Variation In Microbial Community Composition Research Articles

Biotic Interactions Shape Soil Bacterial Beta Diversity Patterns along an Altitudinal Gradient during Invasion

Invasive plants have already been observed in the understory of mountain forests, which are often considered a safe shelter for most native plants. Microorganisms might be drivers of plant invasions. Nevertheless, the mechanisms determining variations in microbial community composition (beta diversity) during invasion along altitudinal gradients remain to be elucidated. Here, the elevational patterns and the driving ecological processes (e.g., environmental filtering, co-occurrence patterns, and community assembly processes) of soil bacterial beta diversity were compared between invasive and native plants on the Qinling Mountains. The species turnover dominated bacterial compositional dissimilarities in both invasive and native communities, and its contribution to total beta diversity decreased during invasion. Total soil bacterial dissimilarities and turnover exhibited significant binominal patterns over an altitudinal gradient, with a tipping point of 1413 m. Further analysis showed that the contributions of assembly processes decreased in parallel with an increase in contributions of co-occurrence patterns during the invasion process, indicating that species interdependence rather than niche partitioning is strongly correlated with the bacterial biogeography of invasive communities. Plant invasion affects the relative contributions of stochastic processes and co-occurrence interactions through the regulation of the physiochemical characteristics of soil, and ultimately determines compositional dissimilarities and the components of the bacterial community along altitudinal gradients.

Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas

Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.

Comparative metagenomic analysis from Sundarbans ecosystems advances our understanding of microbial communities and their functional roles

The Sundarbans mangrove, located at the mouth of the Ganges and Brahmaputra Rivers, is the world’s largest tidal mangrove forest. These mangroves are also one of the most striking sources of microbial diversity, essential in productivity, conservation, nutrient cycling, and rehabilitation. Hence, the main objective of this study was to use metagenome analysis and provide detailed insight into microbial communities and their functional roles in the Sundarbans mangrove ecosystem. A comparative analysis was also done with a non-mangrove region of the Sundarbans ecosystem to assess the capability of the environmental parameters to explain the variation in microbial community composition. The study found several dominant bacteria, viz., Alphaproteobacteria, Actinomycetota, Bacilli, Clostridia, Desulfobacterota, Gammaproteobacteria, and Nitrospira, from the mangrove region. The mangrove sampling site reports several salt-tolerant bacteria like Alkalibacillus haloalkaliphilus, Halomonas anticariensis, and Salinivibrio socompensis. We found some probiotic species, viz., Bacillus clausii, Lactobacillus curvatus, Vibrio mediterranei and Vibrio fluvialis, from the Sundarbans mangrove. Nitrifying bacteria in Sundarbans soils were Nitrococcus mobilis, Nitrosococcus oceani, Nitrosomonas halophila, Nitrospirade fluvii, and others. Methanogenic archaea, viz., Methanoculleus marisnigri, Methanobrevibacter gottschalkii, and Methanolacinia petrolearia, were highly abundant in the mangroves as compared to the non-mangrove soils. The identified methanotrophic bacterial species, viz., Methylobacter tundripaludum, Methylococcus capsulatus, Methylophaga thiooxydans, and Methylosarcina lacus are expected to play a significant role in the degradation of methane in mangrove soil. Among the bioremediation bacterial species identified, Pseudomonas alcaligenes, Pseudomonas mendocina, Paracoccus denitrificans, and Shewanella putrefaciens play a significant role in the remediation of environmental pollution. Overall, our study shows for the first time that the Sundarbans, the largest mangrove ecosystem in the world, has a wide range of methanogenic archaea, methanotrophs, pathogenic, salt-tolerant, probiotic, nitrifying, and bioremediation bacteria.

Metagenomic insights into microbial adaptation to the salinity gradient of a typical short residence-time estuary

BackgroundMicrobial adaptation to salinity has been a classic inquiry in the field of microbiology. It has been demonstrated that microorganisms can endure salinity stress via either the “salt-in” strategy, involving inorganic ion uptake, or the “salt-out” strategy, relying on compatible solutes. While these insights are mostly based on laboratory-cultured isolates, exploring the adaptive mechanisms of microorganisms within natural salinity gradient is crucial for gaining a deeper understanding of microbial adaptation in the estuarine ecosystem.ResultsHere, we conducted metagenomic analyses on filtered surface water samples collected from a typical subtropical short residence-time estuary and categorized them by salinity into low-, intermediate-, and high-salinity metagenomes. Our findings highlighted salinity-driven variations in microbial community composition and function, as revealed through taxonomic and Clusters of Orthologous Group (COG) functional annotations. Through metagenomic binning, 127 bacterial and archaeal metagenome-assembled genomes (MAGs) were reconstructed. These MAGs were categorized as stenohaline—specific to low-, intermediate-, or high-salinity—based on the average relative abundance in one salinity category significantly exceeding those in the other two categories by an order of magnitude. Those that did not meet this criterion were classified as euryhaline, indicating a broader range of salinity tolerance. Applying the Boruta algorithm, a machine learning-based feature selection method, we discerned important genomic features from the stenohaline bacterial MAGs. Of the total 12,162 COGs obtained, 40 were identified as important features, with the “inorganic ion transport and metabolism” COG category emerging as the most prominent. Furthermore, eight COGs were implicated in microbial osmoregulation, of which four were related to the “salt-in” strategy, three to the “salt-out” strategy, and one to the regulation of water channel activity. COG0168, annotated as the Trk-type K+ transporter related to the “salt-in” strategy, was ranked as the most important feature. The relative abundance of COG0168 was observed to increase with rising salinity across metagenomes, the stenohaline strains, and the dominant Actinobacteriota and Proteobacteria phyla.ConclusionsWe demonstrated that salinity exerts influences on both the taxonomic and functional profiles of the microbial communities inhabiting the estuarine ecosystem. Our findings shed light on diverse salinity adaptation strategies employed by the estuarine microbial communities, highlighting the crucial role of the “salt-in” strategy mediated by Trk-type K+ transporters for microorganisms thriving under osmotic stress in the short residence-time estuary.22YT9hkSS5Zn-gk-qyndrEVideo

The spatiotemporal variations of microbial community in relation to water quality in a tropical drinking water reservoir, Southmost China.

It is well-known that water quality has great significance on microbial community composition in aquatic environments. In this study, we detected water column indicates the microbial community composition of nine sampling sites over two seasons using Illumina TruSeq sequencing in Songtao Reservoir, Hainan Province, Southmost China. The study indicated that the dominant phylum was Actinobacteria, Proteobacteria, Bacteroidetes, and Cyanobacteria. The diversity parameters showed that the microbial community composition had significant spatiotemporal variations, including the significantly higher Shannon index and Simpson index upstream than those midstream and downstream. Besides, there were significantly higher Chao1 index, Shannon index, and Simpson index in winter than in summer. Principal coordinates analysis (PCoA) showed the microbial structural composition had significant seasonal differences. The results of microbial community composition further revealed that the eutrophication level upstream was higher than that of midstream and downstream. The redundancy analysis (RDA) diagram indicated that the abundance of microbiology species significantly correlated with temperature, total phosphorus, Se, and Ni. Furthermore, the mantel's test showed that the temperature and total phosphorus significantly affected the community composition of archaea and bacteria. Overall, our finding here partially validated our hypothesis that the spatiotemporal variations of microbial community composition are significantly related to nutrients, physicochemical factors and metals, which has been unknown previously in tropical drinking waterbodies. This study substantially contributed to understanding of the composition of microbial community in tropical drinking water reservoirs and the main environmental driving factors in tropical zones. It also provided a reference for the management of reservoir operation to ensure drinking water safe.

Salinity shapes vertical distribution of sediment microbial community in Ebinur Lake, China

The microbial communities in saline lakes play important roles in maintaining their unique ecosystems. However, little is known about the vertical distribution of the sediment microbial communities in saline lakes. We therefore studied the vertical distribution of the sediment microbial communities and their relationships with environmental factors in Ebinur Lake, China. Our sediment cores, collected in 2018, were analyzed using Illumina MiSeq sequencing. The results indicated that microbial diversity significantly increased in the sediment core with increasing salinity. At the phylum level, the six most abundant microbes were Proteobacteria, Chloroflexi, Bacteroidetes, Firmicutes, Gemmatimonadetes and Deinococcus-Thermus, accounting for 42.9%, 10.7%, 9.6%, 5.2%, 4.6% and 3.6% of the total reads, respectively; At the genus level, the six most abundant genera were Halothiobacillus, Desulfotignum, Truepera, Salipaludibacillus, Marinobacter and Halomonas, accounting for 15.4%, 4.8%, 3.6%, 2.7%, 2.6% and 2.3% of the total reads respectively. There were significant vertical variations in microbial community composition (MCC) between upper layers and lower layers. Canonical correspondence analysis demonstrated that salinity was the dominant environmental factor affecting the vertical variation of sediment MCC. Thus, this study could greatly improve our understanding of the MCC of saline lakes in the arid and semi-arid ecosystems.

Extremophile hypolithic communities in the Vestfold Hills, East Antarctica

Abstract The Vestfold Hills are a 400 km2, isolated ice-free oasis in eastern Antarctica featuring large areas with translucent quartz rocks that provide habitat for hypolithic microbial communities underneath. We used high-throughput DNA sequencing of 16S and 18S ribosomal RNA amplicons to characterize bacterial and eukaryotic hypolithic communities across the Vestfold Hills. We found high-level, local heterogeneity in community structure consistent with limited dispersal between hypoliths. Hypolithic communities were dominated by heterotrophic Bacteroidetes (mean bacterial relative read abundance: 56%) as well as Cyanobacteria (35%), with the eukaryote component often dominated by Chlorophyta (43%). Small but significant proportions of the variation in microbial community composition and function were explained by soil salinity (5–7%) and water availability (8–11%), with distinct taxa associated with different salinities and water availabilities. Furthermore, many inferred bacterial metabolic pathways were enriched in hypolithic communities from either dry or high-salinity sites. Vestfold Hills hypolithic habitats are likely to be local refuges for bacterial and eukaryotic diversity. Gradients in soil salinity and water availability across the Vestfold Hills, in addition to the number and diversity of lake types and fjords as potential source populations, may contribute to the observed variation in the extremophile, hypolithic microbial community composition.

Seasonality and longer-term development generate temporal dynamics in the Populus microbiome.

Temporal variation in community composition is central to our understanding of the assembly and functioning of microbial communities, yet the controls over temporal dynamics for microbiomes of long-lived plants, such as trees, remain unclear. Temporal variation in tree microbiomes could arise primarily from seasonal (i.e., intra-annual) fluctuations in community composition or from longer-term changes across years as host plants age. To test these alternatives, we experimentally isolated temporal variation in plant microbiome composition using a common garden and clonally propagated plants, and we used amplicon sequencing to characterize bacterial/archaeal and fungal communities in the leaf endosphere, root endosphere, and rhizosphere of two Populus spp. over four seasons across two consecutive years. Microbial community composition differed among seasons and years (which accounted for up to 21% of the variation in microbial community composition) and was correlated with seasonal dissimilarity in climatic conditions. However, microbial community dissimilarity was also positively correlated with time, reflecting longer-term compositional shifts as host trees aged. Together, our findings demonstrate that temporal patterns in tree microbiomes arise from both seasonal fluctuations and longer-term changes, which interact to generate unique seasonal patterns each year. In addition to shedding light on two important controls over the assembly of plant microbiomes, our results also suggest future studies of tree microbiomes should account for background temporal dynamics when testing the drivers of spatial patterns in microbial community composition and temporal responses of plant microbiomes to environmental change.IMPORTANCEMicrobiomes are integral to the health of host plants, but we have a limited understanding of the factors that control how the composition of plant microbiomes changes over time. Especially little is known about the microbiome of long-lived trees, relative to annual and non-woody plants. We tested how tree microbiomes changed between seasons and years in poplar (genus Populus), which are widespread and ecologically important tree species that also serve as important biofuel feedstocks. We found the composition of bacterial, archaeal, and fungal communities differed among seasons, but these seasonal differences depended on year. This dependence was driven by longer-term changes in microbial composition as host trees developed across consecutive years. Our findings suggest that temporal variation in tree microbiomes is driven by both seasonal fluctuations and longer-term (i.e., multiyear) development.

Responses of Natural Microorganisms to Land Reclamation and Applications of Functional Microorganisms in Biorestoration of Coal Mining Area

Extensive coal mining causes significant ecological and environmental impacts on the local ecosystem, especially on the terrestrial ecosystem. Mining activities induce the degradation of topsoil physico–chemical characteristics and the succession of soil microbial communities. The soil microbial community is sensitive to soil disturbance and restoration practices, being significant in soil reconstruction and land restoration. Microbes could be effective instruments to restore or reclaim disturbed terrestrial ecosystems and indispensable, unambiguous, indicators to assess reclaimed soils. In the present review, we aimed to provide insight into the effects of mining and subsequent land reclamation on soil microorganisms and the importance and application of microorganisms in the reclamation process. We address changes in the diversity and structure of the soil microbial community after reclamation and discuss the main driving factors of the community. We hypothesize that there is a discernible pattern or regularity in the variation of microbial community composition during the process of restoration succession. By employing the life strategy concept, the study attempts to identify and understand how microbial communities evolve during land reclamation. Land reclamation could improve the nutrients in the soil while increasing the proportion of saprotrophic microorganisms. In community succession, vegetation, soil properties, and reclamation time are key determining factors. Whereas bacteria, fungi, and archaea showed different responses to these factors, as they responded differently to varied soil environments, nutrition, and plants, and occupied different biological niches. Finally, we describe the applications of microorganisms as land reclamation monitors or promoters. This knowledge and understanding can provide comprehensive insight into the soil health condition and strong support for forecasting and decision-making in mine land restoration.

High phenanthrene degrading efficiency by different microbial compositions construction.

Microbial remediation has become the most promising technical means for the remediation of polycyclic aromatic hydrocarbons (PAHs) non-point source contaminated soil due to its low cost of treatment, complete degradation of pollutants, and in-situ remediation. In this study, in order to demonstrate the phenanthrene degrading microbial diversity, phenanthrene was chosen as the representative of PAHs and strains capable of degrading phenanthrene were isolated and screened from the sedimentation sludge and the bottom sludge of oil tank trucks, and high throughput sequencing was used to check the dominant strains with a good degrading effect on phenanthrene. Results showed even more than 50% of phenanthrene was degraded in all samples, the composition of PAH-degrading bacteria was diverse, and different environments constructed different functional microbial groups, which resulted in the microbial adapting to the diversity of the environment. Finally, a series of bacterial species with phenanthrene-degrading functions such as Achromobacter, Pseudomonas, Pseudochelatococcus, Bosea was enriched after nine transferring process. Overall, our study offers value information for the enrichment of functional degrading microbes of phenanthrene or other pollutants that more concern should be paid in not only the degradation rate, but also the diversity variation of microbial community composition.

Explaining nitrogen turnover in sediments and water through variations in microbial community composition and potential function

Anthropogenic activities greatly impact nitrogen (N) biogeochemical cycling in aquatic ecosystems. High N concentrations in coastal aquaculture waters threaten fishery production and aquaculture ecosystems and have become an urgent problem to be solved. Existing microbial flora and metabolic potential significantly regulate N turnover in aquatic ecosystems. To clarify the contribution of microorganisms to N turnover in sediment and water, we investigated three types of aquaculture ecosystems in coastal areas of Guangdong, China. Nitrate nitrogen (NO3−-N) was the dominant component of total nitrogen in the sediment (interstitial water, 90.4%) and water (61.6%). This finding indicates that NO3−-N (1.67–2.86 mg/L and 2.98–7.89 mg/L in the sediment and water) is a major pollutant in aquaculture ecosystems. In water, the relative abundances of assimilation nitrogen reduction and aerobic denitrifying bacteria, as well as the metabolic potentials of nitrogen fixation and dissimilated nitrogen in fish monoculture, were only 61.0%, 31.5%, 47.5%, and 27.2% of fish and shrimp polyculture, respectively. In addition, fish-shrimp polyculture reduced NO3−-N content (2.86 mg/L) compared to fish monoculture (7.89 mg/L), which was consistent with changes in aerobic denitrification and nitrate assimilation, suggesting that polyculture could reduce TN concentrations in water bodies and alleviate nitrogen pollution risks. Further analysis via structural equation modeling (SEM) revealed that functional pathways (36% and 31%) explained TN changes better than microbial groups in sediment and water (13% and 11%), suggesting that microbial functional capabilities explain TN better than microbial community composition and other factors (pH, O2, and aquaculture type). This study enhances our understanding of nitrogen pollution characteristics and microbial community and functional capabilities related to sediment-water nitrogen turnover in three types of aquaculture ecosystems, which can contribute to the preservation of healthy coastal ecosystems.

Mixotrophic denitrification driven by plant carbon sources and influent sulphate for enhancing nitrogen removal in constructed wetlands

A lab-scale horizontal baffled subsurface-flow constructed wetland (HBSFCW) packed with plant litter (reed straws (RS)) was built as a sustained-release carbon source, after which it was fed with synthetic wastewater that simulated the low C/N ratios in tailwater from wastewater treatment plants (WWTPs). The purpose of its operation was to explore the relationship between the nitrogen removal performance and variations in microbial community composition, and propose an enhanced nitrogen removal strategy for constructed wetlands (CWs). The results showed that plant carbon resources and influent sulphate can induce changes in redox conditions and organic matter concentrations at CWs, thereby influencing the microbial community composition and denitrification performance. High-throughput sequencing revealed the formation of richer microbial communities in additional RS units. Conventional heterotrophic denitrifying genera (Dechloromonas, Thauera and Ignavibacterium), sulphate-reducing genera (Desulfobacter, Desulfobulbus) and a sulphur-based denitrification genus (Sulfurimonas) were directly or indirectly affected by the addition of RS and became dominant in additional RS units. This study suggests that plant litter in HBSFCWs and sulphate from WWTP tailwater provide an opportunity to utilize sulphate as an electron-acceptor and reduced sulphur as an electron-donor for nitrate reduction, thus driving mixotrophic denitrification.

Issue Information

Molecular EcologyVolume 32, Issue 10 p. i-ii ISSUE INFORMATIONFree Access Issue Information First published: 09 May 2023 https://doi.org/10.1111/mec.16516AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Graphical Abstract Cover Illustrations: (Left to Right): (Image 1): N/A; (Image 2): Sourdough photography taken on a SEM; (Image 3): Soybean pod with symptoms of anthracnose; (Image 4): Population Genetics provides a link across the three scientific communities interested in improving the durability of plant resistances; (Image 5): Uredinia of the poplar rust fungus Melampsora larici-populina on a poplar leaf; (Image 6): Coffee berries infected with coffee berry disease caused by the fungal pathogen Colletotrichum kahawae which infects the young developing berries causing black sunken lessions on the outer skin of the berries. Eventually the infection covers the whole berries and the berries will be mummified (current stage) and drop from the shrub; (Image 7): The association relationship analysis between the average deoxynivalenol accumulation and Fusarium OTU diversity for different sampling sites; (Image 8): Paddy fields before harvest, Yuanyang Terraces, Yunnan, China; (Image 9): Active sites of multidrug efflux pumps in prominent gut bacterial symbionts of humans contain polymorphisms indicative of a history of balancing selection; (Image 10): Each city subway is distinguishable by a particular microbiome signature. The subway microbiome may be a proxy of the city microbiome itself; (Image 11): We used a combination of sampling, sequencing and culturing to analyse variation of microbial community composition among different locations in Switzerland and different types of shops; (Image 12): Field collection of rhizosphere soil of the model legume Medicago truncatula to culture symbiotic nitrogen-fixing rhizobia in the south of France; (Image 13): Network representing the sharing of plasmid genes among the Lysobacteraceae bacterial family. Photo Credit: (Image 1): J. P. Sampaio; (Image 2): Bernard Onno; (Image 3): Flavia Rogerio; (Image 4): M. Saubin; (Image 5): Benjamin PETRE; (Image 6): Beyene Zewdie; (Image 7): Qiang Wang, Xiaoping Hu; (Image 8): E. FOURNIER, INRAE; (Image 9): Andrew Moeller; (Image 10): Mariana Peimbert; (Image 11): Helena Klein (illuzation-hk.com); (Image 12): Michael Grillo; (Image 13): Damien Richard. Volume32, Issue10Special Issue: EVOLUTIONARY ECOLOGY OF HUMAN‐ASSOCIATED MICROBESMay 2023Pages i-ii RelatedInformation

Characterization of microbiomic and geochemical compositions across the photosynthetic fringe.

Hot spring outflow channels provide geochemical gradients that are reflected in microbial community compositions. In many hot spring outflows, there is a distinct visual demarcation as the community transitions from predominantly chemotrophs to having visible pigments from phototrophs. It has been hypothesized that this transition to phototrophy, known as the photosynthetic fringe, is a result of the pH, temperature, and/or sulfide concentration gradients in the hot spring outflows. Here, we explicitly evaluated the predictive capability of geochemistry in determining the location of the photosynthetic fringe in hot spring outflows. A total of 46 samples were taken from 12 hot spring outflows in Yellowstone National Park that spanned pH values from 1.9 to 9.0 and temperatures from 28.9 to 92.2°C. Sampling locations were selected to be equidistant in geochemical space above and below the photosynthetic fringe based on linear discriminant analysis. Although pH, temperature, and total sulfide concentrations have all previously been cited as determining factors for microbial community composition, total sulfide did not correlate with microbial community composition with statistical significance in non-metric multidimensional scaling. In contrast, pH, temperature, ammonia, dissolved organic carbon, dissolved inorganic carbon, and dissolved oxygen did correlate with the microbial community composition with statistical significance. Additionally, there was observed statistical significance between beta diversity and the relative position to the photosynthetic fringe with sites above the photosynthetic fringe being significantly different from those at or below the photosynthetic fringe according to canonical correspondence analysis. However, in combination, the geochemical parameters considered in this study only accounted for 35% of the variation in microbial community composition determined by redundancy analysis. In co-occurrence network analyses, each clique correlated with either pH and/or temperature, whereas sulfide concentrations only correlated with individual nodes. These results indicate that there is a complex interplay between geochemical variables and the position of the photosynthetic fringe that cannot be fully explained by statistical correlations with the individual geochemical variables included in this study.

Strengthening Fenton-like reactions to improve lignocellulosic degradation performance by increasing lignocellulolytic enzyme core microbes during rice straw composting

This study aimed to explore the effect of Fenton-like reactions on lignocellulosic degradation performance and identify their driving factors during composting. Rice straw was pretreated by inoculating Aspergillus fumigatus Z1 and then adding Fe (II), which resulted in Fenton-like reactions. The treatment groups included CK (control), Fe (addition of Fe (II)), Z1 (inoculation of A. fumigatus Z1), and Fe + Z1 (inoculation of A. fumigatus Z1 and addition of Fe (II)). The results suggested that Fenton-like reactions can produce lignocellulolytic enzymes and degrade lignocellulose, due to the variation in microbial community composition and diversity. In addition, functional modular microbes were identified by network analysis, which can produce endoglucanase and xylanase. Regarding ligninase, bacteria were more favorable for producing manganese peroxidase, and fungi were more favorable for producing laccase. Additionally, reducing sugars, organic matter, total nitrogen and amino acids were key microhabitat factors of functional modular bacteria, while organic matter, reducing sugars, amino acids and C/N were key microhabitat factors of functional modular fungi, thereby promoting the degradation of lignocellulose. This study provides technical support for lignocellulosic degradation based on Fenton-like reactions.

Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage.

Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.

Universal drivers of cheese microbiomes

The culinary value, quality, and safety of cheese are largely driven by the resident bacteria, but comparative analyses of the cheese microbiota across cheese types are scarce. We present the first global synthesis of cheese microbiomes. Following a systematic literature review of cheese microbiology research, we collected 16S rRNA gene amplicon sequence data from 824 cheese samples spanning 58 cheese types and 16 countries. We found a consistent, positive relationship between microbiome richness and pH, and a higher microbial richness in cheeses derived from goat milk. In contrast, we found no relationship between pasteurization, geographic location, or salinity and richness. Milk and cheese type, geographic location, and pasteurization collectively explained 65% of the variation in microbial community composition. Importantly, we identified four universal cheese microbiome types, driven by distinct dominant taxa. Our study reveals notable diversity patterns among the cheese microbiota, which are driven by geography and local environmental variables.

Mycoplasmataceae dominate microbial community differences between gut regions in mammals with a simple gut architecture

AbstractFaunivorous mammals with simple guts are thought to rely primarily on endogenously produced enzymes to digest food, in part because they lack fermentation chambers for facilitating mutualistic interactions with microbes. However, variation in microbial community composition along the length of the gastrointestinal tract has yet to be assessed in faunivorous species with simple guts. We tested for differences in bacterial taxon abundances and community compositions between the small intestines and colons of 26 individuals representing four species of shrew in the genus Crocidura. We sampled these hosts from a single locality on Sulawesi Island, Indonesia, to control for potential geographic and temporal variation. Bacterial community composition differed significantly between the two gut regions and members of the family Mycoplasmataceae contributed substantially to these differences. Three operational taxonomic units (OTUs) of an unclassified genus in this family were more abundant in the small intestine, whereas 1 OTU of genus Ureaplasma was more abundant in the colon. Species of Ureaplasma encode an enzyme that degrades urea, a metabolic byproduct of protein catabolism. Additionally, a Hafnia–Obesumbacterium OTU, a genus known to produce chitinase in bat gastrointestinal tracts, was also more abundant in the colon compared to the small intestine. The presence of putative chitinase- and urease-producing bacteria in shrew guts suggests mutualisms with microorganisms play a role in facilitating the protein-rich, faunivorous diets of simple gut mammals.

Selection, drift and community interactions shape microbial biogeographic patterns in the Pacific Ocean

Despite accumulating data on microbial biogeographic patterns in terrestrial and aquatic environments, we still lack a comprehensive understanding of how these patterns establish, in particular in ocean basins. Here we show the relative significance of the ecological mechanisms selection, dispersal and drift for shaping the composition of microbial communities in the Pacific Ocean over a transect of 12,400 km between subantarctic and subarctic regions. In the epipelagic, homogeneous selection contributes 50–60% and drift least to the three mechanism for the assembly of prokaryotic communities whereas in the upper mesopelagic, drift is relatively most important for the particle-associated subcommunities. Temperature is important for the relative significance of homogeneous selection and dispersal limitation for community assembly. The relative significance of both mechanisms was inverted with increasing temperature difference along the transect. For eukaryotes >8 µm, homogeneous selection is also the most important mechanisms at two epipelagic depths whereas at all other depths drift is predominant. As species interactions are essential for structuring microbial communities we further analyzed co-occurrence-based community metrics to assess biogeographic patterns over the transect. These interaction-adjusted indices explained much better variations in microbial community composition as a function of abiotic and biotic variables than compositional or phylogenetic distance measures like Bray–Curtis or UniFrac. Our analyses are important to better understand assembly processes of microbial communities in the upper layers of the largest ocean and how they adapt to effectively perform in global biogeochemical processes. Similar principles presumably act upon microbial community assembly in other ocean basins.

Acetoclastic methanogenesis pathway stability despite the high microbial taxonomic variability in the transition from acidogenesis to methanogenesis during food waste anaerobic digestion

Anaerobic digestion (AD) is a microbial-mediated biogeochemical process that includes hydrolysis, acidogenesis, acetogenesis and methanogenesis. AD instability usually occurs in the transition from the acidogenesis phase (AP) to the methanogenesis phase (MP) due to over acidification. However, the underlying microbial mechanism of this transition has not been well characterized. In the present study, the transition of bacterial and methanogenic community composition, methanogenesis functional gene expression and metabolic pathways from AP to MP during food waste (FW) AD were investigated in a bioreactor using metagenomics and reverse transcription PCR technology. AP and MP were identified by changes in methane production, gas accumulation, pH and volatile fatty acids (VFAs). Concomitant with the changes in these physiochemical parameters, the bacterial and methanogenic community composition showed succession patterns. The bacterial composition transformed from acidogenic bacteria (Propionispira and Bacteroides) to hydrolytic bacteria (Smithella, Syntrophus and Syntrophorhabdus), and the methanogen composition transformed from the domination of acetoclastic methanogens (Methanosaeta) to the codomination of hydrogenotrophic methanogens (Methanoculleus, Methanolinea and Methanobacterium) and acetoclastic methanogens (Methanosaeta). The expression level of the methanogenesis functional gene mcrA significantly (p < 0.05) increased in response to the increasing methane production. In contrast, acetoclastic methanogenesis as the main methanogenesis metabolic pathway remained stable. These results showed that FWAD key physiochemical parameters drive the variation in microbial community composition and functional genes expression but not the methanogenesis metabolic pathway. The finding suggests that FWAD process may be better predicted by methanogenic functional characteristics than by microbial community composition.