperature dependence shifted to become warm-adapted, with a similar trend for fungal growth. For respiration, there was no shift in the temperature dependence. The shifts in thermal traits were not accompanied by changes in α- or β-diversity of the microbial community. Warming increased the fungal-to-bacterial growth ratio by 33% and decreased the microbial carbon use efficiency by 35%, and both these effects were caused by the reduction in moisture the warming treatments caused, while there was no evidence that substrate depletion had altered microbial processes. The warm-shifted bacterial thermal traits were partially restored within one winter but only fully recovered to match ambient conditions after 1 year. To conclude, a summer heat wave in the Subarctic resulted in (i) shifts in microbial thermal trait distributions; (ii) lower microbial process rates caused by decreased moisture, not substrate depletion; and (iii) no detectable link between the microbial thermal trait shifts and community composition changes.},
}

@article {pmid37994377,
year = {2023},
author = {Lyche Solheim, A and Gundersen, H and Mischke, U and Skjelbred, B and Nejstgaard, JC and Guislain, ALN and Sperfeld, E and Giling, DP and Haande, S and Ballot, A and Moe, SJ and Stephan, S and Walles, TJW and Jechow, A and Minguez, L and Ganzert, L and Hornick, T and Hansson, TH and Stratmann, CN and Järvinen, M and Drakare, S and Carvalho, L and Grossart, HP and Gessner, MO and Berger, SA},
title = {Lake browning counteracts cyanobacteria responses to nutrients: Evidence from phytoplankton dynamics in large enclosure experiments and comprehensive observational data.},
journal = {Global change biology},
volume = {},
number = {},
pages = {e17013},
doi = {10.1111/gcb.17013},
pmid = {37994377},
issn = {1365-2486},
support = {603378, 226273//European Union FP7/ ; 731065//European Union H2020/ ; 01LC1501, 033L041B//German Federal Ministry of Education and Research/ ; GE 1775/2-1//German Research Foundation/ ; K45/2017, SAW-2015-IGB-1//Leibniz Association/ ; GE 1775/2-1//German Research Foundation/ ; //Morsa River Basin authority, Norway/ ; },
abstract = {Lakes worldwide are affected by multiple stressors, including climate change. This includes massive loading of both nutrients and humic substances to lakes during extreme weather events, which also may disrupt thermal stratification. Since multi-stressor effects vary widely in space and time, their combined ecological impacts remain difficult to predict. Therefore, we combined two consecutive large enclosure experiments with a comprehensive time-series and a broad-scale field survey to unravel the combined effects of storm-induced lake browning, nutrient enrichment and deep mixing on phytoplankton communities, focusing particularly on potentially toxic cyanobacterial blooms. The experimental results revealed that browning counteracted the stimulating effect of nutrients on phytoplankton and caused a shift from phototrophic cyanobacteria and chlorophytes to mixotrophic cryptophytes. Light limitation by browning was identified as the likely mechanism underlying this response. Deep-mixing increased microcystin concentrations in clear nutrient-enriched enclosures, caused by upwelling of a metalimnetic Planktothrix rubescens population. Monitoring data from a 25-year time-series of a eutrophic lake and from 588 northern European lakes corroborate the experimental results: Browning suppresses cyanobacteria in terms of both biovolume and proportion of the total phytoplankton biovolume. Both the experimental and observational results indicated a lower total phosphorus threshold for cyanobacterial bloom development in clearwater lakes (10-20 μg P L[-1]) than in humic lakes (20-30 μg P L[-1]). This finding provides management guidance for lakes receiving more nutrients and humic substances due to more frequent extreme weather events.},
}

@article {pmid37991947,
year = {2023},
author = {Arya, S and George, AB and O'Dwyer, JP},
title = {Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {120},
number = {48},
pages = {e2307313120},
doi = {10.1073/pnas.2307313120},
pmid = {37991947},
issn = {1091-6490},
support = {376199//Simons Foundation (SF)/ ; },
abstract = {Microbiome engineering offers the potential to leverage microbial communities to improve outcomes in human health, agriculture, and climate. To translate this potential into reality, it is crucial to reliably predict community composition and function. But a brute force approach to cataloging community function is hindered by the combinatorial explosion in the number of ways we can combine microbial species. An alternative is to parameterize microbial community outcomes using simplified, mechanistic models, and then extrapolate these models beyond where we have sampled. But these approaches remain data-hungry, as well as requiring an a priori specification of what kinds of mechanisms are included and which are omitted. Here, we resolve both issues by introducing a mechanism-agnostic approach to predicting microbial community compositions and functions using limited data. The critical step is the identification of a sparse representation of the community landscape. We then leverage this sparsity to predict community compositions and functions, drawing from techniques in compressive sensing. We validate this approach on in silico community data, generated from a theoretical model. By sampling just [Formula: see text]1% of all possible communities, we accurately predict community compositions out of sample. We then demonstrate the real-world application of our approach by applying it to four experimental datasets and showing that we can recover interpretable, accurate predictions on composition and community function from highly limited data.},
}

@article {pmid37991578,
year = {2023},
author = {Liu, HH and Chen, L and Shao, HB and Gao, S and Hong, XY and Bing, XL},
title = {Environmental Factors and the Symbiont Cardinium Influence the Bacterial Microbiome of Spider Mites Across the Landscape.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {1},
pmid = {37991578},
issn = {1432-184X},
support = {32001905 and 32020103011//National Natural Science Foundation of China/ ; 32001905 and 32020103011//National Natural Science Foundation of China/ ; 2022YFC2601000//National Key Research and Development Program of China/ ; BK20211213//Natural Science Foundation of Jiangsu Province/ ; KJQN202110//Fundamental Research Funds for the Central Universities/ ; },
mesh = {Humans ; Animals ; *Tetranychidae ; RNA, Ribosomal, 16S/genetics ; Bacteroidetes/genetics ; *Arthropods ; *Microbiota ; },
abstract = {Microbes play a key role in the biology, ecology, and evolution of arthropods. Despite accumulating data on microbial communities in arthropods that feed on plants using piercing-sucking mouthparts, we still lack a comprehensive understanding of the composition and assembly factors of the microbiota, particularly in field-collected spider mites. Here, we applied 16S rRNA amplicon sequencing to investigate the characters of the bacterial community in 140 samples representing 420 mite individuals, belonging to eight Tetranychus species (Acari: Tetranychidae) collected from 26 sites in China. The results showed that the bacterial composition of spider mites varied significantly among different species, locations, and plants. The environment showed a significant influence on the bacterial community of spider mites, with different relative contributions. Latitude and precipitation were found to be the main factors influencing the bacterial community composition. The dissimilarity of bacterial community and geographical distance between mite locations were significantly correlated. The assembly of spider mite bacterial communities seemed to be mainly influenced by stochastic processes. Furthermore, the symbiont Cardinium was found to be important in shaping the microbiota of many Tetranychus species. The relative abundance of Cardinium was > 50% in T. viennensis, T. urticae G, T. urticae R, and T. turkestani. Removing Cardinium reads from our analysis significantly changed Shannon diversity index and weighted beta diversity in these species. Altogether, this study provides novel insights into bacterial diversity patterns that contribute to our knowledge of the symbiotic relationships between arthropods and their bacterial communities.},
}

Humans
Animals
*Tetranychidae
RNA, Ribosomal, 16S/genetics
Bacteroidetes/genetics
*Arthropods
*Microbiota

@article {pmid37989722,
year = {2023},
author = {Yuan, M and Na, M and Hicks, LC and Rousk, J},
title = {Limiting resources for soil microbial growth in climate change simulation treatments in the Subarctic.},
journal = {Ecology},
volume = {},
number = {},
pages = {e4210},
doi = {10.1002/ecy.4210},
pmid = {37989722},
issn = {1939-9170},
abstract = {The microbial use of resources to sustain life and reproduce influences e.g., decomposition and plant nutrient provisioning. The study of "limiting factors" has shed light on the interaction between plants and their environment. Here, we investigated whether carbon (C), nitrogen (N) or phosphorus (P) was limiting for soil microorganisms in a subarctic tundra heath, and how changes in resource availability associated with climate change affected this. We studied samples where changes in resource availability due to climate warming were simulated by the addition of birch litter and/or inorganic N. To these soils, we supplied factorial C (as glucose), N (as NH4 NO3) and P (as KH2 PO4 /K2 HPO4) additions ("limiting factor assays"; LFA), to determine the limiting factors. The combination of C and P induced large growth responses in all soils and combined with a systematic tendency for growth increases by C this suggested that total microbial growth was primarily limited by C and secondarily by P. The C limitation was alleviated by the field litter treatment and strengthened by N-fertilization. The microbial growth response to the LFA C and P addition was strongest in the field treatment that combined litter and N addition. We also found that bacteria were closer to P limitation than fungi. Our results suggest that under a climate change scenario, increased C availability resulting from arctic greening, treeline advance and shrubification will reduce the microbial C limitation, while increased N availability resulting from warming will intensify the microbial C limitation. Our results also suggest that the synchronous increase of both C and N availability might lead to a progressive P limitation of microbial growth, primarily driven by bacteria being closer to P limitation. These shifts in microbial resource limitation might lead to a microbial targeting of the limiting element from organic matter, and also trigger competition for nutrients between plants and microorganisms, thus modulating the productivity of the ecosystem. This article is protected by copyright. All rights reserved.},
}

@article {pmid37987191,
year = {2023},
author = {Garbisu, C and Alkorta, I},
title = {A case for the importance of following antibiotic resistant bacteria throughout the soil food web.},
journal = {BioEssays : news and reviews in molecular, cellular and developmental biology},
volume = {45},
number = {12},
pages = {e2300153},
doi = {10.1002/bies.202300153},
pmid = {37987191},
issn = {1521-1878},
support = {PID2020-116495RB-I00//MCIN/AEI/10.13039/501100011033/ ; IT1578-22//Basque Government/ ; //JRL Environmental Antibiotic Resistance/ ; },
mesh = {Animals ; *Soil ; *Bacteria/genetics ; Manure/microbiology ; Food Chain ; Ecosystem ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; },
abstract = {It is necessary to complement next-generation sequencing data on the soil resistome with theoretical knowledge provided by ecological studies regarding the spread of antibiotic resistant bacteria (ARB) in the abiotic and, especially, biotic fraction of the soil ecosystem. Particularly, when ARB enter agricultural soils as a consequence of the application of animal manure as fertilizer, from a microbial ecology perspective, it is important to know their fate along the soil food web, that is, throughout that complex network of feeding interactions among members of the soil biota that has crucial effects on species richness and ecosystem productivity and stability. It is critical to study how the ARB that enter the soil through the application of manure can reach other taxonomical groups (e.g., fungi, protists, nematodes, arthropods, earthworms), paying special attention to their presence in the gut microbiomes of mesofauna-macrofauna and to the possibilities for horizontal gene transfer of antibiotic resistant genes.},
}

Animals
*Soil
*Bacteria/genetics
Manure/microbiology
Food Chain
Ecosystem
Angiotensin Receptor Antagonists
Angiotensin-Converting Enzyme Inhibitors
Anti-Bacterial Agents/pharmacology
Soil Microbiology
Genes, Bacterial

@article {pmid37986012,
year = {2023},
author = {Basbas, C and Garzon, A and Schlesener, C and van Heule, M and Profeta, R and Weimer, BC and Silva-Del-Rio, N and Byrne, BA and Karle, B and Aly, SS and Lima, FS and Pereira, RV},
title = {Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.},
journal = {Animal microbiome},
volume = {5},
number = {1},
pages = {59},
pmid = {37986012},
issn = {2524-4671},
abstract = {BACKGROUND: The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.

RESULTS: All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The α diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted < 0.01) in the diversity of genera between CT and MET samples (R2 = 0.112, P = 0.003) and a non-significant difference between MET and PUS samples (R2 = 0.036, P = 0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.

CONCLUSIONS: The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased α-diversity but decreased β-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.},
}

@article {pmid37984648,
year = {2023},
author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, R},
title = {Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {140743},
doi = {10.1016/j.chemosphere.2023.140743},
pmid = {37984648},
issn = {1879-1298},
abstract = {In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generation.},
}

@article {pmid37982643,
year = {2023},
author = {Lo, H-Y and Wink, K and Nitz, H and Kästner, M and Belder, D and Müller, JA and Kaster, A-K},
title = {scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0099823},
doi = {10.1128/msystems.00998-23},
pmid = {37982643},
issn = {2379-5077},
abstract = {A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.},
}

@article {pmid37981701,
year = {2023},
author = {Sadeghi, J and Chaganti, SR and Johnson, TB and Heath, DD},
title = {Host species and habitat shape fish-associated bacterial communities: phylosymbiosis between fish and their microbiome.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {258},
pmid = {37981701},
issn = {2049-2618},
support = {819047//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Phylogeny ; *Microbiota/genetics ; Fishes ; *Gastrointestinal Microbiome/genetics ; Water ; },
abstract = {BACKGROUND: While many studies have reported that the structure of the gut and skin microbiota is driven by both species-specific and habitat-specific factors, the relative importance of host-specific versus environmental factors in wild vertebrates remains poorly understood. The aim of this study was to determine the diversity and composition of fish skin, gut, and surrounding water bacterial communities (hereafter referred to as microbiota) and assess the extent to which host habitat and phylogeny predict microbiota similarity. Skin swabs and gut samples from 334 fish belonging to 17 species were sampled in three Laurentian Great Lakes (LGLs) habitats (Detroit River, Lake Erie, Lake Ontario). We also collected and filtered water samples at the time of fish collection. We analyzed bacterial community composition using 16S metabarcoding and tested for community variation.

RESULTS: We found that the water microbiota was distinct from the fish microbiota, although the skin microbiota more closely resembled the water microbiota. We also found that environmental (sample location), habitat, fish diet, and host species factors shape and promote divergence or convergence of the fish microbiota. Since host species significantly affected both gut and skin microbiota (separately from host species effects), we tested for phylosymbiosis using pairwise host species phylogenetic distance versus bacterial community dissimilarity. We found significant phylogenetic effects on bacterial community dissimilarity, consistent with phylosymbiosis for both the fish skin and gut microbiota, perhaps reflecting the longstanding co-evolutionary relationship between the host species and their microbiomes.

CONCLUSIONS: Analyzing the gut and skin mucus microbiota across diverse fish species in complex natural ecosystems such as the LGLs provides insights into the potential for habitat and species-specific effects on the microbiome, and ultimately the health, of the host. Video Abstract.},
}

Animals
Phylogeny
*Microbiota/genetics
Fishes
*Gastrointestinal Microbiome/genetics
Water

@article {pmid37980777,
year = {2023},
author = {Acosta, DJ and Alper, HS},
title = {Advances in enzymatic and organismal technologies for the recycling and upcycling of petroleum-derived plastic waste.},
journal = {Current opinion in biotechnology},
volume = {84},
number = {},
pages = {103021},
doi = {10.1016/j.copbio.2023.103021},
pmid = {37980777},
issn = {1879-0429},
abstract = {Biological catalysts are emerging with the capability to depolymerize a wide variety of plastics. Improving and discovering these catalysts has leveraged a range of tools, including microbial ecology studies, high-throughput selections, and computationally guided mutational studies. In this review, we discuss the prospects for biological solutions to plastic recycling and upcycling with a focus on major advances in polyethylene terephthalate depolymerization, expanding the range of polymers with known biological catalysts, and the utilization of derived products. We highlight several recent improvements in enzymes and reaction properties, the discovery of a wide variety of novel plastic-depolymerizing biocatalysts, and how depolymerization products can be utilized in recycling and upcycling.},
}

@article {pmid37979870,
year = {2023},
author = {Xiao, Z and Lu, C and Wu, Z and Li, X and Ding, K and Zhu, Z and Han, R and Zhao, J and Ge, T and Li, G and Zhu, YG},
title = {Continuous cropping disorders of eggplants (Solanum melongena L.) and tomatoes (Solanum lycopersicum L.) in suburban agriculture: Microbial structure and assembly processes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168558},
doi = {10.1016/j.scitotenv.2023.168558},
pmid = {37979870},
issn = {1879-1026},
abstract = {Deciphering the intricate relationships between microorganisms and plants remains a formidable challenge in plant microbial ecology, an area that holds promise for optimizing microbial interventions to enhance stress resilience and agricultural yields. In our investigation, we procured samples during 2019 and 2022 from a suburban agricultural greenhouse. Our study delineated the composition of bacterial and fungal communities across various ecological niches-namely, the rhizosphere soil, bulk soil, and phyllosphere of healthy, Ralstonia solanacearum-infected, and dead eggplants and tomatoes. The structure and composition of both fungal and bacterial communities change significantly under the influence of the host genotype across all samples. In the tomato or eggplant groups, bacterial wilt exerts a more pronounced impact on the bacterial community than on the fungal community. We speculate that the rhizosphere of healthy eggplants and tomatoes harbored more antibiotic-producing (e.g., Amycolatopsis and Penicillium) and biocontrol (e.g., Bacillus) strains, which can lead to have lower absolute abundance of R. solanacearum. In the context of R. solanacearum invasion, deterministic processes were responsible for shaping 70.67 % and 80.63 % of the bacterial community assembly in the rhizosphere of eggplants and tomatoes, respectively. Deterministic processes dominated the assembly of fungal communities in the rhizosphere of R. solanacearum-infected eggplants, whereas the opposite was true in the tomatoes. Homogeneous selection emerged as the predominant force governing the bacterial community assembly in the rhizospheres of R. solanacearum-infected eggplants and tomatoes. The bacterial co-occurrence networks in healthy rhizosphere soil were characterized by reduced vulnerability and enhanced stability (i.e., robustness index) and complexity (i.e., cohesion index), compared to their infected counterparts. In summary, complex microbial networks in rhizosphere soils are more resistant to invasion by soil-borne pathogens. The dynamics of bacterial interactions and community assembly processes are pivotal for effective microbiome management and offer predictive insights into the ecological ramifications of R. solanacearum invasions.},
}

@article {pmid37977011,
year = {2023},
author = {Scaria, SS and Balasubramanian, B and Dandin, VS and Meyyazhagan, A and Pappuswamy, M and Sattanathan, G and Liu, WC and Kadanthottu Sebastian, J and Park, S},
title = {Review on impacts of micro- and nano-plastic on aquatic ecosystems and mitigation strategies.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {265},
number = {},
pages = {106759},
doi = {10.1016/j.aquatox.2023.106759},
pmid = {37977011},
issn = {1879-1514},
abstract = {The rapid proliferation of microplastics (MPs) and nanoplastics (NPs) in our environment presents a formidable hazard to both biotic and abiotic components. These pollutants originate from various sources, including commercial production and the breakdown of larger plastic particles. Widespread contamination of the human body, agroecosystems, and animals occurs through ingestion, entry into the food chain, and inhalation. Consequently, the imperative to devise innovative methods for MPs and NPs remediation has become increasingly apparent. This review explores the current landscape of strategies proposed to mitigate the escalating threats associated with plastic waste. Among the array of methods in use, microbial remediation emerges as a promising avenue for the decomposition and reclamation of MPs and NPs. In response to the growing concern, numerous nations have already implemented or are in the process of adopting regulations to curtail MPs and NPs in aquatic habitats. This paper aims to address this gap by delving into the environmental fate, behaviour, transport, ecotoxicity, and management of MPs and NPs particles within the context of nanoscience, microbial ecology, and remediation technologies. Key findings of this review encompass the intricate interdependencies between MPs and NPs and their ecosystems. The ecological impact, from fate to ecotoxicity, is scrutinized in light of the burgeoning environmental imperative. As a result, this review not only provides an encompassing understanding of the ecological ramifications of MPs and NPs but also highlights the pressing need for further research, innovation, and informed interventions.},
}

@article {pmid37976624,
year = {2023},
author = {Liu, S and Lin, Y and Liu, T and Xu, X and Wang, J and Chen, Q and Sun, W and Dang, C and Ni, J},
title = {Planktonic/benthic Bathyarchaeota as a "gatekeeper" enhance archaeal nonrandom co-existence and deterministic assembling in the Yangtze River.},
journal = {Water research},
volume = {247},
number = {},
pages = {120829},
doi = {10.1016/j.watres.2023.120829},
pmid = {37976624},
issn = {1879-2448},
abstract = {Archaea, the third proposed domain of life, mediate carbon and nutrient cycling in global natural habitats. Compared with bacteria, our knowledge about archaeal ecological modes in large freshwater environments subject to varying natural and human factors is limited. By metabarcoding analysis of 303 samples, we provided the first integrate biogeography about archaeal compositions, co-existence networks, and assembling processes within a 6000 km continuum of the Yangtze River. Our study revealed that, among the major phyla, water samples owned a higher proportion of Thaumarchaeota (62.8%), while sediments had higher proportions of Euryarchaeota (33.4%) and Bathyarchaeota (18.8%). A decline of polarization in phylum abundance profile was observed from plateau/mountain/hill to basin/plain areas, which was attributed to the increase of nutrients and metals. Planktonic and benthic Bathyarchaeota tended to co-occur with both major (e.g., methanogens or Thermoplasmata) and minor (e.g., Asgard or DPANN) taxa in the non-random networks, harboring the highest richness and abundances of keystone species and contributing the most positively to edge number, node degree, and nearest neighbor degree. Furthermore, we noted significantly positive contributions of Bathyarchaeota abundance and network complexity to the dominance of deterministic process in archaeal assembly (water: 65.3%; sediments: 92.6%), since higher carbon metabolic versatility of Bathyarchaeota would benefit archaeal symbiotic relations. Stronger deterministic assembling was identified at the lower-reach plain, and higher concentrations of ammonium and aluminum separately functioning as nutrition and agglomerator were the main environmental drivers. We lastly found that the Three Gorges Dam caused a simultaneous drop of benthic Bathyarchaeota abundance, network co-existence, and deterministic effects immediately downstream due to riverbed erosion as a local interference. These findings highlight that Bathyarchaeota are a "gatekeeper" to promote fluvial archaeal diversity, stability, and predictability under varying macroscopic and microscopic factors, expanding our knowledge about microbial ecology in freshwater biogeochemical cycling globally.},
}

@article {pmid37975506,
year = {2023},
author = {Lequime, S},
title = {The sociality continuum of viruses: a commentary on Leeks et al. 2023.},
journal = {Journal of evolutionary biology},
volume = {36},
number = {11},
pages = {1568-1570},
doi = {10.1111/jeb.14247},
pmid = {37975506},
issn = {1420-9101},
}

@article {pmid37974054,
year = {2023},
author = {Minnebo, Y and De Paepe, K and Raes, J and Van de Wiele, T},
title = {Eating patterns contribute to shaping the gut microbiota in the mucosal simulator of the human intestinal microbial ecosystem.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad149},
pmid = {37974054},
issn = {1574-6941},
abstract = {Eating patterns, i.e. meal frequency and circadian timing of meals, are often modified in weight loss and metabolic healing strategies. However, in-depth research into the effects on the gut microbiome remains scarce, particularly across various colon regions and niches. We identified eating patterns to contribute in shaping the in vitro gut biomass production, metabolism, and microbial community compositions by subjecting four faecal microbiomes to a pattern that is standardised for a dynamic gut model (feeding at 09, 17 and 01h), a typical Western (breakfast, lunch and dinner at 09, 13 and 19h, respectively) and a time-restricted pattern (single meal at 09h). While eating patterns moderately affected the microbiome (2.4% and 1.8% significant variation in proportional and quantitative microbial compositions, respectively), significant changes were noted in the time-restricted pattern, including increased Bacteroides, Butyricicoccus, Dialister, and Faecalibacterium abundances. Sampling every four hours revealed no significant circadian fluctuations in biomass production, microbial community compositions, or functionality. Longer fasting times favoured growth of slower-growing species, like Akkermansia, Dialister and Parasutterella over faster-growers, such as Pseudomonas and Stenotrophomonas. Our findings illustrate the importance of recording and considering eating patterns as a gut microbiome determinant in in vivo and in vitro dietary intervention studies.},
}

@article {pmid37973932,
year = {2023},
author = {Feliu-Paradeda, L and Puig, S and Bañeras, L},
title = {Design and validation of a multiplex PCR method for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {20073},
pmid = {37973932},
issn = {2045-2322},
support = {PCI2019-111932-2//Ministerio de Ciencia e Innovación/ ; 2021 FISDU00132//Generalitat de Catalunya/ ; UdG-AG-575//Universitat de Girona/ ; },
abstract = {Co-cultures of clostridia with distinct physiological properties have emerged as an alternative to increase the production of butanol and other added-value compounds from biomass. The optimal performance of mixed tandem cultures may depend on the stability and fitness of each species in the consortium, making the development of specific quantification methods to separate their members crucial. In this study, we developed and tested a multiplex qPCR method targeting the 16S rRNA gene for the simultaneous quantification of Clostridium acetobutylicum, Clostridium carboxidivorans and Clostridium cellulovorans in co-cultures. Designed primer pairs and probes could specifically quantify the three Clostridium species with no cross-reactions thus allowing significant changes in their growth kinetics in the consortia to be detected and correlated with productivity. The method was used to test a suitable medium composition for simultaneous growth of the three species. We show that higher alcohol productions were obtained when combining C. carboxidivorans and C. acetobutylicum compared to individual cultures, and further improved (> 90%) in the triplet consortium. Altogether, the methodology could be applied to fermentation processes targeting butanol productions from lignocellulosic feedstocks with a higher substrate conversion efficiency.},
}

@article {pmid37971428,
year = {2023},
author = {Silcocks, M and Chang, X and Thuong Thuong, NT and Qin, Y and Minh Ha, DT and Khac Thai, PV and Vijay, S and Anh Thu, DD and Ngoc Ha, VT and Ngoc Nhung, H and Huu Lan, N and Quynh Nhu, NT and Edwards, D and Nath, A and Pham, K and Duc Bang, N and Hong Chau, TT and Thwaites, G and Heemskerk, AD and Chuen Khor, C and Teo, YY and Inouye, M and Ong, RT-H and Caws, M and Holt, KE and Dunstan, SJ},
title = {Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0256223},
doi = {10.1128/spectrum.02562-23},
pmid = {37971428},
issn = {2165-0497},
abstract = {Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.},
}

@article {pmid37971255,
year = {2023},
author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA},
title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0062923},
doi = {10.1128/aem.00629-23},
pmid = {37971255},
issn = {1098-5336},
abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.},
}

@article {pmid37970641,
year = {2023},
author = {Spencer-Williams, I and Meyer, M and DePas, W and Elliott, E and Haig, SJ},
title = {Assessing the Impacts of Lead Corrosion Control on the Microbial Ecology and Abundance of Drinking-Water-Associated Pathogens in a Full-Scale Drinking Water Distribution System.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.3c05272},
pmid = {37970641},
issn = {1520-5851},
abstract = {Increases in phosphate availability in drinking water distribution systems (DWDSs) from the use of phosphate-based corrosion control strategies may result in nutrient and microbial community composition shifts in the DWDS. This study assessed the year-long impacts of full-scale DWDS orthophosphate addition on both the microbial ecology and density of drinking-water-associated pathogens that infect the immunocompromised (DWPIs). Using 16S rRNA gene amplicon sequencing and droplet digital PCR, drinking water microbial community composition and DWPI density were examined. Microbial community composition analysis suggested significant compositional changes after the orthophosphate addition. Significant increases in total bacterial density were observed after orthophosphate addition, likely driven by a 2 log 10 increase in nontuberculous mycobacteria (NTM). Linear effect models confirmed the importance of phosphate addition with phosphorus concentration explaining 17% and 12% of the variance in NTM and L. pneumophila density, respectively. To elucidate the impact of phosphate on NTM aggregation, a comparison of planktonic and aggregate fractions of NTM cultures grown at varying phosphate concentrations was conducted. Aggregation assay results suggested that higher phosphate concentrations cause more disaggregation, and the interaction between phosphate and NTM is species specific. This work reveals new insight into the consequences of orthophosphate application on the DWDS microbiome and highlights the importance of proactively monitoring the DWDS for DWPIs.},
}

@article {pmid37970497,
year = {2023},
author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB},
title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.},
journal = {Journal of animal science and technology},
volume = {65},
number = {4},
pages = {856-864},
pmid = {37970497},
issn = {2055-0391},
abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.},
}

@article {pmid37968548,
year = {2023},
author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A},
title = {Characterization of the soil resistome and mobilome in Namib Desert soils.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {37968548},
issn = {1618-1905},
abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.},
}

@article {pmid37968339,
year = {2023},
author = {Sadiq, FA and De Reu, K and Steenackers, H and Van de Walle, A and Burmølle, M and Heyndrickx, M},
title = {Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms - an example from dairy isolates.},
journal = {ISME communications},
volume = {3},
number = {1},
pages = {118},
pmid = {37968339},
issn = {2730-6151},
support = {101025683//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 35906//Villum Fonden (Villum Foundation)/ ; },
abstract = {Identifying interspecies interactions in mixed-species biofilms is a key challenge in microbial ecology and is of paramount importance given that interactions govern community functionality and stability. We previously reported a bacterial four-species biofilm model comprising Stenotrophomonas rhizophila, Bacillus licheniformis, Microbacterium lacticum, and Calidifontibacter indicus that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture. The present study confirms that the observed community synergy results from dynamic social interactions, encompassing commensalism, exploitation, and amensalism. M. lacticum appears to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of M. lacticum) also contributed towards the synergy in biofilm mass. Biofilm inducing effects of bacterial cell-free-supernatants were observed for some combinations, revealing the nature of the observed synergy, and addition of additional species to dual-species combinations confirmed the presence of higher-order interactions within the biofilm community. Our findings provide understanding of bacterial interactions in biofilms which can be used as an interaction-mediated approach for cultivating, engineering, and designing synthetic bacterial communities.},
}

@article {pmid37830797,
year = {2023},
author = {Stapelfeldt, HRD and Lanclos, VC and Henson, MW and Thrash, JC},
title = {Draft genome sequence of the BAL58 Betaproteobacteria representative strain LSUCC0117.},
journal = {Microbiology resource announcements},
volume = {12},
number = {11},
pages = {e0062023},
pmid = {37830797},
issn = {2576-098X},
support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; },
abstract = {Here, we present the draft genome sequence of strain LSUCC0117, a representative of the abundant aquatic BAL58 Betaproteobacteria group which we isolated from a coastal site in the northern Gulf of Mexico. The genome is estimated at over 99% complete, with a genome size of 2,687,225 bp.},
}

@article {pmid37812006,
year = {2023},
author = {Phillips, EK and Shaffer, JMC and Henson, MW and Coelho, JT and Martin, MO and Thrash, JC},
title = {Genome sequences of four agarolytic bacteria from the Bacteroidia and Gammaproteobacteria.},
journal = {Microbiology resource announcements},
volume = {12},
number = {11},
pages = {e0066723},
pmid = {37812006},
issn = {2576-098X},
support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; OCE-1945279, EF-2125191//National Science Foundation (NSF)/ ; },
abstract = {Here we present the genomes of four marine agarolytic bacteria belonging to the Bacteroidota and Proteobacteria. Two genomes are closed and two are in draft form, but all are at least 99% complete and offer new opportunities to study agar-degradation in marine bacteria.},
}

@article {pmid37966591,
year = {2024},
author = {Heinrichs, ME and Piedade, GJ and Popa, O and Sommers, P and Trubl, G and Weissenbach, J and Rahlff, J},
title = {Breaking the Ice: A Review of Phages in Polar Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2738},
number = {},
pages = {31-71},
pmid = {37966591},
issn = {1940-6029},
mesh = {*Bacteriophages ; Ecosystem ; Biomass ; Biological Evolution ; Cell Death ; *Viroids ; },
abstract = {Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.},
}

*Bacteriophages
Ecosystem
Biomass
Biological Evolution
Cell Death
*Viroids

@article {pmid37966223,
year = {2023},
author = {Liu, S and Greenhut, IV and Heist, EP and Heist, MR and Moe, LA},
title = {Bacterial community dynamics during distilled spirit fermentation: influence of mash recipes and fermentation processes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0162423},
doi = {10.1128/spectrum.01624-23},
pmid = {37966223},
issn = {2165-0497},
abstract = {Production of ethanol from sugars and yeast is an ancient, ostensibly simple process. The source of sugars varies depending on the desired product and can include fruits, vegetables, molasses, honey, or grains, among other things. The source of yeast can be natural in the case of spontaneous ferments, but dry yeast addition is typical for large-scale fermentations. While the polymicrobial nature of some alcoholic fermentations is appreciated (e.g., for wine), most grain-based ethanol producers view microbes, apart from the added yeast, as "contaminants" meant to be controlled in order to maximize efficiency of ethanol production per unit of sugar. Nonetheless, despite rigorous cleaning-in-place measures and cooking the mash, bacteria are routinely cultured from these fermentations. We now know that bacteria can contribute to fermentation efficiency on an industrial scale, yet nothing is known about the makeup and stability of microbial communities in distilled spirit fermentations. The work here establishes the roles of mash recipes and distillery practices in microbial community assembly and dynamics over the course of fermentation. This represents an important first step in appreciating the myriad roles of bacteria in the production of distilled spirits.},
}

@article {pmid37966203,
year = {2023},
author = {Miliotis, G and McDonagh, F and Singh, NK and O'Connor, L and Tuohy, A and Morris, D and Venkateswaran, K},
title = {Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0189723},
doi = {10.1128/spectrum.01897-23},
pmid = {37966203},
issn = {2165-0497},
abstract = {The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.},
}

@article {pmid37965618,
year = {2023},
author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN},
title = {Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data.},
journal = {Data in brief},
volume = {51},
number = {},
pages = {109726},
pmid = {37965618},
issn = {2352-3409},
abstract = {The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224-1702 enzyme classes, 84,833-198,397 gene families, and 280-400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.},
}

@article {pmid37964521,
year = {2023},
author = {Brunetti, AE and Lyra, ML and Monteiro, JPC and Zurano, JP and Baldo, D and Haddad, CFB and Moeller, AH},
title = {Convergence of gut microbiota in myrmecophagous amphibians.},
journal = {Proceedings. Biological sciences},
volume = {290},
number = {2011},
pages = {20232223},
doi = {10.1098/rspb.2023.2223},
pmid = {37964521},
issn = {1471-2954},
abstract = {The gut microbiome composition of terrestrial vertebrates is known to converge in response to common specialized dietary strategies, like leaf-eating (folivory) or ant- and termite-eating (myrmecophagy). To date, such convergence has been studied in mammals and birds, but has been neglected in amphibians. Here, we analysed 15 anuran species (frogs and toads) representing five Neotropical families and demonstrated the compositional convergence of the gut microbiomes of distantly related myrmecophagous species. Specifically, we found that the gut microbial communities of bufonids and microhylids, which have independently evolved myrmecophagy, were significantly more similar than expected based on their hosts' evolutionary divergence. Conversely, we found that gut microbiome composition was significantly associated with host evolutionary history in some cases. For instance, the microbiome composition of Xenohyla truncata, one of the few known amphibians that eat fruits, was not different from those of closely related tree frogs with an arthropod generalist diet. Bacterial taxa overrepresented in myrmecophagous species relative to other host families include Paludibacter, Treponema, and Rikenellaceae, suggesting diet-mediated selection and prey-to-predator transmission likely driving the observed compositional convergence. This study provides a basis for examining the roles of the gut microbiome in host tolerance and sequestration of toxic alkaloids from ants and termites.},
}

@article {pmid37961388,
year = {2023},
author = {Karim, S and Zenzal, TJ and Beati, L and Sen, R and Adegoke, A and Kumar, D and Downs, LP and Keko, M and Nussbaum, A and Becker, DJ and Moore, FR},
title = {Ticks without borders: Microbial communities of immature Neotropical tick species parasitizing migratory landbirds along northern Gulf of Mexico.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.10.22.563347},
pmid = {37961388},
abstract = {The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can lead to the emergence of novel tick-borne pathogens or the re-emergence of previously eradicated ones. This study assessed the prevalence of exotic tick species parasitizing resident, short-distance, and long-distance songbirds during spring and autumn at stopover sites in the northern Gulf of Mexico using the mitochondrial 12S rDNA gene. Birds were captured for tick collection from six different sites from late August to early November in both 2018 and 2019. The highest number of ticks were collected in the 2019 season. Most ticks were collected off the Yellow-breasted Chat (Icteria virens) and Common Yellowthroat (Geothlypis trichas), and 54% of the total ticks collected were from Grand Chenier, LA. A high throughput 16S ribosomal RNA sequencing approach was followed to characterize the microbial communities and identify pathogenic microbes in all tick samples. Tick microbial communities, diversity, and community structure were determined using quantitative insight into microbial ecology (QIIME). The sparse correlations for compositional data (SparCC) approach was then used to construct microbial network maps and infer microbial correlations. A total of 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre was the most abundant tick genus and species, respectively. Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant bacteria include the pathogenic Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma . BLAST analysis and phylogenetic reconstruction of the Rickettsia sequences revealed the highest similarities to pathogenic spotted and non-spotted fever groups, including R . buchneri, R. conorii, R. prowazekii, R. bellii, R. australis, R. parkeri, R. monacensis, and R. monteiroi . Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also observed a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium . Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing means dispersal distances from 421-5003 kilometers. These findings strongly highlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.},
}

@article {pmid37959068,
year = {2023},
author = {Bettera, L and Levante, A and Bancalari, E and Bottari, B and Cirlini, M and Neviani, E and Gatti, M},
title = {Lacticaseibacillus Strains Isolated from Raw Milk: Screening Strategy for Their Qualification as Adjunct Culture in Cheesemaking.},
journal = {Foods (Basel, Switzerland)},
volume = {12},
number = {21},
pages = {},
doi = {10.3390/foods12213949},
pmid = {37959068},
issn = {2304-8158},
support = {FIL-Quota Incentivante//University of Parma/ ; },
abstract = {The microbial ecology fundamentals of raw milk and long-ripened cheeses consist of a complex interaction between starter lactic acid bacteria (SLAB) and non-starter LAB (NSLAB). Although NSLAB aromatic properties are paramount, other phenotypic traits need to be considered for their use as adjunct cultures, such as the capability to endure technological parameters encountered during cheesemaking. The present study focused on the isolation and characterization of NSLAB from spontaneously fermented raw cow's milk coming from 20 dairies that produce Grana Padano PDO cheese. From 122 isolates, the screening process selected the 10 most diverse strains belonging to Lacticaseibacillus spp. to be phenotypically characterized. The strains were tested for their growth performance in milk in combination with the application of technological stresses, for their ability to produce volatile compounds after their growth in milk, and for their ability to use different nutrient sources and resist chemicals. The complex characterization qualified the strains 5959_Lbparacasei and 5296_Lbparacasei as the best candidates to be used as adjunct strains in the production of raw milk and long-ripened cheeses, provided that antibiotic resistance is measured before their employment. Other strains with interesting aromatic capabilities but lower heat resistance were 5293_Lbparacasei, 5649_Lbparacasei and 5780_Lbparacasei, which could be candidates as adjunct strains for uncooked cheese production.},
}

@article {pmid37957741,
year = {2023},
author = {Moldovan, OT and Carrell, AA and Bulzu, PA and Levei, E and Bucur, R and Sitar, C and Faur, L and Mirea, IC and Șenilă, M and Cadar, O and Podar, M},
title = {The gut microbiome mediates adaptation to scarce food in Coleoptera.},
journal = {Environmental microbiome},
volume = {18},
number = {1},
pages = {80},
pmid = {37957741},
issn = {2524-6372},
support = {R01DE024463/NH/NIH HHS/United States ; R01DE024463/NH/NIH HHS/United States ; },
abstract = {Beetles are ubiquitous cave invertebrates worldwide that adapted to scarce subterranean resources when they colonized caves. Here, we investigated the potential role of gut microbiota in the adaptation of beetles to caves from different climatic regions of the Carpathians. The beetles' microbiota was host-specific, reflecting phylogenetic and nutritional adaptation. The microbial community structure further resolved conspecific beetles by caves suggesting microbiota-host coevolution and influences by local environmental factors. The detritivore species hosted a variety of bacteria known to decompose and ferment organic matter, suggesting turnover and host cooperative digestion of the sedimentary microbiota and allochthonous-derived nutrients. The cave Carabidae, with strong mandibula, adapted to predation and scavenging of animal and plant remains, had distinct microbiota dominated by symbiotic lineages Spiroplasma or Wolbachia. All beetles had relatively high levels of fermentative Carnobacterium and Vagococcus involved in lipid accumulation and a reduction of metabolic activity, and both features characterize adaptation to caves.},
}

@article {pmid37956766,
year = {2023},
author = {Dong, CD and Huang, CP and Chen, CW and Hung, CM},
title = {The remediation of marine sediments containing polycyclic aromatic hydrocarbons by peroxymonosulfate activated with Sphagnum moss-derived biochar and its benthic microbial ecology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {122912},
doi = {10.1016/j.envpol.2023.122912},
pmid = {37956766},
issn = {1873-6424},
abstract = {This research was to study the efficiency of Sphagnum moss-derived biochar (SMBC) in removing polycyclic aromatic hydrocarbons (PAHs) from marine sediment using a peroxymonosulfate (PMS)-based carbon-advanced oxidation process (PMS-CAOPs). Sphagnum moss-derived biochar (SMBC) was generated via a simple thermochemical process for PMS activation toward enhancing decontamination of sediments. At pH 6, the SMBC/PMS system achieved a PAH removal efficiency exceeding 78% in 12 h reaction time. Moreover, PAHs of 6-, 5-, 4-, 3-, and 2-ring structures exhibited 98%, 74%, 68%, 85%, and 91%, of removal, respectively. The SMBC activation of PMS generated both radicals (SO4[•-] and HO•) and nonradical ([1]O2), species responsible for PAHs degradation, attributed primarily to inherent iron and carbon moieties. The significant PAHs degradation efficiency showcased by the SMBC/PMS process holds promise for augmenting the performance of indigenous benthic microbial activity in sediment treatment contexts. The response of sediment microbial communities to PAH-induced stress was particularly associated with the Proteobacteria phylum, specifically the Sulfurovum genus. The findings of the present study highlight the efficacy of environmentally benign reactive radical/nonradical-based PMS-CAOP using pristine carbon materials, offering a sustainable strategy for sediment treatment.},
}

@article {pmid37956735,
year = {2023},
author = {Cohen, E and Azriel, S and Auster, O and Gal, A and Mikhlin, S and Crauwels, S and Rahav, G and Gal-Mor, O},
title = {A new Salmonella enterica serovar that was isolated from a wild sparrow presents a distinct genetic, metabolic and virulence profile.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105249},
doi = {10.1016/j.micinf.2023.105249},
pmid = {37956735},
issn = {1769-714X},
abstract = {Salmonella enterica is a ubiquitous and clinically-important bacterial pathogen, able to infect and cause different diseases in a wide range of hosts. Here, we report the isolation and characterization of a new S. enterica serovar (13,23:i:-; S. Tirat-Zvi), belonging to the Havana supper-lineage that was isolated from a wild house sparrow (Passer domesticus) in Israel. Whole genome sequencing and complete assembly of its genome indicated a plasmid-free, 4.7 Mb genome that carries the Salmonella pathogenicity islands 1-6, 9, 19 and an integrative and conjugative element (ICE), encoding arsenic resistance genes. Phenotypically, S. Tirat-Zvi isolate TZ282 was motile, readily formed biofilm, more versatile in carbon source utilization than S. Typhimurium and highly tolerant to arsenic, but impaired in host cell invasion. In-vivo infection studies indicated that while S. Tirat-Zvi was able to infect and cause an acute inflammatory enterocolitis in young chicks, it was compromised in mice colonization and did not cause an inflammatory colitis in mice compared to S. Typhimurium. We suggest that these phenotypes reflect the distinctive ecological niche of this new serovar and its evolutionary adaptation to passerine birds, as a permissive host. Moreover, these results further illuminate the genetic, phenotypic and ecological diversity of S. enterica pathovars.},
}

@article {pmid37956179,
year = {2023},
author = {Sauters, TJC and Roth, C and Murray, D and Sun, S and Floyd Averette, A and Onyishi, CU and May, RC and Heitman, J and Magwene, PM},
title = {Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.},
journal = {PLoS pathogens},
volume = {19},
number = {11},
pages = {e1011763},
doi = {10.1371/journal.ppat.1011763},
pmid = {37956179},
issn = {1553-7374},
abstract = {The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.},
}

@article {pmid37954239,
year = {2023},
author = {Al-Khlifeh, E and Khadem, S and Hausmann, B and Berry, D},
title = {Microclimate shapes the phylosymbiosis of rodent gut microbiota in Jordan's Great Rift Valley.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1258775},
pmid = {37954239},
issn = {1664-302X},
abstract = {Host phylogeny and the environment play vital roles in shaping animal microbiomes. However, the effects of these variables on the diversity and richness of the gut microbiome in different bioclimatic zones remain underexplored. In this study, we investigated the effects of host phylogeny and bioclimatic zone on the diversity and composition of the gut microbiota of two heterospecific rodent species, the spiny mouse Acomys cahirinus and the house mouse Mus musculus, in three bioclimatic zones of the African Great Rift Valley (GRV). We confirmed host phylogeny using the D-loop sequencing method and analyzed the influence of host phylogeny and bioclimatic zone parameters on the rodent gut microbiome using high-throughput amplicon sequencing of 16S rRNA gene fragments. Phylogenetic analysis supported the morphological identification of the rodents and revealed a marked genetic difference between the two heterospecific species. We found that bioclimatic zone had a significant effect on the gut microbiota composition while host phylogeny did not. Microbial alpha diversity of heterospecific hosts was highest in the Mediterranean forest bioclimatic zone, followed by the Irano-Turanian shrubland, and was lowest in the Sudanian savanna tropical zone. The beta diversity of the two rodent species showed significant differences across the Mediterranean, Irano-Turanian, and Sudanian regions. The phyla Firmicutes and Bacteroidetes were highly abundant, and Deferribacterota, Cyanobacteria and Proteobacteria were also prominent. Amplicon sequence variants (ASVs) were identified that were unique to the Sudanian bioclimatic zone. The core microbiota families recovered in this study were consistent among heterospecific hosts. However, diversity decreased in conspecific host populations found at lower altitudes in Sudanian bioclimatic zone. The composition of the gut microbiota is linked to the adaptation of the host to its environment, and this study underscores the importance of incorporating climatic factors such as elevation and ambient temperature, in empirical microbiome research and is the first to describe the rodent gut microbiome from the GRV.},
}

@article {pmid37951257,
year = {2023},
author = {Ye, J and Li, J and Li, L and Zhang, S and Chen, J and Zhu, D and Zhang, C and Xie, B and Zhang, B and Hou, K},
title = {Trends in global ambient fine particulate matter pollution and diabetes mortality rates attributable to it in the 1990-2019: 30 years systematic analysis of global burden of disease.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168358},
doi = {10.1016/j.scitotenv.2023.168358},
pmid = {37951257},
issn = {1879-1026},
abstract = {AIM: To analyze the trends in ambient fine particulate matter pollution (PM2.5) and the age-standardized mortality rate (ASMR) of diabetes attributable to it from 1990 to 2019 by region, country, and socio-economic development status.

METHODS: The main data, including the summary exposure value (SEV) of ambient PM2.5 and the ASMR of diabetes due to ambient PM2.5, was collected from the Global Burden of Disease 2019 database. The socio-demographic index (SDI) was employed for assessing a particular region or country's degree of socio-economic development. Joinpoint regression analysis was used to assess the changes of ambient PM2.5 and ASMR of diabetes attributable to it.

RESULTS: Globally, the SEV of ambient PM2.5 increased from 15.65 μg/m[3] in 1990 to 26.22 μg/m[3] in 2019, with an annual average percent change (AAPC) of 1.788 (95 % CI 1.687-1.889) μg/m[3]. The ASMR of diabetes attributable to ambient PM2.5 increased from 1.57 per 100,000 population in 1990 to 2.47 per 100.000 population in 2019 (AAPC = 1.569 [95 % CI 1.42-1.718]). Most regions and countries had an increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to ambient PM2.5. The largest increase of SEV of ambient PM2.5 was observed in South Asia (AAPC = 3.556 [95 % CI 3.329-3.875]), while the largest increase of ASMR of diabetes was in Central Asia (AAPC = 5.170 [95%CI 4.696-5.647]). Moreover, the increase of SEV of ambient PM2.5 and ASMR of diabetes attributable to it were positively associated with SDI in low SDI countries (SDI < 0.46), whereas the opposite result was observed when SDI ≥ 0.46.

CONCLUSION: From 1990 to 2019, the population's exposure to ambient PM2.5 and ASMR of diabetes attributable to it increased generally, especially in low-middle SDI regions. Ambient PM2.5 remains a threat to global health. Greater investment in ambient PM2.5 and the mortality attributable to it are needed.},
}

@article {pmid37950563,
year = {2023},
author = {White, A and Giannetto, M and Mulla, L and Del Rosario, A and Lim, T and Culver, E and Timmer, M and Bushell, J and Lambert, MR and Hernández-Gómez, O},
title = {Bacterial communities of the threatened Western Pond Turtle maybe impacted by land use.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiad143},
pmid = {37950563},
issn = {1574-6941},
abstract = {As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e., species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.},
}

@article {pmid37942081,
year = {2023},
author = {Han, X and Beck, K and Bürgmann, H and Frey, B and Stierli, B and Frossard, A},
title = {Synthetic oligonucleotides as quantitative PCR standards for quantifying microbial genes.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1279041},
pmid = {37942081},
issn = {1664-302X},
abstract = {Real-time quantitative PCR (qPCR) has been widely used to quantify gene copy numbers in microbial ecology. Despite its simplicity and straightforwardness, establishing qPCR assays is often impeded by the tedious process of producing qPCR standards by cloning the target DNA into plasmids. Here, we designed double-stranded synthetic DNA fragments from consensus sequences as qPCR standards by aligning microbial gene sequences (10-20 sequences per gene). Efficiency of standards from synthetic DNA was compared with plasmid standards by qPCR assays for different phylogenetic marker and functional genes involved in carbon (C) and nitrogen (N) cycling, tested with DNA extracted from a broad range of soils. Results showed that qPCR standard curves using synthetic DNA performed equally well to those from plasmids for all the genes tested. Furthermore, gene copy numbers from DNA extracted from soils obtained by using synthetic standards or plasmid standards were comparable. Our approach therefore demonstrates that a synthetic DNA fragment as qPCR standard provides comparable sensitivity and reliability to a traditional plasmid standard, while being more time- and cost-efficient.},
}

@article {pmid37941937,
year = {2023},
author = {Zhang, H and Wei, T and Li, Q and Fu, L and He, L and Wang, Y},
title = {Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16257},
pmid = {37941937},
issn = {2167-8359},
mesh = {DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Water ; *Microbiota/genetics ; Sulfates ; },
abstract = {Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.},
}

DNA, Ribosomal/genetics
RNA, Ribosomal, 16S/genetics
Phylogeny
*Water
*Microbiota/genetics
Sulfates

@article {pmid37941395,
year = {2022},
author = {Blumberg, K and Miller, M and Ponsero, A and Hurwitz, B},
title = {Ontology-driven analysis of marine metagenomics: what more can we learn from our data?.},
journal = {GigaScience},
volume = {12},
number = {},
pages = {},
pmid = {37941395},
issn = {2047-217X},
support = {OCE-1639614//National Science Foundation/ ; 481471//Simons Foundation/ ; },
mesh = {*Ecology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {BACKGROUND: The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.

RESULTS: Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.

CONCLUSIONS: In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.},
}

*Ecology
*Microbiota/genetics
Metagenome
Metagenomics

@article {pmid37938754,
year = {2022},
author = {Díaz Rodríguez, CA and Díaz-García, L and Bunk, B and Spröer, C and Herrera, K and Tarazona, NA and Rodriguez-R, LM and Overmann, J and Jiménez, DJ},
title = {Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {89},
pmid = {37938754},
issn = {2730-6151},
abstract = {The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.},
}

@article {pmid37938751,
year = {2022},
author = {Jia, X and Dini-Andreote, F and Salles, JF},
title = {Unravelling the interplay of ecological processes structuring the bacterial rare biosphere.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {96},
pmid = {37938751},
issn = {2730-6151},
abstract = {Most ecological communities harbor many rare species (i.e., the rare biosphere), however, relatively little is known about how distinct ecological processes structure their existence. Here, we used spatiotemporal data on soil bacterial communities along a natural ecosystem gradient to model the relative influences of assembly processes structuring the rare and common biospheres. We found a greater influence of homogeneous selection (i.e., imposed by spatiotemporally constant variables) mediating the assembly of the rare biosphere, whereas the common biosphere was mostly governed by variable selection (i.e., imposed by spatial and/or temporal fluctuating variables). By partitioning the different types of rarity, we found homogeneous selection to explain the prevalence of permanently rare taxa, thus suggesting their persistence at low abundances to be restrained by physiological traits. Conversely, the dynamics of conditionally rare taxa were mostly structured by variable selection, which aligns with the ability of these taxa to switch between rarity and commonness as responses to environmental spatiotemporal variations. Taken together, our study contributes to the establishment of a link between conceptual and empirical developments in the ecology of the soil microbial rare biosphere. Besides, this study provides a framework to better understand, model, and predict the existence and dynamics of microbial rare biospheres across divergent systems and scales.},
}

@article {pmid37938693,
year = {2022},
author = {Zauner, S and Vogel, M and Polzin, J and Yuen, B and Mußmann, M and El-Hacen, EM and Petersen, JM},
title = {Microbial communities in developmental stages of lucinid bivalves.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {56},
pmid = {37938693},
issn = {2730-6151},
abstract = {Bivalves from the family Lucinidae host sulfur-oxidizing bacterial symbionts, which are housed inside specialized gill epithelial cells and are assumed to be acquired from the environment. However, little is known about the Lucinidae life cycle and symbiont acquisition in the wild. Some lucinid species broadcast their gametes into the surrounding water column, however, a few have been found to externally brood their offspring by the forming gelatinous egg masses. So far, symbiont transmission has only been investigated in one species that reproduces via broadcast spawning. Here, we show that the lucinid Loripes orbiculatus from the West African coast forms egg masses and these are dominated by diverse members of the Alphaproteobacteria, Clostridia, and Gammaproteobacteria. The microbial communities of the egg masses were distinct from those in the environments surrounding lucinids, indicating that larvae may shape their associated microbiomes. The gill symbiont of the adults was undetectable in the developmental stages, supporting horizontal transmission of the symbiont with environmental symbiont acquisition after hatching from the egg masses. These results demonstrate that L. orbiculatus acquires symbionts from the environment independent of the host's reproductive strategy (brooding or broadcast spawning) and reveal previously unknown associations with microbes during lucinid early development.},
}

@article {pmid37938753,
year = {2022},
author = {Alcolombri, U and Pioli, R and Stocker, R and Berry, D},
title = {Single-cell stable isotope probing in microbial ecology.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {55},
pmid = {37938753},
issn = {2730-6151},
support = {P27831- B28//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; DE- SC0019012//U.S. Department of Energy (DOE)/ ; GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
abstract = {Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.},
}

@article {pmid37938301,
year = {2022},
author = {McDaniel, EA and van Steenbrugge, JJM and Noguera, DR and McMahon, KD and Raaijmakers, JM and Medema, MH and Oyserman, BO},
title = {TbasCO: trait-based comparative 'omics identifies ecosystem-level and niche-differentiating adaptations of an engineered microbiome.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {111},
pmid = {37938301},
issn = {2730-6151},
support = {MCB-1518130//National Science Foundation (NSF)/ ; MCB-1518130//National Science Foundation (NSF)/ ; },
abstract = {A grand challenge in microbial ecology is disentangling the traits of individual populations within complex communities. Various cultivation-independent approaches have been used to infer traits based on the presence of marker genes. However, marker genes are not linked to traits with complete fidelity, nor do they capture important attributes, such as the timing of gene expression or coordination among traits. To address this, we present an approach for assessing the trait landscape of microbial communities by statistically defining a trait attribute as a shared transcriptional pattern across multiple organisms. Leveraging the KEGG pathway database as a trait library and the Enhanced Biological Phosphorus Removal (EBPR) model microbial ecosystem, we demonstrate that a majority (65%) of traits present in 10 or more genomes have niche-differentiating expression attributes. For example, while many genomes containing high-affinity phosphorus transporter pstABCS display a canonical attribute (e.g. up-regulation under phosphorus starvation), we identified another attribute shared by many genomes where transcription was highest under high phosphorus conditions. Taken together, we provide a novel framework for unravelling the functional dynamics of uncultivated microorganisms by assigning trait-attributes through genome-resolved time-series metatranscriptomics.},
}

@article {pmid37934729,
year = {2023},
author = {Vasileiou, D and Karapiperis, C and Baltsavia, I and Chasapi, A and Ahrén, D and Janssen, PJ and Iliopoulos, I and Promponas, VJ and Enright, AJ and Ouzounis, CA},
title = {CGG toolkit: Software components for computational genomics.},
journal = {PLoS computational biology},
volume = {19},
number = {11},
pages = {e1011498},
doi = {10.1371/journal.pcbi.1011498},
pmid = {37934729},
issn = {1553-7358},
abstract = {Public-domain availability for bioinformatics software resources is a key requirement that ensures long-term permanence and methodological reproducibility for research and development across the life sciences. These issues are particularly critical for widely used, efficient, and well-proven methods, especially those developed in research settings that often face funding discontinuities. We re-launch a range of established software components for computational genomics, as legacy version 1.0.1, suitable for sequence matching, masking, searching, clustering and visualization for protein family discovery, annotation and functional characterization on a genome scale. These applications are made available online as open source and include MagicMatch, GeneCAST, support scripts for CoGenT-like sequence collections, GeneRAGE and DifFuse, supported by centrally administered bioinformatics infrastructure funding. The toolkit may also be conceived as a flexible genome comparison software pipeline that supports research in this domain. We illustrate basic use by examples and pictorial representations of the registered tools, which are further described with appropriate documentation files in the corresponding GitHub release.},
}

@article {pmid37934609,
year = {2023},
author = {Qiao, N and Gaur, G and Modesto, M and Chinnici, F and Scarafile, D and Borruso, LM and Marin, AC and Spiezio, C and Valente, D and Sandri, C and Gänzle, MG and Mattarelli, P},
title = {Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxad255},
pmid = {37934609},
issn = {1365-2672},
abstract = {AIMS: Indri indri is a lemur of Madagascar which is Critically Endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lp. plantarum isolates from indris.

METHODS AND RESULTS: Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from 2 individuals. The three isolates were closely related to each other, with fewer than 10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. Genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype.

CONCLUSIONS: Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.},
}

@article {pmid37933257,
year = {2023},
author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Moreno, L and Moraga, CA and Gaete, K and Eguiarte, LE and Souza, V},
title = {Body site microbiota of Magellanic and king penguins inhabiting the Strait of Magellan follow species-specific patterns.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e16290},
pmid = {37933257},
issn = {2167-8359},
mesh = {Animals ; *Spheniscidae ; RNA, Ribosomal, 16S ; *Microbiota ; Soil ; },
abstract = {Animal hosts live in continuous interaction with bacterial partners, yet we still lack a clear understanding of the ecological drivers of animal-associated bacteria, particularly in seabirds. Here, we investigated the effect of body site in the structure and diversity of bacterial communities of two seabirds in the Strait of Magellan: the Magellanic penguin (Spheniscus magellanicus) and the king penguin (Aptenodytes patagonicus). We used 16S rRNA gene sequencing to profile bacterial communities associated with body sites (chest, back, foot) of both penguins and the nest soil of Magellanic penguin. Taxonomic composition showed that Moraxellaceae family (specifically Psychrobacter) had the highest relative abundance across body sites in both penguin species, whereas Micrococacceae had the highest relative abundance in nest soil. We were able to detect a bacterial core among 90% of all samples, which consisted of Clostridium sensu stricto and Micrococcacea taxa. Further, the king penguin had its own bacterial core across its body sites, where Psychrobacter and Corynebacterium were the most prevalent taxa. Microbial alpha diversity across penguin body sites was similar in most comparisons, yet we found subtle differences between foot and chest body sites of king penguins. Body site microbiota composition differed across king penguin body sites, whereas it remained similar across Magellanic penguin body sites. Interestingly, all Magellanic penguin body site microbiota composition differed from nest soil microbiota. Finally, bacterial abundance in penguin body sites fit well under a neutral community model, particularly in the king penguin, highlighting the role of stochastic process and ecological drift in microbiota assembly of penguin body sites. Our results represent the first report of body site bacterial communities in seabirds specialized in subaquatic foraging. Thus, we believe it represents useful baseline information that could serve for long-term comparisons that use marine host microbiota to survey ocean health.},
}

Animals
*Spheniscidae
RNA, Ribosomal, 16S
*Microbiota
Soil

@article {pmid37932283,
year = {2023},
author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K},
title = {Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {19207},
pmid = {37932283},
issn = {2045-2322},
support = {19-12829-26/NASA/NASA/United States ; },
mesh = {Humans ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Prevalence ; Phenotype ; *Paenibacillus/genetics ; Fatty Acids/analysis ; DNA ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; },
abstract = {With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (= NRRL B-65660[T] = DSM 115933[T]), Leifsonia virtsii F6_8S_P_1A[T] (= NRRL B-65661[T] = DSM 115931[T]), Leifsonia williamsii F6_8S_P_1B[T] (= NRRL B-65662[T] = DSM 115932[T]), Paenibacillus vandeheii F6_3S_P_1C[T] (= NRRL B-65663[T] = DSM 115940[T]), and Sporosarcina highlanderae F6_3S_P_2[T] (= NRRL B-65664[T] = DSM 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.},
}

Humans
*Metagenome
Phylogeny
RNA, Ribosomal, 16S/genetics
Prevalence
Phenotype
*Paenibacillus/genetics
Fatty Acids/analysis
DNA
DNA, Bacterial/genetics
Sequence Analysis, DNA
Bacterial Typing Techniques

@article {pmid37938683,
year = {2022},
author = {Marasco, R and Fusi, M and Ramond, JB and Van Goethem, MW and Seferji, K and Maggs-Kölling, G and Cowan, DA and Daffonchio, D},
title = {The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {47},
pmid = {37938683},
issn = {2730-6151},
abstract = {Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.},
}

@article {pmid37938286,
year = {2022},
author = {Yeh, YC and Fuhrman, JA},
title = {Contrasting diversity patterns of prokaryotes and protists over time and depth at the San-Pedro Ocean Time series.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {36},
pmid = {37938286},
issn = {2730-6151},
support = {1737409//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 3779//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 549943//Simons Foundation/ ; },
abstract = {Community dynamics are central in microbial ecology, yet we lack studies comparing diversity patterns among marine protists and prokaryotes over depth and multiple years. Here, we characterized microbes at the San-Pedro Ocean Time series (2005-2018), using SSU rRNA gene sequencing from two size fractions (0.2-1 and 1-80 μm), with a universal primer set that amplifies from both prokaryotes and eukaryotes, allowing direct comparisons of diversity patterns in a single set of analyses. The 16S + 18S rRNA gene composition in the small size fraction was mostly prokaryotic (>92%) as expected, but the large size fraction unexpectedly contained 46-93% prokaryotic 16S rRNA genes. Prokaryotes and protists showed opposite vertical diversity patterns; prokaryotic diversity peaked at mid-depth, protistan diversity at the surface. Temporal beta-diversity patterns indicated prokaryote communities were much more stable than protists. Although the prokaryotic communities changed monthly, the average community stayed remarkably steady over 14 years, showing high resilience. Additionally, particle-associated prokaryotes were more diverse than smaller free-living ones, especially at deeper depths, contributed unexpectedly by abundant and diverse SAR11 clade II. Eukaryotic diversity was strongly correlated with the diversity of particle-associated prokaryotes but not free-living ones, reflecting that physical associations result in the strongest interactions, including symbioses, parasitism, and decomposer relationships.},
}

@article {pmid37938248,
year = {2022},
author = {Song, J and Beule, L and Jongmans-Hochschulz, E and Wichels, A and Gerdts, G},
title = {The travelling particles: community dynamics of biofilms on microplastics transferred along a salinity gradient.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {35},
pmid = {37938248},
issn = {2730-6151},
support = {03F0789B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 03F0789B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
abstract = {Microplastics (MP), as novel substrata for microbial colonization within aquatic ecosystems, are a matter of growing concern due to their potential to propagate foreign or invasive species across different environments. MP are known to harbour a diversity of microorganisms, yet little is understood of the dynamics of their biofilms and their capacity to successfully displace these microorganisms across different aquatic ecosystems typically marked by steep salinity gradients. To address this, we performed an in situ sequential incubation experiment to simulate MP transport from riverine to coastal seawaters using synthetic (high-density polyethylene, HDPE and tyre wear, TW) and natural (Wood) substrata. Bacterial communities on incubated particles were compared to each other as well as to those in surrounding waters, and their dynamics along the gradient investigated. All communities differed significantly from each other in their overall structure along the salinity gradient and were shaped by different ecological processes. While HDPE communities were governed by environmental selection, those on TW and Wood were dominated by stochastic events of dispersal and drift. Upon transfer into coastal seawaters, an almost complete turnover was observed among HDPE and TW communities. While synthetic particles displaced a minor proportion of communities across the salinity gradient, some of these comprised putatively pathogenic and resistant taxa. Our findings present an extensive assessment of MP biofilms and their dynamics upon displacement across different aquatic systems, presenting new insights into the role of MP as transport vectors.},
}

@article {pmid37938679,
year = {2022},
author = {Junkins, EN and McWhirter, JB and McCall, LI and Stevenson, BS},
title = {Environmental structure impacts microbial composition and secondary metabolism.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {15},
pmid = {37938679},
issn = {2730-6151},
support = {80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19K0479//National Aeronautics and Space Administration (NASA)/ ; },
abstract = {Determining the drivers of microbial community assembly is a central theme of microbial ecology, and chemical ecologists seek to characterize how secondary metabolites mediate these assembly patterns. Environmental structure affects how communities assemble and what metabolic pathways aid in that assembly. Here, we bridged these two perspectives by addressing the chemical drivers of community assembly within a spatially structured landscape with varying oxygen availability. We hypothesized that structured environments would favor higher microbial diversity and metabolite diversity. We anticipated that the production of a compound would be more advantageous in a structured environment (less mixing) compared to an unstructured environment (more mixing), where the molecule would have a diminished local effect. We observed this to be partially true in our experiments: structured environments had similar microbial diversity compared to unstructured environments but differed significantly in the metabolites produced. We also found that structured environments selected for communities with higher evenness, rather than communities with higher richness. This supports the idea that when characterizing the drivers of community assembly, it matters less about who is there and more about what they are doing. Overall, these data contribute to a growing effort to approach microbial community assembly with interdisciplinary tools and perspectives.},
}

@article {pmid37938685,
year = {2022},
author = {Jiang, G and Zhang, Y and Gan, G and Li, W and Wan, W and Jiang, Y and Yang, T and Zhang, Y and Xu, Y and Wang, Y and Shen, Q and Wei, Z and Dini-Andreote, F},
title = {Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation.},
journal = {ISME communications},
volume = {2},
number = {1},
pages = {10},
pmid = {37938685},
issn = {2730-6151},
abstract = {The development of strategies for effectively manipulating and engineering beneficial plant-associated microbiomes is a major challenge in microbial ecology. In this sense, the efficacy and potential implications of rhizosphere microbiome transplant (RMT) in plant disease management have only scarcely been explored in the literature. Here, we initially investigated potential differences in rhizosphere microbiomes of 12 Solanaceae eggplant varieties and accessed their level of resistance promoted against bacterial wilt disease caused by the pathogen Ralstonia solanacearum, in a 3-year field trial. We elected 6 resistant microbiomes and further tested the broad feasibility of using RMT from these donor varieties to a susceptible model Solanaceae tomato variety MicroTom. Overall, we found the rhizosphere microbiome of resistant varieties to enrich for distinct and specific bacterial taxa, of which some displayed significant associations with the disease suppression. Quantification of the RMT efficacy using source tracking analysis revealed more than 60% of the donor microbial communities to successfully colonize and establish in the rhizosphere of recipient plants. RTM from distinct resistant donors resulted in different levels of wilt disease suppression, reaching up to 47% of reduction in disease incidence. Last, we provide a culture-dependent validation of potential bacterial taxa associated with antagonistic interactions with the pathogen, thus contributing to a better understanding of the potential mechanism associated with the disease suppression. Our study shows RMT from appropriate resistant donors to be a promising tool to effectively modulate protective microbiomes and promote plant health. Together we advocate for future studies aiming at understanding the ecological processes and mechanisms mediating rates of coalescence between donor and recipient microbiomes in the plant rhizosphere.},
}

@article {pmid37938641,
year = {2021},
author = {Röttjers, L and Vandeputte, D and Raes, J and Faust, K},
title = {Null-model-based network comparison reveals core associations.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {36},
pmid = {37938641},
issn = {2730-6151},
support = {STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; STG/16/006//KU Leuven (Katholieke Universiteit Leuven)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 801747//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; 30770923//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Microbial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.},
}

@article {pmid37938227,
year = {2021},
author = {Reitmeier, S and Hitch, TCA and Treichel, N and Fikas, N and Hausmann, B and Ramer-Tait, AE and Neuhaus, K and Berry, D and Haller, D and Lagkouvardos, I and Clavel, T},
title = {Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {31},
pmid = {37938227},
issn = {2730-6151},
abstract = {16S rRNA gene amplicon sequencing is a popular approach for studying microbiomes. However, some basic concepts have still not been investigated comprehensively. We studied the occurrence of spurious sequences using defined microbial communities based on data either from the literature or generated in three sequencing facilities and analyzed via both operational taxonomic units (OTUs) and amplicon sequence variants (ASVs) approaches. OTU clustering and singleton removal, a commonly used approach, delivered approximately 50% (mock communities) to 80% (gnotobiotic mice) spurious taxa. The fraction of spurious taxa was generally lower based on ASV analysis, but varied depending on the gene region targeted and the barcoding system used. A relative abundance of 0.25% was found as an effective threshold below which the analysis of spurious taxa can be prevented to a large extent in both OTU- and ASV-based analysis approaches. Using this cutoff improved the reproducibility of analysis, i.e., variation in richness estimates was reduced by 38% compared with singleton filtering using six human fecal samples across seven sequencing runs. Beta-diversity analysis of human fecal communities was markedly affected by both the filtering strategy and the type of phylogenetic distances used for comparison, highlighting the importance of carefully analyzing data before drawing conclusions on microbiome changes. In summary, handling of artifact sequences during bioinformatic processing of 16S rRNA gene amplicon data requires careful attention to avoid the generation of misleading findings. We propose the concept of effective richness to facilitate the comparison of alpha-diversity across studies.},
}

@article {pmid37938246,
year = {2021},
author = {Hill, JE and Raaijmakers, JM and Smidt, H},
title = {Editorial.},
journal = {ISME communications},
volume = {1},
number = {1},
pages = {10},
doi = {10.1038/s43705-021-00013-3},
pmid = {37938246},
issn = {2730-6151},
}

@article {pmid37931689,
year = {2023},
author = {Álvarez-Pérez, S and Lievens, B and de Vega, C},
title = {Floral nectar and honeydew microbial diversity and their role in biocontrol of insect pests and pollination.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101138},
doi = {10.1016/j.cois.2023.101138},
pmid = {37931689},
issn = {2214-5753},
abstract = {Sugar-rich plant-related secretions, such as floral nectar and honeydew, that are commonly used as nutrient sources by insects and other animals, are also the ecological niche for diverse microbial communities. Recent research has highlighted the great potential of nectar and honeydew microbiomes in biological pest control and improved pollination, but the exploitation of these microbiomes requires a deep understanding of their community dynamics and plant-microbe-insect interactions. Additionally, the successful application of microbes in crop fields is conditioned by diverse ecological, legal, and ethical challenges that should be taken into account. In this article we provide an overview of the nectar and honeydew microbiomes and discuss their potential applications in sustainable agricultural practices.},
}

@article {pmid37931135,
year = {2023},
author = {Naik, AT and Kamensky, KM and Hellum, AM and Moisander, PH},
title = {Disturbance frequency directs microbial community succession in marine biofilms exposed to shear.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0024823},
doi = {10.1128/msphere.00248-23},
pmid = {37931135},
issn = {2379-5042},
abstract = {Marine biofilm growth poses significant challenges across marine industries ("biofouling"). Understanding the microbial communities involved in biofouling processes is crucial for developing effective mitigation strategies. These communities experience strong disturbances under antifouling pressure, the implications of which must be considered when developing new technologies due to their potential to alter succession, invertebrate settlement, and invasive species establishment risk. We leveraged the development of a shear-based antifouling technique to examine marine biofilm community assembly and stability under disturbance. The influence of repeated underwater shear on microbial community succession and biofilm matrix stability was assessed over 37 days on uncoated and "foul release" paint-coated surfaces. Foul-release coating decreased matrix biomass, and uncoated and coated surfaces hosted different biofilm communities with converging bacterial compositions and diverging eukaryotic compositions over time. On both surfaces, highly frequent shear strongly shifted the community composition and enriched several shear-tolerant bacteria, diatoms, green algae, and ciliates. Infrequent shear decreased matrix biomass, resulted in weaker compositional shifts and fewer enriched taxa, and additionally prevented macrofouling growth when combined with foul-release coating. A cross-domain co-occurrence network revealed mostly positive correlations persisting through the disturbance continuum and identified the diatom Melosira as a highly connected genus. Infrequent shear on anti-biofouling paint-coated surfaces was the most effective biofilm removal strategy, demonstrating that longer recovery periods enabled continued biomass removal and fewer shear-tolerant taxa. The results support the idea that variability in the frequency of a stress disturbance can significantly alter microbial community succession and biomass stability in marine biofilms, resulting in a varied potential for species invasiveness. IMPORTANCE Disturbances are major drivers of community succession in many microbial systems; however, relatively little is known about marine biofilm community succession, especially under antifouling disturbance. Antifouling technologies exert strong local disturbances on marine biofilms, and resulting biomass losses can be accompanied by shifts in biofilm community composition and succession. We address this gap in knowledge by bridging microbial ecology with antifouling technology development. We show that disturbance by shear can strongly alter marine biofilm community succession, acting as a selective filter influenced by frequency of exposure. Examining marine biofilm succession patterns with and without shear revealed stable associations between key prokaryotic and eukaryotic taxa, highlighting the importance of cross-domain assessment in future marine biofilm research. Describing how compounded top-down and bottom-up disturbances shape the succession of marine biofilms is valuable for understanding the assembly and stability of these complex microbial communities and predicting species invasiveness.},
}

@article {pmid37926855,
year = {2023},
author = {Minnebo, Y and Delbaere, K and Goethals, V and Raes, J and Van de Wiele, T and De Paepe, K},
title = {Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {240},
pmid = {37926855},
issn = {2049-2618},
support = {EOS program no. 30770923//Research Foundation - Flanders (Fonds Wetenschappelijk Onderzoek)/ ; EOS program no. 30770923//Research Foundation - Flanders (Fonds Wetenschappelijk Onderzoek)/ ; FWO no. 1SE1721N//Research Foundation - Flanders (Fonds Wetenschappelijk Onderzoek)/ ; BOF/GOA 01G03122//Universiteit Gent/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Butyrates/metabolism ; Nutrients ; Fermentation ; Carbohydrates ; Feces/microbiology ; },
abstract = {BACKGROUND: Transit time is an important modulator of the human gut microbiome. The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research. We singled out gut transit time in an unprecedented in vitro approach by subjecting faecal microbial communities from six individuals with either short, medium or long in vivo transit times, to three different colonic transit times of 21, 32 and 63 h in the validated human gut in vitro model, SHIME.

RESULTS: Transit time was identified as the single most important driver of microbial cell concentrations (52%), metabolic activity (45%) and quantitative (24%) and proportional (22%) community composition. Deceleration of transit was characterised by a significant decrease of specific Bifidobacterium and Veillonella spp. and increase of specific fibre degrading bacteria and nutrient specialists, such as Bacteroides, Prevotella, Ruminococcus, Bilophila and Akkermansia spp. These microbial communities reached a higher population density and net carbohydrate fermentation, leading to an increased SCFA production at longer transit times. In contrast, the carbohydrate-to-biomass production efficiency was increased at shorter transits, particularly in well-adapted faecal microbiomes from donors with short in vivo transit. Said adaptation was also reflected in the carbohydrate-to-SCFA conversion efficiency which varied with donor, but also colon region and SCFA chain length. A long transit time promoted propionate production, whereas butyrate production and butyrate producers were selectively enriched in the proximal colon at medium transit time.

CONCLUSION: Microbial growth rates and nutrient utilisation efficiency mediate the species-specific gut microbiota response to in vitro transit time variation, which is the main driver of in vitro microbial load, metabolism and community composition. Given the in vivo transit time variation within and between individuals, the personalisation of in vitro transit time based on in vivo data is required to accurately study intra- and inter-individual differences in gut microbiome structure, functionality and interactions with host and environmental modulators. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome
*Microbiota
Butyrates/metabolism
Nutrients
Fermentation
Carbohydrates
Feces/microbiology

@article {pmid37925991,
year = {2023},
author = {Chen, C and Li, P and Yin, M and Wang, J and Sun, Y and Ju, W and Liu, L and Li, ZH},
title = {Deciphering characterization of seasonal variations in microbial communities of marine ranching: Diversity, co-occurrence network patterns, and assembly processes.},
journal = {Marine pollution bulletin},
volume = {197},
number = {},
pages = {115739},
doi = {10.1016/j.marpolbul.2023.115739},
pmid = {37925991},
issn = {1879-3363},
abstract = {Offshore coastal marine ranching ecosystems are one of the most productive ecosystems. The results showed that the composition and structure of the microbial communities varied considerably with the season. Co-occurrence network analysis demonstrated that the microbial network was more complex in summer and positively correlated links (cooperative or symbiotic) were dominated in autumn and winter. Null model indicated that the ecological processes of the bacterial communities were mainly governed by deterministic processes (mainly homogeneous selection) in summer. For microeukaryotic communities, assembly processes were more regulated by stochastic processes in all seasons. For rare taxa, assembly processes were regulated by stochastic processes and were not affected by seasonality. Changes in water temperature due to seasonal variations were the main, but not the only, environmental factor driving changes in microbial communities. This study will improve the understanding of offshore coastal ecosystems through the perspective of microbial ecology.},
}

@article {pmid37925029,
year = {2023},
author = {Ghosh, A and Yash, and Kumar, C and Bhadury, P},
title = {Cascading effects of trace metals enrichment on phytoplankton communities of the River Ganga in South Asia.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {140607},
doi = {10.1016/j.chemosphere.2023.140607},
pmid = {37925029},
issn = {1879-1298},
abstract = {Globally freshwater ecosystems and associated biota including phytoplankton communities are at extreme risk from trace metal pollution originating from geogenic as well as from anthropogenic sources such as from untreated industrial effluents. In the present study the influence of iron- and arsenic-enrichments on structure and metabolism of phytoplankton communities of River Ganga, one of the largest rivers of South Asia, was assessed under laboratory-based microcosm experiments. Surface water samples were collected and subsequently enriched with higher than recommended concentrations of iron (10 mg/L) and arsenic (10 μg/L). The set-up comprised of nine containers of 25 L volume with three containers each for iron- and arsenic-enrichment and was maintained for 30 days. Trace metal enrichment rapidly changed the phytoplankton community structure and chemistry of nutrients uptake. Iron-enrichment prompted diatom blooms comprising of Thalassiosira, succeeded by green algae Coelastrum. Arsenic-enrichment maintained cyanobacteria for longer time-spans compared to the control and iron-enriched containers but significantly lesser abundance of diatoms. Variations in community composition was also reflected in nutrient uptake rates with silicate release in the arsenic-enriched containers at the end of the experiment. Changes in macronutrient dynamics also altered genus growth rates wherein both iron- and arsenic appeared to lower the death rate of Thalassosira but stimulate other genera including Skeletonema and Pandorina. Iron appeared to influence lesser number of genera compared to arsenic which altered growth rates of both diatoms and green algae. This consequently influenced the gross primary productivity values which lowered both in the iron- and arsenic-enriched containers compared to the control owing to decrease in phytoplankton diversity. Iron appears to drive phytoplankton communities toward a less general and more specialized composition with high abundance of selective species comprising of small diatoms such as Thalassiorira, whereas arsenic appears to select for green algal enrichment in freshwater ecosystems.},
}

@article {pmid37920817,
year = {2023},
author = {Talavera-Marcos, S and Parras-Moltó, M and Aguirre de Cárcer, D},
title = {Leveraging phylogenetic signal to unravel microbiome function and assembly rules.},
journal = {Computational and structural biotechnology journal},
volume = {21},
number = {},
pages = {5165-5173},
pmid = {37920817},
issn = {2001-0370},
abstract = {Clarifying the general rules behind microbial community assembly will foster the development of microbiome-based technological solutions. Here, we study microbial community assembly through a computational analysis of phylogenetic core groups (PCGs): discrete portions of the bacterial phylogeny with high prevalence in the ecosystem under study. We first show that the existence of PCGs was a predominant feature of the varied set of microbial ecosystems studied. Then, we re-analyzed an in vitro experimental dataset using a PCG-based approach, drawing only from its community composition data and from publicly available genomic databases. Using mainly genome scale metabolic models and population dynamics modeling, we obtained ecological insights on metabolic niche structure and population dynamics comparable to those gained after canonical experimentation. Thus, leveraging phylogenetic signal to help unravel microbiome function and assembly rules offers a potential avenue to gain further insight on Earth's microbial ecosystems.},
}

@article {pmid37920261,
year = {2023},
author = {Poirier, S and Coeuret, G and Champomier-Vergès, MC and Desmonts, MH and Werner, D and Feurer, C and Frémaux, B and Guillou, S and Luong, NM and Rué, O and Loux, V and Zagorec, M and Chaillou, S and , },
title = {Holistic integration of omics data reveals the drivers that shape the ecology of microbial meat spoilage scenarios.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1286661},
pmid = {37920261},
issn = {1664-302X},
abstract = {BACKGROUND: The use of omics data for monitoring the microbial flow of fresh meat products along a production line and the development of spoilage prediction tools from these data is a promising but challenging task. In this context, we produced a large multivariate dataset (over 600 samples) obtained on the production lines of two similar types of fresh meat products (poultry and raw pork sausages). We describe a full analysis of this dataset in order to decipher how the spoilage microbial ecology of these two similar products may be shaped differently depending on production parameter characteristics.

METHODS: Our strategy involved a holistic approach to integrate unsupervised and supervised statistical methods on multivariate data (OTU-based microbial diversity; metabolomic data of volatile organic compounds; sensory measurements; growth parameters), and a specific selection of potential uncontrolled (initial microbiota composition) or controlled (packaging type; lactate concentration) drivers.

RESULTS: Our results demonstrate that the initial microbiota, which is shown to be very different between poultry and pork sausages, has a major impact on the spoilage scenarios and on the effect that a downstream parameter such as packaging type has on the overall evolution of the microbial community. Depending on the process, we also show that specific actions on the pork meat (such as deboning and defatting) elicit specific food spoilers such as Dellaglioa algida, which becomes dominant during storage. Finally, ecological network reconstruction allowed us to map six different metabolic pathways involved in the production of volatile organic compounds involved in spoilage. We were able connect them to the different bacterial actors and to the influence of packaging type in an overall view. For instance, our results demonstrate a new role of Vibrionaceae in isopropanol production, and of Latilactobacillus fuchuensis and Lactococcus piscium in methanethiol/disylphide production. We also highlight a possible commensal behavior between Leuconostoc carnosum and Latilactobacillus curvatus around 2,3-butanediol metabolism.

CONCLUSION: We conclude that our holistic approach combined with large-scale multi-omic data was a powerful strategy to prioritize the role of production parameters, already known in the literature, that shape the evolution and/or the implementation of different meat spoilage scenarios.},
}

@article {pmid37920009,
year = {2023},
author = {Yuan, X and Song, W and Li, Y and Wang, Q and Qing, J and Zhi, W and Han, H and Qin, Z and Gong, H and Hou, G and Li, Y},
title = {Using Bayesian networks with tabu algorithm to explore factors related to chronic kidney disease with mental illness: A cross-sectional study.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {20},
number = {9},
pages = {16194-16211},
doi = {10.3934/mbe.2023723},
pmid = {37920009},
issn = {1551-0018},
abstract = {While Bayesian networks (BNs) offer a promising approach to discussing factors related to many diseases, little attention has been poured into chronic kidney disease with mental illness (KDMI) using BNs. This study aimed to explore the complex network relationships between KDMI and its related factors and to apply Bayesian reasoning for KDMI, providing a scientific reference for its prevention and treatment. Data was downloaded from the online open database of CHARLS 2018, a population-based longitudinal survey. Missing values were first imputed using Random Forest, followed by propensity score matching (PSM) for class balancing regarding KDMI. Elastic Net was then employed for variable selection from 18 variables. Afterwards, the remaining variables were included in BNs model construction. Structural learning of BNs was achieved using tabu algorithm and the parameter learning was conducted using maximum likelihood estimation. After PSM, 427 non-KDMI cases and 427 KDMI cases were included in this study. Elastic Net identified 11 variables significantly associated with KDMI. The BNs model comprised 12 nodes and 24 directed edges. The results suggested that diabetes, physical activity, education levels, sleep duration, social activity, self-report on health and asset were directly related factors for KDMI, whereas sex, age, residence and Internet access represented indirect factors for KDMI. BN model not only allows for the exploration of complex network relationships between related factors and KDMI, but also could enable KDMI risk prediction through Bayesian reasoning. This study suggests that BNs model holds great prospects in risk factor detection for KDMI.},
}

@article {pmid37919394,
year = {2023},
author = {Dougherty, PE and Nielsen, TK and Riber, L and Lading, HH and Forero-Junco, LM and Kot, W and Raaijmakers, JM and Hansen, LH},
title = {Widespread and largely unknown prophage activity, diversity, and function in two genera of wheat phyllosphere bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37919394},
issn = {1751-7370},
support = {NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 801199//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; },
abstract = {Environmental bacteria host an enormous number of prophages, but their diversity and natural functions remain largely elusive. Here, we investigate prophage activity and diversity in 63 Erwinia and Pseudomonas strains isolated from flag leaves of wheat grown in a single field. Introducing and validating Virion Induction Profiling Sequencing (VIP-Seq), we identify and quantify the activity of 120 spontaneously induced prophages, discovering that some phyllosphere bacteria produce more than 10[8] virions/mL in overnight cultures, with significant induction also observed in planta. Sequence analyses and plaque assays reveal E. aphidicola prophages contribute a majority of intraspecies genetic diversity and divide their bacterial hosts into antagonistic factions engaged in widespread microbial warfare, revealing the importance of prophage-mediated microdiversity. When comparing spontaneously active prophages with predicted prophages we also find insertion sequences are strongly correlated with non-active prophages. In conclusion, we discover widespread and largely unknown prophage diversity and function in phyllosphere bacteria.},
}

@article {pmid37914532,
year = {2023},
author = {Ray, AE and Tribbia, DZ and Cowan, DA and Ferrari, BC},
title = {Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0004823},
doi = {10.1128/mmbr.00048-23},
pmid = {37914532},
issn = {1098-5557},
abstract = {SUMMARYAtmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.},
}

@article {pmid37914126,
year = {2023},
author = {Abkar, L and Moghaddam, HS and Fowler, J},
title = {Microbial ecology of drinking water from source to tap.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {168077},
doi = {10.1016/j.scitotenv.2023.168077},
pmid = {37914126},
issn = {1879-1026},
abstract = {As drinking water travels from its source, through various treatment processes, hundreds to thousands of kilometres of distribution network pipes, to the taps in private homes and public buildings, it is exposed to numerous environmental changes, as well as other microbes living in both water and on surfaces. This review aims to identify the key locations and factors that are associated with changes in the drinking water microbiome throughout conventional urban drinking water systems from the source to the tap water. Over the past 15 years, improvements in cultivation-independent methods have enabled studies that allow us to answer such questions. As a result, we are beginning to move towards predicting the impacts of disturbances and interventions resulting ultimately in management of drinking water systems and microbial communities rather than mere observation. Many challenges still exist to achieve effective management, particularly within the premise plumbing environment, which exhibits diverse and inconsistent conditions that may lead to alterations in the microbiota, potentially presenting public health risks. Finally, we recommend the establishment of global collaborative projects on the drinking water microbiome that will enhance our current knowledge and lead to tools for operators and researchers alike to improve global access to high-quality drinking water.},
}

@article {pmid37909775,
year = {2023},
author = {Mason, G and Footer, MJ and Rojas, ER},
title = {Mechanosensation induces persistent bacterial growth during bacteriophage predation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0276622},
doi = {10.1128/mbio.02766-22},
pmid = {37909775},
issn = {2150-7511},
abstract = {Although the relationship between bacteria and lytic bacteriophage is fundamentally antagonistic, these microbes not only coexist but thrive side by side in myriad ecological environments. The mechanisms by which coexistence is achieved, however, are not fully understood. By examining Escherichia coli and bacteriophage T7 population dynamics at the single-cell and single-virion level using a novel microfluidics assay, we observed bacteria growing "persistently" when perfused with high-titer bacteriophage. Bacteriophage persistence occurred at a frequency five orders of magnitude higher than is expected from the natural selection of bacteriophage-resistant mutants. Rather, the frequency of persistence was correlated with the degree to which the bacteria were mechanically compressed by the microfluidic perfusion chamber. Using a combination of mutagenesis and fluorescent imaging techniques, we discovered that compression induces persistence by activating the Rcs phosphorelay pathway, which results in the synthesis of extracellular capsule that sterically blocks bacteriophage adsorption. Other forms of mechanical perturbation also promoted Rcs activity and persistence. These findings have important implications for our understanding of microbial ecology in many important environments, including the gut and the soil, where bacteria grow in confinement. IMPORTANCE Bacteria and bacteriophage form one of the most important predator-prey relationships on earth, yet how the long-term stability of this ecological interaction is achieved is unclear. Here, we demonstrate that Escherichia coli can rapidly grow during bacteriophage predation if they are doing so in spatially confined environments. This discovery revises our understanding of bacteria-bacteriophage population dynamics in many real-world environments where bacteria grow in confinement, such as the gut and the soil. Additionally, this result has clear implications for the potential of bacteriophage therapy and the role of mechanosensation during bacterial pathogenesis.},
}

@article {pmid37909659,
year = {2023},
author = {Quiroga, MV and Stegen, JC and Mataloni, G and Cowan, D and Lebre, PH and Valverde, A},
title = {Microdiverse bacterial clades prevail across Antarctic wetlands.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.17189},
pmid = {37909659},
issn = {1365-294X},
support = {PICT 2016-2517//ANPCyT - Argentina/ ; PICT 2020-3113//ANPCyT - Argentina/ ; //European Union/ ; //Instituto Antártico Argentino - Dirección Nacional del Antártico/ ; CLU-2019-05 IRNASA/CSIC//Junta de Castilla y León/ ; //NRF - South Africa/ ; Contract DE-AC05-76RL01830 -JCS//U.S. Department of Energy-BER program/ ; },
abstract = {Antarctica's extreme environmental conditions impose selection pressures on microbial communities. Indeed, a previous study revealed that bacterial assemblages at the Cierva Point Wetland Complex (CPWC) are shaped by strong homogeneous selection. Yet which bacterial phylogenetic clades are shaped by selection processes and their ecological strategies to thrive in such extreme conditions remain unknown. Here, we applied the phyloscore and feature-level βNTI indexes coupled with phylofactorization to successfully detect bacterial monophyletic clades subjected to homogeneous (HoS) and heterogenous (HeS) selection. Remarkably, only the HoS clades showed high relative abundance across all samples and signs of putative microdiversity. The majority of the amplicon sequence variants (ASVs) within each HoS clade clustered into a unique 97% sequence similarity operational taxonomic unit (OTU) and inhabited a specific environment (lotic, lentic or terrestrial). Our findings suggest the existence of microdiversification leading to sub-taxa niche differentiation, with putative distinct ecotypes (consisting of groups of ASVs) adapted to a specific environment. We hypothesize that HoS clades thriving in the CPWC have phylogenetically conserved traits that accelerate their rate of evolution, enabling them to adapt to strong spatio-temporally variable selection pressures. Variable selection appears to operate within clades to cause very rapid microdiversification without losing key traits that lead to high abundance. Variable and homogeneous selection, therefore, operate simultaneously but on different aspects of organismal ecology. The result is an overall signal of homogeneous selection due to rapid within-clade microdiversification caused by variable selection. It is unknown whether other systems experience this dynamic, and we encourage future work evaluating the transferability of our results.},
}

@article {pmid37903921,
year = {2023},
author = {Jansson, JK and McClure, R and Egbert, RG},
title = {Soil microbiome engineering for sustainability in a changing environment.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {37903921},
issn = {1546-1696},
abstract = {Recent advances in microbial ecology and synthetic biology have the potential to mitigate damage caused by anthropogenic activities that are deleteriously impacting Earth's soil ecosystems. Here, we discuss challenges and opportunities for harnessing natural and synthetic soil microbial communities, focusing on plant growth promotion under different scenarios. We explore current needs for microbial solutions in soil ecosystems, how these solutions are being developed and applied, and the potential for new biotechnology breakthroughs to tailor and target microbial products for specific applications. We highlight several scientific and technological advances in soil microbiome engineering, including characterization of microbes that impact soil ecosystems, directing how microbes assemble to interact in soil environments, and the developing suite of gene-engineering approaches. This Review underscores the need for an interdisciplinary approach to understand the composition, dynamics and deployment of beneficial soil microbiomes to drive efforts to mitigate or reverse environmental damage by restoring and protecting healthy soil ecosystems.},
}

@article {pmid37902333,
year = {2023},
author = {van der Meij, A and Elsayed, SS and Du, C and Willemse, J and Wood, TM and Martin, NI and Raaijmakers, JM and van Wezel, GP},
title = {The plant stress hormone jasmonic acid evokes defensive responses in streptomycetes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0123923},
doi = {10.1128/aem.01239-23},
pmid = {37902333},
issn = {1098-5336},
abstract = {Actinobacteria are prevalent in the rhizosphere and phyllosphere of diverse plant species where they help to enhance tolerance of plants against biotic and abiotic stresses. Here, we show that the plant hormones jasmonic acid (JA) and methyl jasmonate (MeJA) affect the growth, development, and specialized metabolism of Streptomyces. Exposure of Streptomyces coelicolor to JA or MeJA led to enhanced production of the polyketide antibiotic actinorhodin. JA also exhibited toxicity toward Streptomyces and Streptacidiphilus at higher concentrations, whereby streptomycetes were more tolerant to JA than members of the genus Streptacidiphilus. Tolerance to JA could be linked to its conjugation by the bacteria with glutamine. Additionally, JA conjugates with valine, tyrosine, phenylalanine, and leucine/isoleucine were identified. In contrast to JA, synthetic JA conjugates failed to activate antibiotic production and showed significantly reduced toxicity. Thus, our findings provide insights into a previously unknown defense mechanism deployed by Streptomycetaceae to a plant hormone. The underlying mechanism encompasses the attachment of amino acids to JA, which in turn safeguards the bacteria against the harmful impacts of the plant hormone. This study adds to the growing body of evidence that plant hormones can have a significant impact on members of the plant microbiome by affecting their growth, development, and secondary metabolism.IMPORTANCEMicroorganisms that live on or inside plants can influence plant growth and health. Among the plant-associated bacteria, streptomycetes play an important role in defense against plant diseases, but the underlying mechanisms are not well understood. Here, we demonstrate that the plant hormones jasmonic acid (JA) and methyl jasmonate directly affect the life cycle of streptomycetes by modulating antibiotic synthesis and promoting faster development. Moreover, the plant hormones specifically stimulate the synthesis of the polyketide antibiotic actinorhodin in Streptomyces coelicolor. JA is then modified in the cell by amino acid conjugation, thereby quenching toxicity. Collectively, these results provide new insight into the impact of a key plant hormone on diverse phenotypic responses of streptomycetes.},
}

@article {pmid37901816,
year = {2023},
author = {Li, Y and Hou, Y and Hou, Q and Long, M and Wang, Z and Rillig, MC and Liao, Y and Yong, T},
title = {Soil microbial community parameters affected by microplastics and other plastic residues.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1258606},
pmid = {37901816},
issn = {1664-302X},
abstract = {INTRODUCTION: The impact of plastics on terrestrial ecosystems is receiving increasing attention. Although of great importance to soil biogeochemical processes, how plastics influence soil microbes have yet to be systematically studied. The primary objectives of this study are to evaluate whether plastics lead to divergent responses of soil microbial community parameters, and explore the potential driving factors.

METHODS: We performed a meta-analysis of 710 paired observations from 48 published articles to quantify the impact of plastic on the diversity, biomass, and functionality of soil microbial communities.

RESULTS AND DISCUSSION: This study indicated that plastics accelerated soil organic carbon loss (effect size = -0.05, p = 0.004) and increased microbial functionality (effect size = 0.04, p = 0.003), but also reduced microbial biomass (effect size = -0.07, p < 0.001) and the stability of co-occurrence networks. Polyethylene significantly reduced microbial richness (effect size = -0.07, p < 0.001) while polypropylene significantly increased it (effect size = 0.17, p < 0.001). Degradable plastics always had an insignificant effect on the microbial community. The effect of the plastic amount on microbial functionality followed the "hormetic dose-response" model, the infection point was about 40 g/kg. Approximately 3564.78 μm was the size of the plastic at which the response of microbial functionality changed from positive to negative. Changes in soil pH, soil organic carbon, and total nitrogen were significantly positively correlated with soil microbial functionality, biomass, and richness (R[2] = 0.04-0.73, p < 0.05). The changes in microbial diversity were decoupled from microbial community structure and functionality. We emphasize the negative impacts of plastics on soil microbial communities such as microbial abundance, essential to reducing the risk of ecological surprise in terrestrial ecosystems. Our comprehensive assessment of plastics on soil microbial community parameters deepens the understanding of environmental impacts and ecological risks from this emerging pollution.},
}

@article {pmid37897125,
year = {2023},
author = {Seppey, CVW and Cabrol, L and Thalasso, F and Gandois, L and Lavergne, C and Martinez-Cruz, K and Sepulveda-Jauregui, A and Aguilar-Muñoz, P and Astorga-España, MS and Chamy, R and Dellagnezze, BM and Etchebehere, C and Fochesatto, GJ and Gerardo-Nieto, O and Mansilla, A and Murray, A and Sweetlove, M and Tananaev, N and Teisserenc, R and Tveit, AT and Van de Putte, A and Svenning, MM and Barret, M},
title = {Biogeography of microbial communities in high-latitude ecosystems: Contrasting drivers for methanogens, methanotrophs and global prokaryotes.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16526},
pmid = {37897125},
issn = {1462-2920},
support = {Project MATCH C16B03//ECOS sud CONICYT/ ; grant no. 256132/H30//ECOS sud CONICYT/ ; project METHANOBASE (ELAC2014_DCC-0092)//ERANet-LAC program/ ; //French Ministries of Foreign Affairs and International Development (MAEDI)/ ; //German Federal Ministry of Education and Research, WISNA program/ ; grant no. 277238//Mexican National Council for Science and Technology (CONACYT)/ ; //National Education, Superior Education and Research (MENESR)/ ; MillenniumScienceInitiativeProgram-ICN2021_002//Chilean National Agency of Research and Development (ANID)/ ; },
abstract = {Methane-cycling is becoming more important in high-latitude ecosystems as global warming makes permafrost organic carbon increasingly available. We explored 387 samples from three high-latitudes regions (Siberia, Alaska and Patagonia) focusing on mineral/organic soils (wetlands, peatlands, forest), lake/pond sediment and water. Physicochemical, climatic and geographic variables were integrated with 16S rDNA amplicon sequences to determine the structure of the overall microbial communities and of specific methanogenic and methanotrophic guilds. Physicochemistry (especially pH) explained the largest proportion of variation in guild composition, confirming species sorting (i.e., environmental filtering) as a key mechanism in microbial assembly. Geographic distance impacted more strongly beta diversity for (i) methanogens and methanotrophs than the overall prokaryotes and, (ii) the sediment habitat, suggesting that dispersal limitation contributed to shape the communities of methane-cycling microorganisms. Bioindicator taxa characterising different ecological niches (i.e., specific combinations of geographic, climatic and physicochemical variables) were identified, highlighting the importance of Methanoregula as generalist methanogens. Methylocystis and Methylocapsa were key methanotrophs in low pH niches while Methylobacter and Methylomonadaceae in neutral environments. This work gives insight into the present and projected distribution of methane-cycling microbes at high latitudes under climate change predictions, which is crucial for constraining their impact on greenhouse gas budgets.},
}

@article {pmid37895286,
year = {2023},
author = {Aboushaala, K and Wong, AYL and Barajas, JN and Lim, P and Al-Harthi, L and Chee, A and Forsyth, CB and Oh, CD and Toro, SJ and Williams, FMK and An, HS and Samartzis, D},
title = {The Human Microbiome and Its Role in Musculoskeletal Disorders.},
journal = {Genes},
volume = {14},
number = {10},
pages = {},
pmid = {37895286},
issn = {2073-4425},
support = {R21AR079679/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; Bacteria ; *Musculoskeletal Diseases ; Oxygen ; },
abstract = {Musculoskeletal diseases (MSDs) are characterized as injuries and illnesses that affect the musculoskeletal system. MSDs affect every population worldwide and are associated with substantial global burden. Variations in the makeup of the gut microbiota may be related to chronic MSDs. There is growing interest in exploring potential connections between chronic MSDs and variations in the composition of gut microbiota. The human microbiota is a complex community consisting of viruses, archaea, bacteria, and eukaryotes, both inside and outside of the human body. These microorganisms play crucial roles in influencing human physiology, impacting metabolic and immunological systems in health and disease. Different body areas host specific types of microorganisms, with facultative anaerobes dominating the gastrointestinal tract (able to thrive with or without oxygen), while strict aerobes prevail in the nasal cavity, respiratory tract, and skin surfaces (requiring oxygen for development). Together with the immune system, these bacteria have coevolved throughout time, forming complex biological relationships. Changes in the microbial ecology of the gut may have a big impact on health and can help illnesses develop. These changes are frequently impacted by lifestyle choices and underlying medical disorders. The potential for safety, expenses, and efficacy of microbiota-based medicines, even with occasional delivery, has attracted interest. They are, therefore, a desirable candidate for treating MSDs that are chronic and that may have variable progression patterns. As such, the following is a narrative review to address the role of the human microbiome as it relates to MSDs.},
}

Humans
*Microbiota
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
Bacteria
*Musculoskeletal Diseases
Oxygen

@article {pmid37894228,
year = {2023},
author = {Jech, SD and Day, N and Barger, NN and Antoninka, A and Bowker, MA and Reed, S and Tucker, C},
title = {Cultivating Resilience in Dryland Soils: An Assisted Migration Approach to Biological Soil Crust Restoration.},
journal = {Microorganisms},
volume = {11},
number = {10},
pages = {},
pmid = {37894228},
issn = {2076-2607},
support = {RC18-1322//Department of Defense Strategic Environmental Research and Development Program/ ; NA//Canyonlands Research Center/ ; NA//Wildlife Conservation Society Climate Adaptation Fund/ ; },
abstract = {Land use practices and climate change have driven substantial soil degradation across global drylands, impacting ecosystem functions and human livelihoods. Biological soil crusts, a common feature of dryland ecosystems, are under extensive exploration for their potential to restore the stability and fertility of degraded soils through the development of inoculants. However, stressful abiotic conditions often result in the failure of inoculation-based restoration in the field and may hinder the long-term success of biocrust restoration efforts. Taking an assisted migration approach, we cultivated biocrust inocula sourced from multiple hot-adapted sites (Mojave and Sonoran Deserts) in an outdoor facility at a cool desert site (Colorado Plateau). In addition to cultivating inoculum from each site, we created an inoculum mixture of biocrust from the Mojave Desert, Sonoran Desert, and Colorado Plateau. We then applied two habitat amelioration treatments to the cultivation site (growth substrate and shading) to enhance soil stability and water availability and reduce UV stress. Using marker gene sequencing, we found that the cultivated mixed inoculum comprised both local- and hot-adapted cyanobacteria at the end of cultivation but had similar cyanobacterial richness as each unmixed inoculum. All cultivated inocula had more cyanobacterial 16S rRNA gene copies and higher cyanobacterial richness when cultivated with a growth substrate and shade. Our work shows that it is possible to field cultivate biocrust inocula sourced from different deserts, but that community composition shifts toward that of the cultivation site unless habitat amelioration is employed. Future assessments of the function of a mixed inoculum in restoration and its resilience in the face of abiotic stressors are needed to determine the relative benefit of assisted migration compared to the challenges and risks of this approach.},
}