State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.
Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China.
Appl Environ Microbiol. 2021 Feb 26;87(6). doi: 10.1128/AEM.02440-20.
Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N-fixing and alkane-oxidizing species were documented in the karst cave microbiome. Two clusters of the β-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research. Karst caves are oligotrophic environments that are dark and humid and have a relatively stable annual temperature. The diversity of bacteria and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data mining to explore the compositions and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and their genomes sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.
喀斯特洞穴是广泛分布的地下系统，其中的微生物组被认为是洞穴演化和生物地球化学循环的驱动力。在过去的几年中，已经对洞穴系统的微生物组进行了非培养依赖性研究，但仍需要进行密集的微生物培养，以验证基于序列的假设，并揭示洞穴生态系统中的微生物功能。在这项研究中，对中国西南部贵州省的两个喀斯特洞穴的微生物组进行了研究。从岩石、水和沉积物样本中培养了 3562 株细菌菌株，发现了 102 属 329 种（包括 14 种新描述的物种）。我们通过从一个喀斯特洞穴微生物组中提取 204 个数据库衍生基因组和测序 14 个新的细菌基因组，创建了一个包含 218 个细菌基因组的洞穴细菌基因组文库。本研究中获得的培养基因组文库和以前研究的宏基因组数据用于研究细菌代谢以及在洞穴生态系统中参与碳、氮和硫生物地球化学循环的潜力。在喀斯特洞穴微生物组中记录了新的固氮和烷烃氧化物种。在培养微生物组和宏基因组数据中都大量存在的两个β-酮戊二酸途径簇被鉴定出来，并且从培养的细菌基因组中代表它们的功能得到了证明。这项大规模的洞穴微生物培养代表了迄今为止最密集的洞穴细菌资源收集，为未来的洞穴生物地球化学研究提供了有价值的信息和多样化的微生物资源。喀斯特洞穴是贫营养、黑暗、潮湿且年温度相对稳定的环境。细菌的多样性及其代谢对于理解洞穴生态系统中的生物地球化学循环至关重要。我们将大规模的细菌培养与宏基因组数据挖掘相结合，以探索两个喀斯特洞穴系统中微生物组的组成和代谢。我们的结果揭示了高度多样化的洞穴细菌群落的存在，并描述了 14 个新的细菌物种并对其基因组进行了测序。在这项研究中，我们获得了迄今为止最密集的来自喀斯特洞穴的培养微生物资源收集，并预测了洞穴生态系统中元素生物地球化学循环的各种重要途径。
