Microbial Diversity in Paleolithic Caves: A Study Case on the Phototrophic Biofilms of the Cave of Bats (Zuheros, Spain)

Urzı̀, Clara; Leo, Filomena De; Bruno, Laura; Albertano, Patrizia

doi:10.1007/s00248-010-9710-x

Cited by 89 publications

(50 citation statements)

References 43 publications

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“…Although Firmicutes (Bacillus sp) along with Escherichia coli and Staphylococcus have been considered as indicators of human impact on caves (Lavoie & Northup, 2006), their detection in the community profiles of all the caves suggested that they were indigenous to these caves. Bacillus sp have been isolated in caves (Fernandez-Cortes et al, 2011;Urzì et al, 2010) and their dispersal throughout the cave ecosystem is enhanced by their abilities to produce spores. Phylogenetic trees of other DGGE sequences showed that these can be grouped under Acidobacteria, Actinobacteria and Proteobacteria and similar groups have also been detected on cave walls (Schabereiter-Gurtner et al, 2002;Ikner et al, 2007;Urzì et al, 2010).…”

Section: Culture Independent and Dependent Surveymentioning

confidence: 99%

“…Bacillus sp have been isolated in caves (Fernandez-Cortes et al, 2011;Urzì et al, 2010) and their dispersal throughout the cave ecosystem is enhanced by their abilities to produce spores. Phylogenetic trees of other DGGE sequences showed that these can be grouped under Acidobacteria, Actinobacteria and Proteobacteria and similar groups have also been detected on cave walls (Schabereiter-Gurtner et al, 2002;Ikner et al, 2007;Urzì et al, 2010). Cave walls, cave animals, insects and human visitors (Chelius & Moore, 2004;Portillo et al, 2009b) are therefore potential sources of bacterial species in cave sediments.…”

Section: Culture Independent and Dependent Surveymentioning

confidence: 99%

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Bacterial community survey of sediments at Naracoorte Caves, Australia

Adetutu¹,

Thorpe²,

Shahsavari³

et al. 2012

IJS

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Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial communities in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible) and control caves. Other detected sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey also showed differences in bacterial diversity in caves with human access compared to the control cave with the control cave having unique microbial sequences (Acinetobacter, Agromyces, Micrococcus and Streptomyces). The show caves had higher bacterial counts, different 16S rDNA based DGGE cluster patterns and principal component groupings compared to Strawhaven. Different factors such as human access, cave use and configurations could have been responsible for the differences observed in the bacterial community cluster patterns (tourist accessible and inaccessible areas) of these caves. Cave sediments can therefore act as reservoirs of microorganisms. This might have some implications on cave conservation activities especially if these sediments harbor rock art degrading microorganisms in caves with rock art.Keywords: caves; tourism; 16S rDNA; denaturing gradient gel electrophoresis factors attracting tourists (Russell & MacLean, 2008;Bastian et al., 2009; Stomeo et al., 2009).Cave microorganisms range from bacterial groups such as Proteobacteria, Actinobacteria, and Firmicutes to yeasts and saprophytic fungus such as Penicillium, Fusarium and Trichurus (Barton & Jurado, 2007;Zhou et al., 2007;Bastian et al., 2009;Portillo et al., 2009a; Jurado et al., 2010; Adetutu et al., 2011; Vaughan et al., 2011). These microbial communities are affected by the geological nature of the caves, prevailing environmental conditions, soil or sediment factors and cave factors (configuration and use) (Ikner et al., 2007; Shapiro & Pringle, 2010; Adetutu et al., 2011). Cave microorganisms in nutrient rich or limited environments (high and low energy caves) are metabolically versatile acquiring energy from cave compounds, gases and by oxidizing metals from rocks. Through these activities, these microorganisms play critical roles in caves' biogeochemical cycles and in the formation of cave features such as stalactites and stalagmites (Barton & Jurado, 2007). This delicate microbial balance can however be disrupted by uncontrolled human access with adverse effects on the cave environment (Bastian et al., 2010).Abstract:

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Section: Culture Independent and Dependent Surveymentioning

confidence: 99%

Section: Culture Independent and Dependent Surveymentioning

confidence: 99%

Bacterial community survey of sediments at Naracoorte Caves, Australia

Adetutu¹,

Thorpe²,

Shahsavari³

et al. 2012

IJS

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“…On the other hand, the genus Herbiconiux was only isolated from the KT. Several studies reported that Actinobacteria members cause biodeterioration of mural paintings in caves (Adetutu and Ball, 2014;Cuezva et al, 2012;Diaz-Herraiz et al, 2013;Urzì et al, 2010). The major taxa of actinobacterial colonizers in these caves belonged to the genera Streptomyces, Nocardia, and Pseudonocardia.…”

Section: -9mentioning

confidence: 99%

Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

Sugiyama¹,

Kiyuna²,

Nishijima³

et al. 2017

J. Gen. Appl. Microbiol.

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Microbial outbreaks and related biodeterioration problems have affected the 1300-year-old multicolor (polychrome) mural paintings of the special historic sites Takamatsuzuka Tumulus (TT) and Kitora Tumulus (KT). Those of TT are designated as a national treasure. The microbiomes of these tumuli, both located in Asuka village, Nara, Japan, are critically reviewed as the central subject of this report. Using culture-dependent methods (conventional isolation and cultivation), we conducted polyphasic studies of the these microbial communities and identified the major microbial colonizers (Fusarium spp., Trichoderma spp., Penicillium spp., dark Acremonium spp., novel Candida yeast spp., Bacillus spp., Ochrobactrum spp., Stenotrophomonas tumulicola, and a few actinobacterial genera) and noteworthy microbial members (Kendrickiella phycomyces, Cephalotrichum verrucisporum (∫ ∫ ∫ ∫ ∫Doratomyces verrucisporus), Sagenomella striatispora, Sagenomella griseoviridis, two novel Cladophialophora spp., Burgoa anomala, one novel species Prototheca tumulicola, five novel Gluconacetobacter spp., three novel Bordetella spp., and one novel genus and species Krasilnikoviella muralis) involved in the biodeterioration of mural paintings, plaster walls, and stone chamber interiors. In addition, we generated microbial community data from TT and KT samples using cultureindependent methods (molecular biological methods, including PCR-DGGE, clone libraries, and pyrosequence analysis). These data are comprehensively presented, in contrast to those derived from culture-dependent methods. Furthermore, the microbial communities detected using both methods are analytically compared, and, as a result, the complementary roles of these methods and approaches are highlighted. In related contexts, knowledge of similar biodeterioration problems affecting other prehistoric cave paintings, mainly at Lascaux in France and Altamira in Spain, are referred to and commented upon. Based on substrate preferences (or ecological grouping) and mapping (plotting detection sites of isolates), we speculate on the possible origins and invasion routes whereby the major microbial colonizers invaded the TT stone chamber interior. Finally, concluding remarks, lessons, and future perspectives based on our microbiological surveys of these ancient tumuli, and similar treasures outside of Japan, are briefly presented. A list of the microbial taxa that have been identified and fully or briefly described by us as known and novel taxa for TT and KT isolates since 2008 is presented in Supplementary Materials. 64SUGIYAMA et al.

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“…Other strains as for example Enterobacter hormaechei or Bacillus cereus displayed RISA profiles formed by three bands of different size. The RISA method was applied by previous authors for clustering the bacterial strains isolated from different environments (Pangallo et al 2004;Belgacem et al 2009;Urzi et al 2010), other kinds of DNA fingerprints methods were used in clustering the PAH degrading bacteria (La Rosa et al 2006;Abd-Elsalam et al 2009;Ruggeri et al 2009). …”

Section: Resultsmentioning

confidence: 99%

Diversity and PAH growth abilities of bacterial strains isolated from a contaminated soil in Slovakia

et al. 2013

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Different abandoned industrial areas contaminated by polycyclic aromatic hydrocarbons (PAHs) are present in Slovakia. These environmental burdens are very dangerous to the health of human and environment. The bioremediation, based on the use of hydrocarbons degrading microorganisms, is a promising strategy to sanitize these polluted sites. The aim of this investigation was to assess the bacterial diversity of a PAHs-contaminated soil and to select the potential hydrocarbonoclastic bacteria which can be used for different bioremediation approaches. The bacterial strains were isolated on minimal medium agar supplemented with a mixture of PAHs. Seventy-three isolated strains were grouped by ribosomal interspacer analysis in 15 different clusters and representatives of each cluster were identified by 16S rRNA sequencing. The PAHs degradation abilities of all bacterial isolates were estimated by the 2,6-dichlorophenol indophenol assay and by their growth on minimal broth amended with a mixture of PAHs. Different kinds of strains, members of the genus Pseudomonas, Enterobacter, Bacillus, Arthrobacter, Acinetobacter and Sphingomonas, were isolated from the contaminated soil. Four isolates (Pseudomonas putida, Arthrobacter oxydans, Sphingomonas sp. and S. paucimobilis) showed promising PAHs-degrading abilities and therefore their possible employing in bioremediation strategies.

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Microbial Diversity in Paleolithic Caves: A Study Case on the Phototrophic Biofilms of the Cave of Bats (Zuheros, Spain)

Cited by 89 publications

References 43 publications

Bacterial community survey of sediments at Naracoorte Caves, Australia

Bacterial community survey of sediments at Naracoorte Caves, Australia

Polyphasic insights into the microbiomes of the Takamatsuzuka Tumulus and Kitora Tumulus

Diversity and PAH growth abilities of bacterial strains isolated from a contaminated soil in Slovakia

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