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The discharging zones of thermal karst caves provide special environmental conditions for bacteria involved in the biogeochemical processes. The taxonomic composition of bacterial communities inhabiting these still active natural habitats is largely unknown. The aim of this study was to reveal and compare the bacterial diversity of upwelling thermal waters, rock surface biofilms, and cave deposits using high-throughput next-generation sequencing. Two thermal karst caves formed in carbonate rocks and located at the discharging endpoints of the Transdanubian Range (Hungary) were studied: a sublacustrine spring cave and a phreatic hypogene cave. The results of 16S rRNA gene-based Illumina MiSeq amplicon sequencing revealed that almost all samples were dominated by Proteobacteria and/or Epsilonbacteraeota. Other abundant phyla showed habitat-dependent and diverse distributions. Sequences of the thermal waters were mainly associated with different chemolithotrophic sulfur-oxidizing bacteria (genera  Thiovirga ,  Thiofaba , and  Arcobacter  in the sublacustrine thermal spring cave, whereas genera  Sulfurovum ,  Sulfuricurvum , and  Sulfurifustis  were characteristic of the phreatic hypogene thermal cave) in accordance with the difference in environmental parameters. Sequences belonging to ammonia-oxidizing (unclassified Nitrosococcaceae) and nitrite-oxidizing bacteria ( Nitrospira ) were characteristic of the hypogene cave. Sequences related to photoautotrophic bacteria from the lake water and chemoheterotrophic bacteria from the sediment were only found in the sublacustrine spring cave samples.

Impacts of Different Habitats on the Composition of Bacterial Communities at the Discharging Endpoints of a Hypogene Thermal Karst System