The use of high-throughput DNA sequencing (HTS) has revealed the great diversity of rhizobacteria in plant rhizospheres; however, only a minor portion (≤ 1%) of rhizobacteria belonging to few taxa can be cultured under laboratory conditions. In recent years, in situ cultivation has opened a window to explore a greater diversity of bacterial taxa in the environment. Here, we explored the total and culturable rhizobacterial communities associated with the rhizosphere of wheat plants by using 16S rRNA-based HTS and in situ cultivation with microwell chambers (MWCs), respectively. Results by HTS revealed to phyla Proteobacteria (29–39%), Acidobacteria (17%), Actinobacteria (11–15%), and Bacteroidetes (5–12%) as the most abundant rhizobacterial taxa in rhizosphere samples. A total of 206 isolates (26 genera) were obtained with MWCs, where coincidentally with HTS, the most abundant phyla were Proteobacteria (70.4%), Firmicutes (24%), Actinobacteria (4%), and Bacteroidetes (1.5%). At the genus level, the most of isolates (72%) belonged to Pseudomonas , followed by Bacillus , Stenotrophomonas , Delftia , and Herbaspirillum . Members of rare taxa ( Lelliottia , Rhodococcus , Micrococcus , Variovorax , and Bosea ) also were isolated by MWCs. In addition, a high proportion (82%) of isolates showed high similarity with plant beneficial and environmental non-pathogenic bacteria whereas a minor proportion (18%) of isolates showed high similarity to human and plant pathogenic bacteria. This study demonstrates that in situ cultivation represents a useful tool to isolate a greater number of rhizobacterial taxa, which can be investigated under laboratory conditions in bioprospecting (e.g., plant growth–promoting bacteria) and public health (e.g., human opportunist and plant pathogens) studies.

中文翻译：

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增加植物根际群落可培养细菌多样性的原位培养方法

高通量 DNA 测序 (HTS) 的使用揭示了植物根际中根际细菌的巨大多样性；然而，在实验室条件下，只有一小部分 (≤ 1%) 属于少数分类群的根际细菌可以培养。近年来，原位培养为探索环境中更多样化的细菌分类群打开了一扇窗。在这里，我们分别使用基于 16S rRNA 的 HTS 和微孔室 (MWC) 原位培养探索了与小麦植物根际相关的总的和可培养的根际细菌群落。HTS 的结果显示，变形菌门 (29–39%)、酸杆菌门 (17%)、放线菌门 (11–15%) 和拟杆菌门 (5–12%) 是根际样本中最丰富的根际细菌分类群。使用 MWC 共获得 206 个分离株（26 个属），与 HTS 巧合的是，最丰富的门是变形菌门 (70.4%)、厚壁菌门 (24%)、放线菌门 (4%) 和拟杆菌门 (1.5%)。在属水平上，大多数分离株（72%）属于假单胞菌属，其次是芽孢杆菌属、狭养单胞菌属、代尔夫特菌属和草螺菌属。稀有分类群（Lelliottia、Rhodococcus、Micrococcus、Variovorax 和 Bosea）的成员也通过 MWC 进行了分离。此外，高比例 (82%) 的分离株与植物有益和环境非致病细菌表现出高度相似性，而一小部分 (18%) 分离株与人类和植物致病细菌表现出高度相似性。这项研究表明，原位培养代表了一种分离更多根际细菌分类群的有用工具，可以在实验室条件下进行生物勘探（例如