Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, Haryana, 125001, India.
National Centre for Microbial Resource, National Centre for Cell Science, Savitribai Phule Pune University Campus, Pune, 411021, India.
Arch Microbiol. 2022 Jul 17;204(8):495. doi: 10.1007/s00203-022-02916-8.
The microbial diversity in the Indian caves is inadequately characterized. This study reports on the culturable microbial communities in caves from the Indian sub-continent. This study aims to expand the current understanding of bacterial diversity in the speleothems and wall deposits from Krem Soitan, Krem Lawbah, Krem Mawpun in Khasi Hills, Meghalaya, India. A culture-dependent approach was employed for elucidating the community structure in the caves using MALDI-TOF spectrometry and 16S rRNA gene sequencing. A high bacterial diversity and a greater bacterial taxonomic diversity is reported using MALDI-TOF spectrometry and 16S rRNA gene sequencing. High microbial enumerations were observed on dilute nutrient agar (5.3 × 10 to 8.8 × 10) followed by M9 minimal medium (4 × 10 to 1.7 × 10) and R2A medium (1.0 × 10 to 5.7 × 10). A total of 826 bacterial isolates were selected and preserved for the study. 295 bacterial isolates were identified using MALDI-TOF spectrometry and the isolates which showed no reliable peaks were further identified by 16S rRNA gene sequencing. A total 91% of the bacterial diversity was dominated by Proteobacteria (61%) and Actinobacteria (30%). In addition, bacterial phyla include Firmicutes (7.45%), Deinococcus-Thermus (0.33%) and Bacteroidetes (0.67%) were found in the samples. At the genus level, Pseudomonas (55%) and Arthrobacter (23%) were ubiquitous followed by Acinetobacter, Bacillus, Brevundimonas, Deinococcus, Flavobacterium, Paenibacillus, Pseudarthrobacter. Multivariate statistical analysis indicated that the bacterial genera formed separate clusters depending on the geochemical constituents in the spring waters suitable for their growth and metabolism. To the best of our knowledge, there are no previous geomicrobiological investigations in these caves and this study is a pioneering culture dependent study of the microbial community with many cultured isolates.
印度洞穴中的微生物多样性尚未得到充分描述。本研究报告了来自印度次大陆洞穴中的可培养微生物群落。本研究旨在扩大对喀尔西亚丘陵克里姆索坦、克里姆劳巴和克里姆马蓬洞穴中方解石和墙壁沉积物中细菌多样性的现有认识。采用依赖于培养的方法，使用 MALDI-TOF 光谱仪和 16S rRNA 基因测序来阐明洞穴中的群落结构。使用 MALDI-TOF 光谱仪和 16S rRNA 基因测序报告了较高的细菌多样性和更大的细菌分类多样性。在稀营养琼脂（5.3×10 到 8.8×10）上观察到较高的微生物计数，其次是 M9 最小培养基（4×10 到 1.7×10）和 R2A 培养基（1.0×10 到 5.7×10）。总共选择并保存了 826 个细菌分离物用于研究。使用 MALDI-TOF 光谱仪鉴定了 295 个细菌分离物，对于没有可靠峰的分离物进一步通过 16S rRNA 基因测序进行鉴定。细菌多样性的 91%由变形菌门（61%）和放线菌门（30%）主导。此外，在样品中还发现了厚壁菌门（7.45%）、Deinococcus-Thermus（0.33%）和拟杆菌门（0.67%）。在属水平上，假单胞菌（55%）和节杆菌（23%）普遍存在，其次是不动杆菌属、芽孢杆菌属、短小杆菌属、Deinococcus、黄杆菌属、类芽孢杆菌属、假节杆菌属。多变量统计分析表明，根据适合其生长和代谢的泉水的地球化学成分，细菌属形成了不同的聚类。据我们所知，以前在这些洞穴中没有进行过地质微生物学研究，本研究是对微生物群落的首次依赖于培养的研究，有许多培养的分离物。
