Dror Barak, Wang Zongqiang, Brady Sean F, Jurkevitch Edouard, Cytryn Eddie
Institute of Soil, Water and Environmental Sciences, Agricultural Research Organization, Rishon-Lezion, Israel.
Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
mSystems. 2020 Dec 22;5(6):e00866-20. doi: 10.1128/mSystems.00866-20.
Polyketides (PKs) and nonribosomal peptides (NRPs) are two microbial secondary metabolite (SM) families known for their variety of functions, including antimicrobials, siderophores, and others. Despite their involvement in bacterium-bacterium and bacterium-plant interactions, root-associated SMs are largely unexplored due to the limited cultivability of bacteria. Here, we analyzed the diversity and expression of SM-encoding biosynthetic gene clusters (BGCs) in root microbiomes by culture-independent amplicon sequencing, shotgun metagenomics, and metatranscriptomics. Roots (tomato and lettuce) harbored distinct compositions of nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) relative to the adjacent bulk soil, and specific BGC markers were both enriched and highly expressed in the root microbiomes. While several of the highly abundant and expressed sequences were remotely associated with known BGCs, the low similarity to characterized genes suggests their potential novelty. Low-similarity genes were screened against a large set of soil-derived cosmid libraries, from which five whole BGCs of unknown function were retrieved. Three clusters were taxonomically affiliated with , while the remaining were not associated with known bacteria. One -derived BGC was predicted to encode a polyene with potential antifungal activity, while the others were too novel to predict chemical structure. Screening against a suite of metagenomic data sets revealed higher abundances of retrieved clusters in roots and soil samples. In contrast, they were almost completely absent in aquatic and gut environments, supporting the notion that they might play an important role in root ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of undiscovered SMs. We identified distinct secondary-metabolite-encoding genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems yet almost completely absent in human gut and aquatic environments. Several of the genes were distantly related to genes encoding antimicrobials and siderophores, and their high sequence variability relative to known sequences suggests that they may encode novel metabolites and may have unique ecological functions. This study demonstrates that plant roots harbor a diverse array of unique secondary-metabolite-encoding genes that are highly enriched and expressed in the root ecosystem. The secondary metabolites encoded by these genes might assist the bacteria that produce them in colonization and persistence in the root environment. To explore this hypothesis, future investigations should assess their potential role in interbacterial and bacterium-plant interactions.
聚酮化合物（PKs）和非核糖体肽（NRPs）是两个微生物次级代谢产物（SM）家族，以其多种功能而闻名，包括抗菌、铁载体等。尽管它们参与了细菌与细菌以及细菌与植物的相互作用，但由于细菌的可培养性有限，根际相关的SMs在很大程度上尚未得到充分研究。在这里，我们通过不依赖培养的扩增子测序、鸟枪法宏基因组学和宏转录组学分析了根际微生物群落中编码SM的生物合成基因簇（BGCs）的多样性和表达情况。相对于相邻的大块土壤，根（番茄和生菜）中含有不同组成的非核糖体肽合成酶（NRPSs）和聚酮合成酶（PKSs），并且特定的BGC标记在根际微生物群落中既富集又高度表达。虽然一些高度丰富和表达的序列与已知的BGCs有较远的关联，但与已鉴定基因的低相似性表明它们可能具有新颖性。针对大量土壤来源的黏粒文库筛选低相似性基因，从中检索到五个功能未知的完整BGCs。三个簇在分类学上与 相关，而其余的与已知细菌无关。一个源自 的BGC被预测编码一种具有潜在抗真菌活性的多烯，而其他的则过于新颖以至于无法预测化学结构。针对一系列宏基因组数据集进行筛选发现，在根和土壤样本中检索到的簇丰度更高。相比之下，它们在水生和肠道环境中几乎完全不存在，这支持了它们可能在根际生态系统中发挥重要作用的观点。总体而言，我们的结果表明根际微生物群落中存在一组特定的未被发现的SMs。我们鉴定出了独特的编码次级代谢产物的基因，这些基因在根际生态系统中（相对于相邻的大块土壤）富集并表达，但在人类肠道和水生环境中几乎完全不存在。其中一些基因与编码抗菌剂和铁载体的基因有较远的关系，并且它们相对于已知序列的高序列变异性表明它们可能编码新的代谢产物并可能具有独特的生态功能。这项研究表明，植物根系中含有大量独特的编码次级代谢产物的基因，这些基因在根际生态系统中高度富集并表达。这些基因编码的次级代谢产物可能有助于产生它们的细菌在根际环境中定殖和存活。为了探索这一假设，未来的研究应该评估它们在细菌间和细菌与植物相互作用中的潜在作用。
