Abstract
BackgroundDue to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. However, it has been well documented that microorganisms play important roles in cave development. Survival of microbes in this unique habitat likely involves a broad range of adaptive capabilities. Recently, cave microbiomes all over the world are of great scientific interest. However, the majority of investigations focused mostly on small subunit ribosomal RNA (16S rRNA) gene, leaving the ecological role of the microbial community largely unknown. Here, we are particularly interested in exploring the taxonomic composition and metabolic potential of microorganisms in soil from Manao-Pee cave, a subterranean limestone cave in the western part of Thailand, by using high-throughput shotgun metagenomic sequencing.ResultsFrom taxonomic composition analysis using ribosomal RNA genes (rRNA), the results confirmed that Actinobacteria (51.2%) and Gammaproteobacteria (24.4%) were the dominant bacterial groups in the cave soil community. Metabolic potential analysis, based on six functional modules of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, revealed that functional genes involved in microbial metabolisms are highly represented in this community (40.6%). To better understand how microbes thrive under unfavorable cave condition, we focused on microbial energy metabolism. The results showed that microbial genes involved in oxidative phosphorylation were the most dominant (28.8%) in Manao-Pee cave, and were followed by methane metabolism (20.5%), carbon fixation (16.0%), nitrogen metabolism (14.7%), and sulfur metabolism (6.3%). In addition, microbial genes involved in xenobiotic biodegradation (26 pathways) and in production of secondary metabolites (27 pathways) were also identified.ConclusionIn addition to providing information on microbial diversity, we also gained insights into microbial adaptations and survival strategies under cave conditions. Based on rRNA genes, the results revealed that bacteria belonging to the Actinobacteria and Gammaproteobacteria were the most abundant in this community. From metabolic potential analysis, energy and nutrient sources that sustain diverse microbial population in this community might be atmospheric gases (methane, carbon dioxide, nitrogen), inorganic sulfur, and xenobiotic compounds. In addition, the presence of biosynthetic pathways of secondary metabolites suggested that they might play important ecological roles in the cave microbiome.
Highlights
Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive
We are interested in the cave soil since we wanted to know how microorganisms survive under nutrientlimited cave condition
Consistent with the 16S ribosomal RNA genes (rRNA)-based community structure study, the shotgun metagenomic sequencing performed in the current study confirmed that Actinobacteria and Proteobacteria were the dominant bacterium phyla in Manao-Pee cave community (Additional file 14: Figure S5)
Summary
Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. 16S rRNA gene is usually directly amplified from extracted metagenomic DNA of environmental samples for the exploration of prokaryotic diversity [1, 2]. Recent high-throughput sequencing technologies are robust and economical for microbial ecology study. It is well-known that PCR-based studies have several limitations [3]. Primer selection is very important in a PCR-based microbial ecology study As this technique gives only the relative abundance information, the ecological roles of microbial communities largely remained unknown [8, 9]
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