The microbial community structure of the Dupnisa cave in Kırklareli, Turkey

Abstract

Cave ecosystems count to be extreme environments due to their stable temperature, darkness, high humidity rates, and limited organic materials. In this context, these ecosystems represent invaluable laboratories for microbiological studies. Although there are common features between the microorganism groups obtained from the culture-based microbiological studies conducted in the caves and the groups highlighted through molecular methods, the microorganism groups determined through this last method are richer. The detected microorganisms are variable depending on the characteristics of each cave. The aim of this study is to determine the microbial diversity in samples taken from 5 different regions (including regions visited by tourists) of Dupnisa Cave and to reveal the differences between these regions. This is the first microbiological study running in cave sediments of Dupnisa Cave System situated in the north-western of Turkey. In this study, using the Illumina MiSeq next-generation sequencing approach for analyses of Dupnisa Cave samples, 14 phyla and 298 genera as well as 2 phyla and 20 genera can be attributed to bacterial and archaea OTUs, respectively. Moreover, the bacterial community is dominated by the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Gemmatimonadetes, Firmicutes, Nitrospirae, Chloroflexi and Acidobacteria distributed with 1 % and above. Archaeal community is represented by Thaumarchaeota and Euryarchaeota phyla. Proteobacteria is the most dominant bacterial phylum and Thaumarchaeota dominates the archaeal phyla. The highest number of types of bacteria according to Chao 1 richness estimation index were found at point AF (cave entrance / sediment), and that of types of archaea were found at point F2 (touristic area 2 / cave sediment). F2 was determined as the sampling point with the highest diversity of archaeal and bacterial genera according to Shannon-Wiener diversity index.

Keywords

• cave microbiology
• bacterial diversity
• archaeal diversity
• next generation metagenomic sequencing