Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

Jiao, Shuo; Yang, Yunfeng; Xu, Ye; Zhang, Jie; Lu, Yahai

doi:10.1038/s41396-019-0522-9

Cited by 642 publications

(412 citation statements)

References 87 publications

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“…These limitations together with the missing environmental variables could be the reason that a large proportion of variation remains unexplained for both bacterial and fungal communities in the variation partitioning (Additional le 1: Figure S5). Actually, addressing the effect of all potentially biotic and abiotic variables is impractical, especially for a broad-scale eld survey and this is consistent with previous studies that 50% − 90% variation remains unexplained [28,38,41].…”

Section: Biological Interactions Of Microbial Communities In Termite supporting

confidence: 82%

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

Chen¹,

Hu²,

Yan³

et al. 2020

Preprint

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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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Section: Biological Interactions Of Microbial Communities In Termite supporting

confidence: 82%

“…Habitat niche breadth at the community level was estimated as the average B-values from all OTUs in a single community (Bcom) [38]. A microbial group with a wider niche breadth is more metabolically exible at the community level [41].…”

Section: Discussionmentioning

confidence: 99%

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

Chen¹,

Hu²,

Yan³

et al. 2020

Preprint

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“…Distance decay relationship is widely used to observe microbial biogeography and microbial community turnover rates and is known to signi cantly differ at different sampling scales [31]. The microbial community exhibited a stronger DDR in our results than large scale studies (when transferred to the same units), which is potentially a result of undersampling [17,32,33]. Undersampling causes decreased detection of low abundance taxa, leading to the community appearing to have less taxonomic turnover across space.…”

Section: Discussionmentioning

confidence: 63%

Deciphering Centimeter-Scale Microbial Biogeographic Patterns and Community Assembly Processes From A 3D Perspective

Xue¹,

Zhao²,

Yu³

et al. 2020

Preprint

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Background: Revealing the effects of multi-dimensional spatial distribution on microorganisms is crucial for the further understanding of microbial diversity, turnover and ecological processes. However, microbial community assembly and the factors that shape it are still unknown from a three dimensional (3D) perspective. Here, a 3D model was created by performing an exhaustive sampling strategy to a 4x4x4 soil matrix. We examined the dynamics of microbial diversity, biogeographic patterns and microbial assembly processes when transfroming sampling scheme from 2D to 3D.Results: Our results indicated that dispersion of microbial community and significance of distance decay relationship was higher in the 3D compared with 2D sampling scheme, suggesting increased microbial turnover when transforming the model from 2D to 3D. Only a small fraction of community variation can be explained by environmental, spatial factors and spatial canonical axes, possibly due to unmeasured environmental variables. The assembly of microbial community was dominated by deterministic processes that shifted from homogeneous selection to variable selection as we transformed the model from 2D to 3D. The importance of stochasticity increased when homogeneous and variable selection processes were well balanced. However, heterogeneity of existing environmental and spatial variables failed to explain the dynamics of community assembly.Conclusions: Our study revealed significant dynamics of microbial diversity and assembly processes when assessed from 2D and 3D perspectives. As microorganisms are spatially distributed in soil, this spatial dependent diversity and assembly suggests that microbial ecological questions need to be considered in more dimensions than they usually are. Further, new models that integrate all data sets are still needed to disengle the microbial processes in multiple dimensions.

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“…For example, nodes with higher node-level topological feature values play central roles in the network, whereas lower topological feature values indicate a peripheral position [11,25,33]. Network-level topological features with a high value (such as average degree, clustering coefficient, and density) indicate a more connected network, whereas those with lower values (such as average path length and diameter) suggest closer connections within the network [10,11,33]. Here, closer relationships and similar environmental preferences were observed between soil archaeal and bacterial taxa in the alpine grasslands.…”

Section: Discussionmentioning

confidence: 99%

Increasing soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau

Chen

Luo

et al. 2019

Preprint

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Background: Soil functioning and processes are driven by complex microbial interactions. It is therefore critical to understand the co-occurrence patterns of soil microbiota, especially in fragile alpine ecosystems. Here we explored the geographic patterns of the topological features and the major drivers shaping the topological structure of the co-occurrence network for bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau based on high-throughput sequencing.Results: Soil pH was the most important environmental variable for predicting the topological features of the microbial network at both network and node levels. Associations among soil microbiota were enhanced with increasing pH (5.17-8.92), and the network was the most stable at neutral pH (7).Node-level topological features suggested that taxa of the high-pH cluster had more important roles in maintaining complex network connections than taxa of the low-pH cluster. Network-level features revealed closer relationships among soil microbiota in the steppe ecosystem than in the meadow ecosystem. Archaeal operational taxonomic units (OTUs) with higher values for node-level topological features appeared to be more important than bacterial OTUs in maintaining complex connections. The co-occurrence patterns of bacterial OTUs with lower node-level feature values followed a power-law distribution, whereas those of archaeal OTUs did not.Conclusions: Soil pH plays a decisive role in determining the complex interactions among soil microbiota in alpine grassland ecosystems of the Tibetan Plateau, with a more stable co-occurrence network at neutral pH. Bacterial and archaeal taxa, which occupy distinct network niches, have closer relationships in alpine steppe than in alpine meadow ecosystems.

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Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

Cited by 642 publications

References 87 publications

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

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

Deciphering Centimeter-Scale Microbial Biogeographic Patterns and Community Assembly Processes From A 3D Perspective

Increasing soil pH enhances the network interactions among bacterial and archaeal microbiota in alpine grasslands of the Tibetan Plateau

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