Jeevamrut, a bioenhancer used in natural farming, enriches plant-growth-promoting microbial consortia

Jeevamrut, a traditional on-farm fermented bio-formulation used in natural farming, improves soil fertility and crop productivity, yet its microbial ecology remains poorly understood. Here, we report the first integrated shotgun metagenomics and culturomics study to decode the microbial succession and functional potential of Jeevamrut during a 21-day fermentation. Initially Jeevamrut shared microbial profiles similar to cow dung but underwent marked restructuring, with a decline in Bacteroidota and enrichment of Firmicutes, particularly lactic acid bacteria: Leuconostoc, Lactiplantibacillus, Lactococcus, alongside beneficial yeasts such as Saccharomyces cerevisiae. Functional analysis revealed enrichment of genes linked to stress tolerance, phytohormone biosynthesis, nitrogen fixation, and siderophore transport, peaking between days 7 and 10. Culturomic validation confirmed that mid-fermentation isolates exhibited strong plant growth-promoting traits, including auxin production and nutrient solubilization. These findings demonstrate that fermentation transforms Jeevamrut into a bioactive microbial consortium and that days 7-10 represent the optimal window for its application in sustainable natural farming.

吉瓦姆鲁特（Jeevamrut）是一种应用于天然农业的传统农场发酵生物制剂，可提升土壤肥力与作物生产力，但目前学界对其微生物生态的认知仍较为匮乏。本研究首次结合鸟枪宏基因组学（shotgun metagenomics）与培养组学（culturomics）技术，解析了吉瓦姆鲁特在21天发酵过程中的微生物演替与功能潜力。发酵初期，吉瓦姆鲁特的微生物群落组成与牛粪相似，但随后发生了显著的群落重构：拟杆菌门（Bacteroidota）丰度下降，厚壁菌门（Firmicutes）丰度显著富集，其中尤以乳酸菌类群为主，包括明串珠菌属（Leuconostoc）、植物乳杆菌属（Lactiplantibacillus）、乳球菌属（Lactococcus），同时伴随有益酵母酿酒酵母（Saccharomyces cerevisiae）的增殖。功能基因分析显示，与胁迫耐受、植物激素生物合成、固氮作用以及铁载体转运相关的基因丰度显著提升，并在发酵第7至10天达到峰值。培养组学验证结果证实，发酵中期分离得到的菌株表现出优异的促植物生长特性，包括生长素合成与养分溶解能力。本研究结果表明，发酵过程可将吉瓦姆鲁特转化为具有生物活性的微生物群落集合体，且发酵第7至10天为其应用于可持续天然农业的最佳窗口期。