scholarly journals Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

mSystems ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Lu Luan ◽  
Chao Liang ◽  
Lijun Chen ◽  
Haotian Wang ◽  
Qinsong Xu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Bacterial Community ◽  
Community Assembly ◽  
Carbon Metabolism ◽  
Structural Equation ◽  
Equation Modeling ◽  
Deep Soil ◽  
Deterministic Processes ◽  
Stochastic Dispersal ◽  
Microbial Community Assembly

ABSTRACT Soil microbial community assembly is crucial for understanding the mechanisms of microbial communities that regulate ecosystem-level functioning. The relative contributions of stochastic and deterministic processes to microbial community assembly remain poorly defined, and major questions exist concerning the soil organic carbon (SOC) dynamics of microbial community assembly in deep soil. Here, the bacterial community assembly processes were explored across five soil profile depths (up to 80 cm) during a 15-year field experiment involving four fertilization regimes. We found that the bacterial community assembly was initially governed by deterministic selection in topsoil but was progressively structured by increasing stochastic dispersal with depth. The migration rate (m) and β-null deviation pattern supported the hypothesis of a relatively greater influence of dispersal in deep soil, which was correlated with bacterial community assembly by stochastic processes. These changes in the entire community assembly reflected consistent assembly processes of the two most dominant phyla, Acidobacteria and Chloroflexi. Structural equation modeling showed that soil features (pH and total phosphorus) and bacterial interactions (competition and network complexity) were significantly related to bacterial community assembly in the 0-to-10-cm and 10-to-20-cm layers. Partial Mantel tests, structural equation modeling, and random forest modeling consistently indicated a strong and significant correlation between bacterial community assemblages and SOC dynamics, implying that bacterial assembly processes would potentially suppress SOC metabolism and mineralization when the contributions of stochastic dispersal to communities increased in deeper layers. Our results have important implications for integrating bacterial community assembly processes into the predictions of SOC dynamics. IMPORTANCE We have provided a framework to better understand the mechanisms governing the balance between stochastic and deterministic processes and to integrate the shifts in community assembly processes with microbial carbon metabolism. Our study reinforced that environmental filtering and bacterial cooccurrence patterns influence the stochastic/deterministic continuum of soil bacterial community assembly and that stochasticity may act through deeper soil layers to influence carbon metabolism. Delineating theoretically the potential linkages between community assembly and SOC dynamics across a broad range of microbial systems represents an interesting topic for future research.

scholarly journals Deterministic Selection Dominates Microbial Community Assembly in Termite Mounds Across a Large Spatial Area

2020 ◽  
Author(s):  
Qing-Lin Chen ◽  
Hang-Wei Hu ◽  
Zhen-Zhen Yan ◽  
Chao-Yu Li ◽  
Bao-Anh Thi Nguyen ◽  
...  
Keyword(s):  
Microbial Community ◽  
Stochastic Processes ◽  
Microbial Communities ◽  
Fungal Community ◽  
Community Assembly ◽  
Distance Decay ◽  
Termite Mounds ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Abstract Background: Termites are ubiquitous insects in tropical and subtropical habitats, where they construct massive mounds from soil, their saliva and excreta. Termite mounds harbor an enormous amount of microbial inhabitants, which regulate multiple ecosystem functions such as mitigating methane emissions and increasing ecosystem resistance to climate change. However, we lack a mechanistic understanding about the role of termite mounds in modulating the microbial community assembly processes, which are essential to unravel the biological interactions of soil fauna and microorganisms, the major components of soil food webs. We conducted a large-scale survey across a >1500 km transect in northern Australia to investigate biogeographical patterns of bacterial and fungal community in 134 termite mounds and the relative importance of deterministic versus stochastic processes in microbial community assembly. Results: Microbial alpha (number of phylotypes) and beta (changes in bacterial and fungal community composition) significantly differed between termite mounds and surrounding soils. Microbial communities in termite mounds exhibited a significant distance-decay pattern, and fungal communities had a stronger distance-decay relationship (slope = -1.91) than bacteria (slope = -0.21). Based on the neutral community model (fitness < 0.7) and normalized stochasticity ratio index (NST) with a value below the 50% boundary point, deterministic selection, rather than stochastic forces, predominated the microbial community assembly in termite mounds. Deterministic processes exhibited significantly weaker impacts on bacteria (NST = 45.23%) than on fungi (NST = 33.72%), probably due to the wider habitat niche breadth and higher potential migration rate of bacteria. The abundance of antibiotic resistance genes (ARGs) was negatively correlated with bacterial/fungal biomass ratios, indicating that ARG content might be an important biotic factor that drove the biogeographic pattern of microbial communities in termite mounds. Conclusions: Deterministic processes play a more important role than stochastic processes in shaping the microbial community assembly in termite mounds, an unique habitat ubiquitously distributed in tropical and subtropical ecosystems. An improved understanding of the biogeographic patterns of microorganisms in termite mounds is crucial to decipher the role of soil faunal activities in shaping microbial community assembly, with implications for their mediated ecosystems functions and services.

scholarly journals Prokaryotic Diversity in Mangrove Sediments across Southeastern China Fundamentally Differs from That in Other Biomes

mSystems ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Cui-Jing Zhang ◽  
Jie Pan ◽  
Chang-Hai Duan ◽  
Yong-Ming Wang ◽  
Yang Liu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Diversity ◽  
Community Assembly ◽  
Alpha Diversity ◽  
Mean Annual Precipitation ◽  
Mangrove Sediments ◽  
Southeastern China ◽  
Deterministic Process ◽  
Deterministic Processes ◽  
Microbial Community Assembly

ABSTRACT Mangroves, as a blue carbon reservoir, provide an environment for a variety of microorganisms. Mangroves lie in special locations connecting coastal and estuarine areas and experience fluctuating conditions, which are expected to intensify with climate change, creating a need to better understand the relative roles of stochastic and deterministic processes in shaping microbial community assembly. Here, a study of microbial communities inhabiting mangrove sediments across southeastern China, spanning mangroves in six nature reserves, was conducted. We performed high-throughput DNA sequencing of these samples and compared them with data of 1,370 sediment samples collected from the Earth Microbiome Project (EMP) to compare the microbial diversity of mangroves with that of other biomes. Our results showed that prokaryotic alpha diversity in mangroves was significantly higher than that in other biomes and that microbial beta diversity generally clustered according to biome types. The core operational taxonomic units (OTUs) in mangroves were mostly assigned to Gammaproteobacteria, Deltaproteobacteria, Chloroflexi, and Euryarchaeota. The majority of beta nearest-taxon index values were higher than 2, indicating that community assembly in mangroves was better explained through a deterministic process than through a stochastic process. Mean annual precipitation (MAP) and total organic carbon (TOC) were main deterministic factors explaining variation in the microbial community. This study fills a gap in addressing the unique microbial diversity of mangrove ecosystems and their microbial community assembly mechanisms. IMPORTANCE Understanding the underlying mechanisms of microbial community assembly patterns is a vital issue in microbial ecology. Mangroves, as an important and special ecosystem, provide a unique environment for examining the relative importance of stochastic and deterministic processes. We made the first global-scale comparison and found that microbial diversity was significantly different in mangrove sediments compared to that of other biomes. Furthermore, our results suggest that a deterministic process is more important in shaping microbial community assembly in mangroves.

scholarly journals Deterministic processes dominate soil microbial community assembly in subalpine coniferous forests on the Loess Plateau

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6746 ◽  
Author(s):  
Pengyu Zhao ◽  
Jiabing Bao ◽  
Xue Wang ◽  
Yi Liu ◽  
Cui Li ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Soil Microbial Community ◽  
Coniferous Forests ◽  
The Loess Plateau ◽  
Soil Microbial ◽  
Deterministic Processes ◽  
Microbial Community Assembly

Microbial community assembly is influenced by a continuum (actually the trade-off) between deterministic and stochastic processes. An understanding of this ecological continuum is of great significance for drawing inferences about the effects of community assembly processes on microbial community structure and function. Here, we investigated the driving forces of soil microbial community assembly in three different environmental contexts located on subalpine coniferous forests of the Loess Plateau in Shanxi, China. The variation in null deviations and phylogenetic analysis showed that a continuum existed between deterministic and stochastic processes in shaping the microbial community structure, but deterministic processes prevailed. By integrating the results of redundancy analysis (RDA), multiple regression tree (MRT) analysis and correlation analysis, we found that soil organic carbon (SOC) was the main driver of the community structure and diversity patterns. In addition, we also found that SOC had a great influence on the community assembly processes. In conclusion, our results show that deterministic processes always dominated assembly processes in shaping bacterial community structure along the three habitat contexts.

Microbial community assembly in soil aggregates: A dynamic interplay of stochastic and deterministic processes

2021 ◽  
Vol 163 ◽  
pp. 103911
Author(s):  
Menghui Dong ◽  
George A. Kowalchuk ◽  
Hongjun Liu ◽  
Wu Xiong ◽  
Xuhui Deng ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Soil Aggregates ◽  
Deterministic Processes ◽  
Microbial Community Assembly ◽  
Dynamic Interplay

scholarly journals Stochastic Community Assembly: Does It Matter in Microbial Ecology?

2017 ◽  
Vol 81 (4) ◽  
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.

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

2020 ◽  
Vol 86 (8) ◽  
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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