Drivers Of Microbial Community Composition Research Articles

Gut dysbiosis: Ecological causes and causative effects on human disease.

The gut microbiota plays a role in many human diseases, but high-throughput sequence analysis does not provide a straightforward path for defining healthy microbial communities. Therefore, understanding mechanisms that drive compositional changes during disease (gut dysbiosis) continues to be a central goal in microbiome research. Insights from the microbial pathogenesis field show that an ecological cause for gut dysbiosis is an increased availability of host-derived respiratory electron acceptors, which are dominant drivers of microbial community composition. Similar changes in the host environment also drive gut dysbiosis in several chronic human illnesses, and a better understanding of the underlying mechanisms informs approaches to causatively link compositional changes in the gut microbiota to an exacerbation of symptoms. The emerging picture suggests that homeostasis is maintained by host functions that control the availability of resources governing microbial growth. Defining dysbiosis as a weakening of these host functions directs attention to the underlying cause and identifies potential targets for therapeutic intervention.

Vegetation, topography, and soil depth drive microbial community structure in two Swedish grasslands.

Soil microbial diversity and community composition are shaped by various factors linked to land management, topographic position, and vegetation. To study the effects of these drivers, we characterized fungal and bacterial communities from bulk soil at four soil depths ranging from the surface to below the rooting zone of two Swedish grasslands with differing land-use histories, each including both an upper and a lower catenary position. We hypothesized that differences in plant species richness and plant functional group composition between the four study sites would drive the variation in soil microbial community composition and correlate with microbial diversity, and that microbial biomass and diversity would decrease with soil depth following a decline in resource availability. While vegetation was identified as the main driver of microbial community composition, the explained variation was significantly higher for bacteria than for fungi, and the communities differed more between grasslands than between catenary positions. Microbial biomass derived from DNA abundance decreased with depth, but diversity remained relatively stable, indicating diverse microbial communities even below the rooting zone. Finally, plant-microbial diversity correlations were significant only for specific plant and fungal functional groups, emphasizing the importance of functional interactions over general species richness.

Biogeochemical and historical drivers of microbial community composition and structure in sediments from Mercer Subglacial Lake, West Antarctica

Ice streams that flow into Ross Ice Shelf are underlain by water-saturated sediments, a dynamic hydrological system, and subglacial lakes that intermittently discharge water downstream across grounding zones of West Antarctic Ice Sheet (WAIS). A 2.06 m composite sediment profile was recently recovered from Mercer Subglacial Lake, a 15 m deep water cavity beneath a 1087 m thick portion of the Mercer Ice Stream. We examined microbial abundances, used 16S rRNA gene amplicon sequencing to assess community structures, and characterized extracellular polymeric substances (EPS) associated with distinct lithologic units in the sediments. Bacterial and archaeal communities in the surficial sediments are more abundant and diverse, with significantly different compositions from those found deeper in the sediment column. The most abundant taxa are related to chemolithoautotrophs capable of oxidizing reduced nitrogen, sulfur, and iron compounds with oxygen, nitrate, or iron. Concentrations of dissolved methane and total organic carbon together with water content in the sediments are the strongest predictors of taxon and community composition. δ¹³C values for EPS (−25 to −30‰) are consistent with the primary source of carbon for biosynthesis originating from legacy marine organic matter. Comparison of communities to those in lake sediments under an adjacent ice stream (Whillans Subglacial Lake) and near its grounding zone provide seminal evidence for a subglacial metacommunity that is biogeochemically and evolutionarily linked through ice sheet dynamics and the transport of microbes, water, and sediments beneath WAIS.

Clinically relevant pathogens on surfaces display differences in survival and transcriptomic response in relation to probiotic and traditional cleaning strategies

Indoor surfaces are paradoxically presumed to be both colonized by pathogens, necessitating disinfection, and “microbial wastelands.” In these resource-poor, dry environments, competition and decay are thought to be important drivers of microbial community composition. However, the relative contributions of these two processes have not been specifically evaluated. To bridge this knowledge gap, we used microcosms to evaluate whether interspecies interactions occur on surfaces. We combined transcriptomics and traditional microbiology techniques to investigate whether competition occurred between two clinically important pathogens, Acinetobacter baumannii and Klebsiella pneumoniae, and a probiotic cleaner containing a consortium of Bacillus species. Probiotic cleaning seeks to take advantage of ecological principles such as competitive exclusion, thus using benign microorganisms to inhibit viable pathogens, but there is limited evidence that competitive exclusion in fact occurs in environments of interest (i.e., indoor surfaces). Our results indicate that competition in this setting has a negligible impact on community composition but may influence the functions expressed by active organisms. Although Bacillus spp. remained viable on surfaces for an extended period of time after application, viable colony forming units (CFUs) of A. baumannii recovered following exposure to a chemical-based detergent with and without Bacillus spp. showed no statistical difference. Similarly, for K. pneumoniae, there were small statistical differences in CFUs between cleaning scenarios with or without Bacillus spp. in the chemical-based detergent. The transcriptome of A. baumannii with and without Bacillus spp. exposure shared a high degree of similarity in overall gene expression, but the transcriptome of K. pneumoniae differed in overall gene expression, including reduced response in genes related to antimicrobial resistance. Together, these results highlight the need to fully understand the underlying biological and ecological mechanisms for community assembly and function on indoor surfaces, as well as having practical implications for cleaning and disinfection strategies for infection prevention.

Low Diversity and Instability of the Sinus Microbiota over Time in Adults with Cystic Fibrosis.

ABSTRACTChronic rhinosinusitis (CRS) is a common, yet underreported and understudied manifestation of upper respiratory disease in people with cystic fibrosis (CF). Recently developed standard of care guidelines for the management of CF CRS suggest treatment of upper airway disease may ameliorate lower airway disease. We sought to determine whether changes to sinus microbial community diversity and specific taxa known to cause CF lung disease are associated with increased respiratory disease and inflammation. We performed 16S rRNA gene sequencing, supplemented with cytokine analyses, microscopy, and bacterial culturing, on samples from the sinuses of 27 adults with CF CRS. At each study visit, participants underwent endoscopic paranasal sinus sampling and clinical evaluation. We identified key drivers of microbial community composition and evaluated relationships between diversity and taxa with disease outcomes and inflammation. Sinus community diversity was low, and the composition was unstable, with many participants exhibiting alternating dominance between Pseudomonas aeruginosa and staphylococci over time. Despite a tendency for dominance by these two taxa, communities were highly individualized and shifted composition during exacerbation of sinus disease symptoms. Exacerbations were also associated with communities dominated by Staphylococcus spp. Reduced microbial community diversity was linked to worse sinus disease and the inflammatory status of the sinuses (including increased interleukin-1β [IL-1β]). Increased IL-1β was also linked to worse sinus endoscopic appearance, and other cytokines were linked to microbial community dynamics. Our work revealed previously unknown instability of sinus microbial communities and a link between inflammation, lack of microbial community diversity, and worse sinus disease.IMPORTANCE Together with prior sinus microbiota studies of adults with CF chronic rhinosinusitis, our study underscores similarities between sinus and lower respiratory tract microbial community structures in CF. We show how community structure tracks with inflammation and several disease measures. This work strongly suggests that clinical management of CRS could be leveraged to improve overall respiratory health in CF. Our work implicates elevated IL-1β in reduced microbiota diversity and worse sinus disease in CF CRS, suggesting applications for existing therapies targeting IL-1β. Finally, the widespread use of highly effective cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy has led to less frequent availability of spontaneous expectorated sputum for microbiological surveillance of lung infections. A better understanding of CF sinus microbiology could provide a much-needed alternative site for monitoring respiratory infection status by important CF pathogens.

Changes in vegetation types affect soil microbial communities in tropical islands of southern China

Soil microbial communities are the key drivers of nutrient cycling in ecosystems. However, the functional response of soil microbial community composition to contrasting vegetation types in tropical coral islands is still unclear. Tropical coral islands provide a unique, extreme habitat characterized by higher soil pH and P, but lower N and soil water contents. To determine the responses of soil microbial communities to changes in vegetation types, soil microbial biomass and community composition were investigated by determination of phospholipid fatty acids (PLFAs) under three vegetation types (including tree, shrub, and herb-vine) on Dong Island and Yongxing Island of southern China. Redundancy analysis (RDA) has been used to determine the driving factors (soil properties) for shaping soil microbial community composition. The results showed that the total biomass of PLFAs, as well as the specific microbial taxa [such as bacteria, Gram-positive bacteria (G+), Gram-negative bacteria (G-), fungi, arbuscular mycorrhizal fungi (AMF), and actinomycetes] increased in the soils from herb-vine via shrub to tree. Furthermore, along the above vegetation types gradient, the ratios of Gram-positive to Gram-negative bacteria (G+:G-), total saturated to total monounsaturated fatty acids (sat:mono), and fungi to bacteria (F:B) ratio decreased, indicating a shift in soil microbial community towards lower stress and copiotrophic dominance. Our findings indicate that soil microbial groups have a sensitive response to shifting plant communities in tropical coral islands, and soil water content, the ratios of soil organic matter and N content to P content, and soil pH might be the critical drivers of microbial community composition and structure in the study region.

Specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data

BackgroundUnderstanding the factors that influence microbes’ environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, “specificity” is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao’s (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3 ) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.ResultsWe present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.Conclusionsspecificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity’s companion package, specificity.shiny.

The soil microbiomics of intact, degraded and partially-restored semi-arid succulent thicket (Albany Subtropical Thicket).

This study examines the soil bacterial diversity in the Portulacaria afra-dominated succulent thicket vegetation of the Albany Subtropical Thicket biome; this biome is endemic to South Africa. The aim of the study was to compare the soil microbiomes between intact and degraded zones in the succulent thicket and identify environmental factors which could explain the community compositions. Bacterial diversity, using 16S amplicon sequencing, and soil physicochemistry were compared across three zones: intact (undisturbed and vegetated), degraded (near complete removal of vegetation due to browsing) and restored (a previously degraded area which was replanted approximately 11 years before sampling). Amplicon Sequence Variant (ASV) richness was similar across the three zones, however, the bacterial community composition and soil physicochemistry differed across the intact and degraded zones. We identified, via correlation, the potential drivers of microbial community composition as soil density, pH and the ratio of Ca to Mg. The restored zone was intermediate between the intact and degraded zones. The differences in the microbial communities appeared to be driven by the presence of plants, with plant-associated taxa more common in the intact zone. The dominant taxa in the degraded zone were cosmopolitan organisms, that have been reported globally in a wide variety of habitats. This study provides baseline information on the changes of the soil bacterial community of a spatially restricted and threatened biome. It also provides a starting point for further studies on community composition and function concerning the restoration of degraded succulent thicket ecosystems.

Plant Biomass and Soil Nutrients Mainly Explain the Variation of Soil Microbial Communities During Secondary Succession on the Loess Plateau.

Soil microorganisms play an important role in the circulation of materials and nutrients between plants and soil ecosystems, but the drivers of microbial community composition and diversity remain uncertain in different vegetation restoration patterns. We studied soil physicochemical properties (i.e., soil moisture, bulk density, pH, soil nutrients, available nutrients), plant characteristics (i.e., Shannon index [HPlant] and Richness index [SPlant], litter biomass [LB], and fine root biomass [FRB]), and microbial variables (biomass, enzyme activity, diversity, and composition of bacterial and fungal communities) in different plant succession patterns (Robinia pseudoacacia [MF], Caragana korshinskii [SF], and grassland [GL]) on the Loess Plateau. The herb communities, soil microbial biomass, and enzyme activities were strongly affected by vegetation restoration, and soil bacterial and fungal communities were significantly different from each other at the sites. Correlation analysis showed that LB and FRB were significantly positively correlated with the Chao index of soil bacteria, soil microbial biomass, enzyme activities, Proteobacteria, Zygomycota, and Cercozoa, while negatively correlated with Actinobacteria and Basidiomycota. In addition, soil water content (SW), pH, and nutrients have important effects on the bacterial and fungal diversities, as well as Acidobacteria, Proteobacteria, Actinobacteria, Nitrospirae, Zygomycota, and microbial biomass. Furthermore, plant characteristics and soil properties modulated the composition and diversity of soil microorganisms, respectively. Overall, the relative contribution of vegetation and soil to the diversity and composition of soil bacterial and fungal communities illustrated that plant characteristics and soil properties may synergistically modulate soil microbial communities, and the composition and diversity of soil bacterial and fungal communities mainly depend on plant biomass and soil nutrients.

Spatial Metagenomics of Three Geothermal Sites in Pisciarelli Hot Spring Focusing on the Biochemical Resources of the Microbial Consortia.

Terrestrial hot springs are of great interest to the general public and to scientists alike due to their unique and extreme conditions. These have been sought out by geochemists, astrobiologists, and microbiologists around the globe who are interested in their chemical properties, which provide a strong selective pressure on local microorganisms. Drivers of microbial community composition in these springs include temperature, pH, in-situ chemistry, and biogeography. Microbes in these communities have evolved strategies to thrive in these conditions by converting hot spring chemicals and organic matter into cellular energy. Following our previous metagenomic analysis of Pisciarelli hot springs (Naples, Italy), we report here the comparative metagenomic study of three novel sites, formed in Pisciarelli as result of recent geothermal activity. This study adds comprehensive information about phylogenetic diversity within Pisciarelli hot springs by peeking into possible mechanisms of adaptation to biogeochemical cycles, and high applicative potential of the entire set of genes involved in the carbohydrate metabolism in this environment (CAZome). This site is an excellent model for the study of biodiversity on Earth and biosignature identification, and for the study of the origin and limits of life.

Microbial community size is a potential predictor of nematode functional group in limed grasslands

Agronomic management practices can impose structural change within soil biotic communities that may negatively impact soil processes including function and biodiversity. Thus, optimizing sustainable crop production that confers minimal impacts on the structure and function of soil biota is an imperative to deliver healthy, functional and resilient production systems. Liming is a management intervention to mitigate soil acidification with a generally positive effect on crop biomass. The application of lime changes soil pH, a known driver of microbial community composition, but it is unknown whether pH derived shifts in bacterial communities result in altered nematode communities. In this study we used qPCR, next generation sequencing and nematode directed T-RFLP to characterise microbial and nematode communities in a liming field trial with a control and three liming applications to incrementally increase pH by 0.5, 0.75 and 1 pH unit. We demonstrate over a 14-month experimental period an interaction between microbial and nematode communities in managed grasslands. Liming had a limited effect on nematode and microbial community structures. However bacterial and archaeal abundance as measured by 16S rRNA gene copy number was found to be a potential predictor of nematode functional group, based on recognized trophic strategies, with increased abundance of omnivorous and predatory nematodes, that are known to prey upon bacterivorous nematodes, with a concomitant increase of 16S rRNA gene copy number. Thus, indirectly suggesting suppression of the bacterial and archaeal community in the presence of bacterivorous nematodes. Where populations of bacterivorous nematodes were highest the relative abundance of both predatory and omnivorous nematodes was lowest. Thus, this study demonstrates clear connectivity between soil microbial and nematode communities in grassland soil.

Identifying drivers of microbial community composition associated with aquatic primary producers: metagenomic analysis of cyanobacterial cultures

The energy derived from aquatic primary production is fundamental to driving Earth’s life support systems – but they don’t achieve all this by themselves. Heterotrophic bacteria found in the photic zones of aquatic environments have a fundamental role in this too. Our group’s interest is in understanding how heterotrophs help autotrophs: who in these communities are important, and how and why they are important. Answering this is important in both natural and manmade environments so we can model these environments, and as appropriate, manipulate them, such as applying designer microbiomes to aid industrialisation of algal cultivation. Metagenomic analysis of 31 marine and freshwater cyanobacterial cultures from the Culture Collection of Algae & Protozoa resulted in assembly of >400 bacterial metagenomes (MAGs) with ca. 14 unique MAGs per culture. Community composition was clearly partitioned by salinity as a driver but collectively niche accounted for most community taxonomic variation. No universal core microbiome was identified, but taxonomic composition of marine cultures bore notable similarities to marine eukaryotic algal communities and to a natural cyanobacterial mat community found next to a northern Chilean geyser. Stable taxonomic associations imply that these taxa may have functional importance to their algal host. Functional analysis of the MAGs is underway and we will test whether the relative taxonomic variability contrasts with low functional variation between communities. If true, this implies that primary producers drive community assembly in a functionally predictable way, and that function, not taxonomy, is the more important parameter to understand.

Environmental Controls on Microbial Diversity in Arctic Lakes of West Greenland.

We assessed the microbial community structure of six arctic lakes in West Greenland and investigated relationships to lake physical and chemical characteristics. Lakes from the ice sheet region exhibited the highest species richness, while inland and plateau lakes had lower observed taxonomical diversity. Lake habitat differentiation during summer stratification appeared to alter within lake microbial community composition in only a subset of lakes, while lake variability across regions was a consistent driver of microbial community composition in these arctic lakes. Principal coordinate analysis revealed differentiation of communities along two axes: each reflecting differences in morphometric (lake surface area), geographic (latitude and distance from the ice sheet), physical lake variables (water clarity), and lakewater chemistry (dissolved organic carbon [DOC], dissolved oxygen [DO], total nitrogen [TN], and conductivity). Understanding these relationships between environmental variables and microbial communities is especially important as heterotrophic microorganisms are key to organic matter decomposition, nutrient cycling, and carbon flow through nutrient poor aquatic environments in the Arctic.

Microbial communities associated with decomposing deadwood of downy birch in a natural forest in Khibiny Mountains (Kola Peninsula, Russian Federation)

Deadwood plays an important role in the forest ecosystems, providing nutrients and habitat for a wide range of organisms, preventing soil erosion, and improving carbon storage. Microorganisms are primary agents in wood decomposition. The aim of the present research is to describe the changes in diversity, structure and abundance of microbial communities over downy birch lying deadwood decomposition in a boreal forest under natural conditions. This study also included investigations on the potential involvement of deadwood in climate change.The decomposition of deadwood was visually assessed using a five-class system. The microbial community diversity and composition were assessed with polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting. Real time PCR was used to evaluate the absolute and relative microbial abundance. The potential involvement of deadwood in climate change was assessed by in situ-measuring of the carbon dioxide (CO2) emissions from downy birch lying deadwood and from soil.The results obtained indicate that deadwood represents a substrate whose physico-chemical and microbiological property change with time. Higher diversity of fungi, bacteria, and archaea were recorded in the decay class 5. Conversely, actinobacteria showed the lowest values of diversity in decay class 5. We observed a succession of dominant microbial taxa over the decomposition progress. Overall, the abundance of each microbial group increases with the advance of decomposition. Among the estimated physico-chemical properties, nitrogen content, that increased with decay, and pH were the most important candidate drivers of microbial community composition and abundance. CO2 emissions were recorded higher in the decay class 5 and in soil of plots with the highest amount of lying deadwood.Bacteria dominated the microbial community and may play a more important role in the late stages of wood decomposition conversely to fungi and actinobacteria that are assumed to be primary involved in early stages of wood colonization. Archaea are shown to be an integral and dynamic component of decaying wood biota. The presence of large amounts of deadwood may affect greenhouse gas (GHG) emissions, especially in the event of an increase in temperatures that could reduce the carbon (C) sink capacity of the boreal forests.

The pH optimum of soil exoenzymes adapt to long term changes in soil pH

Soil exoenzymes released by microorganisms break down organic matter and are crucial in regulating C, N and P cycling. Soil pH is known to influence enzyme activity, and is also a strong driver of microbial community composition; but little is known about how alterations in soil pH affect enzymatic activity and how this is mediated by microbial communities. To assess long term enzymatic adaptation to soil pH, we conducted enzyme assays at buffered pH levels on two historically managed soils maintained at either pH 5 or 7 from the Rothamsted Park Grass Long-term experiment. The pH optima for a range of exoenzymes involved in C, N, P cycling, differed between the two soils, the direction of the shift being toward the source soil pH, indicating the production of pH adapted isoenzymes by the soil microbial community. Soil bacterial and fungal communities determined by amplicon sequencing were clearly distinct between pH 5 and soil pH 7 soils, possibly explaining differences in enzymatic responses. Furthermore, β-glucosidase gene sequences extracted from metagenomes revealed an increased abundance of Acidobacterial producers in the pH 5 soils, and Actinobacteria in pH 7 soils. Our findings demonstrate that the pH optimum of soil exoenzymes adapt to long term changes in soil pH, the direction being dependent on the soil pH shift; and we provide further evidence that changes in functional microbial communities may underpin this phenomena, though new research is now needed to directly link change in enzyme activity optima with microbial communities. More generally, our new findings have large implications for modelling the efficiency of different microbial enzymatic processes under changing environmental conditions.

Relationship between microbial community and environmental conditions in a constructed wetland system treating greywater

Knowledge of the diversity of microbial communities and their relationship with biogeochemical cycles is a key factor in understanding and improving the performance of constructed wetland (CW) systems, allowing improvements in design and operation methods to reach the desired effluent quality. Assemblies of microbial groups in CWs are driven by several factors, including the environmental conditions of the mesocosm and substrate availability. This study combined physicochemical analyses, high-throughput DNA sequencing, and statistical methods to gain an insight into the influence of operational conditions on the bacteria and archaea communities in a modified constructed wetland system treating raw-light greywater. The EvaTAC system is composed of an upflow evapotranspiration and treatment tank (CEvaT) which has an inbuilt anaerobic chamber (AnC), followed by a horizontal subsurface flow constructed wetland (HSSF-CW). Samples were collected after five years of system operation in both units: sludge from the AnC, coarse gravel from the CEvaT, and fine gravel from the CW. The results showed that the system operated predominantly in anaerobic conditions, with redox potential (Eh) increasing from the inlet (−364.1 mV) to the outlet (−240.4 mV) zone. The Eh was the environmental condition that most influenced the microbial community diversity and richness, and, as well as Eh, increased along the light greywater (LGW) flow. Conversely, the chemical oxygen demand (COD) decreased, thus suggesting a negative correlation among these factors. The clustering analyses of microbial community showed that, besides environmental conditions, the media filter and related depth could also be drivers of microbial community composition. The bottom layer of CEvaT was assigned to the Proteobacteria and Synergistetes phyla indicating the accomplishment of the first steps of anaerobic digestion. The next layer was characterised by the presence of Desulfovibrio, Syntrophobacter, and Methanobacterium, microorganisms responsible for the sulfidogenesis and methanogenesis processes. Finally, in the CW zone, the community composition was dominated by microorganisms involved in the methane oxidation, such as Methylosinus, Bradyrhizobium, and Candidatus Koribacter. This study explored the universe of bacteria and archaea communities, and is an initial step in elucidating microbial diversity conversions in CW systems treating greywater, which is important knowledge to steer the conversion pathway and establish the ideal environmental conditions for the development of desired microbial communities in these systems.

Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures.

Temperature is a primary driver of microbial community composition and taxonomic diversity; however, it is unclear to what extent temperature affects characteristics of central carbon metabolic pathways (CCMPs) at the community level. In this study, 16S rRNA gene amplicon and metagenome sequencing were combined with 13C-labeled metabolite probing of the CCMPs to assess community carbon metabolism along a temperature gradient (60–95°C) in Great Boiling Spring, NV. 16S rRNA gene amplicon diversity was inversely proportional to temperature, and Archaea were dominant at higher temperatures. KO richness and diversity were also inversely proportional to temperature, yet CCMP genes were similarly represented across the temperature gradient and many individual metagenome-assembled genomes had complete pathways. In contrast, genes encoding cellulosomes and many genes involved in plant matter degradation and photosynthesis were absent at higher temperatures. In situ 13C-CO2 production from labeled isotopomer pairs of glucose, pyruvate, and acetate suggested lower relative oxidative pentose phosphate pathway activity and/or fermentation at 60°C, and a stable or decreased maintenance energy demand at higher temperatures. Catabolism of 13C-labeled citrate, succinate, L-alanine, L-serine, and L-cysteine was observed at 85°C, demonstrating broad heterotrophic activity and confirming functioning of the TCA cycle. Together, these results suggest that temperature-driven losses in biodiversity and gene content in geothermal systems may not alter CCMP function or maintenance energy demands at a community level.

Plant host identity and soil macronutrients explain little variation in sapling endophyte community composition: Is disturbance an alternative explanation?

Abstract Bacterial endophytes may be fairly host‐specific; nonetheless, an important subset of taxa may be shared among numerous host species forming a community‐wide core microbiome. Moreover, other key factors, particularly the supply of limiting macronutrients and disturbances, may supersede the importance of host identity. We tested the following four non‐mutually exclusive hypotheses: (a) The Host Identity Hypothesis: endophytes vary substantially among different host‐plant species. (b) The Core Microbiome Hypothesis: a subset of microbial taxa will be shared among all host‐plant species. (c). The Soil Resource Supply Hypothesis: endophytes vary substantially among habitats with experimentally elevated levels of macronutrients. (d) The Disturbance–Disruption Hypothesis: disturbances created by the periodic application of antibiotics structure bacterial endophyte communities. We tested these hypotheses by characterizing endophytes using high‐throughput sequencing among seedlings of five phylogenetically diverse tree species nested within a long‐term, full factorial nitrogen, phosphorus and potassium soil fertilization experiment. We artificially disturbed one of our focal species by applying antibiotics every 10–14 days for 29 months within the soil (N, P, K) fertilization experiment. While we detected a significant effect of host identity and soil nutrient additions, together they explained little variation in endophyte community composition (<10%). We found unequivocal evidence for a core microbiome shared by all species. Specifically, we inferred that nine OTUs were present among 95% or more of all control saplings, representing a third of the total reads. These bacterial taxa belonged to the Actinobacteria. In contrast, disturbance (antibiotics) explained more endophyte variation than all nutrient addition combinations combined and twice the variation explained by host identity for all five tree species. Synthesis. Our results challenge the idea that host identity is a primary filter shaping bacterial endophyte communities; this suggests that many of the same bacterial taxa occur inside plant hosts even if those host plants are phylogenetically diverse. Moreover, we documented a distinct core microbiome shared among our five focal tree species. Finally, we found that disturbance rather than host identity and soil nutrient availability was an important driver of microbial community composition, which parallels the importance of disturbance in other areas of community ecology.

Impact of Phaeobacter inhibens on marine eukaryote-associated microbial communities.

Bacteria-host interactions are universal in nature and have significant effects on host functionality. Bacterial secondary metabolites are believed to play key roles in such interactions as well as in interactions within the host-associated microbial community. Hence, prominent secondary metabolite-producing bacteria may be strong drivers of microbial community composition in natural host-associated microbiomes. This has, however, not been rigorously tested, and the purpose of this study was to investigate how the secondary metabolite producer Phaeobacter inhibens affects the diversity and composition of microbiomes associated with the microalga Emiliania huxleyi and the European flat oyster, Ostrea edulis. Roseobacters were indigenous to both communities exhibiting relative abundances between 2.8% and 7.0%. Addition of P. inhibens caused substantial changes in the overall structure of the low-complexity microbiome of E. huxleyi, but did not shape microbial community structure to the same degree in the more complex oyster microbiomes. Species-specific interactions occurred in both microbiomes and specifically the abundances of other putative secondary metabolite-producers such as vibrios and pseudoalteromonads were reduced. Thus, the impact of a bioactive strain like P. inhibens on host-associated microbiomes depends on the complexity and composition of the existing microbiome.

B Vitamins and Their Congeners as Potential Drivers of Microbial Community Composition in an Oligotrophic Marine Ecosystem

AbstractDetermining the factors that influence marine microbial growth and community structure are critical for the understanding of global carbon cycling. Since the early twentieth century, it has been known that B vitamins play an important role in phytoplankton community dynamics. Limited oceanic dissolved B vitamin distributions indicate that these important coenzymes are present at picomolar levels, which could be too low to support maximal phytoplankton growth, and vast regions of the ocean exist where they are undetectable. Despite their importance, particulate B vitamin concentrations of field microbial populations are unknown. Here we report B vitamin concentrations measured in both the particulate and dissolved fractions, including multiple biochemically relevant B vitamin congeners. We establish their spatial distributions spanning distinct biogeographic and oceanographic regimes in the Mediterranean Sea and the Eastern Atlantic Ocean and show that all congeners are present both dissolved in seawater and in suspended particles. We observe that B vitamins cooccur in patches defined by regional biogeographic and oceanographic features. Additionally, distinct patterns of congener relative abundance in the dissolved and particulate pools provide insight to biological and chemical cycling of these compounds between and within the dissolved and particulate pools. Finally, linear model results demonstrate that model fits of microbial assemblages are strongest when they include both inorganic nutrients and dissolved B vitamin concentrations. We believe that these findings represent an advance in our understanding of B vitamin oceanographic distributions and point to interesting hypotheses of their influence on marine microbial ecology.