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Gutierrez‐Patricio S, Osman JR, Gonzalez‐Pimentel JL, Jurado V, Laiz L, Concepción AL, Saiz‐Jimenez C, Miller AZ. Microbiological exploration of the Cueva del Viento lava tube system in Tenerife, Canary Islands. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13245. [PMID: 38643985 PMCID: PMC11033209 DOI: 10.1111/1758-2229.13245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/15/2024] [Indexed: 04/23/2024]
Abstract
Cueva del Viento, located in the Canary Islands, Spain, is the Earth's sixth-longest lava tube, spanning 18,500 m, and was formed approximately 27,000 years ago. This complex volcanic cave system is characterized by a unique geomorphology, featuring an intricate network of galleries. Despite its geological significance, the geomicrobiology of Cueva del Viento remains largely unexplored. This study employed a combination of culture-dependent techniques and metabarcoding data analysis to gain a comprehensive understanding of the cave's microbial diversity. The 16S rRNA gene metabarcoding approach revealed that the coloured microbial mats (yellow, red and white) coating the cave walls are dominated by the phyla Actinomycetota, Pseudomonadota and Acidobacteriota. Of particular interest is the high relative abundance of the genus Crossiella, which is involved in urease-mediated biomineralization processes, along with the presence of genera associated with nitrogen cycling, such as Nitrospira. Culture-dependent techniques provided insights into the morphological characteristics of the isolated species and their potential metabolic activities, particularly for the strains Streptomyces spp., Paenarthrobacter sp. and Pseudomonas spp. Our findings underscore the potential of Cueva del Viento as an ideal environment for studying microbial diversity and for the isolation and characterization of novel bacterial species of biotechnological interest.
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Affiliation(s)
| | - Jorge R. Osman
- Instituto de Geología Económica Aplicada (GEA)Universidad de ConcepciónConcepciónChile
| | - José Luis Gonzalez‐Pimentel
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
- Laboratorio HERCULESUniversidade de ÉvoraÉvoraPortugal
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
| | | | - Cesareo Saiz‐Jimenez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
| | - Ana Zélia Miller
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS‐CSIC)SevillaSpain
- Laboratorio HERCULESUniversidade de ÉvoraÉvoraPortugal
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Gogoleva N, Chervyatsova O, Balkin A, Kuzmina L, Shagimardanova E, Kiseleva D, Gogolev Y. Microbial tapestry of the Shulgan-Tash cave (Southern Ural, Russia): influences of environmental factors on the taxonomic composition of the cave biofilms. ENVIRONMENTAL MICROBIOME 2023; 18:82. [PMID: 37990336 PMCID: PMC10662634 DOI: 10.1186/s40793-023-00538-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/09/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Cave biotopes are characterized by stable low temperatures, high humidity, and scarcity of organic substrates. Despite the harsh oligotrophic conditions, they are often inhabited by rich microbial communities. Abundant fouling with a wide range of morphology and coloration of colonies covers the walls of the Shulgan-Tash cave in the Southern Urals. This cave is also famous for the unique Paleolithic painting discovered in the middle of the last century. We aimed to investigate the diversity, distribution, and potential impact of these biofilms on the cave's Paleolithic paintings, while exploring how environmental factors influence the microbial communities within the cave. RESULTS The cave's biofilm morphotypes were categorized into three types based on the ultrastructural similarities. Molecular taxonomic analysis identified two main clusters of microbial communities, with Actinobacteria dominating in most of them and a unique "CaveCurd" community with Gammaproteobacteria prevalent in the deepest cave sections. The species composition of these biofilms reflects changes in environmental conditions, such as substrate composition, temperature, humidity, ventilation, and CO2 content. Additionally, it was observed that cave biofilms contribute to biocorrosion on cave wall surfaces. CONCLUSIONS The Shulgan-Tash cave presents an intriguing example of a stable extreme ecosystem with diverse microbiota. However, the intense dissolution and deposition of carbonates caused by Actinobacteria pose a potential threat to the preservation of the cave's ancient rock paintings.
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Affiliation(s)
- Natalia Gogoleva
- Research Department for Limnology, Mondsee, Universität Innsbruck, Mondsee, 5310, Austria.
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia.
| | | | - Alexander Balkin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Institute for Cellular and Intracellular Symbiosis, Ural Branch of the Russian Academy of Sciences, Orenburg, 460000, Russia
| | - Lyudmila Kuzmina
- Ufa Institute of Biology, Ufa Federal Research Center, Russian Academy of Sciences, Ufa, 450054, Russia
| | - Elena Shagimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Loginov Moscow Clinical Scientific Center, Moscow, 111123, Russia
| | - Daria Kiseleva
- Institute of Geology and Geochemistry, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, 620016, Russia
- Institute of Fundamental Education, Ural Federal University named after the first President of Russia B.N. Yeltsin, Ekaterinburg, 620002, Russia
| | - Yuri Gogolev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420111, Russia
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center "Kazan Scientific Center of the Russian Academy of Sciences", Kazan, 420111, Russia
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Theodorescu M, Bucur R, Bulzu PA, Faur L, Levei EA, Mirea IC, Cadar O, Ferreira RL, Souza-Silva M, Moldovan OT. Environmental Drivers of the Moonmilk Microbiome Diversity in Some Temperate and Tropical Caves. MICROBIAL ECOLOGY 2023; 86:2847-2857. [PMID: 37606696 DOI: 10.1007/s00248-023-02286-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023]
Abstract
Moonmilk is a cave deposit that was used for medical and cosmetic purposes and has lately raised interest for its antimicrobial potential. We studied five moonmilk samples from four caves with different microclimatic conditions, two temperate in north-western and northern Romania (Ferice, Fața Apei, and Izvorul Tăușoarelor caves) and one tropical in Minas Gerais, Brazil (Nestor Cave). The physicochemical and mineralogical analyses confirmed the presence of calcite and dolomite as the main phase in the moonmilk. A 16S rRNA gene-based metabarcoding approach showed the most abundant bacteria phyla Proteobacteria, GAL15, Actinobacteriota, and Acidobacteriota. The investigated caves differed in the dominant orders of bacteria, with the highest distance between the Romanian and Nestor Cave samples. Climate and, implicitly, the soil microbiome can be responsible for some differences we found between all the samples. However, other factors can be involved in shaping the moonmilk microbiome, as differences were found between samples in the same cave (Ferice). In our five moonmilk samples, 1 phylum, 70 orders (~ 36%), and 252 genera (~ 47%) were unclassified, which hints at the great potential of cave microorganisms for future uses.
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Affiliation(s)
- Mihail Theodorescu
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Clinicilor 5, 400006, Cluj-Napoca, Romania
| | - Ruxandra Bucur
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Clinicilor 5, 400006, Cluj-Napoca, Romania
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania
| | - Paul-Adrian Bulzu
- Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Academy of Sciences of the Czech Republic, 37005, České Budějovice, Czech Republic
| | - Luchiana Faur
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania
- Emil Racovita Institute of Speleology, 13 Septembrie 13, 050711, Bucharest, Romania
| | - Erika Andrea Levei
- Research Institute for Analytical Instrumentation subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Donath 67, 400293, Cluj-Napoca, Romania
| | - Ionuț Cornel Mirea
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania
- Emil Racovita Institute of Speleology, 13 Septembrie 13, 050711, Bucharest, Romania
| | - Oana Cadar
- Research Institute for Analytical Instrumentation subsidiary, National Institute of Research and Development for Optoelectronics INOE 2000, Donath 67, 400293, Cluj-Napoca, Romania
| | - Rodrigo Lopes Ferreira
- Centro de Estudos em Biologia Subterrânea, Setor de Biodiversidade Subterrânea, Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Campus Universitário, Lavras, Minas Gerais, 37202-553, Brazil
| | - Marconi Souza-Silva
- Centro de Estudos em Biologia Subterrânea, Setor de Biodiversidade Subterrânea, Departamento de Ecologia e Conservação, Universidade Federal de Lavras, Campus Universitário, Lavras, Minas Gerais, 37202-553, Brazil
| | - Oana Teodora Moldovan
- Cluj-Napoca Department, Emil Racovita Institute of Speleology, Clinicilor 5, 400006, Cluj-Napoca, Romania.
- Romanian Institute of Science and Technology, Virgil Fulicea 3, 400022, Cluj-Napoca, Romania.
- Centro Nacional sobre la Evolucion Humana, Paseo Sierra de Atapuerca 3, 09002, Burgos, Spain.
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Martin-Pozas T, Fernandez-Cortes A, Cuezva S, Cañaveras JC, Benavente D, Duarte E, Saiz-Jimenez C, Sanchez-Moral S. New insights into the structure, microbial diversity and ecology of yellow biofilms in a Paleolithic rock art cave (Pindal Cave, Asturias, Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165218. [PMID: 37419360 DOI: 10.1016/j.scitotenv.2023.165218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/13/2023] [Accepted: 06/28/2023] [Indexed: 07/09/2023]
Abstract
In the absence of sunlight, caves harbor a great diversity of microbial colonies to extensive biofilms with different sizes and colors visible to the naked eye. One of the most widespread and visible types of biofilm are those with yellow hues that can constitute a serious problem for the conservation of cultural heritage in many caves, such as Pindal Cave (Asturias, Spain). This cave, declared a World Heritage Site by UNESCO for its Paleolithic parietal art, shows a high degree of development of yellow biofilms that represents a real threat to the conservation of painted and engraved figures. This study aims to: 1) identify the microbial structures and the most characteristic taxa composing the yellow biofilms, 2) seek the linked microbiome reservoir primarily contributing to their growth; 3) seed light on the driving vectors that contribute to their formation and determine the subsequent proliferation and spatial distribution. To achieve this goal, we used amplicon-based massive sequencing, in combination with other techniques such as microscopy, in situ hybridization and environmental monitoring, to compare the microbial communities of yellow biofilms with those of drip waters, cave sediments and exterior soil. The results revealed microbial structures related to the phylum Actinomycetota and the most characteristic bacteria in yellow biofilms, represented by the genera wb1-P19, Crossiella, Nitrospira, and Arenimonas. Our findings suggest that sediments serve as potential reservoirs and colonization sites for these bacteria that can develop into biofilms under favorable environmental and substrate conditions, with a particular affinity for speleothems and rugged-surfaced rocks found in condensation-prone areas. This study presents an exhaustive study of microbial communities of yellow biofilms in a cave, which could be used as a procedure for the identification of similar biofilms in other caves and to design effective conservation strategies in caves with valuable cultural heritage.
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Affiliation(s)
- Tamara Martin-Pozas
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
| | | | - Soledad Cuezva
- Department of Geology, Geography and Environment, University of Alcala, Campus Cientifico-Tecnologico, 28802 Alcala de Henares, Spain.
| | - Juan Carlos Cañaveras
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - David Benavente
- Department of Environmental and Earth Sciences, University of Alicante, Campus San Vicente del Raspeig, 03690 Alicante, Spain.
| | - Elsa Duarte
- Department of History, University of Oviedo, 33011 Oviedo, Spain.
| | - Cesareo Saiz-Jimenez
- Department of Agrochemistry, Environmental Microbiology and Soil and Water Protection, Institute of Natural Resources and Agricultural Biology (IRNAS-CSIC), 41012 Seville, Spain.
| | - Sergio Sanchez-Moral
- Department of Geology, National Museum of Natural Sciences (MNCN-CSIC), 28006 Madrid, Spain.
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Nicolosi G, Gonzalez-Pimentel JL, Piano E, Isaia M, Miller AZ. First Insights into the Bacterial Diversity of Mount Etna Volcanic Caves. MICROBIAL ECOLOGY 2023; 86:1632-1645. [PMID: 36750476 PMCID: PMC10497698 DOI: 10.1007/s00248-023-02181-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
While microbial communities in limestone caves across the world are relatively understood, knowledge of the microbial composition in lava tubes is lagging behind. These caves are found in volcanic regions worldwide and are typically lined with multicolored microbial mats on their walls and ceilings. The Mount Etna (Sicily, S-Italy) represents one of the most active volcanos in the world. Due to its outstanding biodiversity and geological features, it was declared Natural Heritage of Humanity by the UNESCO in 2013. Despite the presence of more than 200 basaltic lava tubes, the microbial diversity of these hypogean systems has never been investigated so far. Here, we investigated bacterial communities in four lava tubes of Mount Etna volcano. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features. We documented an abundant presence of microbial cells with different morphotypes including rod-shaped, filamentous, and coccoidal cells with surface appendages, resembling actinobacteria reported in other lava tubes across the world. Based on 16S rRNA gene analysis, the colored microbial mats collected were mostly composed of bacteria belonging to the phyla Actinomycetota, Pseudomonadota, Acidobacteriota, Chloroflexota, and Cyanobacteria. At the genus level, the analysis revealed a dominance of the genus Crossiella, which is actively involved in biomineralization processes, followed by Pseudomonas, Bacillus, Chujaibacter, and Sphingomonas. The presence of these taxa is associated with the carbon, nitrogen, and ammonia cycles, and some are possibly related to the anthropic disturbance of these caves. This study provides the first insight into the microbial diversity of the Etna volcano lava tubes, and expands on previous research on microbiology of volcanic caves across the world.
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Affiliation(s)
- Giuseppe Nicolosi
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
- Centro Speleologico Etneo, Catania, Italy
| | | | - Elena Piano
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Ana Z Miller
- HERCULES Laboratory, University of Évora, Évora, Portugal.
- Instituto de Recursos Naturales Y Agrobiologia de Sevilla (IRNAS-CSIC), Seville, Spain.
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Djebaili R, Mignini A, Vaccarelli I, Pellegrini M, Spera DM, Del Gallo M, D’Alessandro AM. Polyhydroxybutyrate-producing cyanobacteria from lampenflora: The case study of the “Stiffe” caves in Italy. Front Microbiol 2022; 13:933398. [PMID: 35966678 PMCID: PMC9366245 DOI: 10.3389/fmicb.2022.933398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
This study aimed to estimate the green formation lampenflora of “Stiffe” caves in order to evaluate their suitability as an isolation source of cyanobacteria useful for the production of polyhydroxyalkanoates (PHAs). The cave system was chosen as the sampling site due to its touristic use and the presence of high-impact illuminations. The biofilms and the mats of the illuminated walls were sampled. Samples were investigated by 16S rRNA gene analysis and culturable cyanobacteria isolation. The isolated strains were then screened for the production of PHAs under typical culturing and nutritional starvation. Cultures were checked for PHA accumulation, poly-β-hydroxybutyrate (PHB) presence (infrared spectroscopy), and pigment production. The 16S rRNA gene metabarcoding. Highlighted a considerable extent of the pressure exerted by anthropogenic activities. However, the isolation yielded eleven cyanobacteria isolates with good PHA (mainly PHB)-producing abilities and interesting pigment production rates (chlorophyll a and carotenoids). Under normal conditions (BG110), the accumulation abilities ranged from 266 to 1,152 ng mg dry biomass–1. The optimization of bioprocesses through nutritional starvation resulted in a 2.5-fold increase. Fourier transform infrared (FTIR) studies established the occurrence of PHB within PHAs extracted by cyanobacteria isolates. The comparison of results with standard strains underlined good production rates. For C2 and C8 strains, PHA accumulation rates under starvation were higher than Azospirillum brasilense and similar to Synechocystis cf. salina 192. This study broadened the knowledge of the microbial communities of mats and biofilms on the lightened walls of the caves. These findings suggested that these structures, which are common in tourist caves, could be used to isolate valuable strains before remediation measures are adopted.
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Affiliation(s)
- Rihab Djebaili
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Amedeo Mignini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Ilaria Vaccarelli
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- *Correspondence: Marika Pellegrini,
| | | | - Maddalena Del Gallo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Anna Maria D’Alessandro
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
- Anna Maria D’Alessandro,
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Prescott RD, Zamkovaya T, Donachie SP, Northup DE, Medley JJ, Monsalve N, Saw JH, Decho AW, Chain PSG, Boston PJ. Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles. Front Microbiol 2022; 13:934708. [PMID: 35935195 PMCID: PMC9349362 DOI: 10.3389/fmicb.2022.934708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022] Open
Abstract
Lava caves, tubes, and fumaroles in Hawai‘i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing methods, we investigated the phylogenetic distinctness and diversity and identified microbial interactions and consortia through co-occurrence networks in 70 samples from lava tubes, geothermal lava caves, and fumaroles on the island of Hawai‘i. Our data illustrate that lava caves and geothermal sites harbor unique microbial communities, with very little overlap between caves or sites. We also found that older lava tubes (500–800 yrs old) hosted greater phylogenetic diversity (Faith's PD) than sites that were either geothermally active or younger (<400 yrs old). Geothermally active sites had a greater number of interactions and complexity than lava tubes. Average phylogenetic distinctness, a measure of the phylogenetic relatedness of a community, was higher than would be expected if communities were structured at random. This suggests that bacterial communities of Hawaiian volcanic environments are phylogenetically over-dispersed and that competitive exclusion is the main driver in structuring these communities. This was supported by network analyses that found that taxa (Class level) co-occurred with more distantly related organisms than close relatives, particularly in geothermal sites. Network “hubs” (taxa of potentially higher ecological importance) were not the most abundant taxa in either geothermal sites or lava tubes and were identified as unknown families or genera of the phyla, Chloroflexi and Acidobacteria. These results highlight the need for further study on the ecological role of microbes in caves through targeted culturing methods, metagenomics, and long-read sequence technologies.
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Affiliation(s)
- Rebecca D. Prescott
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, United States
- *Correspondence: Rebecca D. Prescott
| | - Tatyana Zamkovaya
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, United States
| | - Stuart P. Donachie
- School of Life Sciences, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Diana E. Northup
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Joseph J. Medley
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Natalia Monsalve
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
| | - Jimmy H. Saw
- Department of Biological Sciences, The George Washington University, Washington, DC, United States
| | - Alan W. Decho
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States
| | - Patrick S. G. Chain
- Biosciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Penelope J. Boston
- National Aeronautics and Space Administration (NASA) Ames Research Center, Moffett Field, CA, United States
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Into the Unknown: Microbial Communities in Caves, Their Role, and Potential Use. Microorganisms 2022; 10:microorganisms10020222. [PMID: 35208677 PMCID: PMC8877592 DOI: 10.3390/microorganisms10020222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/10/2022] [Accepted: 01/15/2022] [Indexed: 02/05/2023] Open
Abstract
Caves have been an item of amateur and professional exploration for many years. Research on the karst caves has revealed great diversity of bacteria, algae, and fungi living on stone walls and speleothems, in mud puddles or sediments. They have become the source of interest for various research groups including geologists, chemists, ecologists, or microbiologists. The adaptations of cave-dwelling organisms applied to their survival are complex and some of their properties show potential to be used in various areas of human life. Secondary metabolites produced by cave’s bacteria show strong antimicrobial, anti-inflammatory, or anticancer properties. Furthermore, bacteria that can induce mineral precipitation could be used in the construction industry and for neutralization of radioisotopes. In this review we focus on bacteria and algae present in cave ecosystems, their role in shaping such specific environment, and their biotechnological and medical potential.
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Gonzalez-Pimentel JL, Martin-Pozas T, Jurado V, Miller AZ, Caldeira AT, Fernandez-Lorenzo O, Sanchez-Moral S, Saiz-Jimenez C. Prokaryotic communities from a lava tube cave in La Palma Island (Spain) are involved in the biogeochemical cycle of major elements. PeerJ 2021; 9:e11386. [PMID: 34026356 PMCID: PMC8121065 DOI: 10.7717/peerj.11386] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/10/2021] [Indexed: 11/21/2022] Open
Abstract
Lava caves differ from karstic caves in their genesis and mineral composition. Subsurface microbiology of lava tube caves in Canary Islands, a volcanic archipelago in the Atlantic Ocean, is largely unknown. We have focused the investigation in a representative lava tube cave, Fuente de la Canaria Cave, in La Palma Island, Spain, which presents different types of speleothems and colored microbial mats. Four samples collected in this cave were studied using DNA next-generation sequencing and field emission scanning electron microscopy for bacterial identification, functional profiling, and morphological characterization. The data showed an almost exclusive dominance of Bacteria over Archaea. The distribution in phyla revealed a majority abundance of Proteobacteria (37-89%), followed by Actinobacteria, Acidobacteria and Candidatus Rokubacteria. These four phyla comprised a total relative abundance of 72-96%. The main ecological functions in the microbial communities were chemoheterotrophy, methanotrophy, sulfur and nitrogen metabolisms, and CO2 fixation; although other ecological functions were outlined. Genome annotations of the especially representative taxon Ga0077536 (about 71% of abundance in moonmilk) predicted the presence of genes involved in CO2 fixation, formaldehyde consumption, sulfur and nitrogen metabolisms, and microbially-induced carbonate precipitation. The detection of several putative lineages associated with C, N, S, Fe and Mn indicates that Fuente de la Canaria Cave basalts are colonized by metabolically diverse prokaryotic communities involved in the biogeochemical cycling of major elements.
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Affiliation(s)
| | | | - Valme Jurado
- Environmental Microbiology, Instituto de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
| | | | | | | | | | - Cesareo Saiz-Jimenez
- Environmental Microbiology, Instituto de Recursos Naturales y Agrobiologia, CSIC, Sevilla, Spain
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10
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Colored Microbial Coatings in Show Caves from the Galapagos Islands (Ecuador): First Microbiological Approach. COATINGS 2020. [DOI: 10.3390/coatings10111134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The Galapagos Islands (Ecuador) have a unique ecosystem on Earth due to their outstanding biodiversity and geological features. This also extends to their subterranean heritage, such as volcanic caves, with plenty of secondary mineral deposits, including coralloid-type speleothems and moonmilk deposits. In this study, the bacterial communities associated with speleothems from two lava tubes of Santa Cruz Island were investigated. Field emission scanning electron microscopy (FESEM) was carried out for the morphological characterization and detection of microbial features associated with moonmilk and coralloid speleothems from Bellavista and Royal Palm Caves. Microbial cells, especially filamentous bacteria in close association with extracellular polymeric substances (EPS), were abundant in both types of speleothems. Furthermore, reticulated filaments and Actinobacteria-like cells were observed by FESEM. The analysis of 16S rDNA revealed the presence of different bacterial phylotypes, many of them associated with the carbon, nitrogen, iron and sulfur cycles, and some others with pollutants. This study gives insights into subsurface microbial diversity of the Galapagos Islands and further shows the interest of the conservation of these subterranean geoheritage sites used as show caves.
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11
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Park S, Cho YJ, Jung DY, Jo KN, Lee EJ, Lee JS. Microbial Diversity in Moonmilk of Baeg-nyong Cave, Korean CZO. Front Microbiol 2020; 11:613. [PMID: 32390967 PMCID: PMC7190796 DOI: 10.3389/fmicb.2020.00613] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
The Baeg-nyong cave is a limestone cave which has been nominated as the first critical zone observatory (CZO) in South Korea. Moonmilk is a well-known speleothem composed of various carbonate minerals. To characterize moonmilk from the Baeg-nyong cave, we performed mineralogical analyses and applied high-throughput 16S rRNA gene sequencing to analyze the microbial communities, including bacteria and fungi, of dry and wet moonmilk samples. The results showed that the dry and wet moonmilk samples had different and atypical crystal structures, although they were predominantly composed of CaCO3. Furthermore, metagenomic data revealed that the dry and wet moonmilk samples collected from an oligotrophic environment had completely different bacterial communities when compared to the outside soil, and there was a difference in bacterial communities even between dry and wet moonmilk specimens. Fungal communities, however, did not differ significantly between dry and wet moonmilk samples. This study is the first metagenomic analysis of two different types of moonmilk with different physical properties and the first report on the microbial diversity of moonmilk from a cave in the first CZO in South Korea.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
| | - Yong-Joon Cho
- School of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Da-yea Jung
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
- Division of Geology and Geophysics, College of Natural Sciences, Chuncheon, South Korea
| | - Kyung-nam Jo
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
- Division of Geology and Geophysics, College of Natural Sciences, Chuncheon, South Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
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Yellow coloured mats from lava tubes of La Palma (Canary Islands, Spain) are dominated by metabolically active Actinobacteria. Sci Rep 2018; 8:1944. [PMID: 29386569 PMCID: PMC5792456 DOI: 10.1038/s41598-018-20393-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/16/2018] [Indexed: 11/08/2022] Open
Abstract
Microbial diversity in lava tubes from Canary Islands (Spain) has never been explored thus far offering a unique opportunity to study subsurface microbiology. Abundant yellow coloured mats developing on coralloid speleothems in a lava tube from La Palma Islands were studied by next-generation sequencing and DNA/RNA clone library analyses for investigating both total and metabolically active bacteria. In addition, morphological and mineralogical characterization was performed by field emission scanning electron microscopy (FESEM), micro-computed tomography, X-ray diffraction and infrared spectroscopy to contextualize sequence data. This approach showed that the coralloid speleothems consist of banded siliceous stalactites composed of opal-A and hydrated halloysite. Analytical pyrolysis was also conducted to infer the possible origin of cave wall pigmentation, revealing that lignin degradation compounds can contribute to speleothem colour. Our RNA-based study showed for the first time that members of the phylum Actinobacteria, with 55% of the clones belonging to Euzebyales order, were metabolically active components of yellow mats. In contrast, the DNA clone library revealed that around 45% of clones were affiliated to Proteobacteria. Composition of microbial phyla obtained by NGS reinforced the DNA clone library data at the phylum level, in which Proteobacteria was the most abundant phylum followed by Actinobacteria.
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Karwautz C, Kus G, Stöckl M, Neu TR, Lueders T. Microbial megacities fueled by methane oxidation in a mineral spring cave. ISME JOURNAL 2017; 12:87-100. [PMID: 28949325 PMCID: PMC5739006 DOI: 10.1038/ismej.2017.146] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/23/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
Abstract
Massive biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imaging and molecular analytics. Stable isotope analysis indicated that thermogenic methane emerging into the cave served as an important driver of biofilm formation. The undisturbed cavern atmosphere contained up to 3000 p.p.m. methane and was microoxic. A high abundance and diversity of aerobic methanotrophs primarily within the Methylococcales (Gammaproteobacteria) and methylotrophic Methylophilaceae (Betaproteobacteria) were found in the biofilms, along with a surprising diversity of associated heterotrophic bacteria. The highest methane oxidation potentials were measured for submerged biofilms on the cavern wall. Highly organized globular structures of the biofilm matrix were revealed by fluorescent lectin staining. We propose that the extracellular matrix served not only as an electron sink for nutrient-limited biofilm methylotrophs but potentially also as a diffusive barrier against volatilized iodine species. Possible links between carbon and iodine cycling in this peculiar habitat are discussed.
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Affiliation(s)
- Clemens Karwautz
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Günter Kus
- Bavarian Environment Agency (LfU), Department 10: Geological Survey, Hof/Saale, Germany
| | - Michael Stöckl
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research-UFZ, Magdeburg, Germany
| | - Tillmann Lueders
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
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Lavoie KH, Winter AS, Read KJH, Hughes EM, Spilde MN, Northup DE. Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA. PLoS One 2017; 12:e0169339. [PMID: 28199330 PMCID: PMC5310854 DOI: 10.1371/journal.pone.0169339] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 12/15/2016] [Indexed: 11/26/2022] Open
Abstract
Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community.
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Affiliation(s)
- Kathleen H Lavoie
- Biology, State University of New York, College at Plattsburgh, Plattsburgh, NY, United States of America
| | - Ara S Winter
- Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Kaitlyn J H Read
- Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Evan M Hughes
- Biology, University of New Mexico, Albuquerque, NM, United States of America
| | - Michael N Spilde
- Institute of Meteoritics, University of New Mexico, Albuquerque, NM, United States of America
| | - Diana E Northup
- Biology, University of New Mexico, Albuquerque, NM, United States of America
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Riquelme C, Enes Dapkevicius MDL, Miller AZ, Charlop-Powers Z, Brady S, Mason C, Cheeptham N. Biotechnological potential of Actinobacteria from Canadian and Azorean volcanic caves. Appl Microbiol Biotechnol 2016; 101:843-857. [DOI: 10.1007/s00253-016-7932-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 09/07/2016] [Accepted: 10/12/2016] [Indexed: 12/26/2022]
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