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19 Jun 2021 at 01:34
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Bibliography on: Microbial Ecology


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RJR: Recommended Bibliography 19 Jun 2021 at 01:34 Created: 

Microbial Ecology

Wikipedia: Microbial Ecology (or environmental microbiology) is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life — Eukaryota, Archaea, and Bacteria — as well as viruses. Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Created with PubMed® Query: "microbial ecology" NOT pmcbook NOT ispreviousversion

Citations The Papers (from PubMed®)


RevDate: 2021-06-15

Yan L, Hermans SM, Totsche KU, et al (2021)

Groundwater bacterial communities evolve over time in response to recharge.

Water research, 201:117290 pii:S0043-1354(21)00488-7 [Epub ahead of print].

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than surface oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in bacterial communities of shallow fractured bedrock groundwater, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n = 230) along a hillslope recharge area. We showed that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and exhibited non-linear dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, the microbiomes in shallow fractured-rock groundwater vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the dynamics of bacterial communities in groundwater, which is an essential resource for the provision of clean drinking water; understanding the biological complexities of these systems is therefore crucial.

RevDate: 2021-06-15

Zhang ZF, Pan J, Pan YP, et al (2021)

Biogeography, Assembly Patterns, Driving Factors, and Interactions of Archaeal Community in Mangrove Sediments.

mSystems [Epub ahead of print].

Archaea are a major part of Earth's life. They are believed to play important roles in nutrient biogeochemical cycling in the mangrove. However, only a few studies on the archaeal community in mangroves have been reported. In particular, the assembly processes and interaction patterns that impact the archaeal communities in mangroves have not been investigated to date. Here, the biogeography, assembly patterns, and driving factors of archaeal communities in seven representative mangroves across southeastern China were systematically analyzed. The analysis revealed that the archaeal community is more diverse in surface sediments than in subsurface sediments, and more diverse in mangroves at low latitudes than at high latitudes, with Woesearchaeota and Bathyarchaeota as the most diverse and most abundant phyla, respectively. Beta nearest-taxon index analysis suggested a determinant role of homogeneous selection on the overall archaeon community in all mangroves and in each individual mangrove. In addition, the conditionally rare taxon community was strongly shaped by homogeneous selection, while stochastic processes shaped the dominant taxon and always-rare taxon communities. Further, a moderate effect of environmental selection on the archaeal community was noted, with the smallest effect on the always-rare taxon community. Mangrove location, mean annual temperature, and salinity were the major factors that greatly affected the community composition. Finally, network analysis revealed comprehensive cooccurrence relationships in the archaeal community, with a crucial role of Bathyarchaeota. This study expands the understanding of the biogeography, assembly patterns, driving factors, and cooccurrence relationships of the mangrove archaeal community and inspires functional exploration of archaeal resources in mangrove sediments. IMPORTANCE As a key microbial community component with important ecological roles, archaea merit the attention of biologists and ecologists. The mechanisms controlling microbial community diversity, composition, and biogeography are central to microbial ecology but poorly understood. Mangroves are located at the land-ocean interface and are an ideal environment for examining the above questions. We here provided the first-ever overview of archaeal community structure and biogeography in mangroves located along an over-9,000-km coastline of southeastern China. We observed that archaeal diversity in low-latitude mangroves was higher than that in high-latitude mangroves. Furthermore, our data indicated that homogeneous selection strongly controlled the assembly of the overall and conditionally rare taxon communities in mangrove sediments, while the dominant taxon and always-rare taxon communities were mainly controlled by dispersal limitation.

RevDate: 2021-06-15

Wasmund K, Pelikan C, Schintlmeister A, et al (2021)

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments.

Nature microbiology [Epub ahead of print].

Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.

RevDate: 2021-06-15

Shao K, Yao X, Wu Z, et al (2021)

The bacterial community composition and its environmental drivers in the rivers around eutrophic Chaohu Lake, China.

BMC microbiology, 21(1):179.

BACKGROUND: Bacterial community play a key role in environmental and ecological processes in river ecosystems. Rivers are used as receiving body for treated and untreated urban wastewaters that brings high loads of sewage and excrement bacteria. However, little is known about the bacterial community structure and functional files in the rivers around the eutrophic Chaohu Lake, the fifth largest freshwater lake in China, has been subjected to severe eutrophication and cyanobacterial blooms over the past few decades. Therefore, understanding the taxonomic and functional compositions of bacterial communities in the river will contribute to understanding aquatic microbial ecology. The main aims were to (1) examine the structure of bacterial communities and functional profiles in this system; (2) find the environmental factors of bacterial community variations.

RESULTS: We studied 88 sites at rivers in the Chaohu Lake basin, and determined bacterial communities using Illumina Miseq sequencing of the 16 S rRNA gene, and predicted functional profiles using PICRUSt2. A total of 3,390,497 bacterial 16 S rRNA gene sequences were obtained, representing 17 phyla, and 424 genera; The dominant phyla present in all samples were Bacteroidetes (1.4-82.50 %), followed by Proteobacteria (12.6-97.30 %), Actinobacteria (0.1-17.20 %). Flavobacterium was the most numerous genera, and accounted for 0.12-80.34 % of assigned 16 S reads, followed by Acinetobacter (0.33-49.28 %). Other dominant bacterial genera including Massilia (0.06-25.40 %), Psychrobacter (0-36.23 %), Chryseobacterium (0.01-22.86 %), Brevundimonas (0.01-12.82 %), Pseudomonas (0-59.73 %), Duganella (0.08-23.37 %), Unidentified Micrococcaceae (0-8.49 %). The functional profiles of the bacterial populations indicated an relation with many human diseases, including infectious diseases. Overall results, using the β diversity measures, coupled with heatmap and RDA showed that there were spatial variations in the bacterial community composition at river sites, and Chemical oxygen demand (CODMn) and (NH4+)were the dominant environmental drivers affecting the bacterial community variance.

CONCLUSIONS: The high proportion of the opportunistic pathogens (Acinetobacter, Massilia, Brevundimonas) indicated that the discharge of sewage without adequate treatment into the rivers around Chaohu Lake. We propose that these bacteria could be more effective bioindicators for long-term sewage monitoring in eutrophic lakes.

RevDate: 2021-06-14

Li J, Morrow C, Barnes S, et al (2021)

Gut microbiome composition and serum metabolome profile among individuals with spinal cord injury and normal glucose tolerance or prediabetes/type 2 diabetes.

Archives of physical medicine and rehabilitation pii:S0003-9993(21)00438-X [Epub ahead of print].

OBJECTIVE: To compare the gut microbiome composition and serum metabolome profile among individuals with spinal cord injury (SCI) and normal glucose tolerance (NGT) or prediabetes/type 2 diabetes (P/DM).

DESIGN: Cross-sectional design.

SETTING: Research university.

PARTICIPANTS: A total of 25 adults with SCI were included in the analysis and categorized as NGT (n=16) or P/DM (n=9) based on their glucose concentration at minute 120 during a 75-g oral glucose tolerance test. The American Diabetes Association diagnosis guideline was used for grouping participants.

INTERVENTIONS: Not applicable.

MAIN OUTCOME MEASURE(S): A stool sample was collected and used to assess the gut microbiome composition (alpha and beta diversity, microbial abundance) via the 16s rRNA sequencing technique. A fasting serum sample was used for liquid chromatography-mass spectrometry-based untargeted metabolomics analysis, the results from which reflect the relative quantity of metabolites detected and identified. Gut microbiome and metabolomics data were analyzed by the Quantitative Insights into Microbial Ecology 2 and Metaboanalyst platforms, respectively.

RESULTS: Gut microbiome alpha diversity (Pielou's evenness index, Shannon's index) and beta diversity (weighted UniFrac distances) differed between groups. Compared with participants with NGT, participants with P/DM had less evenness in microbial communities. In particular, those with P/DM had a lower abundance of the Clostridiales order and higher abundance of the Akkermansia genus, as well as higher serum levels of gut-derived metabolites, including indoxyl sulfate and phenylacetylglutamine (P < 0.05 for all).

CONCLUSION(S): Our results provide evidence for altered gut microbiome composition and dysregulation of gut-derived metabolites in participants with SCI and P/DM. Both indoxyl sulfate and phenylacetylglutamine have been implicated in the development of cardiovascular diseases in the able-bodied population. These findings may inform future investigations in the field of SCI and cardio-metabolic health.

RevDate: 2021-06-15

Crous PW, Hernández-Restrepo M, Schumacher RK, et al (2021)

New and Interesting Fungi. 4.

Fungal systematics and evolution, 7:255-343.

An order, family and genus are validated, seven new genera, 35 new species, two new combinations, two epitypes, two lectotypes, and 17 interesting new host and / or geographical records are introduced in this study. Validated order, family and genus: Superstratomycetales and Superstratomycetaceae (based on Superstratomyces). New genera: Haudseptoria (based on Haudseptoria typhae); Hogelandia (based on Hogelandia lambearum); Neoscirrhia (based on Neoscirrhia osmundae); Nothoanungitopsis (based on Nothoanungitopsis urophyllae); Nothomicrosphaeropsis (based on Nothomicrosphaeropsis welwitschiae); Populomyces (based on Populomyces zwinianus); Pseudoacrospermum (based on Pseudoacrospermum goniomae). New species: Apiospora sasae on dead culms of Sasa veitchii (Netherlands); Apiospora stipae on dead culms of Stipa gigantea (Spain); Bagadiella eucalyptorum on leaves of Eucalyptus sp. (Australia); Calonectria singaporensis from submerged leaf litter (Singapore); Castanediella neomalaysiana on leaves of Eucalyptus sp. (Malaysia); Colletotrichum pleopeltidis on leaves of Pleopeltis sp. (South Africa); Coniochaeta deborreae from soil (Netherlands); Diaporthe durionigena on branches of Durio zibethinus (Vietnam); Floricola juncicola on dead culm of Juncus sp. (France); Haudseptoria typhae on leaf sheath of Typha sp. (Germany); Hogelandia lambearum from soil (Netherlands); Lomentospora valparaisensis from soil (Chile); Neofusicoccum mystacidii on dead stems of Mystacidium capense (South Africa); Neomycosphaerella guibourtiae on leaves of Guibourtia sp. (Angola); Niesslia neoexosporioides on dead leaves of Carex paniculata (Germany); Nothoanungitopsis urophyllae on seed capsules of Eucalyptus urophylla (South Africa); Nothomicrosphaeropsis welwitschiae on dead leaves of Welwitschia mirabilis (Namibia); Paracremonium bendijkiorum from soil (Netherlands); Paraphoma ledniceana on dead wood of Buxus sempervirens (Czech Republic); Paraphoma salicis on leaves of Salix cf. alba (Ukraine); Parasarocladium wereldwijsianum from soil (Netherlands); Peziza ligni on masonry and plastering (France); Phyllosticta phoenicis on leaves of Phoenix reclinata (South Africa); Plectosphaerella slobbergiarum from soil (Netherlands); Populomyces zwinianus from soil (Netherlands); Pseudoacrospermum goniomae on leaves of Gonioma kamassi (South Africa); Pseudopyricularia festucae on leaves of Festuca californica (USA); Sarocladium sasijaorum from soil (Netherlands); Sporothrix hypoxyli in sporocarp of Hypoxylon petriniae on Fraxinus wood (Netherlands); Superstratomyces albomucosus on Pycnanthus angolensis (Netherlands); Superstratomyces atroviridis on Pinus sylvestris (Netherlands); Superstratomyces flavomucosus on leaf of Hakea multilinearis (Australia); Superstratomyces tardicrescens from human eye specimen (USA); Taeniolella platani on twig of Platanus hispanica (Germany), and Tympanis pini on twigs of Pinus sylvestris (Spain). Citation: Crous PW, Hernández-Restrepo M, Schumacher RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ, Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E, Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW, Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT, Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM, Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ (2021). New and Interesting Fungi. 4. Fungal Systematics and Evolution7: 255-343. doi: 10.3114/fuse.2021.07.13.

RevDate: 2021-06-15

Prothiwa M, Filz V, Oehler S, et al (2021)

Inhibiting quinolone biosynthesis of Burkholderia.

Chemical science, 12(20):6908-6912.

2-Alkylquinolones are important signalling molecules of Burkholderia species. We developed a substrate-based chemical probe against the central quinolone biosynthesis enzyme HmqD and applied it in competitive profiling experiments to discover the first known HmqD inhibitors. The most potent inhibitors quantitatively blocked quinolone production in Burkholderia cultures with single-digit micromolar efficacy.

RevDate: 2021-06-15

Cyriaque V, Madsen JS, Fievez L, et al (2021)

Lead Drives Complex Dynamics of a Conjugative Plasmid in a Bacterial Community.

Frontiers in microbiology, 12:655903.

Plasmids carrying metal resistance genes (MRGs) have been suggested to be key ecological players in the adaptation of metal-impacted microbial communities, making them promising drivers of bio-remediation processes. However, the impact of metals on plasmid-mediated spread of MRGs through selection, plasmid loss, and transfer is far from being fully understood. In the present study, we used two-member bacterial communities to test the impact of lead on the dispersal of the IncP plasmid pKJK5 from a Pseudomonas putida KT2440 plasmid donor and two distinct recipients, Variovorax paradoxus B4 or Delftia acidovorans SPH-1 after 4 and 10 days of mating. Two versions of the plasmid were used, carrying or not carrying the lead resistance pbrTRABCD operon, to assess the importance of fitness benefit and conjugative potential for the dispersal of the plasmid. The spread dynamics of metal resistance conveyed by the conjugative plasmid were dependent on the recipient and the lead concentration: For V. paradoxus, the pbr operon did not facilitate neither lead resistance nor variation in plasmid spread. The growth gain brought by the pbr operon to D. acidovorans SPH-1 and P. putida KT2440 at 1 mM Pb enhanced the spread of the plasmid. At 1.5 mM Pb after 4 days, the proteomics results revealed an oxidative stress response and an increased abundance of pKJK5-encoded conjugation and partitioning proteins, which most likely increased the transfer of the control plasmid to D. acidovorans SPH-1 and ensured plasmid maintenance. As a consequence, we observed an increased spread of pKJK5-gfp. Conversely, the pbr operon reduced the oxidative stress response and impeded the rise of conjugation- and partitioning-associated proteins, which slowed down the spread of the pbr carrying plasmid. Ultimately, when a fitness gain was recorded in the recipient strain, the spread of MRG-carrying plasmids was facilitated through positive selection at an intermediate metal concentration, while a high lead concentration induced oxidative stress with positive impacts on proteins encoding plasmid conjugation and partitioning.

RevDate: 2021-06-15

Batool M, Blazier JC, Rogovska YV, et al (2021)

Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.

Ticks and tick-borne diseases, 12(5):101768 pii:S1877-959X(21)00121-7 [Epub ahead of print].

Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.

RevDate: 2021-06-12

Zhang L, Gong X, Wang L, et al (2021)

Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system.

The Science of the total environment, 791:148096 pii:S0048-9697(21)03167-3 [Epub ahead of print].

Thermal hydrolysis process (THP) is an effective pre-treatment method to reduce solids volume and improve biogas production during anaerobic digestion (AD) via increasing the biodegradability of waste activated sludge (WAS). However, the effects of THP pre-treated sludge on microbial diversity, interspecies interactions, and metabolism in AD systems remain largely unknown. We therefore setup and operated an anaerobic digester during a long-term period to shed light on the effect of THP pre-treatment on AD microbial ecology in comparison to conventional AD via Illumina based 16S rRNA gene amplicon sequencing and genome-centric metagenomics analysis. Results showed THP sludge significantly reduced the microbial diversity, shaped the microbial community structure, and resulted in more intense microbial interactions. Compared to WAS as the feed sludge, THP sludge shaped the core functional groups, but functional redundancy ensured the system's stability. The metabolic interactions between methanogens and syntrophic bacteria as well as the specific metabolic pathways were further elucidated. Hydrogenotrophic methanogens, Methanospirillum sp. and Methanolinea sp., were the primary contributors for methane production when treating THP and WAS, respectively, which also have potential for acetate oxidation to methane. Collectively, this study provides in-depth information on the interspecies interactions to better understand how THP pre-treatment influences AD microbial community.

RevDate: 2021-06-12

Morales Medina WR, Eramo A, NL Fahrenfeld (2021)

Metabolically Active Prokaryotes and Actively Transcribed Antibiotic Resistance Genes in Sewer Systems: Implications for Public Health and Microbially Induced Corrosion.

Microbial ecology [Epub ahead of print].

Sewer systems are reservoirs of pathogens and bacteria carrying antibiotic resistance genes (ARGs). However, most recent high-throughput studies rely on DNA-based techniques that cannot provide information on the physiological state of the cells nor expression of ARGs. In this study, wastewater and sewer sediment samples were collected from combined and separate sanitary sewer systems. The metabolically active prokaryote community was evaluated using 16S rRNA amplicon sequencing and actively transcribed ARG abundance was measured using mRNA RT-qPCR. Three (sul1, blaTEM, tet(G)) of the eight tested ARGs were quantifiable in select samples. Sewer sediment samples had greater abundance of actively transcribed ARGs compared to wastewater. Microbiome analysis showed the presence of metabolically active family taxa that contain clinically relevant pathogens (Pseudomonadaceae, Enterobacteraceae, Streptococcaceae, Arcobacteraceae, and Clostridiaceae) and corrosion-causing prokaryotes (Desulfobulbaceae and Desulfovibrionaceae) in both matrices. Spirochaetaceae and methanogens were more common in the sediment matrix while Mycobacteraceae were more common in wastewater. The microbiome obtained from 16S rRNA sequencing had a significantly different structure from the 16S rRNA gene microbiome. Overall, this study demonstrates active transcription of ARGs in sewer systems and provides insight into the abundance and physiological state of taxa of interest in the different sewer matrices and sewer types relevant for wastewater-based epidemiology, corrosion, and understanding the hazard posed by different matrices during sewer overflows.

RevDate: 2021-06-11

Vaezzadeh V, Thomes MW, Kunisue T, et al (2021)

Corrigendum to "Examination of barnacles' potential to be used as bioindicators of persistent organic pollutants in coastal ecosystem: A Malaysia case study" [Chemosphere 263 (2021) 128272].

RevDate: 2021-06-11

Vissenaekens H, Smagghe G, Criel H, et al (2021)

Intracellular quercetin accumulation and its impact on mitochondrial dysfunction in intestinal Caco-2 cells.

Food research international (Ottawa, Ont.), 145:110430.

PURPOSE: Flavonoid bioavailability and bioactivity is associated with interindividual variability, which is partially due to differences in health status. Previously, it was demonstrated that cellular stress, especially mitochondrial stress, increases intracellular quercetin uptake and this is associated with beneficial health effects. Here, the impact of quercetin on mitochondrial dysfunction, induced by stressors targeting different sites of the electron transport chain, is investigated. The influence of the mitochondrial stress on quercetin uptake and subcellular location is studied and the accumulated quercetin metabolites in intestinal Caco-2 cells and mitochondria are characterized.

PRINCIPAL RESULTS: It was observed that quercetin counteracted (i) the carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP)-induced decrease in maximum oxygen consumption, (ii) the valinomycin-, oligomycin- and FCCP-induced reactive oxygen species production and (iii) the valinomycin-induced disruption of mitochondrial membrane potential. Using confocal microscopy, it was found that upon mitochondrial stress, the intracellular quercetin accumulation increased and was partially located in the mitochondria. Finally, it was demonstrated that quercetin was present as O-methyl, O-methylglucuronide and O-methylsulfate conjugates in the cell lysate and mitochondria-enriched fraction.

MAJOR CONCLUSIONS: This study shows that quercetin can partially restore, especially FCCP-induced, mitochondrial dysfunction and this protective effect was linked with an intracellular quercetin accumulation in the mitochondria of intestinal cells.

RevDate: 2021-06-10

Rivera AJ, RE Tyx (2021)

Microbiology of the American Smokeless Tobacco.

Applied microbiology and biotechnology [Epub ahead of print].

Smokeless tobacco products (STP) contain diverse microbial communities that contribute to the formation of harmful chemical byproducts. This is concerning since 300 million individuals around the globe are users of smokeless tobacco. Significant evidence has shown that microbial metabolic activities mediate the formation of carcinogens during manufacturing. In recent years, studies have revealed a series of additional health impacts that include lesions and inflammation of the oral mucosa and the gastrointestinal tract, as well as alterations of the endogenous microbiota. These findings are due to recent developments in molecular technologies that allowed researchers to better examine the microbial component of these products. This new information illustrates the scale of the STP microbiota and its diversity in the finished product that is sold for consumption. Additionally, the application of metagenomics and metatranscriptomics has provided the tools to look at phylogenies across bacterial, viral, and eukaryotic groups, their functional capacities, and viability. Here we present key examples of tobacco microbiology research that utilizes newer approaches and strategies to define the microbial component of smokeless tobacco products. We also highlight challenges in these approaches, the knowledge gaps being filled, and those gaps that warrant further study. A better understanding of the microbiology of STP brings vast public health benefits. It will provide important information for the product consumer, impact manufacturing practices, and provide support for the development of attainable and more meaningful regulatory goals. KEY POINTS: Newer technologies allowed quicker and more comprehensive identification of microbes in tobacco samples, encapsulating microorganisms difficult or impossible to culture. Current research in smokeless tobacco microbiology is filling knowledge gaps previously unfilled due to the lack of suitable approaches. The microbial ecology of smokeless tobacco presents a clearer picture of diversity and variability not considered before.

RevDate: 2021-06-10

Irit N, Hana B, Esti KW, et al (2021)

Microscopic and biomolecular complementary approaches to characterize bioweathering processes at petroglyph sites from the Negev Desert, Israel.

Environmental microbiology [Epub ahead of print].

RevDate: 2021-06-10

Zhao T, Zwaenepoel A, Xue JY, et al (2021)

Whole-genome microsynteny-based phylogeny of angiosperms.

Nature communications, 12(1):3498.

Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.

RevDate: 2021-06-10

Flachs A, JD Orkin (2021)

On pickles: biological and sociocultural links between fermented foods and the human gut microbiome.

Journal of ethnobiology and ethnomedicine, 17(1):39.

BACKGROUND: The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa.

METHODS: In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods.

RESULTS: We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes.

CONCLUSIONS: By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.

RevDate: 2021-06-09

Scales BS, Cable RN, Duhaime MB, et al (2021)

Cross-Hemisphere Study Reveals Geographically Ubiquitous, Plastic-Specific Bacteria Emerging from the Rare and Unexplored Biosphere.

mSphere [Epub ahead of print].

While it is now appreciated that the millions of tons of plastic pollution travelling through marine systems carry complex communities of microorganisms, it is still unknown to what extent these biofilm communities are specific to the plastic or selected by the surrounding ecosystem. To address this, we characterized and compared the microbial communities of microplastic particles, nonplastic (natural and wax) particles, and the surrounding waters from three marine ecosystems (the Baltic, Sargasso and Mediterranean seas) using high-throughput 16S rRNA gene sequencing. We found that biofilm communities on microplastic and nonplastic particles were highly similar to one another across this broad geographical range. The similar temperature and salinity profiles of the Sargasso and Mediterranean seas, compared to the Baltic Sea, were reflected in the biofilm communities. We identified plastic-specific operational taxonomic units (OTUs) that were not detected on nonplastic particles or in the surrounding waters. Twenty-six of the plastic-specific OTUs were geographically ubiquitous across all sampled locations. These geographically ubiquitous plastic-specific OTUs were mostly low-abundance members of their biofilm communities and often represented uncultured members of marine ecosystems. These results demonstrate the potential for plastics to be a reservoir of rare and understudied microbes, thus warranting further investigations into the dynamics and role of these microbes in marine ecosystems. IMPORTANCE This study represents one of the largest comparisons of biofilms from environmentally sampled plastic and nonplastic particles from aquatic environments. By including particles sampled through three separate campaigns in the Baltic, Sargasso, and Mediterranean seas, we were able to make cross-geographical comparisons and discovered common taxonomical signatures that define the plastic biofilm. For the first time, we identified plastic-specific bacteria that reoccur across marine regions. Our data reveal that plastics have selective properties that repeatedly enrich for similar bacteria regardless of location, potentially shifting aquatic microbial communities in areas with high levels of plastic pollution. Furthermore, we show that bacterial communities on plastic do not appear to be strongly influenced by polymer type, suggesting that other properties, such as the absorption and/or leaching of chemicals from the surface, are likely to be more important in the selection and enrichment of specific microorganisms.

RevDate: 2021-06-09

Dove NC, Veach AM, Muchero W, et al (2021)

Assembly of the Populus Microbiome Is Temporally Dynamic and Determined by Selective and Stochastic Factors.

mSphere [Epub ahead of print].

Recent work shows that the plant microbiome, particularly the initial assembly of this microbiome, influences plant health, survival, and fitness. Here, we characterize the initial assembly of the Populus microbiome across ten genotypes belonging to two poplar species in a common garden using 16S rRNA gene and ITS2 region amplicon sequencing of the leaf endosphere, leaf surface, root endosphere, and rhizosphere. We sampled these microbiomes three times throughout the first growing season and found that the composition of the microbiome changed dramatically over time across all plant-associated habitats and host genotypes. For archaea and bacteria, these changes were dominated by strong homogenizing selection (accounting for 29 to 62% of pairwise comparisons). However, fungal assembly was generally characterized by multiple ecological assembly processes (i.e., a mix of weak selective and dispersal processes). Interestingly, genotype, while a significant moderator of microbiome composition, generally explained less variation than sample date across plant-associated habitats. We defined a set of core genera that accounted for, on average, 36% of the microbiome. The relative abundance of this core community was consistent over time. Additionally, using source tracking modeling, we determined that new microbial taxa colonize from both aboveground and belowground sources, and combined with our ecological assembly null models, we found that both selective and dispersal processes explained the differences between exo- (i.e., leaf surface and rhizosphere) and endospheric microbiomes. Taken together, our results suggest that the initial assembly of the Populus microbiome is time-, genotype-, and habitat-dependent and is moderated by both selective and stochastic factors. IMPORTANCE The initial assembly of the plant microbiome may establish the trajectory of forthcoming microbiome states, which could determine the overall future health of the plant. However, while much is known about the initial microbiome assembly of grasses and agricultural crops, less is known about the initial microbiome of long-lived trees, such as poplar (Populus spp.). Thus, a greater understanding of initial plant microbiome assembly in an ecologically and economically important plant such as Populus is highly desirable. Here, we show that the initial microbiome community composition and assembly in the first growing season of Populus is temporally dynamic and is determined by a combination of both selective and stochastic factors. Our findings could be used to prescribe ecologically informed microbial inoculations and better predict the composition of the Populus microbiome into the future and to better understand its influence on plant health.

RevDate: 2021-06-09

Naidoo Y, Valverde A, Pierneef RE, et al (2021)

Differences in Precipitation Regime Shape Microbial Community Composition and Functional Potential in Namib Desert Soils.

Microbial ecology [Epub ahead of print].

Precipitation is one of the major constraints influencing the diversity, structure, and activity of soil microbial communities in desert ecosystems. However, the effect of changes in precipitation on soil microbial communities in arid soil microbiomes remains unresolved. In this study, using 16S rRNA gene high-throughput sequencing and shotgun metagenome sequencing, we explored changes in taxonomic composition and functional potential across two zones in the Namib Desert with contrasting precipitation regime. We found that precipitation regime had no effect on taxonomic and functional alpha-diversity, but that microbial community composition and functional potential (beta-diversity) changed with increased precipitation. For instance, Acidobacteriota and 'resistance to antibiotics and toxic compounds' related genes were relatively more abundant in the high-rainfall zone. These changes were largely due to a small set of microbial taxa, some of which were present in low abundance (i.e. members of the rare biosphere). Overall, these results indicate that key climatic factors (i.e. precipitation) shape the taxonomic and functional attributes of the arid soil microbiome. This research provides insight into how changes in precipitation patterns associated with global climate change may impact microbial community structure and function in desert soils.

RevDate: 2021-06-09

Febinia CA, Malik SG, Djuwita R, et al (2021)

Distinctive Microbiome Type Distribution in a Young Adult Balinese Cohort May Reflect Environmental Changes Associated with Modernization.

Microbial ecology [Epub ahead of print].

An important public health question is understanding how changes in human environments can drive changes in the gut microbiota that influence risks associated with human health and wellbeing. It is well-documented that the modernization of societies is strongly correlated with intergenerational change in the frequency of nutrition-related chronic diseases in which microbial dysbiosis is implicated. The population of Bali, Indonesia, is well-positioned to study the interconnection between a changing food environment and microbiome patterns in its early stages, because of a recent history of modernization. Here, we characterize the fecal microbiota and diet history of the young adult women in Bali, Indonesia (n = 41) in order to compare microbial patterns in this generation with those of other populations with different histories of a modern food environment (industrialized supply chain). We found strong support for two distinct fecal microbiota community types in our study cohort at similar frequency: a Prevotella-rich (Type-P) and a Bacteroides-rich (Type-B) community (p < 0.001, analysis of similarity, Wilcoxon test). Although Type-P individuals had lower alpha diversity (p < 0.001, Shannon) and higher incidence of obesity, multivariate analyses with diet data showed that community types significantly influenced associations with BMI. In a multi-country dataset (n = 257), we confirmed that microbial beta diversity across subsistent and industrial populations was significantly associated with Prevotella and Bacteroides abundance (p < 0.001, generalized additive model) and that the prevalence of community types differs between societies. The young adult Balinese microbiota was distinctive in having an equal prevalence of two community types. Collectively, our study showed that the incorporation of community types as an explanatory factor into study design or modeling improved the ability to identify microbiome associations with diet and health metrics.

RevDate: 2021-06-09

Sun Y, Huang Y, Xu S, et al (2021)

Seasonal Variations in the Characteristics of Microbial Community Structure and Diversity in Atmospheric Particulate Matter from Clean Days and Smoggy Days in Beijing.

Microbial ecology [Epub ahead of print].

Microorganisms are an important part of atmospheric particulate matter and are closely related to human health. In this paper, the variations in the characteristics of the chemical components and bacterial communities in PM10 and PM2.5 grouped according to season, pollution degree, particle size, and winter heating stage were studied. The influence of environmental factors on community structure was also analyzed. The results showed that seasonal variations were significant. NO3- contributed the most to the formation of particulate matter in spring and winter, while SO42- contributed the most in summer and autumn. The community structures in summer and autumn were similar, while the community structure in spring was significantly different. The dominant phyla were similar among seasons, but their proportions were different. The dominant genera were no-rank_c_Cyanobacteria, Acidovorax, Escherichia-Shigella and Sphingomonas in spring; Massilia, Bacillus, Acinetobacter, Rhodococcus, and Brevibacillus in summer and autumn; and Rhodococcus in winter. The atmospheric microorganisms in Beijing mainly came from soil, water, and plants. The few pathogens detected were mainly affected by the microbial source on the sampling day, regardless of pollution level. RDA (redundancy analysis) showed that the bacterial community was positively correlated with the concentration of particulate matter and that the wind speed in spring was positively correlated with NO3- levels, NH4+ levels, temperature, and relative humidity in summer and autumn, but there was no clear consistency among winter samples. This study comprehensively analyzed the variations in the characteristics of the airborne bacterial community in Beijing over one year and provided a reference for understanding the source, mechanism, and assessment of the health effects of different air qualities.

RevDate: 2021-06-08

Rochefort A, Simonin M, Marais C, et al (2021)

Transmission of Seed and Soil Microbiota to Seedling.

mSystems [Epub ahead of print].

The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.

RevDate: 2021-06-08

Tracanna V, Ossowicki A, Petrus MLC, et al (2021)

Dissecting Disease-Suppressive Rhizosphere Microbiomes by Functional Amplicon Sequencing and 10× Metagenomics.

mSystems [Epub ahead of print].

Disease-suppressive soils protect plants against soilborne fungal pathogens that would otherwise cause root infections. Soil suppressiveness is, in most cases, mediated by the antagonistic activity of the microbial community associated with the plant roots. Considering the enormous taxonomic and functional diversity of the root-associated microbiome, identification of the microbial genera and mechanisms underlying this phenotype is challenging. One approach to unravel the underlying mechanisms is to identify metabolic pathways enriched in the disease-suppressive microbial community, in particular, pathways that harbor natural products with antifungal properties. An important class of these natural products includes peptides produced by nonribosomal peptide synthetases (NRPSs). Here, we applied functional amplicon sequencing of NRPS-associated adenylation domains (A domains) to a collection of eight soils that are suppressive or nonsuppressive (i.e., conducive) to Fusarium culmorum, a fungal root pathogen of wheat. To identify functional elements in the root-associated bacterial community, we developed an open-source pipeline, referred to as dom2BGC, for amplicon annotation and putative gene cluster reconstruction through analyzing A domain co-occurrence across samples. We applied this pipeline to rhizosphere communities from four disease-suppressive and four conducive soils and found significant similarities in NRPS repertoires between suppressive soils. Specifically, several siderophore biosynthetic gene clusters were consistently associated with suppressive soils, hinting at competition for iron as a potential mechanism of suppression. Finally, to validate dom2BGC and to allow more unbiased functional metagenomics, we performed 10× metagenomic sequencing of one suppressive soil, leading to the identification of multiple gene clusters potentially associated with the disease-suppressive phenotype. IMPORTANCE Soil-borne plant-pathogenic fungi continue to be a major threat to agriculture and horticulture. The genus Fusarium in particular is one of the most devastating groups of soilborne fungal pathogens for a wide range of crops. Our approach to develop novel sustainable strategies to control this fungal root pathogen is to explore and exploit an effective, yet poorly understood naturally occurring protection, i.e., disease-suppressive soils. After screening 28 agricultural soils, we recently identified four soils that were suppressive to root disease of wheat caused by Fusarium culmorum. We also confirmed, via sterilization and transplantation, that the microbiomes of these soils play a significant role in the suppressive phenotype. By adopting nonribosomal peptide synthetase (NRPS) functional amplicon screening of suppressive and conducive soils, we here show how computationally driven comparative analysis of combined functional amplicon and metagenomic data can unravel putative mechanisms underlying microbiome-associated plant phenotypes.

RevDate: 2021-06-08

Timmers LFSM, Peixoto JV, Ducati RG, et al (2021)

SARS-CoV-2 mutations in Brazil: from genomics to putative clinical conditions.

Scientific reports, 11(1):11998.

Due to the high rate of transmissibility, Brazil became the new COVID-19 outbreak epicenter and, since then, is being monitored to understand how SARS-CoV-2 mutates and spreads. We combined genomic and structural analysis to evaluate genomes isolated from different regions of Brazil and show that the most prevalent mutations were located in the S, N, ORF3a and ORF6 genes, which are involved in different stages of viral life cycle and its interaction with the host cells. Structural analysis brought to light the positions of these mutations on protein structures, contributing towards studies of selective structure-based drug discovery and vaccine development.

RevDate: 2021-06-07

Hou D, Zhou R, Zeng S, et al (2021)

Stochastic processes shape the bacterial community assembly in shrimp cultural pond sediments.

Applied microbiology and biotechnology [Epub ahead of print].

Sediment environments harbor a repertoire of microorganisms that contribute to animal health and the microecosystem in aquaculture ecosystems, but their community diversity and the potential factors that control it remain unclear. Here, we applied 16S rRNA gene amplicon sequencing to investigate bacterial diversity and assembly mechanisms in the sediments of shrimp cultural ponds at the mesoscale. Our results showed that sediment bacterial communities contained 10,333 operational taxonomic units (OTUs) but had only 34 core OTUs and that the relative abundances of these core OTUs were significantly correlated with the physicochemical properties of the sediments. Proteobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Acidobacteria, Firmicutes, Actinobacteria, Ignavibacteriae, Spirochaetae and Planctomycetes were the ten most abundant bacterial phyla. Notably, some opportunistic pathogens (e.g. Vibrio and Photobacterium) and potential functional microbes (e.g. Nitrospira, Nitrosomonas, Desulfobulbus and Desulfuromusa) were widely distributed in shrimp cultural pond sediments. More importantly, we found that there was a significant negative but weak distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and that the spatial turnover of these bacterial communities appeared to be largely driven by stochastic processes. Additionally, environmental factors, such as pH and total nitrogen, also played important roles in influencing the sediment bacterial structure. Our findings enhance our understanding of microbial ecology in aquatic ecosystems and facilitate sediment microbiota management in aquaculture. KEY POINTS: • Core bacterial taxa in cultural pond sediments contributed to the shrimp health and element cycling. • There was a significant negative distance-decay relationship among bacterial communities in shrimp culture pond sediments at the mesoscale, and its spatial turnover appeared to be largely driven by stochastic processes. • Environmental factors (e.g. pH and total nitrogen) played important roles in influencing bacterial structure in shrimp cultural pond sediments.

RevDate: 2021-06-07

Kumar S, Kumari N, Talukdar D, et al (2021)

The Vaginal Microbial Signatures of Preterm Birth Delivery in Indian Women.

Frontiers in cellular and infection microbiology, 11:622474.

Background: The incidence of preterm birth (PTB) in India is around 13%. Specific bacterial communities or individual taxon living in the vaginal milieu of pregnant women is a potential risk factor for PTB and may play an important role in its pathophysiology. Besides, bacterial taxa associated with PTB vary across populations.

Objective: Conduct a comparative analysis of vaginal microbiome composition and microbial genomic repertoires of women who enrolled in the Interdisciplinary Group for Advanced Research on Birth Outcomes - A DBT India Initiative (GARBH-Ini) pregnancy cohort to identify bacterial taxa associated with term birth (TB) and PTB in Indian women.

Methods: Vaginal swabs were collected during all three trimesters from 38 pregnant Indian women who delivered spontaneous term (n=20) and preterm (n=18) neonates. Paired-end sequencing of V3-V4 region of 16S rRNA gene was performed using the metagenomic DNA isolated from vaginal swabs (n=115). Whole genome sequencing of bacterial species associated with birth outcomes was carried out by shotgun method. Lactobacillus species were grown anaerobically in the De Man, Rogosa and Sharpe (MRS) agar culture medium for isolation of genomic DNA and whole genome sequencing.

Results: Vaginal microbiome of both term and preterm samples reveals similar alpha diversity indices. However, significantly higher abundance of Lactobacillus iners (p-value All_Trimesters<0.02), Megasphaera sp (p-value1st_Trimester <0.05), Gardnerella vaginalis (p-value2nd_Trimester= 0.01) and Sneathia sanguinegens (p-value2nd_Trimester <0.0001) were identified in preterm samples whereas higher abundance of L. gasseri (p-value3rd_Trimester =0.010) was observed in term samples by Wilcoxon rank-sum test. The relative abundance of L. iners, and Megasphaera sp. were found to be significantly different over time between term and preterm mothers. Analyses of the representative genomes of L. crispatus and L. gasseri indicate presence of secretory transcriptional regulator and several ribosomally synthesized antimicrobial peptides correlated with anti-inflammatory condition in the vagina. These findings indicate protective role of L. crispatus and L. gasseri in reducing the risk of PTB.

Conclusion: Our findings indicate that the dominance of specific Lactobacillus species and few other facultative anaerobes are associated with birth outcomes.

RevDate: 2021-06-07

Pjevac P, Hausmann B, Schwarz J, et al (2021)

An Economical and Flexible Dual Barcoding, Two-Step PCR Approach for Highly Multiplexed Amplicon Sequencing.

Frontiers in microbiology, 12:669776.

In microbiome research, phylogenetic and functional marker gene amplicon sequencing is the most commonly-used community profiling approach. Consequently, a plethora of protocols for the preparation and multiplexing of samples for amplicon sequencing have been developed. Here, we present two economical high-throughput gene amplification and sequencing workflows that are implemented as standard operating procedures at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna. These workflows are based on a previously-published two-step PCR approach, but have been updated to either increase the accuracy of results, or alternatively to achieve orders of magnitude higher numbers of samples to be multiplexed in a single sequencing run. The high-accuracy workflow relies on unique dual sample barcoding. It allows the same level of sample multiplexing as the previously-published two-step PCR approach, but effectively eliminates residual read missasignments between samples (crosstalk) which are inherent to single barcoding approaches. The high-multiplexing workflow is based on combinatorial dual sample barcoding, which theoretically allows for multiplexing up to 299,756 amplicon libraries of the same target gene in a single massively-parallelized amplicon sequencing run. Both workflows presented here are highly economical, easy to implement, and can, without significant modifications or cost, be applied to any target gene of interest.

RevDate: 2021-06-06

Girolamini L, Salaris S, Pascale MR, et al (2021)

Dynamics of Legionella Community Interactions in Response to Temperature and Disinfection Treatment: 7 Years of Investigation.

Microbial ecology [Epub ahead of print].

In man-made water distribution systems, Legionella community interactions remain unknown, due to their ability to change from sessile to planktonic states or live in viable but non-culturable forms, in response to anthropic and environmental stress. During 7 years of hospital Legionella surveillance, in 191 hot water positive samples, the interactions among the Legionella species, temperature, and disinfection treatment were evaluated. Legionella was isolated following ISO 11731:2017, and identification was performed by mip gene sequencing and sequence-based typing (SBT) for L. anisa or L. rubrilucens and L. pneumophila, respectively. The species with the higher frequency of isolation was L. pneumophila serogroup 1 (78.53%; 4865.36 ± 25,479.11 cfu/L), followed by L. anisa (54.45%; 558.79 ± 2637.41 cfu/L) and L. rubrilucens (21.99%; 307.73 ± 1574.95 cfu/L), which were sometimes present together. Spearman's rho correlation test was conducted among the species with respect to temperature and disinfectant (H2O2/Ag+). The results showed a generally positive interaction among these species sharing the same environment, except for competition between L. anisa and L. rubrilucens. High temperature (48.83 ± 2.59 °C) and disinfection treatment (11.58 ± 4.99 mg/L) affected the presence of these species. An exception was observed with L. anisa, which showed disinfection treatment resistance. For the purposes of environmental surveillance, it is fundamental to better understand the interactions and dynamic of the Legionella community in man-made water systems in order to choose the proper physical or chemical treatments. The simultaneous presence of different Legionella species could result in an increased resistance to high temperature and disinfectant treatment, leading to changes in contamination level and species diversity.

RevDate: 2021-06-06

Jaskulska A, Šulčius S, Kokociński M, et al (2021)

Cyanophage Distribution Across European Lakes of the Temperate-Humid Continental Climate Zone Assessed Using PCR-Based Genetic Markers.

Microbial ecology [Epub ahead of print].

Studies of the diversity and distribution of freshwater cyanophages are generally limited to the small geographical areas, in many cases including only one or few lakes. Data from dozens of various lakes distributed at a larger distance are necessary to understand their spatial distribution and sensitivity to biotic and abiotic factors. Thus, the objective of this study was to analyze the diversity and distribution of cyanophages within the infected cells using marker genes (psbA, nblA, and g91) in 21 Polish and Lithuanian lakes. Physicochemical factors that might be related to them were also analyzed. The results demonstrated that genetic markers representing cyanophages were observed in most lakes studied. The frequently detected gene was psbA with 88% of cyanophage-positive samples, while nblA and g91 were found in approximately 50% of lakes. The DNA sequence analyses for each gene demonstrated low variability between them, although the psbA sequences branched within the larger cluster of marine Synechoccocuss counterparts. The principal component analysis allowed to identify significant variation between the lakes that presented high and low cyanobacterial biomass. The lakes with high cyanobacterial biomass were further separated by country and the different diversity of cyanobacteria species, particularly Planktothrix agardhii, was dominant in the Polish lakes and Planktolyngbya limnetica in the Lithuanian lakes. The total phosphorous and the presence of cyanophage genes psbA and nblA were the most important factors that allowed differentiation for the Polish lakes, while the pH and the genes g91 and nblA for the Lithuanian lakes.

RevDate: 2021-06-06

Sun C, Zhang B, Ning D, et al (2021)

Seasonal dynamics of the microbial community in two full-scale wastewater treatment plants: Diversity, composition, phylogenetic group based assembly and co-occurrence pattern.

Water research, 200:117295 pii:S0043-1354(21)00493-0 [Epub ahead of print].

The optimal operation and functional stability of a wastewater treatment plant (WWTP) strongly depend on the properties of its microbial community. However, a knowledge gap remains regarding the seasonal dynamics of microbial community properties, especially phylogenetic group based assembly and co-occurrence patterns. Accordingly, in this study, influent and activated sludge (AS) samples were weekly collected from 2 full-scale WWTPs for one year (89 influent and 103 AS samples in total) and examined by high-throughput Illumina-MiSeq sequencing. The results suggested that the microbial community diversity and composition in the influent fluctuated substantially with season, while those in the AS had a relatively more stable pattern throughout the year. The phylogenetic group based assembly mechanisms of AS community were identified by using "Infer Community Assembly Mechanisms by Phylogenetic-bin-based null model (iCAMP)". The results showed that drift accounted for the largest proportion (52.8%), while homogeneous selection (18.2%) was the most important deterministic process. Deterministic processes dominated in 47 microbial groups (bins), which were also found (~40%) in the AS core taxa dataset. Moreover, the results suggested that Nitrospira were more susceptible to stochastic processes in winter, which may provide a possible explanation for nitrification failure in winter. Network analysis results suggested that the network structure of the AS community could be more stable in summer and autumn. In addition, there were no identical keystone taxa found in different networks (constructed from different plants, sources, and seasons), which supported the context dependency theory. The results of this study deepened our understanding of the microbial ecology in AS systems and provided a foundation for further studies on the community regulation strategy of WWTPs.

RevDate: 2021-06-05

Zhao Z, Cheng M, Li Y, et al (2021)

A Novel Constructed Wetland Combined with Microbial Desalination Cells and its Application.

Microbial ecology [Epub ahead of print].

Wastewater recycling can alleviate the shortage of water resources. Saline water is seldom treated with biological processes, and its recycling rate is low. Constructed wetland (CW) is a safe, economical, and ecological water treatment method. However, the saline water treatment performance of CW is not good. Microbial desalination cells (MDC) utilizing a bioelectrochemical approach achieve functions of desalination and power generation. In this study, MDC was used to strengthen CW to form a composite system, MDC-CW. Through optimization of design parameters, MDC-CW was applied in the treatment of salt-containing water. The average total nitrogen removal rate in MDC-CW-P1 reached 87.33% and the average COD removal rate was 92.79%. The average desalination rate of MDC-CW-P1 was 55.78% and the average voltage of MDC-CW-P1 reached 0.40 mV. Planting Canna indica in the MDC-CW was conducive to the functions of desalination and power generation. The above results were also verified by the microbial analysis results of gravels in the substrate, plant rhizosphere, and electrodes. In addition, the decontamination of the device mainly depended on the function of the bacteria commonly used in water treatment, such as Proteobacteria and Bacteroidetes, whereas the generation of power depended on the function of Geobacter. Salt ions moved spontaneously to the cathode and anode under the influence of current generation so that the desalination function was realized under the selective isolation function of exchange membranes. The device design and laboratory applications of MDC-CW experimentally achieved the electrochemical function and broadened the treatment scale of CW.

RevDate: 2021-06-04

De Paepe J, Clauwaert P, Gritti MC, et al (2021)

Electrochemical In Situ pH Control Enables Chemical-Free Full Urine Nitrification with Concomitant Nitrate Extraction.

Environmental science & technology [Epub ahead of print].

Urine is a valuable resource for nutrient recovery. Stabilization is, however, recommended to prevent urea hydrolysis and the associated risk for ammonia volatilization, uncontrolled precipitation, and malodor. This can be achieved by alkalinization and subsequent biological conversion of urea and ammonia into nitrate (nitrification) and organics into CO2. Yet, without pH control, the extent of nitrification is limited as a result of insufficient alkalinity. This study explored the feasibility of an integrated electrochemical cell to obtain on-demand hydroxide production through water reduction at the cathode, compensating for the acidification caused by nitritation, thereby enabling full nitrification. To deal with the inherent variability of the urine influent composition and bioprocess, the electrochemical cell was steered via a controller, modulating the current based on the pH in the bioreactor. This provided a reliable and innovative alternative to base addition, enabling full nitrification while avoiding the use of chemicals, the logistics associated with base storage and dosing, and the associated increase in salinity. Moreover, the electrochemical cell could be used as an in situ extraction and concentration technology, yielding an acidic concentrated nitrate-rich stream. The make-up of the end product could be tailored by tweaking the process configuration, offering versatility for applications on Earth and in space.

RevDate: 2021-06-04

Jakus N, Blackwell N, Osenbrück K, et al (2021)

Nitrate removal by a novel lithoautotrophic nitrate-reducing iron(II)-oxidizing culture enriched from a pyrite-rich limestone aquifer.

Applied and environmental microbiology [Epub ahead of print].

Nitrate removal in oligotrophic environments is often limited by the availability of suitable organic electron donors. Chemolithoautotrophic bacteria may play a key role in denitrification in aquifers depleted in organic carbon. Under anoxic and circumneutral pH conditions, iron(II) was hypothesized to serve as an electron donor for microbially mediated nitrate reduction by Fe(II)-oxidizing (NRFeOx) microorganisms. However, lithoautotrophic NRFeOx cultures have never been enriched from any aquifer and as such there are no model cultures available to study the physiology and geochemistry of this potentially environmentally relevant process. Using iron(II) as an electron donor, we enriched a lithoautotrophic NRFeOx culture from nitrate-containing groundwater of a pyrite-rich limestone aquifer. In the enriched NRFeOx culture that does not require additional organic co-substrates for growth, within 7-11 days 0.3-0.5 mM of nitrate was reduced and 1.3-2 mM of iron(II) was oxidized leading to a stoichiometric NO3-/Fe(II) ratio of 0.2, with N2 and N2O identified as the main nitrate reduction products. Short-range ordered Fe(III) (oxyhydr)oxides were the product of iron(II) oxidation. Microorganisms were observed to be closely associated with formed minerals but only few cells were encrusted, suggesting that most of the bacteria were able to avoid mineral precipitation at their surface. Analysis of the microbial community by long-read 16S rRNA gene sequencing revealed that the culture is dominated by members of the Gallionellaceae family that are known as autotrophic, neutrophilic, microaerophilic iron(II)-oxidizers. In summary, our study suggests that NRFeOx mediated by lithoautotrophic bacteria can lead to nitrate removal in anthropogenically impacted aquifers. Importance Removal of nitrate by microbial denitrification in groundwater is often limited by low concentrations of organic carbon. In these carbon-poor ecosystems, nitrate-reducing bacteria that can use inorganic compounds such as Fe(II) (NRFeOx) as electron donors could play a major role in nitrate removal. However, no lithoautotrophic NRFeOx culture has been successfully isolated or enriched from this type of environment and as such there are no model cultures available to study the rate-limiting factors of this potentially important process. Here we present the physiology and microbial community composition of a novel lithoautotrophic NRFeOx culture enriched from a fractured aquifer in southern Germany. The culture is dominated by a putative Fe(II)-oxidizer affiliated with the Gallionellaceae family and performs nitrate reduction coupled to Fe(II) oxidation leading to N2O and N2 formation without the addition of organic substrates. Our analyses demonstrate that lithoautotrophic NRFeOx can potentially lead to nitrate removal in nitrate-contaminated aquifers.

RevDate: 2021-06-04

Cao YL, Li YL, Fan YF, et al (2021)

Wolfberry genomes and the evolution of Lycium (Solanaceae).

Communications biology, 4(1):671.

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

RevDate: 2021-06-04

Fabersani E, Portune K, Campillo I, et al (2021)

Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice.

Scientific reports, 11(1):11788.

This study investigated the immune mechanisms whereby administration of Bacteroides uniformis CECT 7771 reduces metabolic dysfunction in obesity. C57BL/6 adult male mice were fed a standard diet or a Western diet high in fat and fructose, supplemented or not with B. uniformis CECT 7771 for 14 weeks. B. uniformis CECT 7771 reduced body weight gain, plasma cholesterol, triglyceride, glucose, and leptin levels; and improved oral glucose tolerance in obese mice. Moreover, B. uniformis CECT 7771 modulated the gut microbiota and immune alterations associated with obesity, increasing Tregs and reducing B cells, total macrophages and the M1/M2 ratio in both the gut and epididymal adipose tissue (EAT) of obese mice. B. uniformis CECT 7771 also increased the concentration of the anti-inflammatory cytokine IL-10 in the gut, EAT and peripheral blood, and protective cytokines TSLP and IL-33, involved in Treg induction and type 2 innate lymphoid cells activation, in the EAT. It also restored the obesity-reduced TLR5 expression in the ileum and EAT. The findings indicate that the administration of a human intestinal bacterium with immunoregulatory properties on the intestinal mucosa helps reverse the immuno-metabolic dysfunction caused by a Western diet acting over the gut-adipose tissue axis.

RevDate: 2021-06-03

Mezzasoma A, Coleine C, Sannino C, et al (2021)

Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica.

Microbial ecology [Epub ahead of print].

The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.

RevDate: 2021-06-03

Zhang T, Wang NF, LY Yu (2021)

Geographic Distance and Habitat Type Influence Fungal Communities in the Arctic and Antarctic Sites.

Microbial ecology [Epub ahead of print].

The Antarctic and Arctic regions are collectively referred to as the "Two Poles" of the earth and have extremely harsh climate conditions and fragile ecosystems. Until now, the biogeography of the fungal communities in the bipolar regions is not well known. In this study, we focused on the fungal communities in 110 samples collected from four habitat types (i.e., soil, vascular plant, freshwater, moss) in the Antarctic and Arctic sites using high-throughput sequencing. The data showed that the diversity and composition of fungal communities were both geographically patterned and habitat-patterned. ANOSIM tests revealed statistically significant differences among fungal communities in the eight sample types (R = 0.5035, p < 0.001) and those in the bipolar regions (R = 0.32859, p < 0.001). Only 396 OTUs (14.8%) were shared between the bipolar sites. Fungal communities in the four habitat types clustered together in the Arctic site but were separate from those of the Antarctic site, indicating that geographic distance was a more important determinant of fungal communities in the bipolar sites. These findings offer insights into the present-day biogeography of fungal communities in the bipolar sites.

RevDate: 2021-06-03

Carbonero F, G Strobel (2021)

Fungal Ecology Special Issue: Editorial.

RevDate: 2021-06-03

Gresse R, Chaucheyras-Durand F, Denis S, et al (2021)

Weaning-associated feed deprivation stress causes microbiota disruptions in a novel mucin-containing in vitro model of the piglet colon (MPigut-IVM).

Journal of animal science and biotechnology, 12(1):75.

BACKGROUND: Risk factors for the etiology of post-weaning diarrhea, a major problem in swine industry associated with enormous economic losses, remain to be fully elucidated. In concordance with the ethical concerns raised by animal experiments, we developed a new in vitro model of the weaning piglet colon (MPigut-IVM) including a mucin bead compartment to reproduce the mucus surface from the gut to which gut microbes can adhere.

RESULTS: Our results indicated that the MPigut-IVM is able to establish a representative piglet archaeal and bacterial colon microbiota in terms of taxonomic composition and function. The MPigut-IVM was consequently used to investigate the potential effects of feed deprivation, a common consequence of weaning in piglets, on the microbiota. The lack of nutrients in the MPigut-IVM led to an increased abundance of Prevotellaceae and Escherichia-Shigella and a decrease in Bacteroidiaceae and confirms previous in vivo findings. On top of a strong increase in redox potential, the feed deprivation stress induced modifications of microbial metabolite production such as a decrease in acetate and an increase in proportional valerate, isovalerate and isobutyrate production.

CONCLUSIONS: The MPigut-IVM is able to simulate luminal and mucosal piglet microbiota and represent an innovative tool for comparative studies to investigate the impact of weaning stressors on piglet microbiota. Besides, weaning-associated feed deprivation in piglets provokes disruptions of MPigut-IVM microbiota composition and functionality and could be implicated in the onset of post-weaning dysbiosis in piglets.

RevDate: 2021-06-02

Cornell CR, Zhang Y, Van Nostrand JD, et al (2021)

Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils.

mSphere [Epub ahead of print].

During the last several decades, viruses have been increasingly recognized for their abundance, ubiquity, and important roles in different ecosystems. Despite known contributions to aquatic systems, few studies examine viral abundance and community structure over time in terrestrial ecosystems. The effects of land conversion and land management on soil microbes have been previously investigated, but their effects on virus population are not well studied. This study examined annual dynamics of viral abundance in soils from a native tallgrass prairie and two croplands, conventional till winter wheat and no-till canola, in Oklahoma. Virus-like particle (VLP) abundance varied across sites, and showed clear seasonal shifts. VLP abundance significantly correlated with environmental variables that were generally reflective of land use, including air temperature, soil nitrogen, and plant canopy coverage. Structural equation modeling supported the effects of land use on soil communities by emphasizing interactions between management, environmental factors, and viral and bacterial abundance. Between the viral metagenomes from the prairie and tilled wheat field, 1,231 unique viral operational taxonomic units (vOTUs) were identified, and only five were shared that were rare in the contrasting field. Only 13% of the vOTUs had similarity to previously identified viruses in the RefSeq database, with only 7% having known taxonomic classification. Together, our findings indicated land use and tillage practices influence virus abundance and community structure. Analyses of viromes over time and space are vital to viral ecology in providing insight on viral communities and key information on interactions between viruses, their microbial hosts, and the environment. IMPORTANCE Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution. Therefore, viruses are considered an important part of soil functions in terrestrial ecosystems. In aquatic environments, virus abundance generally exceeds bacterial counts by an order of magnitude, and they are thought to be one of the greatest genetic reservoirs on the planet. However, data are extremely limited on viruses in soils, and even less is known about their responses to the disturbances associated with land use and management. The study provides important insights into the temporal dynamics of viral abundance and the structure of viral communities in response to the common practice of turning native habitats into arable soils.

RevDate: 2021-06-02

Broadhead R, Craeye L, C Callewaert (2021)

The Future of Functional Clothing for an Improved Skin and Textile Microbiome Relationship.

Microorganisms, 9(6): pii:microorganisms9061192.

The skin microbiome has become a hot field of research in the last few years. The emergence of next-generation sequencing has given unprecedented insights into the impact and involvement of microbiota in skin conditions. More and more cosmetics contain probiotics or bacteria as an active ingredient, with or without scientific data. This research is also acknowledged by the textile industry. There has been a more holistic approach on how the skin and textile microbiome interacts and how they influence the pH, moisture content and odour generation. To date, most of the ingredients have a broad-spectrum antibacterial action. This manuscript covers the current research and industry developments in the field of skin and textiles. It explores the nature of antimicrobial finishing in textiles which can disrupt the skin microbiome, and the benefits of more natural and microbiome friendly therapies to combat skin conditions, malodour and skin infection.

RevDate: 2021-06-02

Romaní-Pérez M, Bullich-Vilarrubias C, López-Almela I, et al (2021)

The Microbiota and the Gut-Brain Axis in Controlling Food Intake and Energy Homeostasis.

International journal of molecular sciences, 22(11): pii:ijms22115830.

Obesity currently represents a major societal and health challenge worldwide. Its prevalence has reached epidemic proportions and trends continue to rise, reflecting the need for more effective preventive measures. Hypothalamic circuits that control energy homeostasis in response to food intake are interesting targets for body-weight management, for example, through interventions that reinforce the gut-to-brain nutrient signalling, whose malfunction contributes to obesity. Gut microbiota-diet interactions might interfere in nutrient sensing and signalling from the gut to the brain, where the information is processed to control energy homeostasis. This gut microbiota-brain crosstalk is mediated by metabolites, mainly short chain fatty acids, secondary bile acids or amino acids-derived metabolites and subcellular bacterial components. These activate gut-endocrine and/or neural-mediated pathways or pass to systemic circulation and then reach the brain. Feeding time and dietary composition are the main drivers of the gut microbiota structure and function. Therefore, aberrant feeding patterns or unhealthy diets might alter gut microbiota-diet interactions and modify nutrient availability and/or microbial ligands transmitting information from the gut to the brain in response to food intake, thus impairing energy homeostasis. Herein, we update the scientific evidence supporting that gut microbiota is a source of novel dietary and non-dietary biological products that may beneficially regulate gut-to-brain communication and, thus, improve metabolic health. Additionally, we evaluate how the feeding time and dietary composition modulate the gut microbiota and, thereby, the intraluminal availability of these biological products with potential effects on energy homeostasis. The review also identifies knowledge gaps and the advances required to clinically apply microbiome-based strategies to improve the gut-brain axis function and, thus, combat obesity.

RevDate: 2021-06-02

Zhu J, Sun X, Zhang ZD, et al (2021)

Effect of Ionizing Radiation on the Bacterial and Fungal Endophytes of the Halophytic Plant Kalidium schrenkianum.

Microorganisms, 9(5): pii:microorganisms9051050.

Endophytic bacteria and fungi colonize plants that grow in various types of terrestrial and aquatic ecosystems. Our study investigates the communities of endophytic bacteria and fungi of halophyte Kalidium schrenkianum growing in stressed habitats with ionizing radiation. The geochemical factors and radiation (at low, medium, high level and control) both affected the structure of endophytic communities. The bacterial class Actinobacteria and the fungal class Dothideomycetes predominated the endophytic communities of K. schrenkianum. Aerial tissues of K. schrenkianum had higher fungal diversity, while roots had higher bacterial diversity. Radiation had no significant effect on the abundance of bacterial classes. Soil pH, total nitrogen, and organic matter showed significant effects on the diversity of root endophytes. Radiation affected bacterial and fungal community structure in roots but not in aerial tissues, and had a strong effect on fungal co-occurrence networks. Overall, the genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments, however negative correlations were found between endophytic bacteria and fungi in the plant. The genetic diversity of both endophytic bacteria and fungi was higher in radioactive environments. Our findings suggest that radiation affects root endophytes, and that the endophytes associated with aerial tissues and roots of K. schrenkianum follow different mechanisms for community assembly and different paradigms in stress response.

RevDate: 2021-06-02

Park T, Yoon J, Kim A, et al (2021)

Comparison of the Gut Microbiota of Jeju and Thoroughbred Horses in Korea.

Veterinary sciences, 8(5): pii:vetsci8050081.

(1) Background: The large intestine of horses is an anaerobic fermentative chamber filled with fibrolytic bacteria that play essential roles in digesting and absorbing nutrients for energy production. Although Jeju horses are a prominent local breed in Korea, few studies have investigated the gut microbiota of Jeju horses; (2) Methods: This study performed sequencing of V3 and V4 hypervariable regions of the partial 16S rRNA genes obtained from horse fecal samples and compared the gut microbiota between Jeju and Thoroughbred horses. Thirty and 24 fecal samples were obtained from Jeju and Thoroughbred horses, respectively; (3) Results: The gut microbiota belonged to 23 phyla and 159 families. Firmicutes and Bacteroidetes were the most abundant and predominant phyla, followed by Verrucomicrobia, Euryachaeota, and Spirochaete. The ratio of Firmicutes to Bacteroidetes (F/B), which is known as a relevant marker of gut dysbiosis, was 1.84 for Jeju horses, whereas it was 1.76 for Thoroughbred horses. Moreover, at the genus level, 21 genera were significantly different between the Jeju and Thoroughbred horses (p < 0.05); (4) Conclusions: The Thoroughbred horse's gut microbiotas had significantly higher diversity than the Jeju horses (p < 0.05). In addition, beneficial commensal bacteria that produce short-chain fatty acids thus providing a significant source of energy are also more abundant in Thoroughbred horses. These results provide novel information on the horse gut microbiota and insights for further studies related to the horse gut microbiota.

RevDate: 2021-06-02

Uriot O, Kebouchi M, Lorson E, et al (2021)

Identification of Streptococcus thermophilus Genes Specifically Expressed under Simulated Human Digestive Conditions Using R-IVET Technology.

Microorganisms, 9(6): pii:microorganisms9061113.

Despite promising health effects, the probiotic status of Streptococcus thermophilus, a lactic acid bacterium widely used in dairy industry, requires further documentation of its physiological status during human gastrointestinal passage. This study aimed to apply recombinant-based in vivo technology (R-IVET) to identify genes triggered in a S. thermophilus LMD-9 reference strain under simulated digestive conditions. First, the R-IVET chromosomal cassette and plasmid genomic library were designed to positively select activated genes. Second, recombinant clones were introduced into complementary models mimicking the human gut, the Netherlands Organization for Applied Scientific Research (TNO) gastrointestinal model imitating the human stomach and small intestine, the Caco-2 TC7 cell line as a model of intestinal epithelium, and anaerobic batch cultures of human feces as a colon model. All inserts of activated clones displayed a promoter activity that differed from one digestive condition to another. Our results also showed that S. thermophilus adapted its metabolism to stressful conditions found in the gastric and colonic competitive environment and modified its surface proteins during adhesion to Caco-2 TC7 cells. Activated genes were investigated in a collection of S. thermophilus strains showing various resistance levels to gastrointestinal stresses, a first stage in the identification of gut resistance markers and a key step in probiotic selection.

RevDate: 2021-06-02

Weiss B, Souza ACO, Constancio MTL, et al (2021)

Unraveling a Lignocellulose-Decomposing Bacterial Consortium from Soil Associated with Dry Sugarcane Straw by Genomic-Centered Metagenomics.

Microorganisms, 9(5): pii:microorganisms9050995.

Second-generation biofuel production is in high demand, but lignocellulosic biomass' complexity impairs its use due to the vast diversity of enzymes necessary to execute the complete saccharification. In nature, lignocellulose can be rapidly deconstructed due to the division of biochemical labor effectuated in bacterial communities. Here, we analyzed the lignocellulolytic potential of a bacterial consortium obtained from soil and dry straw leftover from a sugarcane milling plant. This consortium was cultivated for 20 weeks in aerobic conditions using sugarcane bagasse as a sole carbon source. Scanning electron microscopy and chemical analyses registered modification of the sugarcane fiber's appearance and biochemical composition, indicating that this consortium can deconstruct cellulose and hemicellulose but no lignin. A total of 52 metagenome-assembled genomes from eight bacterial classes (Actinobacteria, Alphaproteobacteria, Bacilli, Bacteroidia, Cytophagia, Gammaproteobacteria, Oligoflexia, and Thermoleophilia) were recovered from the consortium, in which ~46% of species showed no relevant modification in their abundance during the 20 weeks of cultivation, suggesting a mostly stable consortium. Their CAZymes repertoire indicated that many of the most abundant species are known to deconstruct lignin (e.g., Chryseobacterium) and carry sequences related to hemicellulose and cellulose deconstruction (e.g., Chitinophaga, Niastella, Niabella, and Siphonobacter). Taken together, our results unraveled the bacterial diversity, enzymatic potential, and effectiveness of this lignocellulose-decomposing bacterial consortium.

RevDate: 2021-06-01

Siebert A, Hofmann K, Staib L, et al (2021)

Amplicon-sequencing of raw milk microbiota: impact of DNA extraction and library-PCR.

Applied microbiology and biotechnology [Epub ahead of print].

The highly complex raw milk matrix challenges the sample preparation for amplicon-sequencing due to low bacterial counts and high amounts of eukaryotic DNA originating from the cow. In this study, we optimized the extraction of bacterial DNA from raw milk for microbiome analysis and evaluated the impact of cycle numbers in the library-PCR. The selective lysis of eukaryotic cells by proteinase K and digestion of released DNA before bacterial lysis resulted in a high reduction of mostly eukaryotic DNA and increased the proportion of bacterial DNA. Comparative microbiome analysis showed that a combined enzymatic and mechanical lysis procedure using the DNeasy® PowerFood® Microbial Kit with a modified protocol was best suitable to achieve high DNA quantities after library-PCR and broad coverage of detected bacterial biodiversity. Increasing cycle numbers during library-PCR systematically altered results for species and beta-diversity with a tendency to overrepresentation or underrepresentation of particular taxa. To limit PCR bias, high cycle numbers should thus be avoided. An optimized DNA extraction yielding sufficient bacterial DNA and enabling higher PCR efficiency is fundamental for successful library preparation. We suggest that a protocol using ethylenediaminetetraacetic acid (EDTA) to resolve casein micelles, selective lysis of somatic cells, extraction of bacterial DNA with a combination of mechanical and enzymatic lysis, and restriction of PCR cycles for analysis of raw milk microbiomes is optimal even for samples with low bacterial numbers. KEY POINTS: • Sample preparation for high-throughput 16S rRNA gene sequencing of raw milk microbiota. • Reduction of eukaryotic DNA by enzymatic digestion. • Shift of detected microbiome caused by high cycle numbers in library-PCR.

RevDate: 2021-06-01

Zhao XF, Shu WS, YQ Hao (2021)

Seasonal Climate Variations Promote Bacterial α-Diversity in Soil.

Microbial ecology [Epub ahead of print].

Ecological theory suggests that temporal environmental fluctuations can contribute greatly to diversity maintenance. Given bacteria's short generation time and rapid responses to environmental change, seasonal climate fluctuations are very likely to play an important role in maintaining the extremely high α-diversity of soil bacterial community, which has been unfortunately neglected in previous studies. Here, with in-depth analyses of two previously published soil bacterial datasets at global scale, we found that soil bacterial α-diversity was positively correlated with both seasonal variations of temperature and precipitation. Furthermore, piecewise structural equation models showed that seasonal variations of temperature or precipitation had weak but significant positive effect on soil bacterial α-diversity in each dataset. However, it is noteworthy that the importance of seasonal climate variations might be underestimated in the above analyses, due to the potential confounding factors (such as vegetation type) and the lack of sampling across seasons. As a supplement, we analyzed a previously published wheat cropland dataset with samples collected in both winter and the following summer across North China Plain. As expected, bacterial α-diversity was positively correlated with seasonal climate variations in the cropland dataset, and climate seasonality explained a larger proportion of variations in bacterial α-diversity. Collectively, these findings implied that fluctuation-dependent mechanisms of diversity maintenance presumably operate in soil bacterial communities. Based on existing evidence, we speculated that the storage effect may be the main mechanism responsible for diversity maintenance in soil bacterial community, but rigorous experimental tests are needed in the future.

RevDate: 2021-05-31

Paredes GF, Viehboeck T, Lee R, et al (2021)

Anaerobic Sulfur Oxidation Underlies Adaptation of a Chemosynthetic Symbiont to Oxic-Anoxic Interfaces.

mSystems [Epub ahead of print].

Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. However, nothing is known about how these variations affect their physiology. Here, by applying omics, Raman microspectroscopy, and stable isotope labeling, we investigated the effect of oxygen on "Candidatus Thiosymbion oneisti." Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation were upregulated under oxic conditions, together with genes involved in organic carbon assimilation, polyhydroxyalkanoate (PHA) biosynthesis, nitrogen fixation, and urea utilization. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand oxidative stress, and the symbiont appeared to proliferate less. Based on its physiological response to oxygen, we propose that "Ca. T. oneisti" may exploit anaerobic sulfur oxidation coupled to denitrification to proliferate in anoxic sand. However, the ectosymbiont would still profit from the oxygen available in superficial sand, as the energy-efficient aerobic respiration would facilitate carbon and nitrogen assimilation. IMPORTANCE Chemoautotrophic endosymbionts are famous for exploiting sulfur oxidization to feed marine organisms with fixed carbon. However, the physiology of thiotrophic bacteria thriving on the surface of animals (ectosymbionts) is less understood. One longstanding hypothesis posits that attachment to animals that migrate between reduced and oxic environments would boost sulfur oxidation, as the ectosymbionts would alternatively access sulfide and oxygen, the most favorable electron acceptor. Here, we investigated the effect of oxygen on the physiology of "Candidatus Thiosymbion oneisti," a gammaproteobacterium which lives attached to marine nematodes inhabiting shallow-water sand. Surprisingly, sulfur oxidation genes were upregulated under anoxic relative to oxic conditions. Furthermore, under anoxia, the ectosymbiont appeared to be less stressed and to proliferate more. We propose that animal-mediated access to oxygen, rather than enhancing sulfur oxidation, would facilitate assimilation of carbon and nitrogen by the ectosymbiont.

RevDate: 2021-06-01

Guerrero-Cruz S, Vaksmaa A, Horn MA, et al (2021)

Methanotrophs: Discoveries, Environmental Relevance, and a Perspective on Current and Future Applications.

Frontiers in microbiology, 12:678057.

Methane is the final product of the anaerobic decomposition of organic matter. The conversion of organic matter to methane (methanogenesis) as a mechanism for energy conservation is exclusively attributed to the archaeal domain. Methane is oxidized by methanotrophic microorganisms using oxygen or alternative terminal electron acceptors. Aerobic methanotrophic bacteria belong to the phyla Proteobacteria and Verrucomicrobia, while anaerobic methane oxidation is also mediated by more recently discovered anaerobic methanotrophs with representatives in both the bacteria and the archaea domains. The anaerobic oxidation of methane is coupled to the reduction of nitrate, nitrite, iron, manganese, sulfate, and organic electron acceptors (e.g., humic substances) as terminal electron acceptors. This review highlights the relevance of methanotrophy in natural and anthropogenically influenced ecosystems, emphasizing the environmental conditions, distribution, function, co-existence, interactions, and the availability of electron acceptors that likely play a key role in regulating their function. A systematic overview of key aspects of ecology, physiology, metabolism, and genomics is crucial to understand the contribution of methanotrophs in the mitigation of methane efflux to the atmosphere. We give significance to the processes under microaerophilic and anaerobic conditions for both aerobic and anaerobic methane oxidizers. In the context of anthropogenically influenced ecosystems, we emphasize the current and potential future applications of methanotrophs from two different angles, namely methane mitigation in wastewater treatment through the application of anaerobic methanotrophs, and the biotechnological applications of aerobic methanotrophs in resource recovery from methane waste streams. Finally, we identify knowledge gaps that may lead to opportunities to harness further the biotechnological benefits of methanotrophs in methane mitigation and for the production of valuable bioproducts enabling a bio-based and circular economy.

RevDate: 2021-06-01

Trego AC, McAteer PG, Nzeteu C, et al (2021)

Combined Stochastic and Deterministic Processes Drive Community Assembly of Anaerobic Microbiomes During Granule Flotation.

Frontiers in microbiology, 12:666584.

Advances in null-model approaches have resulted in a deeper understanding of community assembly mechanisms for a variety of complex microbiomes. One under-explored application is assembly of communities from the built-environment, especially during process disturbances. Anaerobic digestion for biological wastewater treatment is often underpinned by retaining millions of active granular biofilm aggregates. Flotation of granules is a major problem, resulting in process failure. Anaerobic aggregates were sampled from three identical bioreactors treating dairy wastewater. Microbiome structure was analysed using qPCR and 16S rRNA gene amplicon sequencing from DNA and cDNA. A comprehensive null-model approach quantified assembly mechanisms of floating and settled communities. Significant differences in diversity were observed between floating and settled granules, in particular, we highlight the changing abundances of Methanosaeta and Lactococcus. Both stochastic and deterministic processes were important for community assembly. Homogeneous selection was the primary mechanism for all categories, but dispersal processes also contributed. The lottery model was used to identify clade-level competition driving community assembly. Lottery "winners" were identified with different winners between floating and settled groups. Some groups changed their winner status when flotation occurred. Spirochaetaceae, for example, was only a winner in settled biomass (cDNA-level) and lost its winner status during flotation. Alternatively, Arcobacter butzerli gained winner status during flotation. This analysis provides a deeper understanding of changes that occur during process instabilities and identified groups which may be washed out-an important consideration for process control.

RevDate: 2021-06-01

Rocha FYO, Negrisoli Júnior AS, de Matos GF, et al (2021)

Endophytic Bacillus Bacteria Living in Sugarcane Plant Tissues and Telchin licus licus Larvae (Drury) (Lepidoptera: Castniidae): The Symbiosis That May Open New Paths in the Biological Control.

Frontiers in microbiology, 12:659965.

Bacteria of the genus Bacillus can colonize endophytically and benefit several crops including the control of some pest orders. In view of the benefits provided by these microorganisms and in order to find out an efficient biotechnological control for the giant borer, our interest in studying the microorganisms in symbiosis with sugarcane and the giant borer has arisen, since there is no efficient chemical or biological control method for this pest. Therefore, endophytic Bacillus strains were isolated from three sugarcane niches (apoplast fluid, central internode cylinder and roots) and also from the giant borer larvae living inside sugarcane varieties grown in the Northeast region of Brazil. The taxonomical characterization (16S rRNA) of 157 Gram-positive isolates showed that 138 strains belonged to the Bacillus genus. The most representative species were phylogenetically closely related to B. megaterium (11.5%) followed by B. safensis (10.8%), B. cereus (8.9%), B. oleronius (8.9%), B. amyloliquefaciens (7.0%), and B. pacificus (6.4%). BOX-PCR analyses showed very distinct band pattern profiles suggesting a great diversity of Bacillus species within the sugarcane niches and the digestive tract, while the B. cereus group remained very closely clustered in the dendrogram. According to XRE biomarker analysis, eleven strains (FORCN005, 007, 008, 011, 012, 014, 067, 076, 092, 093, and 135) correspond to B. thuringiensis species. Additional studies using conserved genes (glp, gmk, pta, and tpi) indicated that most of these strains were phylogenetically closely related to B. thuringiensis and may be considered different subspecies. In conclusion, this study suggests that the culturable Bacillus species are greatly diversified within the plant niches and showed Bacillus species in the digestive tract of the giant borer for the first time. These results open new perspectives to understand the role and functions played by these microorganisms in symbiosis with this pest and also the possibility of developing an efficient biological control method for the giant borer using strains identified as the B. thuringiensis species.

RevDate: 2021-05-31

Jang MJ, Kim SY, Ricke SC, et al (2021)

Microbial ecology of alfalfa, radish, and rapeseed sprouts based on culture methods and 16S rRNA microbiome sequencing.

Food research international (Ottawa, Ont.), 144:110316.

Sprouts harbor high populations of bacteria and cause numerous foodborne disease outbreaks, yet little is known about their microbial composition. The present study aimed to define the microbiological ecology of sprouts using 16S rRNA microbiome sequencing and culture-dependent methods. Different types (radish, alfalfa, and rapeseed), brands (A, B, and C), and distribution routes (online and offline) of sprouts (n = 70) were considered for microbiome analysis, as well as quantitative (aerobic plate count and coliforms) and qualitative analyses (Escherichia coli O157:H7, Listeria monocytogenes, and Salmonella Typhimurium). The aerobic plate count ranged from 7 to 8 CFU/g, and the coliforms ranged from 6 to 7 log CFU/g. Microbiome analysis revealed that Proteobacteria was the dominant phylum, accounting for 79.0% in alfalfa sprouts, 68.5% in rapeseed sprouts, and 61.9% in radish sprouts. Enterobacteriaceae was the dominant family in alfalfa sprouts (33.9%) and rapeseed sprouts (14.6%), while Moraxellaceae (11.9%) were prevalent on radish sprouts. The majority of the dominant genera were common in the environment, such as soil or water. Alfalfa sprouts yielded the lowest aerobic plate count but the highest relative abundance of Enterobacteriaceae compared to the other sprouts. These results could explain why alfalfa sprouts are a leading cause of sprout-related foodborne disease outbreaks. Alpha-diversity results (Chao1 and Shannon indices) suggested that species richness was greater on radish sprouts than the other sprout types. Beta-diversity results showed samples were clustered by types, indicating dissimilarity in microbial communities. However, the distribution route had a limited influence on microbial composition. The present study provides a comparative examination of the microbial profiles of sprouts. Microbiome analyses contribute to an in-depth understanding of the microbial ecology of sprouts, leading to potential control measures for ensuring food safety.

RevDate: 2021-05-30

Fernández LD, Seppey CVW, Singer D, et al (2021)

Niche Conservatism Drives the Elevational Diversity Gradient in Major Groups of Free-Living Soil Unicellular Eukaryotes.

Microbial ecology [Epub ahead of print].

Ancestral adaptations to tropical-like climates drive most multicellular biogeography and macroecology. Observational studies suggest that this niche conservatism could also be shaping unicellular biogeography and macroecology, although evidence is limited to Acidobacteria and testate amoebae. We tracked the phylogenetic signal of this niche conservatism in far related and functionally contrasted groups of common soil protists (Bacillariophyta, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida) along a humid but increasingly cold elevational gradient in Switzerland. Protist diversity decreased, and the size of the geographic ranges of taxa increased with elevation and associated decreasing temperature (climate), which is consistent with a macroecological pattern known as the Rapoport effect. Bacillariophyta exhibited phylogenetically overdispersed communities assembled by competitive exclusion of closely related taxa with shared (conserved) niches. By contrast, Cercomonadida, Ciliophora, Euglyphida and Kinetoplastida exhibited phylogenetically clustered communities assembled by habitat filtering, revealing the coexistence of closely related taxa with shared (conserved) adaptations to cope with the humid but temperate to cold climate of the study site. Phylobetadiversity revealed that soil protists exhibit a strong phylogenetic turnover among elevational sites, suggesting that most taxa have evolutionary constraints that prevent them from colonizing the colder and higher sites of the elevation gradient. Our results suggest that evolutionary constraints determine how soil protists colonize climates departing from warm and humid conditions. We posit that these evolutionary constraints are linked to an ancestral adaptation to tropical-like climates, which limits their survival in exceedingly cold sites. This niche conservatism possibly drives their biogeography and macroecology along latitudinal and altitudinal climatic gradients.

RevDate: 2021-06-02

Chandler L, Harford AJ, Hose GC, et al (2021)

Saline mine-water alters the structure and function of prokaryote communities in shallow groundwater below a tropical stream.

Environmental pollution (Barking, Essex : 1987), 284:117318 pii:S0269-7491(21)00900-3 [Epub ahead of print].

Bacteria and archaea (prokaryotes) are vital components for maintaining healthy function of groundwater ecosystems. The prokaryotic community composition and associated putative functional processes were examined in a shallow sandy aquifer in a wet-dry tropical environment. The aquifer had a contaminated gradient of saline mine-water, which primarily consisted of elevated magnesium (Mg2+) and sulfate (SO42-), although other major ions and trace metals were also present. Groundwaters were sampled from piezometers, approximately 2 m in depth, located in the creek channel upstream and downstream of the mine-water influence. Sampling occurred during the dry-season when only subsurface water flow was present. Next generation sequencing was used to analyse the prokaryote assemblages using 16S rDNA and metabolic functions were predicted with FAPROTAX. Significant changes in community composition and functional processes were observed with exposure to mine-waters. Communities in the exposed sites had significantly lower relative abundance of methanotrophs such as Methylococcaceae and methanogens (Methanobacteriaceae), but higher abundance in Nitrososphaeraceae, associated with nitrification, indicating potentially important changes in the biogeochemistry of the exposed sites. The changes were most strongly correlated with concentrations of SO42-, Mg2+ and Na+. This knowledge allows an assessment of the risk of mine-water contamination to groundwater ecosystem function and aids mine-water management.

RevDate: 2021-06-02

Lim JH, Lee CW, Bong CW, et al (2021)

The impact of eutrophication towards selected bacterial process rates in tropical coastal waters.

Marine pollution bulletin, 169:112524 pii:S0025-326X(21)00558-0 [Epub ahead of print].

The dissolved organic nutrient conditions and bacterial process rates at two tropical coastal sites in Peninsular Malaysia (Port Klang and Port Dickson) were initially studied in 2004-2005 period and later revisited in 2010-2011. We observed that dissolved organic nitrogen (DON) increased about two- and ten-fold at Port Klang and Port Dickson, respectively and resulted in a significant change in DOC:DON ratio (t ≥ 2.077, p < 0.05). Among the bacterial processes measured, bacterial respiration (BR) was lower in the 2010-2011 period at both stations (t ≥ 3.390, p < 0.01). BR also correlated to the DOC:DON ratio (R2 ≥ 0.259, p < 0.01). The increase in substrate quality enabled the bacteria to respire less in the dissolved organic matter degradation. As a result, the average bacterial growth efficiency increased slightly in the 2010-2011 period.

RevDate: 2021-06-02

Leung MHY, Tong X, Bøifot KO, et al (2021)

Characterization of the public transit air microbiome and resistome reveals geographical specificity.

Microbiome, 9(1):112.

BACKGROUND: The public transit is a built environment with high occupant density across the globe, and identifying factors shaping public transit air microbiomes will help design strategies to minimize the transmission of pathogens. However, the majority of microbiome works dedicated to the public transit air are limited to amplicon sequencing, and our knowledge regarding the functional potentials and the repertoire of resistance genes (i.e. resistome) is limited. Furthermore, current air microbiome investigations on public transit systems are focused on single cities, and a multi-city assessment of the public transit air microbiome will allow a greater understanding of whether and how broad environmental, building, and anthropogenic factors shape the public transit air microbiome in an international scale. Therefore, in this study, the public transit air microbiomes and resistomes of six cities across three continents (Denver, Hong Kong, London, New York City, Oslo, Stockholm) were characterized.

RESULTS: City was the sole factor associated with public transit air microbiome differences, with diverse taxa identified as drivers for geography-associated functional potentials, concomitant with geographical differences in species- and strain-level inferred growth profiles. Related bacterial strains differed among cities in genes encoding resistance, transposase, and other functions. Sourcetracking estimated that human skin, soil, and wastewater were major presumptive resistome sources of public transit air, and adjacent public transit surfaces may also be considered presumptive sources. Large proportions of detected resistance genes were co-located with mobile genetic elements including plasmids. Biosynthetic gene clusters and city-unique coding sequences were found in the metagenome-assembled genomes.

CONCLUSIONS: Overall, geographical specificity transcends multiple aspects of the public transit air microbiome, and future efforts on a global scale are warranted to increase our understanding of factors shaping the microbiome of this unique built environment.

RevDate: 2021-05-26

Petje LM, Jensen SA, Szikora S, et al (2021)

Functional iron-deficiency in women with allergy rhinitis is associated with symptoms after nasal provocation and lack of iron-sequestering microbes.

RevDate: 2021-05-25

Ao L, Zhao M, Li X, et al (2021)

Different Urban Forest Tree Species Affect the Assembly of the Soil Bacterial and Fungal Community.

Microbial ecology [Epub ahead of print].

The selection of tree species used for the afforestation of urban forests is very important for maintaining the urban ecosystem, while soil microbe is one of the driving factors of material cycling in the urban forest ecosystem and for health of forests. In this study, the characteristics of surface soil bacterial and fungal community structure in four urban forests (primarily composed of Fraxinus mandshurica (Fm), Quercus mongolica (Qm), Pinus sylvestris var. mongolica (Ps), and Pinus tabulaeformis var. Mukdensis (Pt) as the main dominant tree species, respectively) were investigated by high-throughput sequencing. Our results showed that the alpha diversity of the soil microbial community in the Fm urban forest was the highest, while the lowest was in the Ps urban forest. In the bacterial community, Proteobacteria was the most predominant phylum in soils from Fm, Ps, and Pt urban forests. The most relatively abundant phylum of the Qm urban forest soil was Acidobacteria. The relative abundances of the bacterial communities at the genus level in the soil of four urban forests were significantly different. The soil bacterial communities in Ps and Pt urban forests were more similar, and Qm and Fm were also more similar. In the fungal community, Basidiomycota was the most predominant phylum in soils from Qm, Ps, and Pt urban forests. The phylum with the greatest relative abundance in the Fm urban forest soil was Ascomycota. There were differences in the fungal community between Qm, Fm, Ps, and Pt urban forests. Soil microbial community composition was affected by environmental factors: soil bacterial and fungal community compositions were significantly related to soil electrical conductivity (EC), alkali hydrolysable nitrogen (AHN), total nitrogen (TN), and total phosphorus (TP). In conclusion, the soil microbial community structure was related to both forest's tree species and soil properties.

RevDate: 2021-05-25

Yang Y (2021)

Emerging Patterns of Microbial Functional Traits.

Trends in microbiology pii:S0966-842X(21)00112-8 [Epub ahead of print].

Functional traits are measurable characteristics that affect an organism's fitness under certain environmental conditions. The use of functional traits in microbial ecology holds great promise for improving our ability to develop biogeochemical models and predict ecosystem responses to global changes. Notably, functional traits could be decoupled from taxonomic relatedness, owing to horizontal gene transfer among microorganisms and adaptive evolution. In recent years, our knowledge about microbial functional traits has been substantially enhanced, thereby revealing the multitude of ecological processes in driving community assembly and dynamics. Here, I summarize the emerging patterns of how microbial functional traits respond to changing environments, which considerably differ from better-studied microbial taxonomy. I use niche and neutral theories to explain microbial functional traits. Finally, I highlight future challenges to analyze, elucidate, and utilize functional traits in microbial ecology.

RevDate: 2021-06-02

Hildebrandt L, Zimmermann T, Primpke S, et al (2021)

Comparison and uncertainty evaluation of two centrifugal separators for microplastic sampling.

Journal of hazardous materials, 414:125482.

For commonly applied microplastic sampling approaches based on filtration, high throughput and no size-discrimination are conflicting goals. Therefore, we propose two efficient centrifugal separators for small microplastic sampling, namely the utilization of a hydrocyclone as well as a continuous flow centrifuge. Thorough method optimization was followed by application in an extensive sampling study to investigate the separators' retention behavior for particulate plastics from estuarine waters. Microplastic concentrations ranged from 193 to 2072 particles m-3. The most dominant identified polymer types were polypropylene, acrylates, polyvinyl chloride and polyethylene. More than 95% of particles were < 100 µm. For the first time in microplastic research, an expanded uncertainty was calculated according to the "Guide to the expression of Uncertainty in Measurement" (JCGM 100:2008). Bottom-up uncertainty evaluation revealed the different sampling methods (~ 44%), sample replicates (~ 26%) and the different detection techniques (~ 16%) as the major sources of uncertainty. Depending on the number of particles detected in the samples, the relative expanded uncertainty (Urel (k = 2)) ranged from 24% up to > 200% underpinning tremendous importance of sound uncertainty evaluation. Our results indicate that scientist should rethink many "observed patterns" in the literature due to being insignificant and herewith not real.

RevDate: 2021-05-28
CmpDate: 2021-05-28

Glodowska M, Schneider M, Eiche E, et al (2021)

Fermentation, methanotrophy and methanogenesis influence sedimentary Fe and As dynamics in As-affected aquifers in Vietnam.

The Science of the total environment, 779:146501.

High arsenic (As) concentrations in groundwater are a worldwide problem threatening the health of millions of people. Microbial processes are central in the (trans)formation of the As-bearing ferric and ferrous minerals, and thus regulate dissolved As levels in many aquifers. Mineralogy, microbiology and dissolved As levels can vary sharply within aquifers, making high-resolution measurements particularly valuable in understanding the linkages between them. We conducted a high spatial resolution geomicrobiological study in combination with analysis of sediment chemistry and mineralogy in an alluvial aquifer system affected by geogenic As in the Red River delta in Vietnam. Microbial community analysis revealed a dominance of fermenters, methanogens and methanotrophs whereas sediment mineralogy along a 46 m deep core showed a diversity of Fe minerals including poorly crystalline Fe (II/III) and Fe(III) (oxyhydr)oxides such as goethite, hematite, and magnetite, but also the presence of Fe(II)-bearing carbonates and sulfides which likely formed as a result of microbially driven organic carbon (OC) degradation. A potential important role of methane (CH4) as electron donor for reductive Fe mineral (trans)formation was supported by the high abundance of Candidatus Methanoperedens, a known Fe(III)-reducing methanotroph. Overall, these results imply that OC turnover including fermentation, methanogenesis and CH4 oxidation are important mechanisms leading to Fe mineral (trans)formation, dissolution and precipitation, and thus indirectly affecting As mobility by changing the Fe-mineral inventory.

RevDate: 2021-05-28

Zhang Y, Chen M, Zhao YY, et al (2021)

Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern.

The Science of the total environment, 788:147794 pii:S0048-9697(21)02865-5 [Epub ahead of print].

The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.

RevDate: 2021-05-26

Li T, Wu S, Yang W, et al (2021)

How Mycorrhizal Associations Influence Orchid Distribution and Population Dynamics.

Frontiers in plant science, 12:647114.

Orchid distribution and population dynamics are influenced by a variety of ecological factors and the formation of holobionts, which play key roles in colonization and ecological community construction. Seed germination, seedling establishment, reproduction, and survival of orchid species are strongly dependent on orchid mycorrhizal fungi (OMF), with mycorrhizal cheating increasingly observed in photosynthetic orchids. Therefore, changes in the composition and abundance of OMF can have profound effects on orchid distribution and fitness. Network analysis is an important tool for the study of interactions between plants, microbes, and the environment, because of the insights that it can provide into the interactions and coexistence patterns among species. Here, we provide a comprehensive overview, systematically describing the current research status of the effects of OMF on orchid distribution and dynamics, phylogenetic signals in orchid-OMF interactions, and OMF networks. We argue that orchid-OMF associations exhibit complementary and specific effects that are highly adapted to their environment. Such specificity of associations may affect the niche breadth of orchid species and act as a stabilizing force in plant-microbe coevolution. We postulate that network analysis is required to elucidate the functions of fungal partners beyond their effects on germination and growth. Such studies may lend insight into the microbial ecology of orchids and provide a scientific basis for the protection of orchids under natural conditions in an efficient and cost-effective manner.

RevDate: 2021-05-26

Suominen S, van Vliet DM, Sánchez-Andrea I, et al (2021)

Organic Matter Type Defines the Composition of Active Microbial Communities Originating From Anoxic Baltic Sea Sediments.

Frontiers in microbiology, 12:628301.

Carbon cycling in anoxic marine sediments is dependent on uncultured microbial communities. Niches of heterotrophic microorganisms are defined by organic matter (OM) type and the different phases in OM degradation. We investigated how OM type defines microbial communities originating from organic-rich, anoxic sediments from the Baltic Sea. We compared changes in the sediment microbial community, after incubation with different stable isotope labeled OM types [i.e., particulate algal organic matter (PAOM), protein, and acetate], by using DNA stable isotope probing (DNA-SIP). Incorporation of 13C and/or 15N label was predominantly detected in members of the phyla Planctomycetes and Chloroflexi, which also formed the majority (>50%) of the original sediment community. While these phylum-level lineages incorporated label from all OM types, phylogenetic analyses revealed a niche separation at the order level. Members of the MSBL9 (Planctomycetes), the Anaerolineales (Chloroflexi), and the class Bathyarchaeota, were identified as initial degraders of carbohydrate-rich OM, while other uncultured orders, like the CCM11a and Phycisphaerales (Planctomycetes), Dehalococcoidia, and JG30-KF-CM66 (Chloroflexi), incorporated label also from protein and acetate. Our study highlights the importance of initial fermentation of complex carbon pools in shaping anoxic sediment microbial communities and reveals niche specialization at the order level for the most important initial degraders in anoxic sediments.

RevDate: 2021-05-26

You Y, Aho K, Lohse KA, et al (2021)

Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem.

Frontiers in microbiology, 12:569791.

Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.

RevDate: 2021-05-23

Kaur M, Kumari A, R Singh (2021)

The Indigenous Volatile Inhibitor 2-Methyl-2-butene Impacts Biofilm Formation and Interspecies Interaction of the Pathogenic Mucorale Rhizopus arrhizus.

Microbial ecology [Epub ahead of print].

2-Methyl-2-butene has recently been reported to be a quorum-based volatile self-inhibitor of spore germination and growth in pathogenic Mucorale Rhizopus arrhizus. The present study aimed to elucidate if this compound can influence R. arrhizus biofilm formation and interspecies interaction. The compound was found to significantly decrease R. arrhizus biofilm formation (p < 0.001), with nearly 25% and 50% lesser biomass in the biofilms cultured with exposure to 4 and 32 µg/ml of 2-methyl-2-butene, respectively. The growth of pre-formed biofilms was also impacted, albeit to a lesser extent. Additionally, 2-methyl-2-butene was found to self-limit R. arrhizus growth during interspecies interaction with Staphylococcus aureus and was detected at a substantially greater concentration in the headspace of co-cultures (2338.75 µg/ml) compared with monocultures (69.52 µg/ml). Some of the C5 derivatives of this compound (3-methyl-1-butanol, 2-methyl-2-butanol, and 3-methyl-1-butyne) were also observed to partially mimic its action, such as inhibition of spore germination, but did not impact R. arrhizus biofilm formation. Finally, the treated R. arrhizus displayed changes in fungal morphology suggestive of cytoskeletal alterations, such as filopodia formation, blebs, increased longitudinal folds and/or corrugations, and finger-like and sheet-like surface protrusions, depending upon the concentration of the compound(s) and the planktonic or biofilm growth mode.

RevDate: 2021-05-22

Wright ES, Gupta R, KH Vetsigian (2021)

Multi-stable bacterial communities exhibit extreme sensitivity to initial conditions.

FEMS microbiology ecology pii:6280976 [Epub ahead of print].

Microbial communities can have dramatically different compositions even among similar environments. This might be due to the existence of multiple alternative stable states, yet there exist little experimental evidence supporting this possibility. Here we gathered a large collection of absolute population abundances capturing population dynamics in one to four strain communities of soil bacteria with a complex life cycle in a feast-or-famine environment. This dataset led to several observations: (i) some pairwise competitions resulted in bistability with a separatrix near a 1:1 initial ratio across a range of population densities; (ii) bistability propagated to multi-stability in multi-species communities; and (iii) replicate microbial communities reached different stable states when starting close to initial conditions separating basins of attraction, indicating finite-sized regions where the dynamics are unpredictable. The generalized Lotka-Volterra equations qualitatively captured most competition outcomes but were unable to quantitatively recapitulate the observed dynamics. This was partly due to complex and diverse growth dynamics in monocultures that ranged from Allee effects to non-monotonic behaviors. Overall, our results highlight that multi-stability might be generic in multi-species communities and, combined with ecological noise, can lead to unpredictable community assembly, even in simple environments.

RevDate: 2021-05-22

Huang YM, Straub D, Blackwell N, et al (2021)

Meta-omics reveal Gallionellaceae and Rhodanobacter as interdependent key players for Fe(II) oxidation and nitrate reduction in the autotrophic enrichment culture KS.

Applied and environmental microbiology pii:AEM.00496-21 [Epub ahead of print].

Nitrate reduction coupled to iron(II) oxidation (NRFO) has been recognized as an environmentally important microbial process in many freshwater ecosystems. However, well-characterized examples of autotrophic nitrate-reducing iron(II)-oxidizing bacteria are rare and their pathway of electron transfer as well as their interaction with flanking community members remain largely unknown. Here, we applied meta-omics (i.e., metagenomics, metatranscriptomics and metaproteomics) to the nitrate-reducing iron(II)-oxidizing enrichment culture KS, growing under autotrophic compared to heterotrophic conditions, and originating from a freshwater sediment. We constructed four metagenome-assembled genomes with an estimated completeness of ≥95%, including the key players of NRFO in culture KS, identified as Gallionellaceae sp. and Rhodanobacter sp. The presence of Gallionellaceae sp. and Rhodanobacter sp. transcripts and proteins likely involved in iron(II) oxidation (e.g., mtoAB, cyc2, mofA), denitrification (e.g., napGHI) and oxidative phosphorylation (e.g., respiratory chain complexes I-V), along with Gallionellaceae sp. transcripts and proteins for carbon fixation (e.g., rbcL) were detected. Overall, our results indicate that in culture KS, the Gallionellaceae sp. and Rhodanobacter sp. are interdependent: while Gallionellaceae sp. fixes CO2 and provides organic compounds for Rhodanobacter sp., Rhodanobacter sp. likely detoxifies NO through NO reduction and completes denitrification, which cannot be done by Gallionellaceae sp. alone. Additionally, the transcripts and partial proteins of cbb3 - and aa3 - type cytochrome c suggest the possibility for a microaerophilic lifestyle of the Gallionellaceae sp., yet culture KS grows under anoxic conditions. Our findings demonstrate that autotrophic NRFO is performed through cooperation among denitrifying and iron(II)-oxidizing bacteria, which might resemble microbial interactions in freshwater environments.ImportanceNitrate-reducing iron(II)-oxidizing bacteria are widespread in the environment, contribute to nitrate removal, and influence the fate of the greenhouse gases nitrous oxide and carbon dioxide. The autotrophic growth of nitrate-reducing iron(II)-oxidizing bacteria is rarely investigated and not fully understood. The most prominent model system for this type of studies is the enrichment culture KS. To gain insights into the metabolism of nitrate reduction coupled to iron(II) oxidation in the absence of organic carbon and oxygen, we performed metagenomic, metatranscriptomic and metaproteomic analyses of culture KS, and identified Gallionellaceae sp. and Rhodanobacter sp. as interdependent key iron(II)-oxidizers in culture KS. Our work demonstrates that autotrophic nitrate reduction coupled to iron(II) oxidation is not performed by an individual strain but a cooperation of at least two members of the bacterial community in culture KS. These findings serve as foundation for our understanding of nitrate-reducing iron(II)-oxidizing bacteria in the environment.

RevDate: 2021-05-24

Silva DP, Villela HDM, Santos HF, et al (2021)

Multi-domain probiotic consortium as an alternative to chemical remediation of oil spills at coral reefs and adjacent sites.

Microbiome, 9(1):118.

BACKGROUND: Beginning in the last century, coral reefs have suffered the consequences of anthropogenic activities, including oil contamination. Chemical remediation methods, such as dispersants, can cause substantial harm to corals and reduce their resilience to stressors. To evaluate the impacts of oil contamination and find potential alternative solutions to chemical dispersants, we conducted a mesocosm experiment with the fire coral Millepora alcicornis, which is sensitive to environmental changes. We exposed M. alcicornis to a realistic oil-spill scenario in which we applied an innovative multi-domain bioremediator consortium (bacteria, filamentous fungi, and yeast) and a chemical dispersant (Corexit® 9500, one of the most widely used dispersants), to assess the effects on host health and host-associated microbial communities.

RESULTS: The selected multi-domain microbial consortium helped to mitigate the impacts of the oil, substantially degrading the polycyclic aromatic and n-alkane fractions and maintaining the physiological integrity of the corals. Exposure to Corexit 9500 negatively impacted the host physiology and altered the coral-associated microbial community. After exposure, the abundances of certain bacterial genera such as Rugeria and Roseovarius increased, as previously reported in stressed or diseased corals. We also identified several bioindicators of Corexit 9500 in the microbiome. The impact of Corexit 9500 on the coral health and microbial community was far greater than oil alone, killing corals after only 4 days of exposure in the flow-through system. In the treatments with Corexit 9500, the action of the bioremediator consortium could not be observed directly because of the extreme toxicity of the dispersant to M. alcicornis and its associated microbiome.

CONCLUSIONS: Our results emphasize the importance of investigating the host-associated microbiome in order to detect and mitigate the effects of oil contamination on corals and the potential role of microbial mitigation and bioindicators as conservation tools. Chemical dispersants were far more damaging to corals and their associated microbiome than oil, and should not be used close to coral reefs. This study can aid in decision-making to minimize the negative effects of oil and dispersants on coral reefs. Video abstract.

RevDate: 2021-05-21

Kim JH, Kim K, W Kim (2021)

Gut microbiota restoration through fecal microbiota transplantation: a new atopic dermatitis therapy.

Experimental & molecular medicine [Epub ahead of print].

The pathogenesis of atopic dermatitis (AD) involves complex factors, including gut microbiota and immune modulation, which remain poorly understood. The aim of this study was to restore gut microbiota via fecal microbiota transplantation (FMT) to ameliorate AD in mice. FMT was performed using stool from donor mice. The gut microbiota was characterized via 16S rRNA sequencing and analyzed using Quantitative Insights into Microbial Ecology 2 with the DADA2 plugin. Gut metabolite levels were determined by measuring fecal short-chain fatty acid (SCFA) contents. AD-induced allergic responses were evaluated by analyzing blood parameters (IgE levels and eosinophil percentage, eosinophil count, basophil percentage, and monocyte percentage), the levels of Th1 and Th2 cytokines, dermatitis score, and the number of mast cells in the ileum and skin tissues. Calprotectin level was measured to assess gut inflammation after FMT. FMT resulted in the restoration of gut microbiota to the donor state and increases in the levels of SCFAs as gut metabolites. In addition, FMT restored the Th1/Th2 balance, modulated Tregs through gut microbiota, and reduced IgE levels and the numbers of mast cells, eosinophils, and basophils. FMT is associated with restoration of gut microbiota and immunologic balance (Th1/Th2) along with suppression of AD-induced allergic responses and is thus a potential new therapy for AD.

RevDate: 2021-05-24
CmpDate: 2021-05-24

LaMartina EL, Mohaimani AA, RJ Newton (2021)

Urban wastewater bacterial communities assemble into seasonal steady states.

Microbiome, 9(1):116.

BACKGROUND: Microorganisms in urban sanitary sewers exhibit community properties that suggest sewers are a novel ecosystem. Sewer microorganisms present both an opportunity as a control point for wastewater treatment and a risk to human health. If treatment processes are to be improved and health risks quantified, then it is necessary to understand microbial distributions and dynamics within this community. Here, we use 16S rRNA gene sequencing to characterize raw influent wastewater bacterial communities in a 5-year time series from two wastewater treatment plants in Milwaukee, WI; influent wastewater from 77 treatment plants across the USA; and wastewater in 12 Milwaukee residential sewers.

RESULTS: In Milwaukee, we find that in transit from residences to treatment plants, the human bacterial component of wastewater decreases in proportion and exhibits stochastic temporal variation. In contrast, the resident sewer community increases in abundance during transit and cycles seasonally according to changes in wastewater temperature. The result is a bacterial community that assembles into two distinct community states each year according to the extremes in wastewater temperature. Wastewater bacterial communities from other northern US cities follow temporal trends that mirror those in Milwaukee, but southern US cities have distinct community compositions and differ in their seasonal patterns.

CONCLUSIONS: Our findings provide evidence that environmental conditions associated with seasonal change and climatic differences related to geography predictably structure the bacterial communities residing in below-ground sewer pipes. Video abstract.

RevDate: 2021-05-24

Dwużnik-Szarek D, Mierzejewska EJ, Rodo A, et al (2021)

Monitoring the expansion of Dermacentor reticulatus and occurrence of canine babesiosis in Poland in 2016-2018.

Parasites & vectors, 14(1):267.

BACKGROUND: The significance of tick-borne diseases has increased considerably in recent years. Because of the unique distribution of the tick species Dermacentor reticulatus in Poland, comprising two expanding populations, Eastern and Western that are separated by a Dermacentor-free zone, it is important to conduct studies on the process of tick expansion and emergence of canine babesiosis. The main aim of the current study was to monitor the expansion of D. reticulatus populations from spring 2016 to autumn 2018 to determine (1) the actual geographical range of this tick species, and (2) and the seasonal/annual shift in range limits and changes in distance between Western and Eastern populations of ticks (the size of the non-endemic area).

METHODS: Ticks were collected in spring/autumn during a 3-year study. From each season and year at least three pairs of sites from the Western and Eastern populations were selected. Then the mean distance between paired sites was calculated for each season and year. We collected and analyzed data from veterinary clinics on the number of canine babesiosis cases treated in the clinic during a whole year (2018).

RESULTS: Accordingly, further expansion of the two D. reticulatus populations was recorded, mainly along river basins. Marked colonization of the gap zone was observed, with a mean annual shift in the range of 2.5-10 km and a steadily decreasing distance between the two tick populations. The occurrence of babesiosis in different regions revealed low numbers of cases in Western Poland (19 cases/year) and the gap area (only 7 cases/year) and high incidence (up to 250 cases/1000 dogs) and fatality (total 3.65%) in Central and Eastern Poland. Strong associations were found geographically between tick and babesiosis occurrence and temporally in the seasonal patterns of occurrence of ticks and outbreaks of babesiosis.

CONCLUSIONS: We documented the shift in range limits and continued process of colonization of the gap zone accompanied by the emergence of canine babesiosis in the Eastern expansion zone. Updated maps of the distribution of ticks and occurrence of babesiosis in different regions of Poland have allowed us to predict of the emergence of pathogens vectored by D. reticulatus. Incidence (per 1000 dogs) of canine babesiosis in veterinary clinics by current range of D. reticulatus.

RevDate: 2021-05-20

Tibatá VM, Sanchez A, Palmer-Young E, et al (2021)

Africanized honey bees in Colombia exhibit high prevalence but low level of infestation of Varroa mites and low prevalence of pathogenic viruses.

PloS one, 16(5):e0244906 pii:PONE-D-20-39577.

The global spread of the ectoparasitic mite Varroa destructor has promoted the spread and virulence of highly infectious honey bee viruses. This phenomenon is considered the leading cause for the increased number of colony losses experienced by the mite-susceptible European honey bee populations in the Northern hemisphere. Most of the honey bee populations in Central and South America are Africanized honey bees (AHBs), which are considered more resistant to Varroa compared to European honey bees. However, the relationship between Varroa levels and the spread of honey bee viruses in AHBs remains unknown. In this study, we determined Varroa prevalence and infestation levels as well as the prevalence of seven major honey bee viruses in AHBs from three regions of Colombia. We found that although Varroa exhibited high prevalence (92%), its infestation levels were low (4.5%) considering that these populations never received acaricide treatments. We also detected four viruses in the three regions analyzed, but all colonies were asymptomatic, and virus prevalence was considerably lower than those found in other countries with higher rates of mite-associated colony loss (DWV 19.88%, BQCV 17.39%, SBV 23.4%, ABPV 10.56%). Our findings indicate that AHBs possess a natural resistance to Varroa that does not prevent the spread of this parasite among their population, but restrains mite population growth and suppresses the prevalence and pathogenicity of mite-associated viruses.

RevDate: 2021-05-20

Romero-Olivares AL, Morrison EW, Pringle A, et al (2021)

Correction to: Linking Genes to Traits in Fungi.

RevDate: 2021-05-19

Antunes VDC, Freitag D, RV Serrato (2021)

Differential exopolysaccharide production and composition by Herbaspirillum strains from diverse ecological environments.

Archives of microbiology [Epub ahead of print].

Bacteria belonging to the genus Herbaspirillum are found in many different ecological niches. Some species are typically endophytic, while others were reported as free-living organisms that occupy various environments. Also, opportunistic herbaspirilli have been found infecting humans affected by several diseases. We have analyzed the production of exopolysaccharides (EPS) by Herbaspirillum strains isolated from different sources and with distinct ecological characteristics. The monosaccharide composition was determined for the EPS obtained for selected strains including free-living, plant-associated and clinical isolates, and the relationship with the ecological niches occupied by Herbaspirillum spp. is proposed.

RevDate: 2021-05-19

Ketchum RN, Smith EG, Vaughan GO, et al (2021)

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients.

Molecular ecology [Epub ahead of print].

Shifts in microbial communities represent a rapid response mechanism for host organisms to respond to changes in environmental conditions. Therefore, they are likely to be important in assisting the acclimatization of hosts to seasonal temperature changes as well as to variation in temperatures across a species' range. The Persian/Arabian Gulf is the world's warmest sea, with large seasonal fluctuations in temperature (20 °C - 37 °C) and is connected to the Gulf of Oman which experiences more typical oceanic conditions (<32 °C in the summer). This system is an informative model for understanding how symbiotic microbial assemblages respond to thermal variation across temporal and spatial scales. Here, we elucidate the role of temperature on the microbial gut community of the sea urchin Echinometra sp. EZ and identify microbial taxa that are tightly correlated with the thermal environment. We generated two independent datasets with a high degree of geographic and temporal resolution. The results show that microbial communities vary across thermally variable habitats, display temporal shifts that correlate with temperature, and can become more disperse as temperatures rise. The relative abundances of several of the same ASVs significantly correlate with temperature in both independent datasets despite the >300 km distance between the furthest sites and the extreme seasonal variations. Notably, over 50% of the ASVs identified from the two datasets belonged to the family Vibrionaceae. Together, our results identify temperature as a robust predictor of community-level variation and putatively highlight specific microbial taxa involved in the response to thermal environment.

RevDate: 2021-05-19

Hwang Y, Rahlff J, Schulze-Makuch D, et al (2021)

Diverse Viruses Carrying Genes for Microbial Extremotolerance in the Atacama Desert Hyperarid Soil.

mSystems, 6(3):.

Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e., spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.IMPORTANCE Deserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments, supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results demonstrate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.

RevDate: 2021-05-18

Kim J, Heo YM, Yun J, et al (2021)

Changes in Archaeal Community and Activity by the Invasion of Spartina anglica Along Soil Depth Profiles of a Coastal Wetland.

Microbial ecology [Epub ahead of print].

Invasion of Spartina spp. in tidal salt marshes may affect the function and characteristics of the ecosystem. Previous studies reported that the invasion alters biogeochemical and microbial processes in marsh ecosystems, yet our knowledge of changing archaeal community due to the invasion is still limited, whereas archaeal communities play a pivotal role in biogeochemical cycles within highly reduced marsh soils. In this study, we aimed to illustrate the influences of the Spartina anglica invasion on soil archaeal community and the depth profile of the influences. The relative abundance of archaeal phyla demonstrated that the invasion substantially shifted the characteristics of tidal salt marsh from marine to terrestrial soil only in surface layer, while the influences indirectly propagated to the deeper soil layer. In particular, two archaeal phyla, Asgardaeota and Diapherotrites, were strongly influenced by the invasion, indicating a shift from marine to terrestrial archaeal communities. The shifts in soil characteristics spread to the deeper soil layer that results in indirect propagation of the influences of the invasion down to the deeper soil, which was underestimated in previous studies. The changes in the concentration of dissolved organic carbon and salinity were the substantial regulating factors for that. Therefore, changes in biogeochemical and microbial characteristics in the deep soil layer, which is below the root zone of the invasive plant, should be accounted for a more accurate illustration of the consequences of the invasion.

RevDate: 2021-05-16

Ng CK, Putra SL, Kennerley J, et al (2021)

Genetic engineering biofilms in situ using ultrasound-mediated DNA delivery.

Microbial biotechnology [Epub ahead of print].

The ability to directly modify native and established biofilms has enormous potential in understanding microbial ecology and application of biofilm in 'real-world' systems. However, efficient genetic transformation of established biofilms at any scale remains challenging. In this study, we applied an ultrasound-mediated DNA delivery (UDD) technique to introduce plasmid to established non-competent biofilms in situ. Two different plasmids containing genes coding for superfolder green fluorescent protein (sfGFP) and the flavin synthesis pathway were introduced into established bacterial biofilms in microfluidic flow (transformation efficiency of 3.9 ± 0.3 × 10-7 cells in biofilm) and microbial fuel cells (MFCs), respectively, both employing UDD. Gene expression and functional effects of genetically modified bacterial biofilms were observed, where some cells in UDD-treated Pseudomonas putida UWC1 biofilms expressed sfGFP in flow cells and UDD-treated Shewanella oneidensis MR-1 biofilms generated significantly (P < 0.05) greater (61%) bioelectricity production (21.9 ± 1.2 µA cm-2) in MFC than a wild-type control group (~ 13.6 ± 1.6 µA cm-2). The effects of UDD were amplified in subsequent growth under selection pressure due to antibiotic resistance and metabolism enhancement. UDD-induced gene transfer on biofilms grown in both microbial flow cells and MFC systems was successfully demonstrated, with working volumes of 0.16 cm3 and 300 cm3 , respectively, demonstrating a significant scale-up in operating volume. This is the first study to report on a potentially scalable direct genetic engineering method for established non-competent biofilms, which can be exploited in enhancing their capability towards environmental, industrial and medical applications.

RevDate: 2021-05-16

Battistelli N, Perpetuini G, Piva A, et al (2021)

Cultivable microbial ecology and aromatic profile of "mothers" for Vino cotto wine production.

Food research international (Ottawa, Ont.), 143:110311.

The aim of the present study was to assess the cultivable microbiota of "mothers" of Vino cotto collected from production of different years 1890, 1895, 1920, 1975, 2008. A total of 73 yeasts and 81 bacteria were isolated. Starmerella lactis-condensi, Starmerella bacillaris, Hanseniaspora uvarum, Saccharomyces cerevisiae, Hanseniaspora guillermondi and Metschnikowia pulcherrima were identified. Bacteria isolates belonged to lactic acid bacteria (Lactiplantibacillus plantarum and Pediococcus pentosaceus) and acetic acid bacteria (Gluconobacter oxydans). Remarkable biodiversity was observed for Starm. bacillaris, as well as L. plantarum and G. oxydans. Organic acids and volatile compounds were also determined. Malic and succinic acids were the main ones with values ranging from 8.49 g/L to 11.76 g/L and from 4.15 g/L to 7.73 g/L respectively, while citric acid was present at low concentrations (<0.2 g/L) in all samples. Esters and higher alcohols were the main volatile compounds detected followed by alkanes. This study permits to better understand the microbial communities associated to this product and could be considered a starting point for the definition of tailored starter cultures to improve the quality of Vino cotto preserving its typical traits.

RevDate: 2021-05-15

Hartwick M, Berenson A, Whistler CA, et al (2021)

The Seasonal Microbial Ecology of Plankton and Plankton-Associated Vibrio parahaemolyticus in the Northeast US.

Applied and environmental microbiology pii:AEM.02973-20 [Epub ahead of print].

Microbial ecology studies have proven to be important resources for improving infectious disease response and outbreak prevention. Vibrio parahaemolyticus is an ongoing source of shellfish-borne food illness in the Northeast, United States and there is keen interest in understanding the environmental conditions that coincide with V. parahaemolyticus disease risk to aid harvest management and prevent further illness. Zooplankton and chitinous phytoplankton associate with V. parahaemolyticus dynamics elsewhere, however, this relationship is undetermined for the Great Bay estuary (GBE), an important emerging shellfish growing region in the Northeast, US. A comprehensive evaluation of the microbial ecology of V. parahaemolyticus associated with plankton was conducted in the GBE using three years of plankton community, nutrient concentration, water quality and V. parahaemolyticus concentration in plankton data. The concentrations of V. parahaemolyticus associated with plankton were highly seasonal and the highest concentrations of V. parahaemolyticus cultured from zooplankton occurred approximately one month before the highest concentrations of V. parahaemolyticus from phytoplankton. The two V. parahaemolyticus peaks corresponded with different water quality variables and a few highly seasonal plankton taxa. Importantly, V. parahaemolyticus concentrations and plankton community dynamics were poorly associated with nutrient concentrations and chlorophyll-a, commonly applied proxy variables for assessing ecological health risks, and human health risks from harmful plankton and V. parahaemolyticus elsewhere. Together, these statistical associations (or lack thereof) provide valuable insights to characterize the plankton-V. parahaemolyticus dynamic and inform approaches for understanding the potential contribution of plankton to human health risks from V. parahaemolyticus for the Northeast US.IMPORTANCEThe Vibrio-plankton interaction is a focal relationship in Vibrio disease research; however, little is known about this dynamic in the Northeast, US where V. parahaemolyticus is an established public health issue. We integrated phototactic plankton separation with seasonality analysis to determine the dynamics of the plankton community, water quality and V. parahaemolyticus concentrations. Distinct bimodal peaks in the seasonal timing of V. parahaemolyticus abundance from phyto- vs zooplankton and differing associations with water quality variables and plankton taxa highlight that monitoring and forecasting approaches should consider the source of exposure when designing predictive methods for V. parahaemolyticusHeliotheca tamensis has not been previously reported in the GBE. Its detection during this study provides evidence of the changes occurring in the ecology of regional estuaries and potential mechanisms for changes in V. parahaemolyticus populations. The Vibrio monitoring approaches can be translated to aid other areas facing similar public health challenges.

RevDate: 2021-05-21
CmpDate: 2021-05-19

Qian X, Gunturu S, Guo J, et al (2021)

Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.

Microbiome, 9(1):108.

BACKGROUND: Soil is an important reservoir of antibiotic resistance genes (ARGs), but their potential risk in different ecosystems as well as response to anthropogenic land use change is unknown. We used a metagenomic approach and datasets with well-characterized metadata to investigate ARG types and amounts in soil DNA of three native ecosystems: Alaskan tundra, US Midwestern prairie, and Amazon rainforest, as well as the effect of conversion of the latter two to agriculture and pasture, respectively.

RESULTS: High diversity (242 ARG subtypes) and abundance (0.184-0.242 ARG copies per 16S rRNA gene copy) were observed irrespective of ecosystem, with multidrug resistance and efflux pump the dominant class and mechanism. Ten regulatory genes were identified and they accounted for 13-35% of resistome abundances in soils, among them arlR, cpxR, ompR, vanR, and vanS were dominant and observed in all studied soils. We identified 55 non-regulatory ARGs shared by all 26 soil metagenomes of the three ecosystems, which accounted for more than 81% of non-regulatory resistome abundance. Proteobacteria, Firmicutes, and Actinobacteria were primary ARG hosts, 7 of 10 most abundant ARGs were found in all of them. No significant differences in both ARG diversity and abundance were observed between native prairie soil and adjacent long-term cultivated agriculture soil. We chose 12 clinically important ARGs to evaluate at the sequence level and found them to be distinct from those in human pathogens, and when assembled they were even more dissimilar. Significant correlation was found between bacterial community structure and resistome profile, suggesting that variance in resistome profile was mainly driven by the bacterial community composition.

CONCLUSIONS: Our results identify candidate background ARGs (shared in all 26 soils), classify ARG hosts, quantify resistance classes, and provide quantitative and sequence information suggestive of very low risk but also revealing resistance gene variants that might emerge in the future. Video abstract.

RevDate: 2021-05-28

Zhong X, Yu S, H Xu (2021)

Influence of tidal events on the body-size spectrum of periphytic ciliates for marine bioassessment using artificial substrata.

Marine pollution bulletin, 168:112435 pii:S0025-326X(21)00469-0 [Epub ahead of print].

As an internal functional trait of a community, the body-size spectrum is a highly informative indicator for bioassessment of water/environmental quality in aquatic ecosystems. To determine the influence of tidal events on body-size spectra of protozoan periphytons, a 3-month baseline survey was conducted in Korean coastal waters using the polyurethane foam enveloped slide system (PFES) and conventional slide system (CS). The body-size spectrum of the protozoans showed a clear temporal pattern during the study period using both sampling systems. However, the temporal dynamics showed significantly different trajectories in the body-size spectrum between the two sampling methods during the study period. The bootstrapped average analysis revealed that the patterns of the body-size spectrum were significantly different between the PFES and CS systems, especially in terms of frequency of occurrence. These findings suggest that the tidal events may significantly influence body-size spectrum of periphytic ciliates for bioassessment in marine ecosystems.

RevDate: 2021-06-02

Singh NS, Sharma R, Singh SK, et al (2021)

A comprehensive review of environmental fate and degradation of fipronil and its toxic metabolites.

Environmental research, 199:111316 pii:S0013-9351(21)00610-1 [Epub ahead of print].

The use of pesticides to increase crop production has become one of the inevitable components of modern agriculture. Fipronil, a phenylpyrazoles insecticide, is one of the most widely used, systemic, broad-spectrum insecticides. Owing to its unique mode of action and selective toxicity, it was once regarded as safer alternatives to more toxic and persistent organochlorine insecticides. However, with the increased use, many studies have reported the toxicity of fipronil and its metabolites in various non-target organisms during the last two decades. Currently, it is regarded as one of the most persistent and lipophilic insecticides in the market. In the environment, fipronil can undergo oxidation, reduction, hydrolysis, or photolysis to form fipronil sulfone, fipronil sulfide, fipronil amide, or fipronil desulfinyl respectively. These metabolites except fipronil amide are more or less toxic and persistent than fipronil and have been reported from diverse environmental samples. Recently many studies have focused on the degradation and removal of fipronil residues from the environment. However, a comprehensive review summarizing and combining these recent findings is lacking. In the present review, we evaluate, summarize, and combine important findings from recent degradation studies of fipronil and its metabolites. An attempt has been made to elucidate the possible mechanism and pathways of degradation of fipronil and its toxic metabolites.

RevDate: 2021-05-14

Figueiredo G, Gomes M, Covas C, et al (2021)

The Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study.

Microbial ecology [Epub ahead of print].

Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation. This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.

RevDate: 2021-05-14

Girolamini L, Salaris S, Orsini M, et al (2021)

Draft Genome Sequences of Legionella Presumptive Novel Species Isolated during Environmental Surveillance in Artificial Water Systems.

Microbiology resource announcements, 10(19):.

We present the draft genome sequences of three Legionella strains that were isolated from a hotel water distribution system. Legionella species identification was performed by macrophage infectivity potentiator (mip) and RNA polymerase β subunit (rpoB) gene sequencing. Whole-genome sequencing and average nucleotide identity results supported the hypothesis of new Legionella species isolation.

RevDate: 2021-05-13

Stevens BR, Pepine CJ, Richards EM, et al (2021)

Depressive-hypertension: A proposed human endotype of brain/gut microbiome dysbiosis.

American heart journal pii:S0002-8703(21)00122-8 [Epub ahead of print].

BACKGROUND: Hypertension is frequently linked with depression in adults with cardiovascular disease (CVD), yet the underlying mechanism and successful management remain elusive. We approached this knowledge gap through the lens that humans are eukaryote-prokaryote "meta-organisms", such that CVD dysregulation is a mosaic disorder involving dysbiosis of the gut. We hypothesized that patients diagnosed with hypertension plus depression harbor a unique gut microbial ecology with attending functional genomics engaged with their hosts' gut/brain axis physiology.

METHODS: Stool microbiome DNA was analyzed by whole metagenome shotgun sequencing in 54 subjects parsed into cohorts diagnosed with hypertension (HTN)-only (N=18), depression (DEP)-only (N=7), DEP plus HTN (DEP-HTN)(N=8), or reference subjects with neither HTN nor DEP (N=21). A novel battery of machine-learning multivariate analyses of de-noised data yielded effect sizes and permutational covariance-based dissimilarities that significantly differentiated the cohorts (False Discovery Rate (FDR)-adjusted P ≤ 0.05); data clustering within 95% Confidence Interval (CI)).

RESULTS: Metagenomic significant differences extricated the four cohorts. Data of the cohort exhibiting DEP-HTN were germane to the interplay of central control of blood pressure (BP) concomitant with the neuropathology of depressive disorders. DEP-HTN gut bacterial community ecology was defined by co-occurance of Eubacterium siraeum, Alistipes obesi, Holdemania filiformis and Lacnospiraceeae bacterium 1.1.57FAA with Streptococcus salivariu. The corresponding microbial functional genomics of DEP-HTN engaged pathways degrading GABA and beneficial short chain fatty acids (SCFA), and are associated with enhanced sodium absorption and inflammasome induction.

CONCLUSIONS: These data suggest a new putative endotype of hypertension-"depressive-hypertension" (DEP-HTN)-for which we posit a model that is distinctive from either hypertension alone or depression alone. An "endotype" is a subtype of a heterogeneous pathophysiological mechanism. The DEP-HTN model incorporates a unique signature of microbial taxa and functional genomics with crosstalk that putatively intertwines host pathophysiology involving the gastrointestinal tract with disruptions in central control of BP and mood. The DEP-HTN endotype model engages cardiology with gastroenterology and psychiatry, providing a proof-of-concept foundation to explore future treatments, diagnosis, and prevention of hypertension-coupled mood disorders.

RevDate: 2021-05-13

Flieder M, Buongiorno J, Herbold CW, et al (2021)

Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling.

The ISME journal [Epub ahead of print].

Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.

RevDate: 2021-05-22

De Leόn KB (2021)

mSphere of Influence: Surface Sensing in Biofilm Formation.

mSphere, 6(3):.

Kara B. De Leόn works in the field of microbial ecology, environmental biofilms, and microbial genetics. In this mSphere of Influence article, she reflects on how the paper "Multigenerational memory and adaptive adhesion in early bacterial biofilm communities" by C. K. Lee et al. (C. K. Lee, J. de Anda, A. E. Baker, R. R. Bennett, et al., Proc Natl Acad Sci U S A 115:4471-4476, 2018, https://dx.doi.org/10.1073/pnas.1720071115) made an impact on her by changing the way she thinks about initial cell attachment to a surface in an environment.

RevDate: 2021-05-13

Liébana-García R, Olivares M, Bullich-Vilarrubias C, et al (2021)

The gut microbiota as a versatile immunomodulator in obesity and associated metabolic disorders.

Best practice & research. Clinical endocrinology & metabolism pii:S1521-690X(21)00059-2 [Epub ahead of print].

Obesity has reached epidemic proportions and is associated with chronic-low-grade inflammation and metabolic morbidities. Energy-dense diets and a sedentary lifestyle are determinants of obesity. The gut microbiome is a novel biological factor involved in obesity via interactions with the host and the diet. The gut microbiome act as a synergistic force protecting or aggravating the effects of the diet on the metabolic phenotype. The role of the microbiome in the regulation of intestinal and systemic immunity is one of the mechanisms by which it contributes to the host's response to the diet and to the pathophysiology of diet-induced obesity. Here, we review the mechanisms whereby "obesogenic" diets and the microbiome impact immunity, locally and systemically, focusing on the consequences in the gut-adipose tissue axis. We also review the structural and microbial metabolites that influence immunity and how advances in this field could help design microbiome-informed strategies to tackle obesity-related disorders more effectively.

RevDate: 2021-05-19

Jung CE, Estaki M, Chopyk J, et al (2021)

Impact of Vaginal Estrogen on the Urobiome in Postmenopausal Women With Recurrent Urinary Tract Infection.

Female pelvic medicine & reconstructive surgery pii:01436319-900000000-99232 [Epub ahead of print].

OBJECTIVE: The aim of this study was to describe effects of vaginal estrogen (VE) on the urogenital microbiome in postmenopausal women with recurrent urinary tract infections (rUTIs).

METHODS: This is a secondary analysis of 17 participants enrolled in a randomized controlled trial of VE versus placebo on urinary tract infection recurrence in postmenopausal women with rUTIs. Paired clean-catch urine samples were collected at baseline and after 6 months of VE and sequenced using 16S rRNA gene sequencing. Sequence reads were analyzed using Quantitative Insights Into Microbial Ecology 2. Changes in α diversity, β diversity, and differentially abundant genera were measured between paired baseline and 6-month samples and between those with a urinary tract infection at 6 months (failures) and those without (successes).

RESULTS: Of the 17 women, 11 were successes and 6 were failures after 6 months of VE treatment. There was a significant change in α diversity from baseline to month 6 in samples overall (Kruskal-Wallis χ2 = 3.47, P = 0.037) and in the treatment success group (Yuen T = -2.53, P = 0.035). The increase in relative abundance of Lactobacillus crispatus, Lactobacillus gasseri, and Lactobacillus iners AB-1 was correlated with month 6. A relative bloom of L. crispatus compared with L. gasseri was associated with treatment success (Kruskal-Wallis χ2 = 4.9, P = 0.0014).

CONCLUSIONS: Lactobacillus increases in the urogenital microbiome of postmenopausal women with rUTI after 6 months of VE. However, only the relative increase in L. crispatus specifically may be associated with treatment success.

RevDate: 2021-05-14

Eliades SJ, Brown JC, Colston TJ, et al (2021)

Gut microbial ecology of the Critically Endangered Fijian crested iguana (Brachylophus vitiensis): Effects of captivity status and host reintroduction on endogenous microbiomes.

Ecology and evolution, 11(9):4731-4743.

Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release.

RevDate: 2021-05-12

Sieradzki ET, Morando M, JA Fuhrman (2021)

Metagenomics and Quantitative Stable Isotope Probing Offer Insights into Metabolism of Polycyclic Aromatic Hydrocarbon Degraders in Chronically Polluted Seawater.

mSystems, 6(3):.

Bacterial biodegradation is a significant contributor to remineralization of polycyclic aromatic hydrocarbons (PAHs)-toxic and recalcitrant components of crude oil as well as by-products of partial combustion chronically introduced into seawater via atmospheric deposition. The Deepwater Horizon oil spill demonstrated the speed at which a seed PAH-degrading community maintained by chronic inputs responds to acute pollution. We investigated the diversity and functional potential of a similar seed community in the chronically polluted Port of Los Angeles (POLA), using stable isotope probing with naphthalene, deep-sequenced metagenomes, and carbon incorporation rate measurements at the port and in two sites in the San Pedro Channel. We demonstrate the ability of the community of degraders at the POLA to incorporate carbon from naphthalene, leading to a quick shift in microbial community composition to be dominated by the normally rare Colwellia and Cycloclasticus We show that metagenome-assembled genomes (MAGs) belonged to these naphthalene degraders by matching their 16S-rRNA gene with experimental stable isotope probing data. Surprisingly, we did not find a full PAH degradation pathway in those genomes, even when combining genes from the entire microbial community, leading us to hypothesize that promiscuous dehydrogenases replace canonical naphthalene degradation enzymes in this site. We compared metabolic pathways identified in 29 genomes whose abundance increased in the presence of naphthalene to generate genomic-based recommendations for future optimization of PAH bioremediation at the POLA, e.g., ammonium as opposed to urea, heme or hemoproteins as an iron source, and polar amino acids.IMPORTANCE Oil spills in the marine environment have a devastating effect on marine life and biogeochemical cycles through bioaccumulation of toxic hydrocarbons and oxygen depletion by hydrocarbon-degrading bacteria. Oil-degrading bacteria occur naturally in the ocean, especially where they are supported by chronic inputs of oil or other organic carbon sources, and have a significant role in degradation of oil spills. Polycyclic aromatic hydrocarbons are the most persistent and toxic component of crude oil. Therefore, the bacteria that can break those molecules down are of particular importance. We identified such bacteria at the Port of Los Angeles (POLA), one of the busiest ports worldwide, and characterized their metabolic capabilities. We propose chemical targets based on those analyses to stimulate the activity of these bacteria in case of an oil spill in the Port POLA.

RevDate: 2021-05-12

Chuckran PF, Fofanov V, Hungate BA, et al (2021)

Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community.

mSystems, 6(3):.

Episodic inputs of labile carbon (C) to soil can rapidly stimulate nitrogen (N) immobilization by soil microorganisms. However, the transcriptional patterns that underlie this process remain unclear. In order to better understand the regulation of N cycling in soil microbial communities, we conducted a 48-h laboratory incubation with agricultural soil where we stimulated the uptake of inorganic N by amending the soil with glucose. We analyzed the metagenome and metatranscriptome of the microbial communities at four time points that corresponded with changes in N availability. The relative abundances of genes remained largely unchanged throughout the incubation. In contrast, glucose addition rapidly increased the transcription of genes encoding ammonium and nitrate transporters, enzymes responsible for N assimilation into biomass, and genes associated with the N regulatory network. This upregulation coincided with an increase in transcripts associated with glucose breakdown and oxoglutarate production, demonstrating a connection between C and N metabolism. When concentrations of ammonium were low, we observed a transient upregulation of genes associated with the nitrogen-fixing enzyme nitrogenase. Transcripts for nitrification and denitrification were downregulated throughout the incubation, suggesting that dissimilatory transformations of N may be suppressed in response to labile C inputs in these soils. These results demonstrate that soil microbial communities can respond rapidly to changes in C availability by drastically altering the transcription of N cycling genes.IMPORTANCE A large portion of activity in soil microbial communities occurs in short time frames in response to an increase in C availability, affecting the biogeochemical cycling of nitrogen. These changes are of particular importance as nitrogen represents both a limiting nutrient for terrestrial plants as well as a potential pollutant. However, we lack a full understanding of the short-term effects of labile carbon inputs on the metabolism of microbes living in soil. Here, we found that soil microbial communities responded to labile carbon addition by rapidly transcribing genes encoding proteins and enzymes responsible for inorganic nitrogen acquisition, including nitrogen fixation. This work demonstrates that soil microbial communities respond within hours to carbon inputs through altered gene expression. These insights are essential for an improved understanding of the microbial processes governing soil organic matter production, decomposition, and nutrient cycling in natural and agricultural ecosystems.

RevDate: 2021-05-12

Che Y, Yang Y, Xu X, et al (2021)

Reply to Shaw: Challenges for enrichment analysis of AMR gene-bearing plasmids.

Proceedings of the National Academy of Sciences of the United States of America, 118(21):.

RevDate: 2021-06-01

Lima J, Manning T, Rutherford KM, et al (2021)

Taxonomic annotation of 16S rRNA sequences of pig intestinal samples using MG-RAST and QIIME2 generated different microbiota compositions.

Journal of microbiological methods, 186:106235 pii:S0167-7012(21)00103-2 [Epub ahead of print].

Environmental microbiome studies rely on fast and accurate bioinformatics tools to characterize the taxonomic composition of samples based on the 16S rRNA gene. MetaGenome Rapid Annotation using Subsystem Technology (MG-RAST) and Quantitative Insights Into Microbial Ecology 2 (QIIME2) are two of the most popular tools available to perform this task. Their underlying algorithms differ in many aspects, and therefore the comparison of the pipelines provides insights into their best use and interpretation of the outcomes. Both of these bioinformatics tools are based on several specialized algorithms pipelined together, but whereas MG-RAST is a user-friendly webserver that clusters rRNA sequences based on their similarity to create Operational Taxonomic Units (OTU), QIIME2 employs DADA2 in the construction of Amplicon Sequence Variants (ASV) by applying an error model that considers the abundance of each sequence and its similarity to other sequences. Taxonomic compositions obtained from the analyses of amplicon sequences of DNA from swine intestinal gut and faecal microbiota samples using MG-RAST and QIIME2 were compared at domain-, phylum-, family- and genus-levels in terms of richness, relative abundance and diversity. We found significant differences between the microbiota profiles obtained from each pipeline. At domain level, bacteria were relatively more abundant using QIIME2 than MG-RAST; at phylum level, seven taxa were identified exclusively by QIIME2; at family level, samples processed in QIIME2 showed higher evenness and richness (assessed by Shannon and Simpson indices). The genus-level compositions obtained from each pipeline were used in partial least squares-discriminant analyses (PLS-DA) to discriminate between sample collection sites (caecum, colon and faeces). The results showed that different genera were found to be significant for the models, based on the Variable Importance in Projection, e.g. when using sequencing data processed by MG-RAST, the three most important genera were Acetitomaculum, Ruminococcus and Methanosphaera, whereas when data was processed using QIIME2, these were Candidatus Methanomethylophilus, Sphaerochaeta and Anaerorhabdus. Furthermore, the application of differential filtering procedures before the PLS-DA revealed higher accuracy when using non-restricted datasets obtained from MG-RAST, whereas datasets obtained from QIIME2 resulted in more accurate discrimination of sample collection sites after removing genera with low relative abundances (<1%) from the datasets. Our results highlight the differences in taxonomic compositions of samples obtained from the two separate pipelines, while underlining the impact on downstream analyses, such as biomarkers identification.

RevDate: 2021-05-11

Clocchiatti A, Hannula SE, Hundscheid MPJ, et al (2021)

Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings.

Environmental microbiology [Epub ahead of print].

Saprotrophic fungi play an important role in ecosystem functioning and plant performance, but their abundance in intensively managed arable soils is low. Saprotrophic fungal biomass in arable soils can be enhanced with amendments of cellulose-rich materials. Here we examined if sawdust-stimulated saprotrophic fungi extend their activity to the rhizosphere of crop seedlings and influence the composition and activity of other rhizosphere and root inhabitants. After growing carrot seedlings in sawdust-amended arable soil, we determined fungal and bacterial biomass and community structure in roots, rhizosphere and soil. Utilization of root exudates was assessed by stable isotope probing (SIP) following 13 CO2 -pulse-labeling of seedlings. This was combined with analysis of lipid fatty acids (PLFA/NLFA-SIP) and nucleic acids (DNA-SIP). Sawdust-stimulated Sordariomycetes colonized the seedling's rhizosphere and roots and actively consumed root exudates. This did not reduce the abundance and activity of bacteria, yet higher proportions of α-Proteobacteria and Bacteroidia were seen. Biomass and activity of mycorrhizal fungi increased with sawdust amendments, whereas exudate consumption and root colonization by functional groups containing plant pathogens did not change. Sawdust amendment of arable soil enhanced abundance and exudate-consuming activity of saprotrophic fungi in the rhizosphere of crop seedlings and promoted potential beneficial microbial groups in root-associated microbiomes. This article is protected by copyright. All rights reserved.

RevDate: 2021-05-12
CmpDate: 2021-05-12

Moossavi S, Fehr K, Maleki H, et al (2021)

Prevention of COVID-19: Preventive Strategies for General Population, Healthcare Setting, and Various Professions.

Advances in experimental medicine and biology, 1318:575-604.

The disease 2019 (COVID-19) made a public health emergency in early 2020. Despite attempts for the development of therapeutic modalities, there is no effective treatment yet. Therefore, preventive measures in various settings could help reduce the burden of disease. In this chapter, the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19, non-pharmaceutical approaches at individual and population level, chemoprevention, immunoprevention, preventive measures in different healthcare settings and other professions, special considerations in high-risk groups, and the role of organizations to hamper the psychosocial effects will be discussed.


RJR Experience and Expertise


Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.


Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.


Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.


Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.


While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.


Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.


Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.


Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.

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This book covers the ecological activities of microbes in the biosphere with an emphasis on microbial interactions within their environments and communities In thirteen concise and timely chapters, Microbial Ecology presents a broad overview of this rapidly growing field, explaining the basic principles in an easy-to-follow manner. Using an integrative approach, it comprehensively covers traditional issues in ecology as well as cutting-edge content at the intersection of ecology, microbiology,

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Collection of publications by R J Robbins

Reprints and preprints of publications, slide presentations, instructional materials, and data compilations written or prepared by Robert Robbins. Most papers deal with computational biology, genome informatics, using information technology to support biomedical research, and related matters.

Research Gate page for R J Robbins

ResearchGate is a social networking site for scientists and researchers to share papers, ask and answer questions, and find collaborators. According to a study by Nature and an article in Times Higher Education , it is the largest academic social network in terms of active users.

Curriculum Vitae for R J Robbins

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Curriculum Vitae for R J Robbins

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RJR Picks from Around the Web (updated 11 MAY 2018 )