Acharya Shwetha M, Yee Mon Oo, Diamond Spencer, Andeer Peter F, Baig Nameera F, Aladesanmi Omolara T, Northen Trent R, Banfield Jillian F, Chakraborty Romy
Department of Ecology, Earth & Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Earth and Planetary Science, University of California, Berkeley, CA, 94720, USA.
ISME Commun. 2023 Jun 6;3(1):54. doi: 10.1038/s43705-023-00265-1.
For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.
为了更深入、全面地了解根际微生物群的组成和功能，我们需要在标准化生长容器中以单个根的尺度为重点进行研究。即使在幼苗中，根分泌物模式也会沿着根的不同部位发生变化，从而形成空间上不同的微生物生态位。为了解决这个问题，我们使用一种名为EcoFABs的标准化人工生态系统，以及更传统的花盆和试管，分析了在天然土壤中生长的短柄草幼根发育过程中两个空间上不同区域（根尖和根基）的微生物群落。基于16S rRNA的群落分析显示出强烈的根际效应，导致属于放线菌、拟杆菌、厚壁菌和变形菌的几个操作分类单元显著富集。然而，根尖和根基之间或不同生长容器之间的微生物群落组成没有差异。宏基因组学的功能分析揭示了根尖和根际土壤之间的显著差异。与不同代谢途径和根定殖相关的基因在根尖中富集。另一方面，与养分限制和环境胁迫相关的基因在根际土壤中比根尖中更为突出，这意味着相对于根而言，根际土壤中缺乏容易获得的、不稳定的碳和养分。这种对发育中的根与微生物群落之间关系的见解对于明智地理解植物早期发育阶段的植物-微生物相互作用至关重要。
