Special Issue "Microbial Diversity in Caves"

A special issue of Diversity (ISSN 1424-2818).

Deadline for manuscript submissions: closed (30 June 2017)

Special Issue Editor

Guest Editor
Prof. Kathleen Lavoie

State University of New York at Plattsburgh, Plattsburgh, United States
Website | E-Mail
Interests: geomicrobiology; astrobiology; species diversity; distributional diversity; biogeographical diversity; community diversity; genetic diversity; microbes associated with higher organisms; impacts of humans on microbial diversity; microbial conservation; threats to microbial diversity

Special Issue Information

Dear Colleagues;

I am inviting you to consider submitting a manuscript to Diversity for a Special Issue on “Microbial Diversity of Caves”. Life on Earth is mostly microbial, both eukaryotic and prokaryotic, and in the aphotic subsurface. Caves can provide access to the shallow and deep subsurface for the study of these environments. Caves can be classified by the kind of rock and how they were formed. Microbes are directly involved in the solutional formation of karst caves through the flow of slightly acidic water that can be increased by microbial activities that acidify the water as it moves through soil. Another solutional process is sulfuric acid speleogenesis, where sulfuric acid is formed abiotically or though the action of chemolithotrophic bacteria. There are other types of caves, including lava caves, ice caves, talus caves, shelter caves, and so on. Built environments like mines and bunkers are also often studied in Speleomicrobiology. Caves have also been suggested as a model for Astrobiological studies since caves are likely places to harbor life on other planets.

A great deal of interest has focused recently on the intersection of geological processes and microbial action in the study of Geomicrobiology. Most low-energy processes in caves are probably the result of microbial action. Geomicrobiological processes include contributions to the formation of speleothems and secondary mineral deposits, including moonmilk. Microbial involvement includes both depositional and erosional processes. Microbes are involved in ferromanganese deposits, nitrates, and nutrient cycling in caves.

Caves are considered extreme environments due to the lack of sunlight resulting in extremely oligotrophic conditions in most caves. In addition to the lack of food, cave biota are further stressed by high humidity and constant low temperatures. Are there microbes adapted to, and unique to, the cave environment? Caves may also be good places to look for the production of bioactive compounds including antibiotics. Among the big questions are presence vs. activity of microbes; just because something can be found in an environment may not mean the organism and the environment have any impact on the other. How do microbes influence higher organisms, including as parasites and microbial contributors to nutrition of cave crickets? What are the microbiomes of cave-adapted organisms, including bats?

We need to think small, at the level of the microniche. New techniques in geology, chemistry and genomics can offer new insights into microbial diversity of caves. We need more information from basic distributional studies to experimental research. For this Special Issue I am looking for reviews. distributional surveys, and experimental studies relating to any aspect of microbial diversity, both eukaryotic and prokaryotic, in caves of all types.

Thank you for your consideration.

Prof. Kathleen Lavoie
Guest Editor

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Published Papers (5 papers)

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Research

Open AccessArticle
High Levels of Antibiotic Resistance but No Antibiotic Production Detected Along a Gypsum Gradient in Great Onyx Cave, KY, USA
Diversity 2017, 9(4), 42; https://doi.org/10.3390/d9040042
Received: 7 July 2017 / Revised: 12 September 2017 / Accepted: 19 September 2017 / Published: 25 September 2017
Cited by 2 | PDF Full-text (443 KB) | HTML Full-text | XML Full-text
Abstract
A preliminary study of antibiotic production and antibiotic resistance was conducted in Great Onyx Cave in Mammoth Cave National Park, KY, to determine if gypsum (CaSO4∙2H2O) affects these bacterial activities. The cave crosses through the width of Flint Ridge, [...] Read more.
A preliminary study of antibiotic production and antibiotic resistance was conducted in Great Onyx Cave in Mammoth Cave National Park, KY, to determine if gypsum (CaSO4∙2H2O) affects these bacterial activities. The cave crosses through the width of Flint Ridge, and passages under the sandstone caprock are dry with different amounts of gypsum. The Great Kentucky Desert hypothesis posits that gypsum limits the distribution of invertebrates in the central areas of Great Onyx Cave. Twenty-four bacterial isolates were cultivated from swabs and soils. Using three methods (soil crumb, soil crumb with indicator bacteria, and the cross-streak method using isolated bacteria) we did not detect any production of antibiotics. Antibiotic resistance was widespread, with all 24 isolates resistant to a minimum of two antibiotics of seven tested, with three isolates resistant to all. Antibiotic resistance was high and not correlated with depth into the cave or the amount of gypsum. The Great Kentucky Desert hypothesis of the negative effects of gypsum seems to have no impact on bacterial activity. Full article
(This article belongs to the Special Issue Microbial Diversity in Caves)
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Open AccessArticle
In Situ Cultured Bacterial Diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada
Diversity 2017, 9(3), 36; https://doi.org/10.3390/d9030036
Received: 28 June 2017 / Revised: 2 August 2017 / Accepted: 18 August 2017 / Published: 29 August 2017
Cited by 2 | PDF Full-text (7754 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The culturable bacterial diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada was examined. Sixty five bacterial isolates were successfully cultivated, purified, and identified based on 16S rRNA gene sequencing. Four distinguishable phyla, i.e., Actinobacteria (44.61%), Proteobacteria (27.69%), Firmicutes (20%) and Bacteroidetes (7.69%) [...] Read more.
The culturable bacterial diversity from Iron Curtain Cave, Chilliwack, British Columbia, Canada was examined. Sixty five bacterial isolates were successfully cultivated, purified, and identified based on 16S rRNA gene sequencing. Four distinguishable phyla, i.e., Actinobacteria (44.61%), Proteobacteria (27.69%), Firmicutes (20%) and Bacteroidetes (7.69%) were identified. Arthrobacter (21.53%) was identified as the major genus, followed by Sporosarcina (9.23%), Stenotrophomonas (9.23%), Streptomyces (6.15%), Brevundimonas (4.61%), and Crocebacterium (2.8%). Noteworthy, 12.3% of the population was recognized as unidentified bacteria. The isolates were evaluated for their potential antimicrobial activities against multidrug resistant microbial strains. Two species of the genus Streptomyces exhibited a wide range of antimicrobial activities against multidrug resistance (MDR) strains of Escherichia coli and Pseudomonas spp. along with non-resistant strains of Staphylococcus aureus and E. coli. However, all of the antimicrobial activities were only observed when the isolates were grown at 8 °C in different media. To the best of our knowledge, this is the first study conducted on the Iron Curtain Cave’s bacterial diversity, and reveals some bacterial isolates that have never been reported from a cave. Bacterial isolates identified with antimicrobial properties demonstrated that the Iron Curtain Cave can be further considered as a potential habitat for antimicrobial agents. Full article
(This article belongs to the Special Issue Microbial Diversity in Caves)
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Open AccessArticle
A Comparative Analysis of Viral Richness and Viral Sharing in Cave-Roosting Bats
Diversity 2017, 9(3), 35; https://doi.org/10.3390/d9030035
Received: 15 July 2017 / Revised: 11 August 2017 / Accepted: 22 August 2017 / Published: 28 August 2017
Cited by 4 | PDF Full-text (8072 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Caves provide critical roosting habitats for bats globally, but are increasingly disturbed or destroyed by human activities such as tourism and extractive industries. In addition to degrading the habitats of cave-roosting bats, such activities often promote contact between humans and bats, which may [...] Read more.
Caves provide critical roosting habitats for bats globally, but are increasingly disturbed or destroyed by human activities such as tourism and extractive industries. In addition to degrading the habitats of cave-roosting bats, such activities often promote contact between humans and bats, which may have potential impacts on human health. Cave-roosting bats are hosts to diverse viruses, some of which emerged in humans with severe consequences (e.g., severe acute respiratory syndrome coronavirus and Marburg virus). Characterizing patterns of viral richness and sharing among bat species are therefore important first steps for understanding bat-virus dynamics and mitigating future bat-human spillover. Here we compile a database of bat-virus associations and bat species ecological traits, and investigate the importance of roosting behavior as a determinant of viral richness and viral sharing among bat species. We show that cave-roosting species do not host greater viral richness, when accounting for publication bias, diet, body mass, and geographic range size. Our global analyses, however, show that cave-roosting bats do exhibit a greater likelihood of viral sharing, especially those documented in the literature as co-roosting in the same cave. We highlight the importance of caves as critical foci for bat conservation, as well as ideal sites for longitudinal surveillance of bat-virus dynamics. Full article
(This article belongs to the Special Issue Microbial Diversity in Caves)
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Open AccessArticle
16S rRNA Gene-Based Metagenomic Analysis of Ozark Cave Bacteria
Diversity 2017, 9(3), 31; https://doi.org/10.3390/d9030031
Received: 30 June 2017 / Revised: 3 August 2017 / Accepted: 3 August 2017 / Published: 15 August 2017
Cited by 2 | PDF Full-text (1122 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit [...] Read more.
The microbial diversity within cave ecosystems is largely unknown. Ozark caves maintain a year-round stable temperature (12–14 °C), but most parts of the caves experience complete darkness. The lack of sunlight and geological isolation from surface-energy inputs generate nutrient-poor conditions that may limit species diversity in such environments. Although microorganisms play a crucial role in sustaining life on Earth and impacting human health, little is known about their diversity, ecology, and evolution in community structures. We used five Ozark region caves as test sites for exploring bacterial diversity and monitoring long-term biodiversity. Illumina MiSeq sequencing of five cave soil samples and a control sample revealed a total of 49 bacterial phyla, with seven major phyla: Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Chloroflexi, Bacteroidetes, and Nitrospirae. Variation in bacterial composition was observed among the five caves studied. Sandtown Cave had the lowest richness and most divergent community composition. 16S rRNA gene-based metagenomic analysis of cave-dwelling microbial communities in the Ozark caves revealed that species abundance and diversity are vast and included ecologically, agriculturally, and economically relevant taxa. Full article
(This article belongs to the Special Issue Microbial Diversity in Caves)
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Open AccessArticle
Spacio-Temporal Distribution and Tourist Impact on Airborne Bacteria in a Cave (Škocjan Caves, Slovenia)
Diversity 2017, 9(3), 28; https://doi.org/10.3390/d9030028
Received: 29 June 2017 / Revised: 22 July 2017 / Accepted: 27 July 2017 / Published: 1 August 2017
Cited by 2 | PDF Full-text (1517 KB) | HTML Full-text | XML Full-text
Abstract
(1) Background: Airborne microbes are an integral part of a cave ecosystem. Cave allochtonous airborne microbiota, which occurs mainly during aerosolization from an underground river, from animals, and from visitors, is particularly pronounced in show caves. The impacts of tourists and natural river [...] Read more.
(1) Background: Airborne microbes are an integral part of a cave ecosystem. Cave allochtonous airborne microbiota, which occurs mainly during aerosolization from an underground river, from animals, and from visitors, is particularly pronounced in show caves. The impacts of tourists and natural river aerosolization on the cave air were estimated in large cave spaces within the Škocjan Caves; (2) Methods: Simultaneously with the measurements of atmospheric parameters, cultivable airborne bacteria were impacted, counted and identified using MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry); (3) Results: A mix of bacteria typically associated with humans and with natural habitats, including a large percentage of non-identified isolates, was found in the cave air. Few of the isolates were attributed to Risk Group 2. A strong positive correlation between tourist numbers and the rise in the concentration of airborne bacteria was indicated. Concentration of airborne bacteria rises to particularly high levels close to the underground river during periods of high discharge. A 10-times lower discharge reflected an approximately 20-times lower concentration of airborne bacteria; (4) Conclusions: Caves that are open and visited contain a diverse airborne microbiota originating from different sources. Enormous cave chambers that display relatively dynamic cave climate conditions do not normally support the enhancement of airborne bacterial concentrations. Full article
(This article belongs to the Special Issue Microbial Diversity in Caves)
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