Table_6_Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System.XLSX

Tillage and fertilization are common practices used to enhance soil fertility and increase yield. Changes in soil edaphic properties associated with different tillage and fertility regimes have been widely examined, yet, the microbially mediated pathways and ecological niches involved in enhancing soil fertility are poorly understood. The effects of long-term conventional tillage and no-till in parallel with three fertility treatments (No fertilization, N-only, and NPK) on soil microbial communities were investigated in a long-term field study that was established in the 1970’s. Here, we used high-throughput sequencing of bacterial, fungal and oomycetes markers, followed by community-level functional and ecological assembly to discern principles governing tillage and fertility practices’ influence on associated soil microbiomes. Both tillage and fertilizer significantly altered microbial community structure, but the tillage effect was more prominent than the fertilizer effect. Tillage significantly affected bacteria, fungi, fusaria, and oomycete beta-diversity, whereas fertilizer only affected bacteria and fungi beta-diversity. In our study different tillage and fertilizer regimes favored specific networks of metabolic pathways and distinct ecological guilds. No-till selected for beneficial microbes that translocate nutrients and resources and protect the host against pathogens. Notably, ecological guilds featuring arbuscular mycorrhizae, mycoparasites, and nematophagous fungi were favored in no-till soils, while fungal saprotrophs and plant pathogens dominated in tilled soils. Conventional till and fertilizer management shifted the communities toward fast growing competitors. Copiotrophic bacteria and fusarium species were favored under conventional tillage and in the presence of fertilizers. The analysis of the metagenomes revealed a higher abundance of predicted pathways associated with energy metabolism, translation, metabolism of cofactors and vitamins, glycan biosynthesis and nucleotide metabolism in no-till. Furthermore, no specific pathways were found to be enriched under the investigated fertilization regimes. Understanding how tillage and fertilizer management shift microbial diversity, structure and ecological niches, such as presented here, can assist with designing farming systems that can maintain high crop yield, while reducing soil erosion and nutrient losses.

耕作（tillage）与施肥（fertilization）是提升土壤肥力、增加作物产量的常用农艺措施。不同耕作与施肥管理模式下的土壤理化性质变化已得到广泛研究，但人们对介导土壤肥力提升的微生物途径及相关生态位（ecological niches）仍知之甚少。本研究依托1970年代建立的长期定位田间试验，探究了长期常规耕作（conventional tillage）与免耕（no-till）结合三种施肥处理（不施肥、单施氮肥、氮磷钾配施）对土壤微生物群落的影响。本研究通过对细菌、真菌及卵菌（oomycetes）标记基因进行高通量测序（high-throughput sequencing），随后开展群落水平功能与生态组装分析，以阐明耕作与施肥措施对相关土壤微生物组的调控规律。耕作与施肥均显著改变了微生物群落结构，但耕作措施的影响更为显著。耕作显著影响细菌、真菌、镰孢菌属（fusaria）及卵菌的β多样性（beta-diversity），而施肥仅对细菌和真菌的β多样性产生显著影响。本研究中，不同耕作与施肥管理模式分别倾向于形成特定的代谢通路网络与独特的生态功能群（ecological guilds）。免耕土壤中富集了可转运养分与资源、帮助宿主抵御病原菌的有益微生物。值得注意的是，免耕土壤中富集了丛枝菌根（arbuscular mycorrhizae）、重寄生真菌及食线虫真菌类生态功能群，而耕作土壤中则以真菌腐生菌与植物病原菌为优势类群。常规耕作与施肥管理使微生物群落向快速生长的竞争类群转变。常规耕作及施肥条件下，富营养型细菌（copiotrophic bacteria）与镰孢菌属物种更具优势。宏基因组（metagenomes）分析显示，免耕土壤中与能量代谢、翻译过程、辅因子与维生素代谢、聚糖生物合成及核苷酸代谢相关的预测通路丰度更高。此外，在所研究的施肥管理模式下，未发现显著富集的特异性代谢通路。如本研究所示，阐明耕作与施肥管理如何改变微生物多样性、群落结构及生态位，有助于设计既能维持高产作物产量，又能减少土壤侵蚀与养分流失的农业生产系统。