Combined effects of fermentation starters and environmental factors on the microbial community assembly and flavor formation of Zhenjiang aromatic vinegar

AbstractMicrobes assemble into complex, dynamic, and species-rich communities that play critical roles in human health and in the environment. The complexity of natural environments and the large number of niches present in most habitats are often invoked to explain the maintenance of microbial diversity in the presence of competitive exclusion. Here we show that soil and plant-associated microbiota, cultivated ex situ in minimal synthetic environments with a single supplied source of carbon, universally re-assemble into large and dynamically stable communities with strikingly predictable coarse-grained taxonomic and functional compositions. We find that generic, non-specific metabolic cross-feeding leads to the assembly of dense facilitation networks that enable the coexistence of multiple competitors for the supplied carbon source. The inclusion of universal and non-specific cross-feeding in ecological consumer-resource models is sufficient to explain our observations, and predicts a simple determinism in community structure, a property reflected in our experiments.

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

10.21203/rs.3.rs-34782/v1 ◽

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.

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Rhizosheath microbial community assembly of sympatric desert speargrasses is independent of the plant host

Microbiome ◽

10.1186/s40168-018-0597-y ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 25

Author(s):

Ramona Marasco ◽

María J. Mosqueira ◽

Marco Fusi ◽

Jean-Baptiste Ramond ◽

Giuseppe Merlino ◽

...

Keyword(s):

Microbial Community ◽

Community Assembly ◽

Plant Host ◽

Microbial Community Assembly

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Coupling Bacterial Community Assembly to Microbial Metabolism across Soil Profiles

mSystems ◽

10.1128/msystems.00298-20 ◽

2020 ◽

Vol 5 (3) ◽

Cited By ~ 1

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.

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