A comparative molecular analysis of water‐filled limestone sinkholes in north‐eastern Mexico

Abstract

Sistema Zacatón in north-eastern Mexico is host to several deep, water-filled, anoxic, karstic sinkholes (cenotes). These cenotes were explored, mapped, and geochemically and microbiologically sampled by the autonomous underwater vehicle deep phreatic thermal explorer (DEPTHX). The community structure of the filterable fraction of the water column and extensive microbial mats that coat the cenote walls was investigated by comparative analysis of small-subunit (SSU) 16S rRNA gene sequences. Full-length Sanger gene sequence analysis revealed novel microbial diversity that included three putative bacterial candidate phyla and three additional groups that showed high intra-clade distance with poorly characterized bacterial candidate phyla. Limited functional gene sequence analysis in these anoxic environments identified genes associated with methanogenesis, sulfate reduction and anaerobic ammonium oxidation. A directed, barcoded amplicon, multiplex pyrosequencing approach was employed to compare ∼100,000 bacterial SSU gene sequences from water column and wall microbial mat samples from five cenotes in Sistema Zacatón. A new, high-resolution sequence distribution profile (SDP) method identified changes in specific phylogenetic types (phylotypes) in microbial mats at varied depths; Mantel tests showed a correlation of the genetic distances between mat communities in two cenotes and the geographic location of each cenote. Community structure profiles from the water column of three neighbouring cenotes showed distinct variation; statistically significant differences in the concentration of geochemical constituents suggest that the variation observed in microbial communities between neighbouring cenotes are due to geochemical variation.

Biofilm forming bacteria and archaea in thermal karst springs of Gellért Hill discharge area (Hungary)

“…In the Rác Spa Nagy spring biofilm sample originated from the Buda Marl Formation, more than 50% of the molecular clones was members of the phylum Euryarchaeota but they could not be identified more precisely because of the low sequence matches to known taxa. The other part of molecular clones of Rác Spa Nagy spring was closely related to environmental clones of phylum Thaumarchaeota and Crenaechaeota revealed also from phreatic limestone sinkholes in cenote La Palita, Mexico .…”

Molecular diversity and distribution of anammox community in sediments of the Dongjiang River, a drinking water source of Hong Kong

“…About 18% sequences present in all sediment samples were grouped into cluster 1 and affiliated with the sequences obtained from sinkholes in north‐eastern Mexico (Sahl et al . ) (Table and Fig. ).…”

“…; Sahl et al . ). Overall, the C. Jettenia‐ related sequences were the representative and dominant anammox bacteria in the sediments, and the presence of different phylogenetic types of C. Jettenia might be due to the different sediment conditions along the river.…”

Local Conditions Structure Unique Archaeal Communities in the Anoxic Sediments of Meromictic Lake Kivu

“…The phreatic limestone sinkholes that were the origin of many of the best matches to our sequences in this group are freshwater environments characterized by anoxic karstic water with high alkalinity and a tropical temperature regime. [55].…”

“…4b) KSGR-1a and 1c clustered together with several subclusters of the C2 cluster of environmental Crenarchaeota. Many of the Kivu sequences in this group were most closely affiliated with uncultured Crenarchaeota sequences derived from phreatic limestone sinkholes in Mexico [55]. KSGR-1b included two sequences related to cluster Sd-NA and sequence KS9-12 that was up to 96 % similar to Candidatus Nitrososphaera sp., which are members of the Thaumarchaeota [19].…”