Chen Mingfei, Acharya Shwetha M, Yee Mon Oo, Cabugao Kristine Grace M, Chakraborty Romy
Department of Ecology, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
Front Microbiol. 2024 May 23;15:1401794. doi: 10.3389/fmicb.2024.1401794. eCollection 2024.
The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from roots grown in field soil with carbon substrates mimicking root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.
根际微生物群通过调节养分循环、土壤完整性和碳储存，在支持植物生产力和生态系统功能方面发挥着关键作用。然而，由于分类学和功能多样性极为丰富，解读根际内微生物关系之间复杂的相互作用具有挑战性。在此，我们提出了基于微生物共定位和微生物相互作用构建的系统设计框架，以成功组装多个源自根际的简化复杂性菌群（RCC）。我们用模拟根系分泌物的碳底物，从田间土壤中生长的根系富集共定位微生物，产生了768个富集物。通过每3天或7天转移一次富集物，持续10代，我们开发了快速生长和缓慢生长的简化复杂性微生物群落。大多数碳底物在几次转移后就导致了高度稳定的RCC。16S rRNA基因扩增子分析揭示了基于接种物和碳源的不同群落组成，复杂碳源富集了生长缓慢但功能重要的土壤类群，如酸杆菌门和疣微菌门。网络分析表明，微生物群落，无论是按生长速率（快与慢）还是按演替（跨代）区分，都具有显著不同的网络中心性。此外，在这些网络中确定的关键类群属于具有促进植物生长特性的属，突出了它们在塑造根际微生物群落网络中的关键作用。此外，测试的菌群表现出高稳定性和可重复性，确保从甘油菌液中长期存活并成功复苏以供使用。我们的研究代表了朝着基于微生物共定位和相互作用构建根际菌群框架迈出的重要一步，对可持续农业和环境管理具有未来意义。
