利用新型皮升液滴技术富集神秘候选门类辐射细菌的不同类群。

IF 5.1 Q1 ECOLOGY
ISME communications Pub Date : 2024-06-21 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae080
DeDe Kwun Wai Man, Syrie M Hermans, Martin Taubert, Sarahi L Garcia, Sundar Hengoju, Kirsten Küsel, Miriam A Rosenbaum
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引用次数: 0

摘要

候选门辐射(CPR)是一个独特的单系支系,构成了生命树的主要部分。人们主要利用基于测序的技术,广泛致力于破译其成员的功能多样性。然而,培养成功的微生物仍然很少,这带来了巨大的挑战,尤其是在以 CPR 为主导、生物量较低的地下水微生物群中。在这里,我们采用了一种先进的高通量液滴微流控技术来富集地下水中的 CPR 分类群。利用低容量过滤方法,我们成功地获得了与原始地下水微生物群落相似的微生物群落。我们使用一种新型 CPR 特异性引物,通过培养尝试快速跟踪 CPR 部分,对水滴和水体批量培养 30 天的 CPR 富集情况进行了评估。土壤提取物和微生物产生的坏死物质的结合为 CPR 的富集提供了最有利的条件。利用这些补充条件,液滴培养被证明优于散装培养,与散装培养的 1 到 2 倍相比,液滴培养可使 CPR 富集 13 倍。扩增子测序发现了 10 个明显富集的 CPR 顺序。CPR富集度最高的是 Parcubacteria 目中的一些未知成员、Cand.Jorgensenbacteria 和未分类的 UBA9983。此外,我们还发现了共同富集的假定宿主类群,这可能会在后续研究中指导更有针对性的 CPR 分离方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique.

The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.

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