Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

Development of soil microbial communities along ecological succession is crucial for ecosystem functioning and maintenance. However, ecological processes mediating microbial community assembly and microbial co-occurrence patterns along ecological succession remain unclear. Here, we explored community phylogenetic structures, ecological processes driving community phylogenetic turnover, and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing prior studies of microbial phylogeny in community assembly, we proposed two conceptual models to better explain our results. At early successional stages, the significantly increasing phylogenetic clustering of bacterial communities with soil age was co-determined by the environmental selection from soil vegetation cover and by bacterial heterogeneous responses that less phylogenetically similar bacteria differently expanded their population in response to the increasing resource availability in soil along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community structure turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of the phylogeny between co-occurring fungi. This study provides new sights into ecological processes and mechanisms underlying bacterial and fungal community dynamics along ecological succession, thereby boosting our understanding of the interactions between microbial community assembly and soil environment gradients.

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Historical land use has long-term effects on microbial community assembly processes in forest soils

ISME Communications ◽

10.1038/s43705-021-00051-x ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Ernest D. Osburn ◽

Frank O. Aylward ◽

J. E. Barrett

Keyword(s):

Land Use ◽

Microbial Community ◽

Community Assembly ◽

Soil Microbial Communities ◽

Fungal Communities ◽

Long Term Effects ◽

Soil Microbial ◽

Historical Land Use ◽

Microbial Community Assembly

AbstractLand use change has long-term effects on the structure of soil microbial communities, but the specific community assembly processes underlying these effects have not been identified. To investigate effects of historical land use on microbial community assembly, we sampled soils from several currently forested watersheds representing different historical land management regimes (e.g., undisturbed reference, logged, converted to agriculture). We characterized bacterial and fungal communities using amplicon sequencing and used a null model approach to quantify the relative importance of selection, dispersal, and drift processes on bacterial and fungal community assembly. We found that bacterial communities were structured by both selection and neutral (i.e., dispersal and drift) processes, while fungal communities were structured primarily by neutral processes. For both bacterial and fungal communities, selection was more important in historically disturbed soils compared with adjacent undisturbed sites, while dispersal processes were more important in undisturbed soils. Variation partitioning identified the drivers of selection to be changes in vegetation communities and soil properties (i.e., soil N availability) that occur following forest disturbance. Overall, this study casts new light on the effects of historical land use on soil microbial communities by identifying specific environmental factors that drive changes in community assembly.

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Multiple ecological processes jointly drive the soil microbial community assembly in subalpine coniferous forests

10.7287/peerj.preprints.27223v1 ◽

2018 ◽

Author(s):

Pengyu Zhao ◽

Jiabing Bao ◽

Xue Wang ◽

Yi Liu ◽

Cui Li ◽

...

Keyword(s):

Microbial Community ◽

Stochastic Processes ◽

Community Assembly ◽

Soil Microbial Community ◽

Analytical Methods ◽

Community Dynamics ◽

Coniferous Forests ◽

Ecological Processes ◽

Soil Microbial ◽

Microbial Community Assembly

The mechanisms underlying community dynamics, which govern the complicated biogeographical patterns of microbes, have long been a research hotspot in community ecology. However, the mixing of multiple ecological processes and the one-sidedness of analytical methods make it difficult to draw inferences about the community assembly mechanisms. In this study, we investigated the driving forces of the soil microbial community in subalpine coniferous forests of the Loess Plateau in Shanxi, China, by integrating multiple analytical methods. The results of the null model demonstrated that deterministic processes (especially interspecific relationships) were the main driving force of the soil microbial community assembly in this study area, relative to stochastic processes. Based on the results of the net relatedness index (NRI) and nearest taxon index (NTI), we inferred that historical and evolutionary factors, such as climate change and local diversification, may have similar effects on microbial community structure based on the climatic niche conservatism. Based on the results of a functional traits analysis, we found that the effects of ongoing ecological processes on the microbial community assembly varied among sites. Therefore, the functional structures seemed to be more related to ongoing ecological processes, whereas the phylogenetic structures seemed to be more related to historical and evolutionary factors, as well as the tradeoff between deterministic and stochastic processes. The functional and phylogenetic structures were mainly shaped by different ecological processes. By integrating multiple ecological processes, our results provide more details of the mechanisms driving the community assembly

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Hierarchical control of microbial community assembly

10.1101/2021.06.22.449372 ◽

2021 ◽

Author(s):

Sammy Pontrelli ◽

Rachel Szabo ◽

Shaul Pollak ◽

Julia A Schwartzman ◽

Daniela Ledezma-Tejeida ◽

...

Keyword(s):

Organic Matter ◽

Microbial Community ◽

Resource Availability ◽

Community Assembly ◽

Hierarchical Control ◽

Complex Forms ◽

Chain Lengths ◽

Changes Over Time ◽

Microbial Community Assembly ◽

Over Time

Metabolic processes that fuel the growth of heterotrophic microbial communities are initiated by specialized biopolymer degraders that decompose complex forms of organic matter. It is unclear, however, to what extent degraders control the downstream assembly of the community that follows polymer breakdown. Investigating a model marine microbial community that degrades chitin, we show that chitinases secreted by different degraders produce oligomers of specific chain lengths that not only select for specialized consumers but also influence the metabolites secreted by these consumers into a shared resource pool. Each species participating in the breakdown cascade exhibits unique hierarchical preferences for substrates, which underlies the sequential colonization of metabolically distinct groups as resource availability changes over time. By identifying the metabolic underpinnings of microbial community assembly, we reveal a hierarchical crossfeeding structure that allows biopolymer degraders to shape the dynamics of community assembly.

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Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00002-17 ◽

2017 ◽

Vol 81 (4) ◽

Cited By ~ 219

Author(s):

Jizhong Zhou ◽

Daliang Ning

Keyword(s):

Community Structure ◽

Microbial Community ◽

Microbial Ecology ◽

Community Assembly ◽

Community Diversity ◽

Ecological Processes ◽

Experimental Approaches ◽

Deterministic Processes ◽

Deterministic Components ◽

Microbial Community Assembly

SUMMARY Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research.

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Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar

Applied and Environmental Microbiology ◽

10.1128/aem.02283-19 ◽

2020 ◽

Vol 86 (8) ◽

Cited By ~ 9

Author(s):

C. Heys ◽

B. Cheaib ◽

A. Busetti ◽

R. Kazlauskaite ◽

L. Maier ◽

...

Keyword(s):

Life Cycle ◽

Microbial Community ◽

Atlantic Salmon ◽

Salmo Salar ◽

Community Assembly ◽

Wild Fish ◽

Ecological Processes ◽

Deterministic Processes ◽

Microbial Community Assembly

ABSTRACT In recent years, a wealth of studies has examined the relationships between a host and its microbiome across diverse taxa. Many studies characterize the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterized using 16S rRNA gene MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across life cycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we found declining taxonomic and functional microbial community richness as fish mature through different life cycle stages. Alongside neutral community models applied to wild fish, we suggest that declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We found a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma spp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes, such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered. IMPORTANCE A growing number of studies have examined variation in the microbiome to determine the role in modulating host health, physiology, and ecology. However, the ecology of host microbial colonization is not fully understood and rarely tested. The continued increase in production of farmed Atlantic salmon, coupled with increased farmed-wild salmon interactions, has accentuated the need to unravel the potential adaptive function of the microbiome and to distinguish resident from transient gut microbes. Between gut compartments in a farmed system, we found a majority of operational taxonomic units (OTUs) that fit the neutral model, with Mycoplasma species among the key exceptions. In wild fish, deterministic processes account for more OTU differences across life stages than those observed across gut compartments. Unlike previous studies, our results make detailed comparisons between fish from wild and farmed environments, while also providing insight into the ecological processes underpinning microbial community assembly in this ecologically and economically important species.

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