Culture-based analysis of ‘Cave Silver’ biofilms on Rocks in the former Homestake mine in South Dakota, USA

Brar, Amanpreet; Bergmann, David

doi:10.5038/1827-806x.48.2.2226

Cited by 3 publications

(1 citation statement)

References 19 publications

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“…Only the results of culture-independent, MiSeq-generated V3–V4 sequences were reported in this study, although cultivation using the R2A agar plates was tried and resulted in the Sanger sequencing of 16S rRNA genes of four isolates, which were related to Bacillus and Paenibacillus spp., as shown in previous studies on limestone cave microflorae [ 45 , 46 ]. However, their V3–V4 sequences were not found in our dataset from Charles Brewer Cave.…”

Section: Discussionsupporting

confidence: 82%

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

Liu

Naganuma

et al. 2022

Microorganisms

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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.

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Section: Discussionsupporting

confidence: 82%

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

Liu

Naganuma

et al. 2022

Microorganisms

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Bacterial and fungal diversity in the lorandite (TlAsS2) mine ‘Allchar' in the Republic of North Macedonia

Taleski

Dimkić

Boev

et al. 2020

FEMS Microbiology Ecology

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The Allchar mineral mine is one of the oldest arsenic-antimony mines in the Republic of North Macedonia. The mine is a well-known reservoir of the worldwide purest source of the thallium-bearing mineral, lorandite (TlAsS2). The current study evaluated the bacterial and fungal diversity of three As- and Tl-contaminated sites in Allchar mineral mine. We used a combination of high-throughput sequencing and bioinformatic analyses. Trace metal content was detected using inductively coupled plasma optical emission spectrometry. Our analysis showed the presence of 25 elements and confirmed a high concentration of As and Tl. Alpha diversity indices suggested a high diversity and evenness of bacterial and fungal communities. Bacterial phyla that dominated the environment were Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Verrucomicrobia. Looking at the genus level, we found the following groups of bacteria: Chryseolinea, Opitutus, Flavobacterium, Pseudomonas, Terrimonas, Sphingomonas, and Reyranella. For the fungi genera, we report Tetracladium sp., Coprinellus micaceus, Coprinus sp. from Ascomycota, and Basidiomycota phyla in all sites. We also observed a high abundance of the fungal species Pilidium sp., Dendroclathra lignicola, Rosellinia desmazieri, Hypomyces rosellus, and Coprinellus disseminatus. This study is the first to identify specific As- and Tl-tolerant fungal (Pilidium sp., Cladophialophora sp., Neobulgaria sp., and Mycena acicula) and bacterial (Trichococcus, Devosia, Litorilinea, and Gimesia) genera from Allchar mine, suggesting bioremediation and industrial potential.

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Contributions of DNA Sequencing Technologies to the Integrative Monitoring of Karstic Caves

Bontemps,

Moënne-Loccoz,

Hugoni

2024

Applied Sciences

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Cave microbiota knowledge has greatly expanded in the past decades, driven by the development of molecular techniques, which allow an in-depth characterization of diversity and its metabolic potential. This review focuses on the contribution of DNA sequencing technologies to depict the cave microbiome for the three domains of life (Bacteria, Archaea, and Microeukaryotes), assessing their advantages and limits. Cultural methods do not provide a representative view of cave microbial diversity but do offer, subsequently, the possibility to genomically characterize the strains isolated from caves. Next-generation DNA sequencing permits an exhaustive description of microbial biodiversity in caves, using metabarcoding (for taxonomic assessment) or metagenomics (for taxonomic and functional assessments). It proved useful to compare caves, different rooms, or substrata (water, soil, bedrock, etc.) within a cave, or the effect of cave disturbance in Lascaux and elsewhere. The integration of next-generation DNA sequencing with cultivation techniques, physico-chemical characterization, and other complementary approaches is important to understand the global functioning of caves and to provide key information to guide cave conservation strategies.

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Culture-based analysis of ‘Cave Silver’ biofilms on Rocks in the former Homestake mine in South Dakota, USA

Cited by 3 publications

References 19 publications

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

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

Bacterial and fungal diversity in the lorandite (TlAsS2) mine ‘Allchar' in the Republic of North Macedonia

Contributions of DNA Sequencing Technologies to the Integrative Monitoring of Karstic Caves

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