Unraveling negative biotic interactions determining soil microbial community assembly and functioning

AbstractMicrobial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.

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A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming

10.1101/2020.02.22.960872 ◽

2020 ◽

Author(s):

Daliang Ning ◽

Mengting Yuan ◽

Linwei Wu ◽

Ya Zhang ◽

Xue Guo ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Assembly ◽

Soil Microbial Community ◽

Null Model ◽

Relative Importance ◽

Community Based ◽

Grassland Soil ◽

Soil Microbial ◽

Microbial Community Assembly

AbstractUnraveling the drivers controlling community assembly is a central issue in ecology. Selection, dispersal, diversification and drift are conceptually accepted as major community assembly processes. Defining their relative importance in governing biodiversity is compellingly needed, but very challenging. Here, we present a novel framework to quantitatively infer community assembly mechanisms by phylogenetic bin-based null model analysis (iCAMP). Our results with simulated microbial communities showed that iCAMP had high accuracy (0.93 - 0.99), precision (0.80 - 0.94), sensitivity (0.82 - 0.94), and specificity (0.95 - 0.98), which were 10-160% higher than those from the entire community-based approach. Applying it to grassland microbial communities in response to experimental warming, our analysis showed that homogeneous selection (38%) and “drift” (59%) played dominant roles in controlling grassland soil microbial community assembly. Interestingly, warming enhanced homogeneous selection, but decreased “drift” over time. Warming-enhanced selection was primarily imposed on Bacillales in Firmicutes, which were strengthened by increased drought and reduced plant productivity. This general framework should also be useful for plant and animal ecology.

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Dominant Tree Species Shape Soil Microbial Community via Regulating Assembly Processes in Planted Subtropical Forests

Forests ◽

10.3390/f10110978 ◽

2019 ◽

Vol 10 (11) ◽

pp. 978

Author(s):

Ma ◽

Zou ◽

Yang ◽

Hogan ◽

Xu ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Soil Nutrients ◽

Community Assembly ◽

Soil Microbial Community ◽

Soil Microbial Communities ◽

Soil Microbial ◽

Environmental Selection ◽

Α Diversity ◽

Microbial Community Assembly

Understanding the ecological processes that regulate microbial community assembly in different habitats is critical to predict microbial responses to anthropogenic disturbances and environmental changes. Rubber (Hevea brasiliensis) and Eucalypt (Eucalyptus urophylla) plantations (thereafter RP and EP) are rapidly established at the expense of forests in tropical China, greatly affecting tropical soils and their processes. However, the assembly processes of soil microbial communities after forest conversions remain unclear. We investigated soil microbial communities’ attributes and quantified the portion of deterministic assembly variation in two RP (a 3- and a 5-year-old) and two EP (a 2- and a 4-year-old) in Southern China. Shannon and Faith’s Phylogenetic α-diversity of both bacterial and fungal communities were higher in RP than in EP, regardless of plantation age or soil depth (0–50 cm). Bacterial and fungal community structure was significantly different among the four plantations. The dominant microbial taxa in RP closely tracked the availability of nitrogen, phosphorus and potassium (K) while those in EP were closely related to the high total K content. Microbial co-occurrence networks in RP were more modular than those in EP, as governed by more keystone taxa that were strongly dependent on soil available nutrients. Environmental filtering imposed by soil nutrients heterogeneity contributed a considerable portion (33–47%) of bacterial assembly variation in RP, but much less (8–14%) in EP. The relative contribution of environmental selection on fungal assembly was also greater in RP than in EP. Our findings suggest that in RP clear microbial community patterns exist with respect to soil nutrients, whereas in EP microbial community assembly patterns are more stochastic and variable. The large variation in soil microbial community assembly patterns in EP could lead to fragile and unstable microbial-soil relationships, which may be one factor driving soil degradation in EP.

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Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China

Forests ◽

10.3390/f11030285 ◽

2020 ◽

Vol 11 (3) ◽

pp. 285 ◽

Cited By ~ 1

Author(s):

Mengxin Zhao ◽

Jing Cong ◽

Jingmin Cheng ◽

Qi Qi ◽

Yuyu Sheng ◽

...

Keyword(s):

Microbial Community ◽

Community Composition ◽

Community Assembly ◽

Soil Microbial Community ◽

Southern China ◽

Microbial Community Composition ◽

Nitrogen And Phosphorus ◽

Soil Microbial ◽

Microbial Community Assembly ◽

Microbial Functional Gene

Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.

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

PeerJ ◽

10.7717/peerj.6746 ◽

2019 ◽

Vol 7 ◽

pp. e6746 ◽

Cited By ~ 4

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.

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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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