Data from: Community assembly, species richness and nestedness of arbuscular mycorrhizal fungi in agricultural soils

Understanding how communities assemble is a central goal of ecology. This is particularly relevant for communities of arbuscular mycorrhizal fungi (AMF), because the community composition of these beneficial plant symbionts influences important ecosystem processes. Moreover, AMF may be used as sensitive indicators of ecological soil quality if they respond to environmental variation in a predictable way. Here we use a molecular profiling technique (T-RFLP of 25S rRNA gene fragments) to test which factors determine AM fungal community composition in 40 agricultural soils in the Netherlands. In particular, we test whether species richness, dominance structure and community nestedness are influenced by management type (in pairs of organically and conventionally farmed fields), and we examine the contribution of crop species (maize versus potato), soil type (sand versus clay textured soils), and habitat (plant root versus bulk soil) on AMF community characteristics. AMF richness varied from 1 to 11 taxa per field. Communities from species poor fields were found to be subsets of those in richer fields, indicating nestedness and a progressive “loss” from the species pool. AMF taxa richness and occurrence in soil and plant roots were highly correlated, and richness was related to management intensity (phosphate availability and grass cropping history together explained 34% and 50% of richness in roots and soils). Soil type together with soil chemical parameters explained only 17% of variance in AMF community structure. We synthesize these results by discussing the potential contribution of a “bottle-neck effect” on AMF communities through increased stochastic effects under environmental stress.解析群落构建机制是生态学的核心研究目标之一。这对于丛枝菌根真菌（arbuscular mycorrhizal fungi, AMF）群落而言尤为关键，因为这类有益植物共生真菌的群落组成会调控诸多重要的生态系统过程。此外，若AMF能以可预测的方式响应环境变化，其可作为生态土壤质量的敏感指示物。本研究采用分子指纹技术——25S核糖体RNA（25S rRNA）基因片段的末端限制性片段长度多态性（Terminal Restriction Fragment Length Polymorphism, T-RFLP）——对荷兰40份农业土壤中的AMF群落组成的影响因子展开探究。具体而言，本研究旨在验证：物种丰富度、优势度结构及群落嵌套性是否受耕作管理类型（有机耕作与常规耕作配对样地）的影响；同时分析作物种类（玉米与马铃薯）、土壤质地类型（砂土与黏土）以及生境（植物根系与非根际土壤）对AMF群落特征的贡献程度。各样地的AMF物种丰富度介于1至11个分类单元之间。研究发现，物种贫乏样地的AMF群落是物种丰富样地群落的子集，这表明群落存在嵌套性，且物种库呈现出逐步“丢失”分类单元的现象。AMF分类单元丰富度与土壤及植物根系中的AMF检出率呈显著正相关，且丰富度与管理强度密切相关：土壤有效磷含量与草地种植历史可分别解释根系和土壤中34%、50%的AMF丰富度变异。土壤质地与土壤化学参数仅能解释AMF群落结构17%的变异。本研究最后综合上述结果，探讨了环境胁迫下随机过程增强所引发的“瓶颈效应”对AMF群落的潜在调控作用。