Data from: Diffuse symbioses: roles of plant–plant, plant–microbe and microbe–microbe interactions in structuring the soil microbiome

A conceptual model emphasizing direct host–microbe interactions has
dominated work on host-associated microbiomes. To understand
plant–microbiome associations, however, broader influences on microbiome
composition and functioning must be incorporated, such as those arising
from plant–plant and microbe–microbe interactions. We sampled soil
microbiomes associated with target plant species (Andropogon gerardii,
Schizachyrium scoparium, Lespedeza capitata, Lupinus perennis) grown in
communities varying in plant richness (1-, 4-, 8- or 16-species). We
assessed Streptomyces antagonistic activity and analysed bacterial and
Streptomyces populations via 454 pyrosequencing. Host plant species and
plant richness treatments altered networks of coassociation among
bacterial taxa, suggesting the potential for host plant effects on the
soil microbiome to include changes in microbial interaction dynamics and,
consequently, co-evolution. Taxa that were coassociated in the rhizosphere
of a given host plant species often showed consistent correlations between
operational taxonomic unit (OTU) relative abundance and Streptomyces
antagonistic activity, in the rhizosphere of that host. However, in the
rhizosphere of a different host plant species, the same OTUs showed no
consistency, or a different pattern of responsiveness to such biotic
habitat characteristics. The diversity and richness of bacterial and
Streptomyces communities exhibited distinct relationships with biotic and
abiotic soil characteristics. The rhizosphere soil microbiome is
influenced by a complex and nested array of factors at varying spatial
scales, including plant community, plant host, soil edaphics and microbial
taxon and community characteristics.

强调宿主-微生物直接相互作用的概念模型主导了宿主相关微生物组的研究。然而，要理解植物-微生物组关联，必须纳入对微生物组组成和功能的更广泛影响，例如源自植物-植物和微生物-微生物相互作用的影响。我们采集了与目标植物物种（Andropogon gerardii、Schizachyrium scoparium、Lespedeza capitata、Lupinus perennis）相关的土壤微生物组，这些植物生长在植物丰富度不同的群落中（1、4、8或16物种）。我们评估了链霉菌（Streptomyces）的拮抗活性，并通过454焦磷酸测序分析了细菌和链霉菌种群。宿主植物物种和植物丰富度处理改变了细菌类群间的共关联网络，表明宿主植物对土壤微生物组的影响可能包括微生物相互作用动态的变化，进而导致协同进化。在特定宿主植物物种根际中共关联的类群，其操作分类单元（OTU）相对丰度与链霉菌拮抗活性之间通常表现出一致的相关性。然而，在不同宿主植物物种的根际中，相同的OTU未表现出一致性，或对这类生物栖息地特征表现出不同的响应模式。细菌和链霉菌群落的多样性和丰富度与土壤生物和非生物特征表现出显著的相关性。根际土壤微生物组受到不同空间尺度上复杂且嵌套的一系列因素的影响，包括植物群落、宿主植物、土壤理化特征以及微生物类群和群落特征。