Longley Reid, Noel Zachary A, Benucci Gian Maria Niccolò, Chilvers Martin I, Trail Frances, Bonito Gregory
Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.
Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.
Front Microbiol. 2020 Jun 3;11:1116. doi: 10.3389/fmicb.2020.01116. eCollection 2020.
Soybean () is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by and while belowground samples were dominated by and Aboveground fungal communities were dominated by across all management systems, while belowground samples were dominated by and . Specific taxa including potential plant beneficials such as were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.
大豆（）是一种重要的豆科作物，在美国乃至全世界广泛种植。2016年，仅在美国，大豆的价值就达410亿美元。越来越多的大豆种植户采用替代管理策略来提高作物的可持续性和盈利能力。替代管理系统已展现出多种益处，但其对与大豆相关的微生物群落的影响尚不清楚。为了更好地理解作物管理系统对与大豆相关的微生物组的影响，我们采用对内部转录间隔区（ITS）区域和16S rRNA基因进行DNA扩增子测序的方法，来分析与土壤、根、茎和叶相关的真菌和原核生物群落。在整个生长季节的三个时间点，从长期采用传统、免耕和有机管理系统的重复地块中采集大豆植株样本。结果表明，样本来源是与大豆相关的微生物群落中β多样性的主要驱动因素，但管理方式和植物生长阶段也是重要因素。同样，α多样性的差异由区室和样本来源驱动。总体而言，有机管理系统的真菌和细菌香农多样性较低。在原核生物群落中，地上组织以 和 为主，而地下样本以 和 为主。在所有管理系统中，地上真菌群落以 为主，而地下样本以 和 为主。包括潜在植物有益菌如 在内的特定分类群是传统和有机管理系统的指示物种。免耕管理增加了已知含有植物有益生物如 和球囊菌纲的类群的丰度。网络分析表明，每个管理系统中都存在不同的高度连通的枢纽分类群。总体而言，本研究证明了特定的长期种植管理系统如何改变微生物群落，以及这些群落在大豆生长过程中如何变化。
