Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui

Abstract

The diversity of microorganisms associated with speleological sources has mainly been studied in limestone caves, while studies in silicate caves are still under development. Here, we profiled the microbial diversity of opal speleothems from a silicate cave in Guiana Highlands. Bulk DNAs were extracted from three speleothems of two types, i.e., one soft whitish mushroom-like speleothem and two hard blackish coral-like speleothems. The extracted DNAs were amplified for sequencing the V3–V4 region of the bacterial 16S rRNA gene by MiSeq. A total of 210,309 valid reads were obtained and clustered into 3184 phylotypes or operational taxonomic units (OTUs). The OTUs from the soft whitish speleothem were mostly affiliated with Acidobacteriota, Pseudomonadota (formerly, Proteobacteria), and Chloroflexota, with the OTUs ascribed to Nitrospirota being found specifically in this speleothem. The OTUs from the hard blackish speleothems were similar to each other and were mostly affiliated with Pseudomonadota, Acidobacteriota, and Actinomycetota (formerly, Actinobacteria). These OTU compositions were generally consistent with those reported for limestone and silicate caves. The OTUs were further used to infer metabolic features by using the PICRUSt bioinformatic tool, and membrane transport and amino acid metabolism were noticeably featured. These and other featured metabolisms may influence the pH microenvironment and, consequently, the formation, weathering, and re-deposition of silicate speleothems.

Microbiomic Analysis of Bacteria Associated with Rock Tripe Lichens in Continental and Maritime Antarctic Regions

“…The ENS values based on Shannon and Simpson indices were much smaller than the Chao1 values (estimated OTU numbers) as well as the observed OTU numbers and the OTU-derived species numbers ( Table 3 ). Bacterial species richness of a large sample size may be better represented by Chao1, as also reported in other studies [ 52 , 53 ].…”

Bacteriomic Profiles of Rock-Dwelling Lichens from the Venezuelan Guiana Shield and the South African Highveld Plateau

“…All of these species but one showed no overlaps between the regions, Carolina shield lichen ( Canoparmelia caroliniana ) was the only lichen species common to the two regions: six specimens, G07 to G12, from the Guiana Shield and two specimens, SA01 and SA02, from South Africa ( Table 3 ). The associated bacterial microbiomes of the monospecific samples showed apparent regional features ( Figure 3 ), implying that the associated microbiomes are controlled more regionally by climate, particularly by rainfall [ 24 , 25 , 26 , 27 ], than host lichen species. In contrast, the monospecific ( Canoparmelia caroliniana ) samples from grassland and bush, SA01 and SA02, respectively, showed no or little intra-regional variation ( Figure 3 ), which may implicate a case of control by host species rather than inter-regional habitat variety in the vicinity.…”

“…The lichen samples of the Venezuelan Guiana Shield were collected in October 2016 on the summit of the table-top mountain or tepui called Churi (ca. 05°15′ N, 62°00′ W; Figure 1 , Table 1 ) during the speleological expedition to the tepui’s cave system [ 24 ]. Tepuis are typically flat-topped mountains with steep vertical walls rising to 1000 m or more above the surrounding landscape, and with an annual rainfall >3000 mm [ 25 ].…”

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives

“…The ammonia-oxidizing Nitrosospira and nitrite-oxidizing Nitrospira complete the entire nitrification cycle and support primary production in oligotrophic environments ( Lavoie et al, 2017 ; Leuko et al, 2017 ). Nitrospirota members were detected in a variety of subterranean environments, e.g., on a cave wall in the western Loess Plateau of China ( Anda et al, 2020 ), in the Su Bentu limestone cave in Sardinia ( Leuko et al, 2017 ) and the limestone Pindal Cave in Spain ( Martin-Pozas et al, 2023 ), but also in speleothems of a silicate cave in Guiana ( Liu et al, 2022 ) and in the lava tubes of Lava Beds National Monument, USA ( Lavoie et al, 2017 ). Members of Thermodesulfovibrionia , a class of Nitrospirota characterized by hydrogen oxidation, sulfate reduction, nitrate reduction, and sulfur disproportionation, are rare in surface environments but are frequent in marine and terrestrial subsurface aquifers ( D’Angelo et al, 2023 ).…”

“…Other caves are formed by dissolution processes of different rock types. They include evaporite rocks (gypsum, halite, anhydrite), which are relatively young with very rapid morphological evolution ( D’Angeli et al, 2017 ), and silicate caves, which require a very long formation time since they are embedded in rocks that are poorly soluble in water, such as sandstone and quartzite ( Sauro et al, 2018 ; Ghezzi et al, 2022 ; Liu et al, 2022 ).…”