Soil, Water and Environmental Sciences, Volcani Research Center, Rishon LeZion 7505101, Israel.
Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
Int J Mol Sci. 2021 Nov 4;22(21):11948. doi: 10.3390/ijms222111948.
Root selection of their associated microbiome composition and activities is determined by the plant's developmental stage and distance from the root. Total gene abundance, structure and functions of root-associated and rhizospheric microbiomes were studied throughout wheat growth season under field conditions. On the root surface, abundance of the well-known wheat colonizers and decreased and increased, respectively, during spike formation, whereas abundance of was independent of spike formation. Metagenomic analysis combined with functional co-occurrence networks revealed a significant impact of plant developmental stage on its microbiome during the transition from vegetative growth to spike formation. For example, gene functions related to biofilm and sensorial movement, antibiotic production and resistance and carbons and amino acids and their transporters. Genes associated with these functions were also in higher abundance in root vs. the rhizosphere microbiome. We propose that abundance of transporter-encoding genes related to carbon and amino acid, may mirror the availability and utilization of root exudates. Genes related to antibiotic resistance mechanisms were abundant during vegetative growth, while after spike formation, genes related to the biosynthesis of various antibiotics were enriched. This observation suggests that during root colonization and biofilm formation, bacteria cope with competitor's antibiotics, whereas in the mature biofilm stage, they invest in inhibiting new colonizers. Additionally, there is higher abundance of genes related to denitrification in rhizosphere compared to root-associated microbiome during wheat growth, possibly due to competition with the plant over nitrogen in the root vicinity. We demonstrated functional and phylogenetic division in wheat root zone microbiome in both time and space: pre- and post-spike formation, and root-associated vs. rhizospheric niches. These findings shed light on the dynamics of plant-microbe and microbe-microbe interactions in the developing root zone.
根系对其相关微生物群落组成和活性的选择取决于植物的发育阶段和与根系的距离。在田间条件下，研究了整个小麦生长季节中根系相关和根际微生物群落的总基因丰度、结构和功能。在根表面，在穗形成过程中，众所周知的小麦定殖者 和 的丰度分别减少和增加，而 的丰度与穗形成无关。结合功能共现网络的宏基因组分析表明，植物发育阶段对其微生物组在从营养生长向穗形成过渡过程中的显著影响。例如，与生物膜和感觉运动、抗生素产生和抗性以及碳、氨基酸及其转运体相关的基因功能。与这些功能相关的基因在根与根际微生物组中的丰度也更高。我们提出，与碳和氨基酸相关的转运蛋白编码基因的丰度可能反映了根分泌物的可用性和利用。抗生素抗性机制相关基因在营养生长期间丰富，而在穗形成后，各种抗生素生物合成相关基因富集。这一观察结果表明，在根定植和生物膜形成过程中，细菌应对竞争者的抗生素，而在成熟的生物膜阶段，它们投资于抑制新的定植者。此外，与根相关的微生物群落相比，在小麦生长过程中，根际中与反硝化相关的基因丰度更高，这可能是由于植物在根附近争夺氮源所致。我们证明了小麦根区微生物组在时间和空间上的功能和系统发育上的划分：穗形成前后，以及根相关和根际生境。这些发现揭示了发育中的根区中植物-微生物和微生物-微生物相互作用的动态。
