The influence of alfalfa-switchgrass intercropping on microbial community structure and function. Prosser soil metagenome

The use of nitrogen fertilizer on bioenergy crops such as switchgrass results in increased costs, nitrogen leaching, and emissions of N2O, a potent greenhouse gas. Intercropping with nitrogen-fixing alfalfa has been proposed as an environmentally sustainable alternative, but the effects of synthetic fertilizer versus intercropping on soil microbial community functionality remain uncharacterized. We analyzed 24 metagenomes from the upper soil layer of agricultural fields from Prosser, WA over two growing seasons, and representing three agricultural practices: unfertilized switchgrass (control), fertilized switchgrass, and switchgrass intercropped with alfalfa. The synthetic fertilization and intercropping did not result in major shifts of microbial community taxonomic and functional composition compared to the control plots, but a few significant changes were noted. Most notably, mycorrhizal fungi, AOA, and AOB increased in abundance with intercropping and (for AOA/AOB) fertilization. However, only AOB abundance in fertilized plots significantly correlated to N2O emission and companion qPCR data. Collectively, a short period of intercropping elicits minor but significant changes in the soil microbial community toward nitrogen preservation and that intercropping may be a viable alternative to synthetic fertilization. Gene sequences representing novel taxa related to the Nitrosovibrio tenuis and Nitrosospira were also recovered.

在柳枝稷等生物能源作物上施用氮肥，不仅会推高种植成本、造成氮素淋失，还会排放强效温室气体一氧化二氮（N₂O）。有研究提出采用与固氮苜蓿间作的模式作为环境友好型可持续替代方案，但目前尚不清楚合成氮肥施用与间作两种种植模式对土壤微生物群落功能的影响差异。本研究针对美国华盛顿州普罗瑟地区农田的表层土壤样本展开分析，共获取两个生长季的24份宏基因组（metagenome）样本，涵盖三种种植模式：未施氮肥的柳枝稷（对照组）、施用合成氮肥的柳枝稷，以及与苜蓿间作的柳枝稷。与对照组样地相比，合成氮肥施用与间作模式未引发土壤微生物群落分类学与功能组成的显著整体变化，但存在若干具有统计学意义的差异。最为显著的是，间作模式下菌根真菌、氨氧化古菌（Ammonia-Oxidizing Archaea, AOA）与氨氧化细菌（Ammonia-Oxidizing Bacteria, AOB）的丰度均有所提升；而合成氮肥施用仅对AOA与AOB的丰度产生正向影响。不过，仅在施用氮肥的样地中，AOB丰度与N₂O排放量及配套的定量聚合酶链式反应（quantitative Polymerase Chain Reaction, qPCR）检测数据存在显著相关性。综合来看，短期间作可使土壤微生物群落朝着提升氮素固持能力的方向发生小幅但具有统计学意义的变化，表明间作可作为合成氮肥施用的可行替代方案。本研究还成功获取到了与纤细亚硝化弧菌（*Nitrosovibrio tenuis*）和亚硝化螺菌属（*Nitrosospira*）相关的新型分类单元基因序列。