Dispersal alters bacterial diversity and composition in a natural community

Distance-decay equations of antibiotic resistance genes across freshwater reservoirs

Distance-decay (DD) equations can discern the biogeographical pattern of organisms and genes in a better way with advanced statistical methods. Here, we developed a data Compilation, Arrangement, and Statistics framework to advance quantile regression (QR) into the generation of DD equations for antibiotic resistance genes (ARGs) across various spatial scales using freshwater reservoirs as an illustration. We found that QR is superior at explaining dissemination potential of ARGs to the traditionally used least squares regression (LSR). This is because our model is based on the 'law of limiting factors', which reduces influence of unmeasured factors that reduce the efficacy of the LSR method. DD equations generated from the 99th QR model for ARGs were 'Sall = 90.03e-0.01Dall' in water and 'Sall = 92.31e-0.011Dall' in sediment. The 99th QR model was less impacted by uneven sample sizes, resulting in a better quantification of ARGs dissemination. Within an individual reservoir, the 99th QR model demonstrated that there is no dispersal limitation of ARGs at this smaller spatial scale. The QR method not only allows for construction of robust DD equations that better display dissemination of organisms and genes across ecosystems, but also provides new insights into the biogeography exhibited by key parameters, as well as the interactions between organisms and environment.

Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations

BACKGROUND

Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method.

RESULTS

Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations.

CONCLUSIONS

Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.

High immigration rates critical for establishing emigration-driven diversity in microbial communities

Unraveling the mechanisms governing the diversity of ecological communities is a central goal in ecology. Although microbial dispersal constitutes an important ecological process, the effect of dispersal on microbial diversity is poorly understood. Here, we sought to fill this gap by combining a generalized Lotka-Volterra model with experimental investigations. Our model showed that emigration increases the diversity of the community when the immigration rate crosses a defined threshold, which we identified as Ineutral. We also found that at high immigration rates, emigration weakens the relative abundance of fast-growing species and thus enhances the mass effect and increases the diversity. We experimentally confirmed this finding using co-cultures of 20 bacterial strains isolated from the soil. Our model further showed that Ineutral decreases with the increase of species pool size, growth rate, and interspecies interaction. Our work deepens the understanding of the effects of dispersal on the diversity of natural communities.

Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

Long-term (press) disturbances like the climate crisis and other anthropogenic pressures are fundamentally altering ecosystems and their functions. Many critical ecosystem functions, such as biogeochemical cycling, are facilitated by microbial communities. Understanding the functional consequences of microbiome responses to press disturbances requires ongoing observations of the active populations that contribute to functions. This study leverages a 7-year time series of a 60-year-old coal seam fire (Centralia, Pennsylvania, USA) to examine the resilience of soil bacterial microbiomes to a press disturbance. Using 16S rRNA and 16S rRNA gene amplicon sequencing, we assessed the interannual dynamics of the active subset and the 'whole' bacterial community. Contrary to our hypothesis, the whole communities demonstrated greater resilience than active subsets, suggesting that inactive members contributed to overall structural resilience. Thus, in addition to selection mechanisms of active populations, perceived microbiome resilience is also supported by mechanisms of dispersal, persistence, and revival from the local dormant pool.

Unraveling plant-microbe interactions: can integrated omics approaches offer concrete answers?

Advances in high throughput omics techniques provide avenues to decipher plant microbiomes. However, there is limited information on how integrated informatics can help provide deeper insights into plant-microbe interactions in a concerted way. Integrating multi-omics datasets can transform our understanding of the plant microbiome from unspecified genetic influences on interacting species to specific gene-by-gene interactions. Here, we highlight recent progress and emerging strategies in crop microbiome omics research and review key aspects of how the integration of host and microbial omics-based datasets can be used to provide a comprehensive outline of complex crop-microbe interactions. We describe how these technological advances have helped unravel crucial plant and microbial genes and pathways that control beneficial, pathogenic, and commensal plant-microbe interactions. We identify crucial knowledge gaps and synthesize current limitations in our understanding of crop microbiome omics approaches. We highlight recent studies in which multi-omics-based approaches have led to improved models of crop microbial community structure and function. Finally, we recommend holistic approaches in integrating host and microbial omics datasets to achieve precision and efficiency in data analysis, which is crucial for biotic and abiotic stress control and in understanding the contribution of the microbiota in shaping plant fitness.

Bacterial diversity in a continuum from supraglacial habitats to a proglacial lake on the Tibetan Plateau

Mountain glaciers are frequently assessed for their hydrological connectivity from glaciers to proglacial lakes. Ecological process on glacier surfaces and downstream ecosystems have often been investigated separately, but few studies have focused on the connectivity between the different glacial habitats. Therefore, it remains a limited understanding of bacterial community assembly across different habitats along the glacier hydrological continuum. In this study, we sampled along a glacial catchment from supraglacial snow, cryoconite holes, supraglacial runoff, ice-marginal moraine and proglacial lake on the Tibetan Plateau. The bacterial communities in these habitats were analyzed using high-throughput DNA sequencing of the 16S rRNA gene to determine the bacterial composition and assembly. Our results showed that each habitat hosted unique bacterial communities, with higher bacterial α-diversity in transitional habitats (e.g. runoff and ice-marginal moraine). Null model analysis indicated that deterministic processes predominantly shaped bacterial assembly in snow, cryoconite holes and lake, while stochastic process dominantly governed bacterial community in transitional habitats. Collectively, our findings suggest that local environment play a critical role in filtering bacterial community composition within glacier habitats. This study enhances our understanding of microbial assembly process in glacier environments and provides valuable insights into the factors governing bacterial community compositions across different habitats along the glacial hydrological continuum.

Investigating eco-evolutionary processes of microbial community assembly in the wild using a model leaf litter system

Microbial communities are not the easiest to manipulate experimentally in natural ecosystems. However, leaf litter-topmost layer of surface soil-is uniquely suitable to investigate the complexities of community assembly. Here, we reflect on over a decade of collaborative work to address this topic using leaf litter as a model system in Southern California ecosystems. By leveraging a number of methodological advantages of the system, we have worked to demonstrate how four processes-selection, dispersal, drift, and diversification-contribute to bacterial and fungal community assembly and ultimately impact community functioning. Although many dimensions remain to be investigated, our initial results demonstrate that both ecological and evolutionary processes occur simultaneously to influence microbial community assembly. We propose that the development of additional and experimentally tractable microbial systems will be enormously valuable to test the role of eco-evolutionary processes in natural settings and their implications in the face of rapid global change.

Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence

When bacterial communities mix, immigration history can fundamentally affect the community composition as a result of priority effects. Priority effects arise when an early immigrant exhausts resources and/or alters habitat conditions, thereby influencing the establishment success of the late arriver. The strength of priority effects is context-dependent and expected to be stronger if environmental conditions favour the growth of the first arriver. In this study, we conducted a two-factorial experiment testing the importance of nutrient availability and grazing on the strength of priority effects in complex aquatic bacterial communities. We did so by mixing two dissimilar communities, simultaneously, and with a 38 h time-delay. Priority effects were measured as the invasion resistance of the first community to the invading second community. We found stronger priority effects in treatments with high nutrient availability and absence of grazing, but in general, the arrival timing was less important than the selection by nutrients and grazing. At the population level, the results were complex, but priority effects may have been driven by bacteria belonging to for example, the genera Rhodoferax and Herbaspirillum. Our study highlights the importance of arrival timing in complex bacterial communities, especially if environmental conditions favour rapid community growth.

Testing the contribution of dispersal to microbial succession following a wildfire

IMPORTANCE

Identifying the mechanisms underlying microbial community succession is necessary for predicting how microbial communities, and their functioning, will respond to future environmental change. Dispersal is one mechanism expected to affect microbial succession, yet the difficult nature of manipulating microorganisms in the environment has limited our understanding of its contribution. Using a dispersal exclusion experiment, this study isolates the specific effect of environmental dispersal on bacterial and fungal community assembly over time following a wildfire. The work demonstrates the potential to quantify dispersal impacts on soil microbial communities over time and test how dispersal might further interact with other assembly processes in response to environmental change.

Investigating the eco-evolutionary response of microbiomes to environmental change

Microorganisms are the primary engines of biogeochemical processes and foundational to the provisioning of ecosystem services to human society. Free-living microbial communities (microbiomes) and their functioning are now known to be highly sensitive to environmental change. Given microorganisms' capacity for rapid evolution, evolutionary processes could play a role in this response. Currently, however, few models of biogeochemical processes explicitly consider how microbial evolution will affect biogeochemical responses to environmental change. Here, we propose a conceptual framework for explicitly integrating evolution into microbiome-functioning relationships. We consider how microbiomes respond simultaneously to environmental change via four interrelated processes that affect overall microbiome functioning (physiological acclimation, demography, dispersal and evolution). Recent evidence in both the laboratory and the field suggests that ecological and evolutionary dynamics occur simultaneously within microbiomes; however, the implications for biogeochemistry under environmental change will depend on the timescales over which these processes contribute to a microbiome's response. Over the long term, evolution may play an increasingly important role for microbially driven biogeochemical responses to environmental change, particularly to conditions without recent historical precedent.

Plant Community Associates with Rare Rather than Abundant Fungal Taxa in Alpine Grassland Soils

The importance of the rare microbial biosphere in maintaining biodiversity and ecological functions has been highlighted recently. However, the current understanding of the spatial distribution of rare microbial taxa is still limited, with only a few investigations for rare prokaryotes and virtually none for rare fungi. Here, we investigated the spatial patterns of rare and abundant fungal taxa in alpine grassland soils across 2,000 km of the Qinghai-Tibetan plateau. We found that most locally rare fungal taxa remained rare (13.07%) or were absent (82.85%) in other sites, whereas only a small proportion (4.06%) shifted between rare and abundant among sites. Although they differed in terms of diversity levels and compositions, the distance decay relationships of both the rare and the abundant fungal taxa were valid and displayed similar turnover rates. Moreover, the community assemblies of both rare and abundant fungal taxa were predominantly controlled by deterministic rather than stochastic processes. Notably, the community composition of rare rather than abundant fungal taxa associated with the plant community composition. In summary, this study advances our understanding of the biogeographic features of rare fungal taxa in alpine grasslands and highlights the concordance between plant communities and rare fungal subcommunities in soil. IMPORTANCE Our current understanding of the ecology and functions of rare microbial taxa largely relies on research conducted on prokaryotes. Despite the key ecological roles of soil fungi, little is known about the biogeographic patterns and drivers of rare and abundant fungi in soils. In this study, we investigated the spatial patterns of rare and abundant fungal taxa in Qinghai-Tibetan plateau (QTP) alpine grassland soils across 2,000 km, with a special concentration on the importance of the plant communities in shaping rare fungal taxa. We showed that rare fungal taxa generally had a biogeographic pattern that was similar to that of abundant fungal taxa in alpine grassland soils on the QTP. Furthermore, the plant community composition was strongly related to the community composition of rare taxa but not abundant taxa. In summary, this study significantly increases our biogeographic and ecological knowledge of rare fungal taxa in alpine grassland soils.

Bacterioplankton dispersal and biogeochemical function across Alaskan Arctic catchments

In Arctic catchments, bacterioplankton are dispersed through soils and streams, both of which freeze and thaw/flow in phase, seasonally. To characterize this dispersal and its potential impact on biogeochemistry, we collected bacterioplankton and measured stream physicochemistry during snowmelt and after vegetation senescence across multiple stream orders in alpine, tundra, and tundra-dominated-by-lakes catchments. In all catchments, differences in community composition were associated with seasonal thaw, then attachment status (i.e. free floating or sediment associated), and then stream order. Bacterioplankton taxonomic diversity and richness were elevated in sediment-associated fractions and in higher-order reaches during snowmelt. Families Chthonomonadaceae, Pyrinomonadaceae, and Xiphinematobacteraceae were abundantly different across seasons, while Flavobacteriaceae and Microscillaceae were abundantly different between free-floating and sediment-associated fractions. Physicochemical data suggested there was high iron (Fe⁺ ) production (alpine catchment); Fe⁺ production and chloride (Cl^- ) removal (tundra catchment); and phosphorus (SRP) removal and ammonium (NH₄ ⁺ ) production (lake catchment). In tundra landscapes, these 'hot spots' of Fe⁺ production and Cl^- removal accompanied shifts in species richness, while SRP promoted the antecedent community. Our findings suggest that freshet increases bacterial dispersal from headwater catchments to receiving catchments, where bacterioplankton-mineral relations stabilized communities in free-flowing reaches, but bacterioplankton-nutrient relations stabilized those punctuated by lakes.

Routes and rates of bacterial dispersal impact surface soil microbiome composition and functioning

Recent evidence suggests that, similar to larger organisms, dispersal is a key driver of microbiome assembly; however, our understanding of the rates and taxonomic composition of microbial dispersal in natural environments is limited. Here, we characterized the rate and composition of bacteria dispersing into surface soil via three dispersal routes (from the air above the vegetation, from nearby vegetation and leaf litter near the soil surface, and from the bulk soil and litter below the top layer). We then quantified the impact of those routes on microbial community composition and functioning in the topmost litter layer. The bacterial dispersal rate onto the surface layer was low (7900 cells/cm2/day) relative to the abundance of the resident community. While bacteria dispersed through all three routes at the same rate, only dispersal from above and near the soil surface impacted microbiome composition, suggesting that the composition, not rate, of dispersal influenced community assembly. Dispersal also impacted microbiome functioning. When exposed to dispersal, leaf litter decomposed faster than when dispersal was excluded, although neither decomposition rate nor litter chemistry differed by route. Overall, we conclude that the dispersal routes transport distinct bacterial communities that differentially influence the composition of the surface soil microbiome.

The effect of migration and variation on populations of Escherichia coli adapting to complex fluctuating environments

Migration, a critical evolutionary force, can have contrasting effects on adaptation. It can aid as well as impede adaptation. The effects of migration on microbial adaptation have been studied primarily in simple constant environments. Very little is known about the effects of migration on adaptation to complex, fluctuating environments. In our study, we subjected replicate populations of Escherichia coli, adapting to complex and unpredictably fluctuating environments to different proportions of clonal ancestral immigrants. Contrary to the results from simple/constant environments, the presence of clonal immigrants reduced all measured proxies of fitness. However, migration from a source population with a greater variance in fitness resulted in no change in fitness with respect to the no-migration control, except at the highest level of migration. Thus, the presence of variation in the immigrants could counter the adverse effects of migration in complex and unpredictably fluctuating environments. Our study demonstrates that the effects of migration are strongly dependent on the nature of the destination environment and the genetic makeup of immigrants. These results enhance our understanding of the influences of migrating populations, which could help better predict the consequences of migration.

Disentangling the Mechanisms Shaping the Prokaryotic Communities in a Eutrophic Bay

Eutrophication occurring in coastal bays is prominent in impacting local ecosystem structure and functioning. To understand how coastal bay ecosystem function responds to eutrophication, comprehending the ecological processes associated with microbial community assembly is critical. However, quantifying the contribution of ecological processes to the assembly of prokaryotic communities is still limited in eutrophic waters. Moreover, the influence of these ecological processes on microbial interactions is poorly understood. Here, we examined the assembly processes and co-occurrence patterns of prokaryotic communities in a eutrophic bay using 156 surface seawater samples collected over 12 months. The variation of prokaryotic community compositions (PCCs) could be mainly explained by environmental factors, of which temperature was the most important. Under high environmental heterogeneity conditions in low-temperature seasons, heterogeneous selection was the major assembly process, resulting in high β-diversity and more tightly connected co-occurrence networks. When environmental heterogeneity decreased in high-temperature seasons, drift took over, leading to decline in β-diversity and network associations. Microeukaryotes were found to be important biological factors affecting PCCs. Our results first disentangled the contribution of drift and microbial interactions to the large unexplained variation of prokaryotic communities in eutrophic waters. Furthermore, a new conceptual model linking microbial interactions to ecological processes was proposed under different environmental heterogeneity. Overall, our study sheds new light on the relationship between assembly processes and co-occurrence of prokaryotic communities in eutrophic waters. IMPORTANCE A growing number of studies have examined roles of microbial community assembly in modulating community composition. However, the relationships between community assembly and microbial interactions are not fully understood and rarely tested, especially in eutrophic waters. In this study, we built a conceptual model that links seasonal microbial interactions to ecological processes, which has not been reported before. The model showed that heterogeneous selection plays an important role in driving community assembly during low-temperature seasons, resulting in higher β-diversity and more tightly connected networks. In contrast, drift became a dominant force during high-temperature seasons, leading to declines in the β-diversity and network associations. This model could function as a new framework to predict how prokaryotic communities respond to intensified eutrophication induced by climate change in coastal environment.

Elevational Gradients Impose Dispersal Limitation on Streptomyces

Dispersal governs microbial biogeography, but the rates and mechanisms of dispersal remain poorly characterized for most microbial taxa. Dispersal limitation is driven by limits on dissemination and establishment, respectively. Elevation gradients create striking patterns of biogeography because they produce steep environmental gradients at small spatial scales, and these gradients offer a powerful tool to examine mechanisms of dispersal limitation. We focus on Streptomyces, a bacterial genus common to soil, by using a taxon-specific phylogenetic marker, the RNA polymerase-encoding rpoB gene. By targeting Streptomyces, we assess dispersal limitation at finer phylogenetic resolution than is possible using whole community analyses. We characterized Streptomyces diversity at local spatial scales (100 to 3,000 m) in two temperate forest sites located in the Adirondacks region of New York State: Woods Lake (<100 m elevation change), and Whiteface Mountain (>1,000 m elevation change). Beta diversity varied considerably at both locations, indicative of dispersal limitation acting at local spatial scales, but beta diversity was significantly higher at Whiteface Mountain. Beta diversity varied across elevation at Whiteface Mountain, being lowest at the mountain’s base. We show that Streptomyces taxa exhibit elevational preferences, and these preferences are phylogenetically conserved. These results indicate that habitat preferences influence Streptomyces biogeography and suggest that barriers to establishment structure Streptomyces communities at higher elevations. These data illustrate that Streptomyces biogeography is governed by dispersal limitation resulting from a complex mixture of stochastic and deterministic processes.

Farm-scale differentiation of active microbial colonizers

Microbial movement is important for replenishing lost soil microbial biodiversity and driving plant root colonization, particularly in managed agricultural soils, where microbial diversity and composition can be disrupted. Despite abundant survey-type microbiome data in soils, which are obscured by legacy DNA and microbial dormancy, we do not know how active microbial pools are shaped by local soil properties, agricultural management, and at differing spatial scales. To determine how active microbial colonizers are shaped by spatial scale and environmental conditions, we deployed microbial traps (i.e. sterile soil enclosed by small pore membranes) containing two distinct soil types (forest; agricultural), in three neighboring locations, assessing colonization through 16S rRNA gene and fungal ITS amplicon sequencing. Location had a greater impact on fungal colonizers (R2 = 0.31 vs. 0.26), while the soil type within the microbial traps influenced bacterial colonizers more (R2 = 0.09 vs. 0.02). Bacterial colonizers showed greater colonization consistency (within-group similarity) among replicate communities. Relative to bacterial colonizers, fungal colonizers shared a greater compositional overlap to sequences from the surrounding local bulk soil (R2 = 0.08 vs. 0.29), suggesting that these groups respond to distinct environmental constraints and that their in-field management may differ. Understanding how environmental constraints and spatial scales impact microbial recolonization dynamics and community assembly are essential for identifying how soil management can be used to shape agricultural microbiomes.

Ecological and Evolutionary Implications of Microbial Dispersal

Dispersal is simply defined as the movement of species across space and time. Despite this terse definition, dispersal is an essential process with direct ecological and evolutionary implications that modulate community assembly and turnover. Seminal ecological studies have shown that environmental context (e.g., local edaphic properties, resident community), dispersal timing and frequency, and species traits, collectively account for patterns of species distribution resulting in either their persistence or unsuccessful establishment within local communities. Despite the key importance of this process, relatively little is known about how dispersal operates in microbiomes across divergent systems and community types. Here, we discuss parallels of macro- and micro-organismal ecology with a focus on idiosyncrasies that may lead to novel mechanisms by which dispersal affects the structure and function of microbiomes. Within the context of ecological implications, we revise the importance of short- and long-distance microbial dispersal through active and passive mechanisms, species traits, and community coalescence, and how these align with recent advances in metacommunity theory. Conversely, we enumerate how microbial dispersal can affect diversification rates of species by promoting gene influxes within local communities and/or shifting genes and allele frequencies via migration or de novo changes (e.g., horizontal gene transfer). Finally, we synthesize how observed microbial assemblages are the dynamic outcome of both successful and unsuccessful dispersal events of taxa and discuss these concepts in line with the literature, thus enabling a richer appreciation of this process in microbiome research.

Microbial Dispersal, Including Bison Dung Vectored Dispersal, Increases Soil Microbial Diversity in a Grassland Ecosystem

Microbial communities display biogeographical patterns that are driven by local environmental conditions and dispersal limitation, but the relative importance of underlying dispersal mechanisms and their consequences on community structure are not well described. High dispersal rates can cause soil microbial communities to become more homogenous across space and therefore it is important to identify factors that promote dispersal. This study experimentally manipulated microbial dispersal within different land management treatments at a native tallgrass prairie site, by changing the relative openness of soil to dispersal and by simulating vector dispersal via bison dung addition. We deployed experimental soil bags with mesh open or closed to dispersal, and placed bison dung over a subset of these bags, to areas with three different land managements: active bison grazing and annual fire, annual fire but no bison grazing, and no bison grazing with infrequent fire. We expected microbial dispersal to be highest in grazed and burned environments, and that the addition of dung would consistently increase overall microbial richness and lead to homogenization of communities over time. Results show that dispersal rates, as the accumulation of taxa over the course of the 3-month experiment, increase taxonomic richness similarly in all land management treatments. Additionally, bison dung seems to be serving as a dispersal and homogenization vector, based on the consistently higher taxon richness and increased community similarity across contrasting grazing and fire treatments when dung is added. This finding also points to microbial dispersal as an important function that herbivores perform in grassland ecosystems, and in turn, as a function that was lost at a continental scale following bison extermination across the Great Plains of North America in the nineteenth century. This study is the first to detect that dispersal and vector dispersal by grazing mammals promote grassland soil microbial diversity and affect microbial community composition.

A framework for integrating microbial dispersal modes into soil ecosystem ecology

Dispersal is a fundamental community assembly process that maintains soil microbial biodiversity across spatial and temporal scales, yet the impact of dispersal on ecosystem function is largely unpredictable. Dispersal is unique in that it contributes to both ecological and evolutionary processes and is shaped by both deterministic and stochastic forces. The ecosystem-level ramifications of dispersal outcomes are further compounded by microbial dormancy dynamics and environmental selection. Here we review the knowledge gaps and challenges that remain in defining how dispersal, environmental filtering, and microbial dormancy interact to influence the relationship between microbial community structure and function in soils. We propose the classification of microbial dispersal into three categories, through vegetative or active cells, through dormant cells, and through acellular dispersal, each with unique spatiotemporal dynamics and microbial trait associations. This conceptual framework should improve the integration of dispersal in defining soil microbial community structure-function relationships.

When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment

In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.

Soil plastispheres as hotpots of antibiotic resistance genes and potential pathogens

In the Anthropocene, increasing pervasive plastic pollution is creating a new environmental compartment, the plastisphere. How the plastisphere affects microbial communities and antibiotic resistance genes (ARGs) is an issue of global concern. Although this has been studied in aquatic ecosystems, our understanding of plastisphere microbiota in soil ecosystems remains poor. Here, we investigated plastisphere microbiota and ARGs of four types of microplastics (MPs) from diverse soil environments, and revealed effects of manure, temperature, and moisture on them. Our results showed that the MPs select for microbial communities in the plastisphere, and that these plastisphere communities are involved in diverse metabolic pathways, indicating that they could drive diverse ecological processes in the soil ecosystem. The relationship within plastisphere bacterial zero-radius operational taxonomic units (zOTUs) was predominantly positive, and neutral processes appeared to dominate community assembly. However, deterministic processes were more important in explaining the variance in ARGs in plastispheres. A range of potential pathogens and ARGs were detected in the plastisphere, which were enriched compared to the soil but varied across MPs and soil types. We further found that the addition of manure and elevation of soil temperature and moisture all enhance ARGs in plastispheres, and potential pathogens increase with soil moisture. These results suggested that plastispheres are habitats in which an increased potential pathogen abundance is spatially co-located with an increased abundance of ARGs under global change. Our findings provided new insights into the community ecology of the microbiome and antibiotic resistome of the soil plastisphere.

Culturable bacteria are more common than fungi in floral nectar and are more easily dispersed by thrips, a ubiquitous flower visitor

Variation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results with the incidence and abundance of culturable flower-inhabiting bacteria and fungi within naturally occurring flowers across two coflowering communities in California across two flowering seasons. Our microbial dispersal experiment demonstrates that bacteria disperse via thrips among artificial habitat patches more readily than fungi. In the field, incidence and abundance of culturable bacteria and fungi were positively correlated, but bacteria were much more widespread. These patterns suggest shared dispersal routes or habitat requirements among culturable bacteria and fungi, but differences in dispersal or colonization frequency by thrips, common flower visitors. The finding that culturable bacteria are more common among nectar sampled here, in part due to superior thrips-mediated dispersal, may have relevance for microbial life history, community assembly of microbes, and plant-pollinator interactions.

Effects of dispersal on species distribution, abundance, diversity and interaction in a bacterial biofilm metacommunity

AIMS

Dispersal effects on biofilms have not been adequately studied despite their strong potential impacts on biofilm development. We investigated the effects of dispersal on biofilm metacommunity.

METHODS AND RESULTS

A bacterial consortium was allowed to form biofilms on 12 glass beads attached to disposable plates (compartmentalized or not), and biofilms were scrutinized on days 5, 10 and 15 using quantitative PCR and MiSeq sequencing. Biofilm population density was lesser by 2 orders of magnitude on day 5 when dispersal was allowed (p < 0.05). Then, the population rapidly increased by 4.4 orders with dispersal (p < 0.05) but did not change without dispersal. Community analyses revealed that dispersal increased the species diversity at all sampling times (p < 0.05). Dispersal affected the community structure and increased the homogeneity of local communities (p < 0.05). Distance-decay analysis showed that dispersal reduced the dissimilarity among local communities at all distance levels. Furthermore, dispersal reduced the variability of diversity, population and community structure. Network analysis revealed that dispersal increased the clustering coefficient, network density and connectivity.

CONCLUSIONS

Dispersal increased the species diversity, population and interaction and reduced the variability of the diversity, population and structure among local communities.

SIGNIFICANCE AND IMPACT OF STUDY

Our results suggest that dispersal can induce the niche complementarity and mass effects.

Adaptive differentiation and rapid evolution of a soil bacterium along a climate gradient

Increasing evidence suggests that evolutionary processes frequently shape ecological patterns; however, most microbiome studies thus far have focused on only the ecological responses of these communities. By using parallel field experiments and focusing in on a model soil bacterium, we showed that bacterial “species” are differentially adapted to local climates, leading to changes in their composition. Furthermore, we detected strain-level evolution, providing direct evidence that both ecological and evolutionary processes operate on annual timescales. The consideration of eco-evolutionary dynamics may therefore be important to understand the response of soil microbiomes to future environmental change.

Microbial community responses to environmental change are largely associated with ecological processes; however, the potential for microbes to rapidly evolve and adapt remains relatively unexplored in natural environments. To assess how ecological and evolutionary processes simultaneously alter the genetic diversity of a microbiome, we conducted two concurrent experiments in the leaf litter layer of soil over 18 mo across a climate gradient in Southern California. In the first experiment, we reciprocally transplanted microbial communities from five sites to test whether ecological shifts in ecotypes of the abundant bacterium, Curtobacterium, corresponded to past adaptive differentiation. In the transplanted communities, ecotypes converged toward that of the native communities growing on a common litter substrate. Moreover, these shifts were correlated with community-weighted mean trait values of the Curtobacterium ecotypes, indicating that some of the trait variation among ecotypes could be explained by local adaptation to climate conditions. In the second experiment, we transplanted an isogenic Curtobacterium strain and tracked genomic mutations associated with the sites across the same climate gradient. Using a combination of genomic and metagenomic approaches, we identified a variety of nonrandom, parallel mutations associated with transplantation, including mutations in genes related to nutrient acquisition, stress response, and exopolysaccharide production. Together, the field experiments demonstrate how both demographic shifts of previously adapted ecotypes and contemporary evolution can alter the diversity of a soil microbiome on the same timescale.

Microbial Communities in Full-Scale Wastewater Treatment Systems Exhibit Deterministic Assembly Processes and Functional Dependency over Time

Microbial communities constitute the core component of biological wastewater treatment processes. We conducted a meta-analysis based on the 16S rRNA gene of temporal samples obtained from diverse full-scale activated sludge and anaerobic digestion systems treating municipal and industrial wastewater (collected in this study and published previously) to investigate their community assembly mechanism and functional traits over time, which are not currently well understood. The influent composition was found to be the main driver of the microbial community's composition, and relatively large proportions of specialist (26.1% and 18.6%) and transient taxa (67.2% and 68.1%) were estimated in both systems. Deterministic processes, especially homogeneous selection events (accounting for >53.8% of assembly events), were consistently identified as the dominant microbial community assembly mechanisms in both systems over time. Significant and strong correlations (Pearson's r = 0.51-0.92) were detected between the dynamics of the temporal community and the functional compositions in both systems, which suggests functional dependency. In contrast, the occurrence of sludge bulking and foaming in the activated sludge system led to an increase in stochastic assembly processes (i.e., limited dispersal and undominated events), a shift toward functional redundancy and less community diversity, a decreased community niche breadth index, and a more compact co-association network. This study illustrates that the mechanism of microbial community assembly and functional traits over time can be used to diagnose system performance and provide information on potential system malfunction.

Sources and Assembly of Microbial Communities in Vineyards as a Functional Component of Winegrowing

Microbiomes are integral to viticulture and winemaking – collectively termed winegrowing – where diverse fungi and bacteria can exert positive and negative effects on grape health and wine quality. Wine is a fermented natural product, and the vineyard serves as a key point of entry for quality-modulating microbiota, particularly in wine fermentations that are conducted without the addition of exogenous yeasts. Thus, the sources and persistence of wine-relevant microbiota in vineyards critically impact its quality. Site-specific variations in microbiota within and between vineyards may contribute to regional wine characteristics. This includes distinctions in microbiomes and microbiota at the strain level, which can contribute to wine flavor and aroma, supporting the role of microbes in the accepted notion of terroir as a biological phenomenon. Little is known about the factors driving microbial biodiversity within and between vineyards, or those that influence annual assembly of the fruit microbiome. Fruit is a seasonally ephemeral, yet annually recurrent product of vineyards, and as such, understanding the sources of microbiota in vineyards is critical to the assessment of whether or not microbial terroir persists with inter-annual stability, and is a key factor in regional wine character, as stable as the geographic distances between vineyards. This review examines the potential sources and vectors of microbiota within vineyards, general rules governing plant microbiome assembly, and how these factors combine to influence plant-microbe interactions relevant to winemaking.

Stream Microbial Community Structured by Trace Elements, Headwater Dispersal, and Large Reservoirs in Sub-Alpine and Urban Ecosystems

Stream bacterioplankton communities, a crucial component of aquatic ecosystems and surface water quality, are shaped by environmental selection (i.e., changes in taxa abundance associated with more or less favorable abiotic conditions) and passive dispersal (i.e., organisms' abundance and distribution is a function of the movement of the water). These processes are a function of hydrologic conditions such as residence time and water chemistry, which are mediated by human infrastructure. To quantify the role of environmental conditions, dispersal, and human infrastructure (dams) on stream bacterioplankton, we measured bacterioplankton community composition in rivers from sub-alpine to urban environments in three watersheds (Utah, United States) across three seasons. Of the 53 environmental parameters measured (including physicochemical parameters, solute concentrations, and catchment characteristics), trace element concentrations explained the most variability in bacterioplankton community composition using Redundancy Analysis ordination. Trace elements may correlate with bacterioplankton due to the commonality in source of water and microorganisms, and/or environmental selection creating more or less favorable conditions for bacteria. Bacterioplankton community diversity decreased downstream along parts of the stream continuum but was disrupted where large reservoirs increased water residence time by orders of magnitude, potentially indicating a shift in the relative importance of environmental selection and dispersal at these sites. Reservoirs also had substantial effects on community composition, dissimilarity (Bray-Curtis distance) and species interactions as indicated by co-occurrence networks. Communities downstream of reservoirs were enriched with anaerobic Sporichthyaceae, methanotrophic Methylococcaceae, and iron-transforming Acidimicrobiales, suggesting alternative metabolic pathways became active in the hypolimnion of large reservoirs. Our results identify that human activity affects river microbial communities, with potential impacts on water quality through modified biogeochemical cycling.

Local community assembly mechanisms shape soil bacterial β diversity patterns along a latitudinal gradient

Biodiversity patterns across geographical gradients could result from regional species pool and local community assembly mechanisms. However, little has been done to separate the effects of local ecological mechanisms from variation in the regional species pools on bacterial diversity patterns. In this study, we compare assembly mechanisms of soil bacterial communities in 660 plots from 11 regions along a latitudinal gradient in eastern China with highly divergent species pools. Our results show that β diversity does not co-vary with γ diversity, and local community assembly mechanisms appear to explain variation in β diversity patterns after correcting for variation in regional species pools. The variation in environmental conditions along the latitudinal gradient accounts for the variation in β diversity through mediating the strength of heterogeneous selection. In conclusion, our study clearly illustrates the importance of local community assembly processes in shaping geographical patterns of soil bacterial β diversity.

The relative importance of regional species pool and local assembly processes as drivers of beta diversity is unclear. Here the authors investigate soil bacterial diversity patterns along a 3700-km latitudinal gradient in Chinese forests, finding that community assembly processes differ based on environmental heterogeneity.

Soil Bacterial Communities Exhibit Strong Biogeographic Patterns at Fine Taxonomic Resolution

Bacteria have been inferred to exhibit relatively weak biogeographic patterns. To what extent such findings reflect true biological phenomena or methodological artifacts remains unclear. Here, we addressed this question by analyzing the turnover of soil bacterial communities from three data sets. We applied three methodological innovations: (i) design of a hierarchical sampling scheme to disentangle environmental from spatial factors driving turnover; (ii) resolution of 16S rRNA gene amplicon sequence variants to enable higher-resolution community profiling; and (iii) application of the new metric zeta diversity to analyze multisite turnover and drivers. At fine taxonomic resolution, rapid compositional turnover was observed across multiple spatial scales. Turnover was overwhelmingly driven by deterministic processes and influenced by the rare biosphere. The communities also exhibited strong distance decay patterns and taxon-area relationships, with z values within the interquartile range reported for macroorganisms. These biogeographical patterns were weakened upon applying two standard approaches to process community sequencing data: clustering sequences at 97% identity threshold and/or filtering the rare biosphere (sequences lower than 0.05% relative abundance). Comparable findings were made across local, regional, and global data sets and when using shotgun metagenomic markers. Altogether, these findings suggest that bacteria exhibit strong biogeographic patterns, but these signals can be obscured by methodological limitations. We advocate various innovations, including using zeta diversity, to advance the study of microbial biogeography.IMPORTANCE It is commonly thought that bacterial distributions show lower spatial variation than for multicellular organisms. In this article, we present evidence that these inferences are artifacts caused by methodological limitations. Through leveraging innovations in sampling design, sequence processing, and diversity analysis, we provide multifaceted evidence that bacterial communities in fact exhibit strong distribution patterns. This is driven by selection due to factors such as local soil characteristics. Altogether, these findings suggest that the processes underpinning diversity patterns are more unified across all domains of life than previously thought, which has broad implications for the understanding and management of soil biodiversity.

Stochastic Dispersal Rather Than Deterministic Selection Explains the Spatio-Temporal Distribution of Soil Bacteria in a Temperate Grassland

Spatial and temporal processes shaping microbial communities are inseparably linked but rarely studied together. By Illumina 16S rRNA sequencing, we monitored soil bacteria in 360 stations on a 100 square meter plot distributed across six intra-annual samplings in a rarely managed, temperate grassland. Using a multi-tiered approach, we tested the extent to which stochastic or deterministic processes influenced the composition of local communities. A combination of phylogenetic turnover analysis and null modeling demonstrated that either homogenization by unlimited stochastic dispersal or scenarios, in which neither stochastic processes nor deterministic forces dominated, explained local assembly processes. Thus, the majority of all sampled communities (82%) was rather homogeneous with no significant changes in abundance-weighted composition. However, we detected strong and uniform taxonomic shifts within just nine samples in early summer. Thus, community snapshots sampled from single points in time or space do not necessarily reflect a representative community state. The potential for change despite the overall homogeneity was further demonstrated when the focus shifted to the rare biosphere. Rare OTU turnover, rather than nestedness, characterized abundance-independent β-diversity. Accordingly, boosted generalized additive models encompassing spatial, temporal and environmental variables revealed strong and highly diverse effects of space on OTU abundance, even within the same genus. This pure spatial effect increased with decreasing OTU abundance and frequency, whereas soil moisture – the most important environmental variable – had an opposite effect by impacting abundant OTUs more than the rare ones. These results indicate that – despite considerable oscillation in space and time – the abundant and resident OTUs provide a community backbone that supports much higher β-diversity of a dynamic rare biosphere. Our findings reveal complex interactions among space, time, and environmental filters within bacterial communities in a long-established temperate grassland.

Effects of initial microbial biomass abundance on respiration during pine litter decomposition

Microbial biomass is increasingly used to predict respiration in soil organic carbon (SOC) models. Its increased use combined with the difficulty of accurately measuring this variable points a need to directly assess the importance of microbial biomass abundance for carbon (C) cycling. To test the hypothesis that the initial microbial biomass abundance (i.e. biomass abundance on new plant litter) is a strong driver of plant litter C cycling, we manipulated biomass abundance by 10 and 100-fold dilution and composition using 12 source communities on sterile pine litter and measured respiration in microcosms for 30 days. In the first two days of microbial growth on fresh litter, a 100-fold difference in initial biomass abundance caused an average difference in respiration of nearly 300%, but the effect rapidly declined to less than 30% in 10 days and to 14% in 30 days. Parallel simulations with a soil carbon model, SOMIC 1.0, also predicted a 14% difference over 30 days, consistent with the experimental results. Model simulations predicted convergence of cumulative CO₂ to within 10% in three months and within 4% in three years. Rapid microbial growth, evidenced by appearance of visible microbial mats on the litter during the first week of incubation, likely attenuates the effects of large initial differences in biomass abundance. In contrast, the persistence of source community as an explanatory factor in driving differences in respiration across microcosms supports the importance of microbial composition in C cycling. Overall, the results suggest that the initial abundance of microbial biomass on litter is a weak driver of C flux from litter decomposition over long timescales (months to years) when litter communities have equal nutrient availability. By extension, slight variation in the timing of microbial dispersal to fresh litter is likely to be a minor factor in long-term C flux.

Optimization of a Method To Quantify Soil Bacterial Abundance by Flow Cytometry

The ability to quantify bacterial abundance is important for understanding the contributions of microbial communities in soils, but such assays remain difficult and time-consuming. Flow cytometry offers a fast and direct way to count bacterial cells, but several concerns remain in applying the technique to soils. This study aimed to improve the efficiency of the method for soil while quantifying its limitations. We demonstrated that an optimized procedure was sensitive enough to capture differences in bacterial abundances among treatments and ecosystems in two field studies.

Bacterial abundance is a fundamental metric for understanding the population dynamics of soil bacteria and their role in biogeochemical cycles. Despite its importance, methodological constraints hamper our ability to assess bacterial abundance in terrestrial environments. Here, we aimed to optimize the use of flow cytometry (FCM) to assay bacterial abundances in soil while providing a rigorous quantification of its limitations. Soil samples were spiked with Escherichia coli to evaluate the levels of recovery efficiency among three extraction approaches. The optimized method added a surfactant (a tetrasodium pyrophosphate [TSP] buffer) to 0.1 g of soil, applied an intermediate degree of agitation through shaking, and used a Nycodenz density gradient to separate the cells from background debris. This procedure resulted in a high (average, 89%) level of cell recovery. Recovery efficiencies did not differ significantly among sites across an elevation gradient but were positively correlated with percent carbon in the soil samples. Estimated abundances were also highly repeatable between technical replicates. The method was applied to samples from two field studies and, in both cases, was sensitive enough to detect treatment and site differences in bacterial abundances. We conclude that FCM offers a fast and sensitive method to assay soil bacterial abundance from relatively small amounts of soil. Further work is needed to assay differential biases of the method across a wider range of soil types.

IMPORTANCE The ability to quantify bacterial abundance is important for understanding the contributions of microbial communities in soils, but such assays remain difficult and time-consuming. Flow cytometry offers a fast and direct way to count bacterial cells, but several concerns remain in applying the technique to soils. This study aimed to improve the efficiency of the method for soil while quantifying its limitations. We demonstrated that an optimized procedure was sensitive enough to capture differences in bacterial abundances among treatments and ecosystems in two field studies.

Local biotic interactions drive species-specific divergence in soil bacterial communities

It is well accepted that environmental heterogeneity and dispersal are key factors determining soil bacterial community composition, yet little is known about the role of local biotic interactions. Here we address this issue with an abundance-manipulation experiment that was conducted in a semiarid grassland. We manually increased the abundance of six randomly chosen resident bacterial species in separate, closed, communities and allowed the communities to recover in situ for 1 year. The single episode of increase in the abundance of different species drove species-specific community divergence accompanied by a decline in local diversity. Four of the six added species caused a decrease in the abundance of their closely related species, suggesting an important role of interspecific competition in driving the observed community divergence. Our results also suggested a lack of effective population regulations to force the relative abundance of manipulated species to revert to original level, which would allow persistence of the divergence among soil bacterial communities. We concluded that biotic interactions were important in determining soil bacterial community composition, which could result in substantial variation in soil bacterial community composition in abiotically homogenous environment.

Dispersal alters soil microbial community response to drought

Microbial communities will experience novel climates in the future. Dispersal is now recognized as a driver of microbial diversity and function, but our understanding of how dispersal influences responses to novel climates is limited. We experimentally tested how the exclusion of aerially dispersed fungi and bacteria altered the compositional and functional response of soil microbial communities to drought. We manipulated dispersal and drought by collecting aerially deposited microbes after precipitation events and subjecting soil mesocosms to either filter-sterilized rain (no dispersal) or unfiltered rain (dispersal) and to either drought (25% ambient) or ambient rainfall for 6 months. We characterized community composition by sequencing 16S and ITS rRNA regions and function using community-level physiological profiles. Treatments without dispersal had lower soil microbial biomass and metabolic diversity but higher bacterial and fungal species richness. Dispersal also altered soil community response to drought; drought had a stronger effect on bacterial (but not fungal) community composition, and induced greater functional loss, when dispersal was present. Surprisingly, neither immigrants nor drought-tolerant taxa had higher abundance in dispersal treatments. We show experimentally that natural aerial dispersal rate alters soil microbial responses to disturbance. Changes in dispersal rates should be considered when predicting microbial responses to climate change.

Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community

Stochasticity emerging from random differences in replication, death, mutation, and dispersal is thought to alter the composition of ecological communities. However, the importance of stochastic effects remains somewhat speculative because stochasticity is not directly measured but is instead inferred from unexplained variations in beta-diversity. Here, we performed a field experiment to more directly disentangle the role of stochastic processes, environmental selection, and dispersal in the composition and functioning of a natural bacterial decomposer community in the field. To increase our ability to detect these effects, we reduced initial biological and environmental heterogeneity using replicate nylon litterbags in the field. We then applied two treatments: ambient/added precipitation and bacterial and fungal dispersal using "open" litterbags (made from 18.0-μm-pore-size mesh) ("open bacterial dispersal") versus bacterial and fungal dispersal using "closed" litterbags (made from 22.0-μm-pore-size mesh) ("closed bacterial dispersal"). After 5 months, we assayed composition and functioning by the use of three subsamples from each litterbag to disentangle stochastic effects from residual variation. Our results indicate that stochasticity via ecological drift can contribute to beta-diversity in bacterial communities. However, residual variation, which had previously been included in stochasticity estimates, accounted for more than four times as much variability. At the same time, stochastic effects on beta-diversity were not attenuated at the functional level, as measured by genetic functional potential and extracellular enzyme activity. Finally, dispersal was found to interact with precipitation availability to influence the degree to which stochasticity contributed to functional variation. Together, our results demonstrate that the ability to quantify stochastic processes is key to understanding microbial diversity and its role in ecosystem functioning.IMPORTANCE Randomness can alter the diversity and composition of ecological communities. Such stochasticity may therefore obscure the relationship between the environment and community composition and hinder our ability to predict the relationship between biodiversity and ecosystem functioning. This study investigated the role of stochastic processes, environmental selection, and dispersal in microbial composition and its functioning on an intact field community. To do this, we used a controlled and replicated experiment that was similar to that used to study population genetics in the laboratory. Our study showed that, while the stochastic effects on taxonomic composition are smaller than expected, the degree to which stochasticity contributes to variability in ecosystem processes may be much higher than previously assumed.

Bacterial Dispersers along Preferential Flow Paths of a Clay Till Depth Profile

The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

This study assessed the dispersal of five bacterial communities from contrasting compartments along a fractured clay till depth profile comprising plow layer soil, preferential flow paths (biopores and the tectonic fractures below), and matrix sediments, down to 350 cm below the surface. A recently developed expansion of the porous surface model (PSM) was used to capture bacterial communities dispersing under controlled hydration conditions on a soil-like surface. All five communities contained bacteria capable of active dispersal under relatively low hydration conditions (−3.1 kPa). Further testing of the plow layer community revealed active dispersal even at matric potentials of −6.3 to −8.4 kPa, previously thought to be too dry for dispersal on the PSM. Using 16S rRNA gene amplicon sequencing, the dispersing communities were found to be less diverse than their corresponding total communities. The dominant dispersers in most compartments belonged to the genus Pseudomonas and, in the plow layer soil, to Rahnella as well. An exception to this was the dispersing community in the matrix at 350 cm below the surface, which was dominated by Pantoea. Hydrologically connected compartments shared proportionally more dispersing than nondispersing amplicon sequence variants (ASVs), suggesting that active dispersal is important for colonizing these compartments. These results highlight the importance of including soil profile heterogeneity when assessing the role of active dispersal and contribute to discerning the importance of active dispersal in the soil environment.

IMPORTANCE The ability to disperse is considered essential for soil bacteria colonization and survival, yet very little is known about the dispersal ability of communities from different heterogeneous soil compartments. Important factors for dispersal are the thickness and connectivity of the liquid film between soil particles. The present results from a fractured clay till depth profile suggest that dispersal ability is common in various soil compartments and that most are dominated by a few dispersing taxa. Importantly, an increase in shared dispersers among the preferential flow paths of the clay till suggests that active dispersal plays a role in the successful colonization of these habitats.

Microbial Community Dynamics and Assembly Follow Trajectories of an Early-Spring Diatom Bloom in a Semienclosed Bay

Harmful algal blooms (HABs) are serious ecological disasters in coastal areas, significantly influencing biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been widely investigated, but the assembly mechanisms of microbial communities during HABs are poorly understood. Here, using 16S rRNA gene amplicon sequencing, we analyzed the microbial communities during an early-spring diatom bloom, in order to investigate the dynamics of microbial assembly processes. Rhodobacteraceae, Flavobacteriaceae, and Microbacteriaceae were the main bacterial families during the bloom. The 30 most abundant operational taxonomic units (OTUs) segregated into 4 clusters according to specific bloom stages, exhibiting clear successional patterns during the bloom process. The succession of microbial communities correlated with changes in the dynamics of algal species. Based on the β-nearest taxon distance, we constructed a simulation model, which demonstrated that the assembly of microbial communities shifted from strong heterogenous selection in the early stage of the bloom to stochasticity in the middle stage and then to strong homogeneous selection in the late and after-bloom stages. These successions were driven mainly by chlorophyll a contents, which were affected mainly by Skeletonema costatum Moreover, functional prediction of microbial communities showed that microbial metabolic functions were significantly related to nitrogen metabolism. In summary, our results clearly suggested a dominant role of determinacy in microbial community assembly in HABs and will facilitate deeper understanding of the ecological processes shaping microbial communities during the algal bloom process.IMPORTANCE Harmful algal blooms (HABs) significantly influence biogeochemical cycles driven by bacteria. The shifts in microbial communities during HABs have been studied intensively, but the assembly mechanisms of microbial communities during HABs are poorly understood, with limited investigation of the balance of deterministic and stochastic processes in shaping microbial communities in HABs. In this study, the dynamics and assembly of microbial communities in an early-spring diatom bloom process were investigated. Our data both confirm previously observed general microbial successional patterns and show new detailed mechanisms for microbial assembly in HABs. These results will facilitate deeper understanding of the ecological processes shaping microbial communities in HABs. In addition, predictions of metabolic potential in this study will facilitate understanding of the influence of HABs on nitrogen metabolism in marine environments.

Function and functional redundancy in microbial systems

Microbial communities often exhibit incredible taxonomic diversity, raising questions regarding the mechanisms enabling species coexistence and the role of this diversity in community functioning. On the one hand, many coexisting but taxonomically distinct microorganisms can encode the same energy-yielding metabolic functions, and this functional redundancy contrasts with the expectation that species should occupy distinct metabolic niches. On the other hand, the identity of taxa encoding each function can vary substantially across space or time with little effect on the function, and this taxonomic variability is frequently thought to result from ecological drift between equivalent organisms. Here, we synthesize the powerful paradigm emerging from these two patterns, connecting the roles of function, functional redundancy and taxonomy in microbial systems. We conclude that both patterns are unlikely to be the result of ecological drift, but are inevitable emergent properties of open microbial systems resulting mainly from biotic interactions and environmental and spatial processes.

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome

Microbial community assembly is affected by a combination of forces that act simultaneously, but the mechanisms underpinning their relative influences remain elusive. This gap strongly limits our ability to predict human impacts on microbial communities and the processes they regulate. Here, we experimentally demonstrate that increased salinity stress, food web alteration and nutrient loading interact to drive outcomes in salt marsh fungal leaf communities. Both salinity stress and food web alterations drove communities to deterministically diverge, resulting in distinct fungal communities. Increased nutrient loads, nevertheless, partially suppressed the influence of other factors as determinants of fungal assembly. Using a null model approach, we found that increased nutrient loads enhanced the relative importance of stochastic over deterministic divergent processes; without increased nutrient loads, samples from different treatments showed a relatively (deterministic) divergent community assembly whereas increased nutrient loads drove the system to more stochastic assemblies, suppressing the effect of other treatments. These results demonstrate that common anthropogenic modifications can interact to control fungal community assembly. Furthermore, our results suggest that when the environmental conditions are spatially heterogeneous (as in our case, caused by specific combinations of experimental treatments), increased stochasticity caused by greater nutrient inputs can reduce the importance of deterministic filters that otherwise caused divergence, thus driving to microbial community homogenization.