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

Ning, Daliang; Yuan, Mengting; Wu, Linwei; Zhang, Ya Ping; Guo, Xue; Zhou, Xuelong; Yang, Yunfeng; Arkin, Adam P.; Firestone, Mary K.; Zhou, Jizhong

doi:10.1038/s41467-020-18560-z

Cited by 669 publications

(512 citation statements)

References 66 publications

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“…As β‐diversity often depends on community size (α‐diversity; Chase et al, 2011; Kraft et al, 2011; Myers et al, 2015), we also calculated the standard effective size of β‐diversity (i.e., β‐deviation) by comparing observed β‐diversity values to those generated by null models. We generated 999 null local communities within each N treatment, by randomly placing individuals into each local community with probabilities proportional to regional relative cover/abundance of the species, while preserving local α‐diversity (Ning et al, 2019, 2020). The standardized effect size (β‐deviation for Bray–Curtis and Jaccard dissimilarity) was calculated as the difference between the observed β‐diversity and mean β‐diversity of the null communities divided by the standard deviation of β‐diversity of the null communities (Kraft et al, 2011; Ning et al, 2019, 2020).…”

Section: Methodsmentioning

confidence: 99%

Long‐term nitrogen input alters plant and soil bacterial, but not fungal beta diversity in a semiarid grassland

Liu

Yang

et al. 2021

Global Change Biology

108

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Anthropogenic nitrogen (N) input is known to alter plant and microbial α‐diversity, but how N enrichment influences β‐diversity of plant and microbial communities remains poorly understood. Using a long‐term multilevel N addition experiment in a temperate steppe, we show that plant, soil bacterial and fungal communities exhibited different responses in their β‐diversity to N input. Plant β‐diversity decreased linearly as N addition increased, as a result of increased directional environmental filtering, where soil environmental properties largely explained variation in plant β‐diversity. Soil bacterial β‐diversity first increased then decreased with increasing N input, which was best explained by corresponding changes in soil environmental heterogeneity. Soil fungal β‐diversity, however, remained largely unchanged across the N gradient, with plant β‐diversity, soil environmental properties, and heterogeneity together explaining an insignificant fraction of variation in fungal β‐diversity, reflecting the importance of stochastic community assembly. Our study demonstrates the divergent effect of N enrichment on the assembly of plant, soil bacterial and fungal communities, emphasizing the need to examine closely associated fundamental components (i.e., plants and microorganisms) of ecosystems to gain a more complete understanding of ecological consequences of anthropogenic N enrichment.

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Section: Methodsmentioning

confidence: 99%

Long‐term nitrogen input alters plant and soil bacterial, but not fungal beta diversity in a semiarid grassland

Liu

Yang

et al. 2021

Global Change Biology

108

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“…We inferred community assembly mechanisms with a phylogenetic bin-based null model (iCAMP) [44] and found that dispersal limitation and homogenous selection were the key processes driving protist community assembly in both sampling sites during the five sampling times. Dispersal limitation had a larger effect on community assembly at the SL site (67-73%), followed by homogenous selection (23-29%) (Fig.…”

Section: Dispersal Limitation and Homogeneous Selection Shape Rhizospmentioning

confidence: 99%

“…The relative influences of community assembly processes were assessed by a phylogenetic bin-based null model framework, iCAMP, which was recently reported with substantially improved performance [44]. Briefly, iCAMP divided taxa into different phylogenetic groups (bins) to ensure adequate phylogenetic signal to infer selection from phylogenetic diversity; then, the processes (selection, dispersal, and drift or others) dominating each bin were identified, according to the deviation of observed phylogenetic and taxonomic diversity from random patterns simulated by null models; finally, the relative abundance of bins governed by each process was aggregated to evaluate its influence on entire community assembly.…”

Section: Inferring Community Assembly Mechanismsmentioning

confidence: 99%

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

et al. 2021

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Background Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. Results We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists’ community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. Conclusions We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system.

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“…The assembly of microbial community was calculated using a framework to quantitatively infer community assembly mechanisms through phylogenetic bin-based null model analysis (iCAMP) in iCAMP packages (version 1.2.9) under the default parameters with the argument of bin.size.limit = 24 (Ning et al, 2020). In detail, the bins were divided according to the phylogenetic relationships of observed taxa.…”

Section: Microbial Community Assemblymentioning

confidence: 99%

Bacterial and eukaryotic community interactions might contribute to shrimp culture pond soil ecosystem at different culture stages

et al. 2021

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Sedimentary bacterial and eukaryotic communities are major components of the aquatic ecosystem. Revealing the linkages between their community structure and interactions is crucial to understand the diversity and functions of aquatic and soil ecosystems. However, how their diversity and assembly contribute to their interactions on time scale is unclear. This study examined sedimentary bacterial and eukaryotic communities in shrimp culture ponds at different culture stages. The most abundant bacteria were Proteobacteria (38.27%), whereas the most abundant eukaryotes were Chytridiomycota (27.48%). Bacterial and eukaryotic diversities were correlated (P < 0.05), implying the strong interactions between bacteria and eukaryotes. Results showed that the bacterial and eukaryotic communities became increasingly similar on a local scale along with the shrimp culture. Only the eukaryotic community significantly increased in similarity along with the shrimp culture (P < 0.05), suggesting that the sedimentary eukaryotic community structure is sensitive under shrimp culture. Co-occurrence network modeling indicated that positive microbial interactions were dominant. The homogeneous selection was the major driver of community assembly. Bacterial diversity negatively correlated with operational taxonomic units and positive links in networks (P < 0.05), whereas eukaryotic diversities positively correlated with positive links in networks (P < 0.05). This study broadens our knowledge about sedimentary microbial diversity, community assembly, and interaction patterns on time scale, providing a reference for the sustainable management in aquaculture production.

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

Cited by 669 publications

References 66 publications

Long‐term nitrogen input alters plant and soil bacterial, but not fungal beta diversity in a semiarid grassland

Long‐term nitrogen input alters plant and soil bacterial, but not fungal beta diversity in a semiarid grassland

Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop

Bacterial and eukaryotic community interactions might contribute to shrimp culture pond soil ecosystem at different culture stages

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