1
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Zhu HZ, Jiang CY, Liu SJ. Microbial roles in cave biogeochemical cycling. Front Microbiol 2022; 13:950005. [PMID: 36246268 PMCID: PMC9554484 DOI: 10.3389/fmicb.2022.950005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 09/14/2022] [Indexed: 11/23/2022] Open
Abstract
Among fundamental research questions in subterranean biology, the role of subterranean microbiomes playing in key elements cycling is a top-priority one. Karst caves are widely distributed subsurface ecosystems, and cave microbes get more and more attention as they could drive cave evolution and biogeochemical cycling. Research have demonstrated the existence of diverse microbes and their participance in biogeochemical cycling of elements in cave environments. However, there are still gaps in how these microbes sustain in caves with limited nutrients and interact with cave environment. Cultivation of novel cave bacteria with certain functions is still a challenging assignment. This review summarized the role of microbes in cave evolution and mineral deposition, and intended to inspire further exploration of microbial performances on C/N/S biogeocycles.
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Affiliation(s)
- Hai-Zhen Zhu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Shuang-Jiang Liu,
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2
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Alonso L, Pommier T, Kaufmann B, Dubost A, Chapulliot D, Doré J, Douady CJ, Moënne-Loccoz Y. Anthropization level of Lascaux Cave microbiome shown by regional-scale comparisons of pristine and anthropized caves. Mol Ecol 2019; 28:3383-3394. [PMID: 31177607 DOI: 10.1111/mec.15144] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/18/2019] [Accepted: 05/20/2019] [Indexed: 11/29/2022]
Abstract
Limestone areas across the world develop karstic caves, which are populated by a wide range of macro- and microorganisms. Many of these caves display Paleolithic art or outstanding speleothems, and in the last century they have been subjected to anthropization due to touristic management and intense human frequentation. Despite their cultural importance and associated conservation issues, the impact of anthropization on cave biodiversity is not known. Here, we show that anthropization is associated with specific cave biota modifications. We compared diversity in four pristine caves, four anthropized show caves, and the iconic Lascaux Cave with even stronger anthropization. The predominant microbial higher taxa were the same in all caves, but the most anthropized cave (Lascaux) was unique as it differed from the eight others by a higher proportion of Bacteroidetes bacteria and the absence of Euryarchaeota and Woesearchaeota archaea. Anthropization resulted in lower diversity and altered community structure for bacteria and archaea on cave walls, especially in Lascaux, but with a more limited effect on microeukaryotes and arthropods. Our findings fill a key gap in our understanding of the response of karstic communities to anthropization, by revealing that tourism-related anthropization impacts on the prokaryotic microbiome rather than on eukaryotic residents, and that it shapes cave biota irrespective of cave natural features.
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Affiliation(s)
- Lise Alonso
- Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, University de Lyon, Villeurbanne, France
| | - Thomas Pommier
- Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, University de Lyon, Villeurbanne, France
| | - Bernard Kaufmann
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, University de Lyon, Villeurbanne, France
| | - Audrey Dubost
- Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, University de Lyon, Villeurbanne, France
| | - David Chapulliot
- Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, University de Lyon, Villeurbanne, France
| | - Jeanne Doré
- Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, University de Lyon, Villeurbanne, France
| | - Christophe J Douady
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA, University de Lyon, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, University de Lyon, Villeurbanne, France
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3
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Yasir M. Analysis of bacterial communities and characterization of antimicrobial strains from cave microbiota. Braz J Microbiol 2017; 49:248-257. [PMID: 29108974 PMCID: PMC5913830 DOI: 10.1016/j.bjm.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 05/29/2017] [Accepted: 08/15/2017] [Indexed: 02/01/2023] Open
Abstract
In this study for the first-time microbial communities in the caves located in the mountain range of Hindu Kush were evaluated. The samples were analyzed using culture-independent (16S rRNA gene amplicon sequencing) and culture-dependent methods. The amplicon sequencing results revealed a broad taxonomic diversity, including 21 phyla and 20 candidate phyla. Proteobacteria were dominant in both caves, followed by Bacteroidetes, Actinobacteria, Firmicutes, Verrucomicrobia, Planctomycetes, and the archaeal phylum Euryarchaeota. Representative operational taxonomic units from Koat Maqbari Ghaar and Smasse-Rawo Ghaar were grouped into 235 and 445 different genera, respectively. Comparative analysis of the cultured bacterial isolates revealed distinct bacterial taxonomic profiles in the studied caves dominated by Proteobacteria in Koat Maqbari Ghaar and Firmicutes in Smasse-Rawo Ghaar. Majority of those isolates were associated with the genera Pseudomonas and Bacillus. Thirty strains among the identified isolates from both caves showed antimicrobial activity. Overall, the present study gave insight into the great bacterial taxonomic diversity and antimicrobial potential of the isolates from the previously uncharacterized caves located in the world's highest mountains range in the Indian sub-continent.
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Affiliation(s)
- Muhammad Yasir
- King Abdulaziz University, King Fahd Medical Research Center, Special Infectious Agents Unit, Jeddah, Saudi Arabia.
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4
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Sugiyama J, Kiyuna T, Nishijima M, An KD, Nagatsuka Y, Tazato N, Handa Y, Hata-Tomita J, Sato Y, Kigawa R, Sano C. Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus. J GEN APPL MICROBIOL 2017; 63:63-113. [DOI: 10.2323/jgam.2017.01.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | - Yoshinori Sato
- Tokyo National Research Institute for Cultural Properties
| | - Rika Kigawa
- Tokyo National Research Institute for Cultural Properties
| | - Chie Sano
- Tokyo National Research Institute for Cultural Properties
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5
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Reitschuler C, Spötl C, Hofmann K, Wagner AO, Illmer P. Archaeal Distribution in Moonmilk Deposits from Alpine Caves and Their Ecophysiological Potential. MICROBIAL ECOLOGY 2016; 71:686-699. [PMID: 26790864 DOI: 10.1007/s00248-015-0727-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/27/2015] [Indexed: 06/05/2023]
Abstract
(Alpine) caves are, in general, windows into the Earth's subsurface. Frequently occurring structures in caves such as moonmilk (secondary calcite deposits) offer the opportunity to study intraterrestrial microbial communities, adapted to oligotrophic and cold conditions. This is an important research field regarding the dimensions of subsurface systems and cold regions on Earth. On a methodological level, moonmilk deposits from 11 caves in the Austrian Alps were collected aseptically and investigated using a molecular (qPCR and DGGE sequencing-based) methodology in order to study the occurrence, abundance, and diversity of the prevailing native Archaea community. Furthermore, these Archaea were enriched in complex media and studied regarding their physiology, with a media selection targeting different physiological requirements, e.g. methanogenesis and ammonia oxidation. The investigation of the environmental samples showed that all moonmilk deposits were characterized by the presence of the same few habitat-specific archaeal species, showing high abundances and constituting about 50 % of the total microbial communities. The largest fraction of these Archaea was ammonia-oxidizing Thaumarchaeota, while another abundant group was very distantly related to extremophilic Euryarchaeota (Moonmilk Archaea). The archaeal community showed a depth- and oxygen-dependent stratification. Archaea were much more abundant (around 80 %), compared to bacteria, in the actively forming surface part of moonmilk deposits, decreasing to about 5 % down to the bedrock. Via extensive cultivation efforts, it was possible to enrich the enigmatic Moonmilk Archaea and also AOA significantly above the level of bacteria. The most expedient prerequisites for cultivating Moonmilk Archaea were a cold temperature, oligotrophic conditions, short incubation times, a moonmilk surface inoculum, the application of erythromycin, and anaerobic (microaerophilic) conditions. On a physiological level, it seems that methanogenesis is of marginal importance, while ammonia oxidation and a still undiscovered metabolic pathway are vital elements in the (archaeal) moonmilk biome.
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Affiliation(s)
- Christoph Reitschuler
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria.
| | - Christoph Spötl
- Institute of Geology, University of Innsbruck, Innrain 52, A-6020, Innsbruck, Austria
| | - Katrin Hofmann
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Andreas O Wagner
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
| | - Paul Illmer
- Institute of Microbiology, University of Innsbruck, Technikerstrasse 25, A-6020, Innsbruck, Austria
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6
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Axenov-Gibanov DV, Voytsekhovskaya IV, Tokovenko BT, Protasov ES, Gamaiunov SV, Rebets YV, Luzhetskyy AN, Timofeyev MA. Actinobacteria Isolated from an Underground Lake and Moonmilk Speleothem from the Biggest Conglomeratic Karstic Cave in Siberia as Sources of Novel Biologically Active Compounds. PLoS One 2016; 11:e0149216. [PMID: 26901168 PMCID: PMC4764329 DOI: 10.1371/journal.pone.0149216] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 01/28/2016] [Indexed: 12/02/2022] Open
Abstract
Actinobacteria isolated from unstudied ecosystems are one of the most interesting and promising sources of novel biologically active compounds. Cave ecosystems are unusual and rarely studied. Here, we report the isolation and characterization of ten new actinobacteria strains isolated from an ancient underground lake and moonmilk speleothem from the biggest conglomeratic karstic cave in Siberia with a focus on the biological activity of the obtained strains and the metabolite dereplication of one active strain. Streptomyces genera isolates from moonmilk speleothem demonstrated antibacterial and antifungal activities. Some of the strains were able to inhibit the growth of pathogenic Candida albicans.
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Affiliation(s)
| | | | - Bogdan T. Tokovenko
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrucken, Germany
| | | | | | - Yuriy V. Rebets
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrucken, Germany
| | - Andriy N. Luzhetskyy
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrucken, Germany
- Universität des Saarlandes–Pharmazeutische Biotechnologie, Saarbrucken, Germany
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7
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Villa F, Vasanthakumar A, Mitchell R, Cappitelli F. RNA-based molecular survey of biodiversity of limestone tombstone microbiota in response to atmospheric sulphur pollution. Lett Appl Microbiol 2014; 60:92-102. [DOI: 10.1111/lam.12345] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 10/18/2014] [Accepted: 10/19/2014] [Indexed: 11/30/2022]
Affiliation(s)
- F. Villa
- Dipartimento di Scienze per gli Alimenti; la Nutrizione e l'Ambiente; Università degli Studi di Milano; Milano Italy
| | - A. Vasanthakumar
- Laboratory of Applied Microbiology; School of Engineering and Applied Sciences; Harvard University; Cambridge MA USA
| | - R. Mitchell
- Laboratory of Applied Microbiology; School of Engineering and Applied Sciences; Harvard University; Cambridge MA USA
| | - F. Cappitelli
- Dipartimento di Scienze per gli Alimenti; la Nutrizione e l'Ambiente; Università degli Studi di Milano; Milano Italy
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8
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Crenarchaeal heterotrophy in salt marsh sediments. ISME JOURNAL 2014; 8:1534-43. [PMID: 24553469 DOI: 10.1038/ismej.2014.15] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/21/2013] [Accepted: 01/06/2014] [Indexed: 11/08/2022]
Abstract
Mesophilic Crenarchaeota (also known as Thaumarchaeota) are ubiquitous and abundant in marine habitats. However, very little is known about their metabolic function in situ. In this study, salt marsh sediments from New Jersey were screened via stable isotope probing (SIP) for heterotrophy by amending with a single (13)C-labeled compound (acetate, glycine or urea) or a complex (13)C-biopolymer (lipids, proteins or growth medium (ISOGRO)). SIP incubations were done at two substrate concentrations (30-150 μM; 2-10 mg ml(-1)), and (13)C-labeled DNA was analyzed by terminal restriction fragment length polymorphism (TRFLP) analysis of 16S rRNA genes. To test for autotrophy, an amendment with (13)C-bicarbonate was also performed. Our SIP analyses indicate salt marsh crenarchaea are heterotrophic, double within 2-3 days and often compete with heterotrophic bacteria for the same organic substrates. A clone library of (13)C-amplicons was screened to find matches to the (13)C-TRFLP peaks, with seven members of the Miscellaneous Crenarchaeal Group and seven members from the Marine Group 1.a Crenarchaeota being discerned. Some of these crenarchaea displayed a preference for particular carbon sources, whereas others incorporated nearly every (13)C-substrate provided. The data suggest salt marshes may be an excellent model system for studying crenarchaeal metabolic capabilities and can provide information on the competition between crenarchaea and other microbial groups to improve our understanding of microbial ecology.
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Reitschuler C, Lins P, Wagner AO, Illmer P. Cultivation of moonmilk-born non-extremophilic Thaum and Euryarchaeota in mixed culture. Anaerobe 2013; 29:73-9. [PMID: 24513652 DOI: 10.1016/j.anaerobe.2013.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/08/2013] [Accepted: 10/14/2013] [Indexed: 10/26/2022]
Abstract
PCR-DGGE, qPCR and sequencing highlighted a quite homogenous archaeal community prevailing in secondary calcite deposits, so-called moonmilk, within the cold alpine Hundalm cave in Tyrol (Austria). Furthermore, the depth profile of this moonmilk could prove that the Archaea are located in oxygen-rich near- and oxygen-depleted sub-surface layers. To gather these communities we therefore applied an aerobic and anaerobic cultivation approach in oligotrophic and methanotrophic media. The mixed moonmilk community was analyzed with a combination of molecular methods using qPCR, PCR-DGGE and sequencing. Anaerobic and aerobic cultures were additionally investigated with GC and HPLC analyses. It was possible to initially cultivate and enrich the supposed aerobic/microaerophilic and anaerobic archaeal fraction, representing the natural archaeal community. While the naturally less abundant near-surface Archaea are closely related to members of the Thaumarchaeota (Nitrosopumilus maritimus), the highly abundant anaerobic Archaea are more distantly related to members within the Euryarchaeota. It is possible that these cultivable moonmilk-born Archaea represent new ecotypes or are so far undescribed. Based on the sequencing results and the production of very low amounts of methane, a corresponding methanogenic community is thought to represent only a minor abundant archaeal fraction. On a physiological level the cultivated moonmilk community is cold-adapted and basically of oligotrophic and organotrophic character.
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Affiliation(s)
- Christoph Reitschuler
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Philipp Lins
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Andreas Otto Wagner
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
| | - Paul Illmer
- University of Innsbruck, Institute of Microbiology, Technikerstr. 25, A-6020 Innsbruck, Austria.
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10
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Michaelsen A, Pinzari F, Barbabietola N, Piñar G. Monitoring the effects of different conservation treatments on paper-infecting fungi. INTERNATIONAL BIODETERIORATION & BIODEGRADATION 2013; 84:333-341. [PMID: 24092956 PMCID: PMC3728566 DOI: 10.1016/j.ibiod.2012.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Revised: 01/25/2012] [Accepted: 08/22/2012] [Indexed: 05/31/2023]
Abstract
Fungi are among the most degradative organisms inducing biodeterioration of paper-based items of cultural heritage. Appropriate conservation measures and restoration treatments to deal with fungal infections include mechanical, chemical, and biological methods, which entail effects on the paper itself and health hazards for humans. Three different conservation treatments, namely freeze-drying, gamma rays, and ethylene oxide fumigation, were compared and monitored to assess their short- (one month, T1) and long-term (one year, T2) effectiveness to inhibit fungal growth. After the inoculation with fungi possessing cellulose hydrolysis ability - Chaetomium globosum, Trichoderma viride, and Cladosporium cladosporioides - as single strains or as a mixture, different quality paper samples were treated and screened for fungal viability by culture-dependent and -independent techniques. Results derived from both strategies were contradictory. Both gamma irradiation and EtO fumigation showed full efficacy as disinfecting agents when evaluated with cultivation techniques. However, when using molecular analyses, the application of gamma rays showed a short-term reduction in DNA recovery and DNA fragmentation; the latter phenomenon was also observed in a minor degree in samples treated with freeze-drying. When RNA was used as an indicator of long-term fungal viability, differences in the RNA recovery from samples treated with freeze-drying or gamma rays could be observed in samples inoculated with the mixed culture. Only the treatment with ethylene oxide proved negative for both DNA and RNA recovery. Therefore, DNA fragmentation after an ethylene oxide treatment can hamper future paleogenetic and archaeological molecular studies on the objects.
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Affiliation(s)
- Astrid Michaelsen
- Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Flavia Pinzari
- ICRCPAL – Istituto Centrale per il Restauro e la Conservazione del Patrimonio Archivistico e Librario, Laboratorio di Biologia, Ministero per i Beni e le Attivita Culturali, Via Milano 76, 00184 Rome, Italy
| | - Nicoletta Barbabietola
- ICRCPAL – Istituto Centrale per il Restauro e la Conservazione del Patrimonio Archivistico e Librario, Laboratorio di Biologia, Ministero per i Beni e le Attivita Culturali, Via Milano 76, 00184 Rome, Italy
| | - Guadalupe Piñar
- Institute of Applied Microbiology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190 Vienna, Austria
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11
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Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave. ISME JOURNAL 2013; 8:478-91. [PMID: 24030597 DOI: 10.1038/ismej.2013.159] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 08/03/2013] [Accepted: 08/12/2013] [Indexed: 01/06/2023]
Abstract
Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.
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Martin-Sanchez PM, Bastian F, Alabouvette C, Saiz-Jimenez C. Real-time PCR detection of Ochroconis lascauxensis involved in the formation of black stains in the Lascaux Cave, France. THE SCIENCE OF THE TOTAL ENVIRONMENT 2013; 443:478-484. [PMID: 23220137 DOI: 10.1016/j.scitotenv.2012.11.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Revised: 11/06/2012] [Accepted: 11/07/2012] [Indexed: 05/27/2023]
Abstract
A real-time Polymerase Chain Reaction (PCR) assay was developed to detect and quantify Ochroconis lascauxensis in the Lascaux Cave in France. This fungus is the principal causal agent of the black stains threatening the Paleolithic paintings of this UNESCO World Heritage Site. The black stains outbreak could not be stopped in spite of using intensive biocide treatments. A sensitive and time-saving protocol is needed for determining the extent of the colonization. Sets of primers that target the ITS and RPB2 regions were designed and evaluated for specificity against O. lascauxensis. Genomic DNA extracted from five species of Ochroconis and 13 other fungal species frequently isolated from caves were used to test the specificity of each primer set. The specific and sensitive real-time PCR assay using the primers 347F/493R targeting a 147-bp fragment from the RPB2 gene was useful for quantifying the presence of O. lascauxensis in the stains on the walls, sediments and air of the cavity. The results confirmed the association of this fungus with the black stains and its wide dissemination in all cave compartments. The suitability of this method for monitoring fungal outbreaks in cave environments is discussed.
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Affiliation(s)
- Pedro M Martin-Sanchez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, IRNAS-CSIC, Apartado 1052, 41080 Sevilla, Spain
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13
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Diaz-Herraiz M, Jurado V, Cuezva S, Laiz L, Pallecchi P, Tiano P, Sanchez-Moral S, Saiz-Jimenez C. The actinobacterial colonization of Etruscan paintings. Sci Rep 2013; 3:1440. [PMID: 23486535 PMCID: PMC3595702 DOI: 10.1038/srep01440] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 02/25/2013] [Indexed: 02/07/2023] Open
Abstract
The paintings from Tomba della Scimmia, in Tuscany, are representative of the heavy bacterial colonization experienced in most Etruscan necropolises. The tomb remained open until the late 70's when it was closed because of severe deterioration of the walls, ceiling and paintings after decades of visits. The deterioration is the result of environmental changes and impacts suffered since its discovery in 1846. We show scanning electron microscopy and molecular studies that reveal the extent and nature of the biodeterioration. Actinobacteria, mainly Nocardia and Pseudonocardia colonize and grow on the tomb walls and this process is linked to the availability of organic matter, phyllosilicates (e.g. clay minerals) and iron oxides. Nocardia is found metabolically active in the paintings. The data confirm the specialization of the genera Nocardia and Pseudonocardia in the colonization of subterranean niches.
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Affiliation(s)
- Marta Diaz-Herraiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Soledad Cuezva
- Departamento de Ciencias de la Tierra y del Medio Ambiente, Universidad de Alicante, 03690 Conservazione Vicente del Raspeig, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Pasquino Pallecchi
- Soprintendenza per i Beni Archeologici della Toscana, 50143 Firenze, Italy
| | - Piero Tiano
- CNR Istituto per la Conservazione e Valorizzazione dei Beni Culturali, 50019 Sesto Fiorentino, Italy
| | | | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain
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14
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Microbiological and environmental issues in show caves. World J Microbiol Biotechnol 2012; 28:2453-64. [PMID: 22806150 DOI: 10.1007/s11274-012-1070-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/21/2012] [Indexed: 02/01/2023]
Abstract
Cultural tourism expanded in the last half of the twentieth century, and the interest of visitors has come to include caves containing archaeological remains. Some show caves attracted mass tourism, and economical interests prevailed over conservation, which led to a deterioration of the subterranean environment and the rock art. The presence and the role of microorganisms in caves is a topic that is often ignored in cave management. Knowledge of the colonisation patterns, the dispersion mechanisms, and the effect on human health and, when present, over rock art paintings of these microorganisms is of the utmost importance. In this review the most recent advances in the study of microorganisms in caves are presented, together with the environmental implications of the findings.
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Cuezva S, Fernandez-Cortes A, Porca E, Pašić L, Jurado V, Hernandez-Marine M, Serrano-Ortiz P, Hermosin B, Cañaveras JC, Sanchez-Moral S, Saiz-Jimenez C. The biogeochemical role of Actinobacteria in Altamira Cave, Spain. FEMS Microbiol Ecol 2012; 81:281-90. [DOI: 10.1111/j.1574-6941.2012.01391.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 04/06/2012] [Accepted: 04/11/2012] [Indexed: 11/28/2022] Open
Affiliation(s)
- Soledad Cuezva
- Laboratorio de Petrologia Aplicada; Departamento de Ciencias de la Tierra y del Medio Ambiente; Universidad de Alicante; Alicante; Spain
| | | | - Estefania Porca
- Instituto de Recursos Naturales y Agrobiologia IRNAS-CSIC; Sevilla; Spain
| | - Lejla Pašić
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana; Slovenia
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia IRNAS-CSIC; Sevilla; Spain
| | | | | | - Bernardo Hermosin
- Instituto de Recursos Naturales y Agrobiologia IRNAS-CSIC; Sevilla; Spain
| | - Juan Carlos Cañaveras
- Laboratorio de Petrologia Aplicada; Departamento de Ciencias de la Tierra y del Medio Ambiente; Universidad de Alicante; Alicante; Spain
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16
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Portillo MC, Gonzalez JM. Moonmilk deposits originate from specific bacterial communities in Altamira Cave (Spain). MICROBIAL ECOLOGY 2011; 61:182-189. [PMID: 20717660 DOI: 10.1007/s00248-010-9731-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Accepted: 07/21/2010] [Indexed: 05/29/2023]
Abstract
The influence of bacterial communities on the formation of carbonate deposits such as moonmilk was investigated in Altamira Cave (Spain). The study focuses on the relationship between the bacterial communities at moonmilk deposits and those forming white colonizations, which develop sporadically throughout the cave. Using molecular fingerprinting of the metabolically active bacterial communities detected through RNA analyses, the development of white colonizations and moonmilk deposits showed similar bacterial profiles. White colonizations were able to raise the pH as a result of their metabolism (reaching in situ pH values above 8.5), which was proportional to the nutrient supply. Bacterial activity was analyzed by nanorespirometry showing higher metabolic activity from bacterial colonizations than uncolonized areas. Once carbonate deposits were formed, bacterial activity decreased drastically (down to 5.7% of the white colonization activity). This study reports on a specific type of bacterial community leading to moonmilk deposit formation in a cave environment as a result of bacterial metabolism. The consequence of this process is a macroscopic phenomenon of visible carbonate depositions and accumulation in cave environments.
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Affiliation(s)
- Maria C Portillo
- Instituto de Recursos Naturales y Agrobiología, IRNAS-CSIC, Avda. Reina Mercedes 10, Sevilla, 41012, Spain
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17
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Pasić L, Kovce B, Sket B, Herzog-Velikonja B. Diversity of microbial communities colonizing the walls of a Karstic cave in Slovenia. FEMS Microbiol Ecol 2010; 71:50-60. [PMID: 19817862 DOI: 10.1111/j.1574-6941.2009.00789.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Karstic cave systems in Slovenia receive substantial amounts of organic input from adjacent forest and freshwater systems. These caves host microbial communities that consist of distinct small colonies differing in colour and shape. Visible to the naked eye, the colonies cover cave walls and are strewn with light-reflecting water droplets. In this study, the diversity of prokaryotes constituting these unusual microbial communities in Pajsarjeva jama cave was examined. A molecular survey based on small subunit rRNA diversity showed a high diversity within the Bacteria, while members of Archaea were not recovered. A total of eight bacterial phyla were detected. The application of various species richness estimators confirmed the diverse nature of the microbial community sample. Members of Gammaproteobacteria were most abundant in the clone libraries constructed and were followed in abundance by members of Actinobacteria and Nitrospira. In addition, members of Alphaproteobacteria, Betaproteobacteria and Deltaproteobacteria as well as Acidobacteria, Verrucomicrobia, Planctomycetes, Chloroflexi and Gemmatimonadetes were identified in clone libraries. The high number of clones most closely related to environmental 16S rRNA gene clones showed the broad spectrum of unknown and yet to be cultivated microorganisms inhabiting these cave systems.
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Affiliation(s)
- Lejla Pasić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
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18
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Portillo MC, Alloza R, Gonzalez JM. Three different phototrophic microbial communities colonizing a single natural shelter containing prehistoric paintings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:4876-4881. [PMID: 19523664 DOI: 10.1016/j.scitotenv.2009.05.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 05/19/2009] [Accepted: 05/20/2009] [Indexed: 05/27/2023]
Abstract
Three different cases of deterioration were identified in a single natural shelter containing prehistoric paintings. The microbial communities induced by run-off water, a black crust covering a portion of the shelter, and a cryptoendolithic microbial community, were studied. Molecular analyses based both on DNA and RNA were performed to identify the major components of these microbial communities present and metabolically active, respectively, at the studied location. While similar microbial communities were expected due to the proximity of the studied sites, clearly different communities were detected suggesting that specific microorganisms adapt to different micro-environments. Phototrophic microorganisms represented the major portion of total RNA and DNA in the studied microbial communities. Run-off water induced the presence of a large proportion of putative photosynthetic bacteria belonging to Chloroflexi. Different groups of bacteria were associated to phototrophs and were represented by Alpha, Beta, Delta, and Gammaproteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, and Planctomycetes. The present study confirms a need for careful monitoring of microbial communities associated to distinct cases of deterioration even within a single location, underlining the interest of phototrophic microorganisms as indicators of colonization on cultural heritage at natural shelters.
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Affiliation(s)
- M C Portillo
- Instituto de Recursos Naturales y Agrobiología, CSIC, Avda. Reina Mercedes 10, 41012 Sevilla, Spain
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19
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Jurado V, Kroppenstedt RM, Saiz-Jimenez C, Klenk HP, Mouniée D, Laiz L, Couble A, Pötter G, Boiron P, Rodríguez-Nava V. Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm. Int J Syst Evol Microbiol 2009; 59:3105-10. [PMID: 19643882 DOI: 10.1099/ijs.0.008664-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel actinomycete, strain OFN S31(T), was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31(T) formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31(T) (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31(T) is characterized by the absence of mycelium and mycolic acids. Strain OFN S31(T) had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31(T) is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31(T) (=CIP 109864(T) =DSM 45258(T)).
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Affiliation(s)
- Valme Jurado
- Instituto de Recursos Naturales y Agrobiología, CSIC, Apartado 1052, E-41080 Sevilla, Spain
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20
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Assessment of bacterial and fungal growth on natural substrates: consequences for preserving caves with prehistoric paintings. Curr Microbiol 2009; 59:321-5. [PMID: 19536596 DOI: 10.1007/s00284-009-9437-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 05/26/2009] [Accepted: 05/27/2009] [Indexed: 10/20/2022]
Abstract
The most representative bacterium (Pseudonocardia sp.) and fungus (Fusarium sp.) from the microbial communities of a cave containing paleolithic paintings were isolated and their growth on natural substrates assessed. Growth was tested at the in situ and optimal, laboratory growth temperature. Development was analyzed with and without supplemented nutrients (glucose, ammonium, phosphate, peptone). Results showed that the assayed bacterium on natural substrate was able to develop best at in situ temperature and the addition of organic nutrients and/or phosphate enhanced its growth. The growth of the assayed fungus, however, was limited by low temperature and the availability of ammonium. These results confirm a differential behavior of microorganisms between the laboratory and the natural environments and could explain previous invasion of fungi reported for some caves with prehistoric paintings.
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21
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Is the availability of different nutrients a critical factor for the impact of bacteria on subterraneous carbon budgets? Naturwissenschaften 2009; 96:1035-42. [PMID: 19488732 DOI: 10.1007/s00114-009-0562-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 10/20/2022]
Abstract
Bacteria thriving in underground systems, such as karsts, adapt to use a variety of nutrients. Most of these nutrients derive from superficial processes. This study shows that bacteria are able to differentially induce carbonate precipitation or dissolution depending on the availability of nutrients for growth. Different bacterial strains isolated from caves, representing the most common components of these microbial communities, were cultured with different carbon and nitrogen sources (e.g., acetate, glucose, peptone, humic acids) and induced changes in pH were measured during growth. Carbonate can either precipitate or dissolve during bacterial growth. The induction of carbonate precipitates or their dissolution as a function of consumption of specific carbon sources revealed the existence of an active nutrient cycling process in karsts and links nutrients and environmental conditions to the existence of a highly significant carbon sink in subterraneous environments.
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22
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The fungal colonisation of rock-art caves: experimental evidence. Naturwissenschaften 2009; 96:1027-34. [PMID: 19484211 DOI: 10.1007/s00114-009-0561-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2009] [Revised: 04/20/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
The conservation of rock-art paintings in European caves is a matter of increasing interest. This derives from the bacterial colonisation of Altamira Cave, Spain and the recent fungal outbreak of Lascaux Cave, France-both included in the UNESCO World Heritage List. Here, we show direct evidence of a fungal colonisation of rock tablets in a testing system exposed in Altamira Cave. After 2 months, the tablets, previously sterilised, were heavily colonised by fungi and bacteria. Most fungi isolated were labelled as entomopathogens, while the bacteria were those regularly identified in the cave. Rock colonisation was probably promoted by the dissolved organic carbon supplied with the dripping and condensation waters and favoured by the displacement of aerosols towards the interior of the cave, which contributed to the dissemination of microorganisms. The role of arthropods in the dispersal of spores may also help in understanding fungal colonisation. This study evidences the fragility of rock-art caves and demonstrates that microorganisms can easily colonise bare rocks and materials introduced into the cavity.
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Bastian F, Alabouvette C, Saiz-Jimenez C. The impact of arthropods on fungal community structure in Lascaux Cave. J Appl Microbiol 2009; 106:1456-62. [DOI: 10.1111/j.1365-2672.2008.04121.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Bastian F, Alabouvette C, Jurado V, Saiz-Jimenez C. Impact of biocide treatments on the bacterial communities of the Lascaux Cave. Naturwissenschaften 2009; 96:863-8. [PMID: 19404600 DOI: 10.1007/s00114-009-0540-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 02/13/2009] [Accepted: 03/06/2009] [Indexed: 11/28/2022]
Abstract
The Lascaux Cave contains a remarkable set of paintings from the Upper Palaeolithic. Shortly after discovery in 1940, the cave was modified for public viewing and, in 2001, was invaded by a Fusarium solani species complex. Benzalkonium chloride was used from 2001 to 2004 to eliminate the fungal outbreak. In this study, we carried out a sampling in most of the cave halls and galleries. Sequence analysis and isolation methods detected that the most abundant genera of bacteria were Ralstonia and Pseudomonas. We suggest that, as a result of years of benzalkonium chloride treatments, the indigenous microbial community has been replaced by microbial populations selected by biocide application.
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Affiliation(s)
- Fabiola Bastian
- UMR Microbiologie du Sol et de l'Environnement, INRA-Université de Bourgogne, BP 86510, 21065, Dijon Cedex, France
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25
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Portillo MC, Gonzalez JM. Comparing bacterial community fingerprints from white colonizations in Altamira Cave (Spain). World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0021-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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26
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Portillo MC, Gonzalez JM. Sulfate-reducing bacteria are common members of bacterial communities in Altamira Cave (Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2009; 407:1114-1122. [PMID: 19027143 DOI: 10.1016/j.scitotenv.2008.10.045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 10/16/2008] [Accepted: 10/17/2008] [Indexed: 05/27/2023]
Abstract
The conservation of paleolithic paintings such as those in Altamira Cave (Spain) is a primary objective. Recent molecular studies have shown the existence of unknown microbial communities in this cave including anaerobic microorganisms on cave walls. Herein, we analyzed an anaerobic microbial group, the sulfate-reducing bacteria (SRB), from Altamira Cave with potential negative effects on painting conservation. In the present work, the communities of bacteria and SRB were studied through PCR-DGGE analysis. Data suggest that SRB communities represent a significant, highly diverse bacterial group in Altamira Cave. These findings represent a first report on this physiological group on caves with paleolithic paintings and their potential biodegradation consequences. Expanding our knowledge on microbial communities in Altamira Cave is a priority to design appropriate conservation strategies.
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Affiliation(s)
- M Carmen Portillo
- Instituto de Recursos Naturales y Agrobiología, CSIC, Avda. Reina Mercedes 10, 41012, Sevilla, Spain
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27
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Portillo MC, Saiz-Jimenez C, Gonzalez JM. Molecular characterization of total and metabolically active bacterial communities of “white colonizations” in the Altamira Cave, Spain. Res Microbiol 2009; 160:41-7. [DOI: 10.1016/j.resmic.2008.10.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2008] [Revised: 10/02/2008] [Accepted: 10/02/2008] [Indexed: 11/28/2022]
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28
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Laiz L, Miller AZ, Jurado V, Akatova E, Sanchez-Moral S, Gonzalez JM, Dionísio A, Macedo MF, Saiz-Jimenez C. Isolation of five Rubrobacter strains from biodeteriorated monuments. Naturwissenschaften 2008; 96:71-9. [PMID: 18953520 DOI: 10.1007/s00114-008-0452-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Revised: 09/07/2008] [Accepted: 09/14/2008] [Indexed: 10/21/2022]
Abstract
In the last few years, the microbial colonisation of mural paintings in ancient monuments has been attracting the attention of microbiologists and conservators. The genus Rubrobacter is commonly found in biodeteriorated monuments, where it has been reported to cause rosy discolouration. However, to date, only three species of this genus have been isolated, all from thermophilic environments. In this paper, we studied three monuments: the Servilia and Postumio tombs in the Roman Necropolis of Carmona (Spain), and Vilar de Frades church (Portugal), in search of Rubrobacter strains. In all cases, biodeterioration and the formation of efflorescences were observed, and five Rubrobacter strains were isolated. These isolates showed different physiology and migration in denaturing gradient gel electrophoresis, suggesting they might represent new species within this genus. The isolates reproduced some biodeterioration processes in the laboratory and revealed their biomediation in crystal formation.
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Affiliation(s)
- L Laiz
- Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080, Seville, Spain
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29
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Use of attenuated total reflectance Fourier transform infrared spectroscopy to identify microbial metabolic products on carbonate mineral surfaces. Appl Environ Microbiol 2008; 74:4553-9. [PMID: 18502924 DOI: 10.1128/aem.02936-07] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This paper demonstrates the use of attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to detect microbial metabolic products on carbonate mineral surfaces. By creating an ATR-FTIR spectral database for specific organic acids using ATR-FTIR spectroscopy we were able to distinguish metabolic acids on calcite surfaces following Escherichia coli growth. The production of these acids by E. coli was verified using high-performance liquid chromatography with refractive index detection. The development of this technique has allowed us to identify microbial metabolic products on carbonate surfaces in nutrient-limited cave environments.
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30
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Microbial communities and immigration in volcanic environments of Canary Islands (Spain). Naturwissenschaften 2007; 95:307-15. [DOI: 10.1007/s00114-007-0330-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 11/12/2007] [Accepted: 11/15/2007] [Indexed: 10/22/2022]
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31
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Portillo MC, Gonzalez JM, Saiz-Jimenez C. Metabolically active microbial communities of yellow and grey colonizations on the walls of Altamira Cave, Spain. J Appl Microbiol 2007; 104:681-91. [PMID: 17927740 DOI: 10.1111/j.1365-2672.2007.03594.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS To determine the major components of total and metabolically active microbial communities of yellow and grey colonizations threatening the conservation of palaeolithic paintings in Altamira Cave (Spain). METHODS AND RESULTS Micro-organisms present in yellow and grey colonizations were determined from DNA analysis with those showing metabolic activity determined from RNA analysis. Microbial community fingerprints were obtained by denaturing gradient gel electrophoresis (DGGE) and 16S rDNA libraries were constructed from PCR amplified products. Proteobacteria was the most frequent bacterial phylum. Other phyla detected from RNA-based microbial surveys were Acidobacteria, Actinobacteria, Firmicutes, Nitrospirae and Gemmatimonadetes. The detected metabolically active micro-organisms represented only a fraction of the total bacterial community present in the studied colonizations as compared from DGGE analysis. CONCLUSIONS The major bacterial participants in the development of yellow and grey colonizations in Altamira Cave were determined using RNA-based molecular techniques. Micro-organisms showing undetectable activity represent a potential risk for the conservation of these paintings if environmental conditions experience variations. SIGNIFICANCE AND IMPACT OF THE STUDY Caves with palaeolithic paintings are affected by microbial deterioration. Assessing the composition of the microbial communities colonizing these caves represents a first stage to understand and control these colonizations.
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Affiliation(s)
- M C Portillo
- Instituto de Recursos Naturales y Agrobiología, CSIC, Avda. Reina Mercedes, Sevilla, Spain
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32
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Jurado V, Gonzalez JM, Laiz L, Saiz-Jimenez C. Aurantimonas altamirensis sp. nov., a member of the order Rhizobiales isolated from Altamira Cave. Int J Syst Evol Microbiol 2007; 56:2583-2585. [PMID: 17082395 DOI: 10.1099/ijs.0.64397-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A bacterial strain, S21BT, was isolated from Altamira Cave (Cantabria, Spain). The cells were Gram-negative, short rods growing aerobically. Comparative 16S rRNA gene sequence analysis revealed that strain S21BT represented a separate subline of descent within the family 'Aurantimonadaceae' (showing 96% sequence similarity to Aurantimonas coralicida) in the order Rhizobiales (Alphaproteobacteria). The major fatty acids detected were C16:0 and C18:1omega7c. The G+C content of the DNA from strain S21BT was 71.8 mol%. Oxidase and catalase activities were present. Strain S21BT utilized a wide range of substrates for growth. On the basis of the results of this polyphasic study, isolate S21BT represents a novel species of the genus Aurantimonas, for which the name Aurantimonas altamirensis sp. nov. is proposed. The type strain is S21BT (=CECT 7138T=LMG 23375T).
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Affiliation(s)
- Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain
| | - Juan M Gonzalez
- Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, CSIC, Apartado 1052, 41080 Sevilla, Spain
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33
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Cañaveras JC, Cuezva S, Sanchez-Moral S, Lario J, Laiz L, Gonzalez JM, Saiz-Jimenez C. On the origin of fiber calcite crystals in moonmilk deposits. Naturwissenschaften 2005; 93:27-32. [PMID: 16240102 DOI: 10.1007/s00114-005-0052-3] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2005] [Accepted: 09/02/2005] [Indexed: 10/25/2022]
Abstract
In this study, we show that moonmilk subaerial speleothems in Altamira Cave (Spain) consist of a network of fiber calcite crystals and active microbial structures. In Altamira moonmilks, the study of the typology and distribution of fiber crystals, extracellular polymeric substances, and microorganisms allowed us to define the initial stages of fiber crystal formation in recent samples as well as the variations in the microstructural arrangement in more evolved stages. Thus, we have been able to show the existence of a relationship among the different types of fiber crystals and their origins. This allowed us to outline a model that illustrates the different stages of formation of the moonmilk, developed on different substrata, concluding that microbes influence physicochemical precipitation, resulting in a variety of fiber crystal morphologies and sizes.
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Affiliation(s)
- Juan Carlos Cañaveras
- Unidad Asociada CSIC-UA, Laboratorio de Petrologia Aplicada, Departamento de Ciencias de la Tierra, Universidad de Alicante, Alicante, Spain
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