A Practical Guide to Studying the Microbiology of Karst Aquifers

Hershey, Olivia S.; Kallmeyer, Jens; Barton, Hazel A.

doi:10.1007/978-3-319-77368-1_7

Cited by 3 publications

(2 citation statements)

References 49 publications

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“…Given the remoteness of the cave sample site and the narrow size of cave passages traversed, all equipment had to be battery powered with its largest dimension no greater than the narrowest passage height (20 cm; Figure 1A ). We therefore collected cells via filtration through a Nalgene disposable 0.2 μm filter unit using a SP200 variable speed peristaltic pump (Global Water Instrumentation, Gold River, CA, United States) with a pump rate of 1 L min -1 ( Hershey et al, 2018 ). To filter at the wells, samples were collected using the same Nalgene filter set-up, with well water flowing into a 18 L, sterile, acid-washed bucket in which the filter unit was floated.…”

Section: Methodsmentioning

confidence: 99%

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

et al. 2018

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Despite the importance of karst aquifers as a source of drinking water, little is known about the role of microorganisms in maintaining the quality of this water. One of the limitations in exploring the microbiology of these environments is access, which is usually limited to wells and surface springs. In this study, we compared the microbiology of the Madison karst aquifer sampled via the potentiometric lakes of Wind Cave with surface sampling wells and a spring. Our data indicated that only the Streeter Well (STR), which is drilled into the same hydrogeologic domain as the Wind Cave Lakes (WCL), allowed access to water with the same low biomass (1.56–9.25 × 103 cells mL-1). Filtration of ∼300 L of water from both of these sites through a 0.2 μm filter allowed the collection of sufficient cells for DNA extraction, PCR amplification of 16S rRNA gene sequences, and identification through pyrosequencing. The results indicated that bacteria (with limited archaea and no detectable eukaryotic organisms) dominated both water samples; however, there were significant taxonomic differences in the bacterial populations of the samples. The STR sample was dominated by a single phylotype within the Gammaproteobacteria (Order Acidithiobacillales), which dramatically reduced the overall diversity and species richness of the population. In WCL, despite less organic carbon, the bacterial population was significantly more diverse, including significant contributions from the Gammaproteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Planctomycetes, Fusobacter, and Omnitrophica phyla. Comparisons with similar oligotrophic environments suggest that karst aquifers have a greater species richness than comparable surface environs. These data also demonstrate that Wind Cave provides a unique opportunity to sample a deep, subterranean aquifer directly, and that the microbiology of such aquifers may be more complex than previously anticipated.

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Section: Methodsmentioning

confidence: 99%

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

et al. 2018

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“…For in-lab studies, cell count is also a key parameter to estimate the microbial population size in different cave matrices (e.g., biofilm, air, sediment, and groundwater). Several methods have been proposed for the quantification of bacteria in water ( Hershey et al, 2019 ) and soil ( Lee et al, 2021 ). Fluorescence in situ hybridization (FISH) can identify and quantify specific microbial taxa in environmental samples, allowing for direct microscopic observation using epifluorescence or confocal laser scanning microscopies ( Jones et al, 2023 ).…”

Section: Good Practices In Future Cave Microbiome Studiesmentioning

confidence: 99%

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

Turrini,

Chebbi,

Riggio

et al. 2024

Front. Microbiol.

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Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.

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Yüksek Rakımlı Karstik Bir Mağara Deresinin (Güvercinkaya Mağarası: Çanakkale, Türkiye) Hidrokimyasal ve Bakteriyolojik Durumu ile Sucul Makroomurgasız Bulguları

Odabaşi

Odabaşı

Deniz

et al. 2022

Çanakkale Onsekiz Mart University Journal of Marine Sciences and Fisheries

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Caves are laboratories for many disciplines that work in natural sciences including mineralogy, biology, hydrogeology, and archaeology. In this study, bi-monthly samplings were carried out from three sampling locations within and around the Güvercinkaya Cave, a high-altitude cave located in northwestern Turkey, to evaluate the hydrochemical and microbiological properties and the aquatic macroinvertebrates of the cave stream. Some parameters of the water including pH, electrical conductivity, temperature, oxidation-reduction potential, and dissolved oxygen were measured in-situ, while elemental (70 in total) and ionic composition of water were analyzed in the laboratory. Microbiological analyses of the cave stream were examined through analyses of total bacteria, total coliforms, fecal coliforms, fecal Streptococcus, and Escherichia coli. According to the Piper diagram of hydrochemical data, the cave stream had mainly Ca-Mg-HCO3 character, on the other hand, the Schoeller diagram indicated a common water source in Güvercinkaya cave due to the similar components of the main ionic components of the water. As a result of microbiological analysis, fecal contamination was determined, indicating active wildlife in the cave. Additionally, several aquatic macroinvertebrates taxa, Rhynchelmis limosella, Dugesia sp., Gammarus uludagi which have non-troglobiont character were found in the cave stream. Rhynchelmis limosella detected in this study is the first record for the Turkish fauna.

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A Practical Guide to Studying the Microbiology of Karst Aquifers

Cited by 3 publications

References 49 publications

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

High Microbial Diversity Despite Extremely Low Biomass in a Deep Karst Aquifer

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

Yüksek Rakımlı Karstik Bir Mağara Deresinin (Güvercinkaya Mağarası: Çanakkale, Türkiye) Hidrokimyasal ve Bakteriyolojik Durumu ile Sucul Makroomurgasız Bulguları

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