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Demergasso C, Neilson JW, Tebes-Cayo C, Véliz R, Ayma D, Laubitz D, Barberán A, Chong-Díaz G, Maier RM. Hyperarid soil microbial community response to simulated rainfall. Front Microbiol 2023; 14:1202266. [PMID: 37779711 PMCID: PMC10537920 DOI: 10.3389/fmicb.2023.1202266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.
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Affiliation(s)
- Cecilia Demergasso
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Julia W. Neilson
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Cinthya Tebes-Cayo
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Roberto Véliz
- Biotechnology Center “Profesor Alberto Ruíz”, Universidad Católica del Norte, Antofagasta, Chile
| | - Diego Ayma
- Department of Mathematics, Faculty of Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Daniel Laubitz
- Steele Steele Children’s Research Center, Department of Pediatrics, University of Arizona, Tucson, AZ, United States
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
| | - Guillermo Chong-Díaz
- Department of Geology, Faculty of Engineering and Geological Sciences, Universidad Católica del Norte, Antofagasta, Chile
| | - Raina M. Maier
- Department of Environmental Science, University of Arizona, Tucson, AZ, United States
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Villa F, Wu YL, Zerboni A, Cappitelli F. In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface. Bioscience 2022; 72:1156-1175. [PMID: 36451971 PMCID: PMC9699719 DOI: 10.1093/biosci/biac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.
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Tait AW, Wilson SA, Tomkins AG, Hamilton JL, Gagen EJ, Holman AI, Grice K, Preston LJ, Paterson DJ, Southam G. Preservation of Terrestrial Microorganisms and Organics Within Alteration Products of Chondritic Meteorites from the Nullarbor Plain, Australia. ASTROBIOLOGY 2022; 22:399-415. [PMID: 35100042 DOI: 10.1089/ast.2020.2387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Meteorites that fall to Earth quickly become contaminated with terrestrial microorganisms. These meteorites are out of chemical equilibrium in the environments where they fall, and equilibration promotes formation of low-temperature alteration minerals that can entomb contaminant microorganisms and thus preserve them as microfossils. Given the well-understood chemistry of meteorites and their recent discovery on Mars by rovers, a similarly weathered meteorite on Mars could preserve organic and fossil evidence of a putative past biosphere at the martian surface. Here, we used several techniques to assess the potential of alteration minerals to preserve microfossils and biogenic organics in terrestrially weathered ordinary chondrites from the Nullarbor Plain, Australia. We used acid etching of ordinary chondrites to reveal entombed fungal hyphae, modern biofilms, and diatoms within alteration minerals. We employed synchrotron X-ray fluorescence microscopy of alteration mineral veins to map the distribution of redox-sensitive elements of relevance to chemolithotrophic organisms, such as Mn-cycling bacteria. We assessed the biogenicity of fungal hyphae within alteration veins using a combination of Fourier-transform infrared spectroscopy and pyrolysis gas chromatography-mass spectrometry, which showed that alteration minerals sequester and preserve organic molecules at various levels of decomposition. Our combined analyses results show that fossil microorganisms and the organic molecules they produce are preserved within calcite-gypsum admixtures in meteorites. Furthermore, the distributions of redox-sensitive elements (e.g., Mn) within alteration minerals are localized, which qualitatively suggests that climatically or microbially facilitated element mobilization occurred during the meteorite's residency on Earth. If returned as part of a sample suite from the martian surface, ordinary chondrites could preserve similar, recognizable evidence of putative past life and/or environmental change.
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Affiliation(s)
- Alastair W Tait
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Victoria, Australia
| | - Siobhan A Wilson
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Victoria, Australia
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew G Tomkins
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Victoria, Australia
| | - Jessica L Hamilton
- School of Earth, Atmosphere and Environment, Monash University, Melbourne, Victoria, Australia
- Australian Synchrotron, ANSTO, Clayton, Victoria, Australia
| | - Emma J Gagen
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Queensland, Australia
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Alex I Holman
- Western Australian Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, Western Australia, Australia
| | - Kliti Grice
- Western Australian Organic and Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, Curtin University, Perth, Western Australia, Australia
| | - Louisa J Preston
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | | | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Queensland, Australia
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Chaddha AS, Sharma A, Singh NK. Clay minerals identification in rock varnish by XRD: A one-step reduction approach. MethodsX 2021; 8:101511. [PMID: 34754782 PMCID: PMC8563653 DOI: 10.1016/j.mex.2021.101511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/06/2021] [Indexed: 11/29/2022] Open
Abstract
Rock varnishes are known to be fine, dark, glossy submicron films found in deserts bare rock surfaces. The oxides and hydroxides of manganese and iron bind together the clay minerals present in the varnish layer. The processes of oxide-hydroxide accumulation at varnish sites are due to iron and manganese oxidizing bacteria which may require clay minerals for additional nutrition. Quantification and identification of clay minerals in this biofilm is needed to understand its formation. Past attempts to analyze the mineralogical composition of rock varnish have led to inconclusive results as varnish is a submicron thin layer composed of a complex mineral matrix. The elimination of non-crystalline cementing groups comprising of free iron oxides is a key step in the identification of many types of clay minerals, particularly in soil/sediment mineral studies.The Fe-Mn oxide-hydroxide coatings, acting as cementing materials, can be easily removed using a one-step reduction method employing Na2S2O4 at 70 °C, leading to separation of clay minerals. We have taken the lead from earlier reported Jackson (1958) method, wherein a combination of reagents was used such as sodium acetate, sodium citrate, hydrogen peroxide, sodium bicarbonate, and sodium dithionite for removing carbonate, organic carbon and Fe-Mn oxy-hydroxide coatings respectively from sediment grains to segregate individual grains from each other. Our modification helps in the unveiling of clay minerals from a solid substrate and reports the X-ray diffraction peaks, which are elsewise hard to detect and therefore earlier studies are inconclusive.
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Affiliation(s)
- Amritpal Singh Chaddha
- Birbal Sahni Institute of Palaeosciences, Lucknow-226007, India.,Department of Chemistry, University of Lucknow, Lucknow-226007, India
| | - Anupam Sharma
- Birbal Sahni Institute of Palaeosciences, Lucknow-226007, India
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Unveiling the Hidden Diversity of Rock-Inhabiting Fungi: Chaetothyriales from China. J Fungi (Basel) 2020; 6:jof6040187. [PMID: 32987844 PMCID: PMC7711927 DOI: 10.3390/jof6040187] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 11/16/2022] Open
Abstract
Rock-inhabiting fungi (RIF) are nonlichenized fungi that naturally colonize rock surfaces and subsurfaces. The extremely slow growth rate and lack of distinguishing morphological characteristics of RIF resulted in a poor understanding on their biodiversity. In this study, we surveyed RIF colonizing historical stone monuments and natural rock formations from throughout China. Among over 1000 isolates, after preliminary delimitation using the internal transcribed spacer region (ITS) sequences, representative isolates belonging to Trichomeriaceae and Herpotrichiellaceae were selected for a combined analysis of ITS and the nuclear ribosomal large subunit (nucLSU) to determine the generic placements. Eight clades representing seven known genera and one new genus herein named as Anthracina were placed in Trichomeriaceae. While, for Herpotrichiellaceae, two clades corresponded to two genera: Cladophialophora and Exophiala. Fine-scale phylogenetic analyses using combined sequences of the partial actin gene (ACT), ITS, mitochondrial small subunit ribosomal DNA (mtSSU), nucLSU, the largest subunit of RNA polymerase II (RPB1), small subunit of nuclear ribosomal RNA gene (SSU), translation elongation factor (TEF), and β-tubulin gene (TUB) revealed that these strains represented 11 and 6 new species, respectively, in Trichomeriaceae and Herpotrichiellaceae. The 17 new species were described, illustrated for their morphologies and compared with similar taxa. Our study demonstrated that the diversity of RIF is surprisingly high and still poorly understood. In addition, a rapid strategy for classifying RIF was proposed to determine the generic and familial placements through preliminary ITS and nucLSU analyses, followed by combined analyses of five loci selected from ACT, ITS, mtSSU, nucLSU, RPB1, and/or the second subunit of RNA polymerase II gene (RPB2), SSU, TEF, and TUB regions to classify RIF to the species level.
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Geomicrobial Investigations of Colored Outer Coatings from an Ethiopian Rock Art Gallery. COATINGS 2020. [DOI: 10.3390/coatings10060536] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The open rock shelter of Yabelo in Ethiopia hosts diverse Holocene paintings of great cultural importance. The paintings are characterized by the presence of different mineral coatings, whose features have not been studied yet. Our goal was to understand whether different rock samples from the Yabelo paintings collected in close proximity may reveal coatings with different minerology and biology. Thus, elemental analyses combined with microscopic and molecular investigations were performed on two coatings, one whitish (sample 1) and one reddish (sample 2). Although both samples were dominated by heterotrophic bacteria, the two coatings showed distinct mineralogical and microbiological characteristics. Sample 1 contained higher amounts of Ca and P than sample 2, which was likely related to the presence of organic matter. Sample 1 hosted bacterial genera that are potentially involved in biomineralization processes, metal redox cycles and metal resistance. In contrast, sample 2 showed mainly pathogenic and commensal bacteria that are characteristic of animal and human microbiota, and other microorganisms that are involved in nitrogen and metal biogeochemical cycles. Overall, our results indicated that the bacterial communities were particular to the coating mineralogy, suggesting a potential role of the biological components in the crust genesis.
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Samuels T, Bryce C, Landenmark H, Marie‐Loudon C, Nicholson N, Stevens AH, Cockell C. Microbial Weathering of Minerals and Rocks in Natural Environments. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/9781119413332.ch3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Evolutionary conservation of within-family biodiversity patterns. Nat Commun 2020; 11:882. [PMID: 32060281 PMCID: PMC7021778 DOI: 10.1038/s41467-020-14720-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 01/29/2020] [Indexed: 11/08/2022] Open
Abstract
The tendency for species to retain their ancestral biological properties has been widely demonstrated, but the effect of phylogenetic constraints when progressing from species to ensemble-level properties requires further assessment. Here we test whether community-level patterns (environmental shifts in local species richness and turnover) are phylogenetically conserved, assessing whether their similarity across different families of lichens, insects, and birds is dictated by the relatedness of these families. We show a significant phylogenetic signal in the shape of the species richness-elevation curve and the decay of community similarity with elevation: closely related families share community patterns within the three major taxa. Phylogenetic influences are partly explained by similarities among families in conserved traits defining body plan and interactions, implying a scaling of phylogenetic effects from the organismal to the community level. Consequently, the phylogenetic signal in community-level patterns informs about how the historical legacy of a taxon and shared responses among related taxa to similar environments contribute to community assembly and diversity patterns.
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Esposito A, Borruso L, Rattray JE, Brusetti L, Ahmed E. Taxonomic and functional insights into rock varnish microbiome using shotgun metagenomics. FEMS Microbiol Ecol 2019; 95:5626342. [DOI: 10.1093/femsec/fiz180] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/13/2019] [Indexed: 12/21/2022] Open
Abstract
ABSTRACTRock varnish is a microbial habitat, characterised by thin (5–500 μm) and shiny coatings of iron (Fe) and manganese (Mn) oxides associated with clay minerals. This structure is well studied by geologists, and recently there have been reports about the taxonomical composition of its microbiome. In this study, we investigated the rock varnish microbiome using shotgun metagenomics together with analyses of elemental composition, lipid and small molecule biomarkers, and rock surface analyses to explore the biogeography of microbial communities and their functional features. We report taxa and encoded functions represented in metagenomes retrieved from varnish or non-varnish samples, additionally, eight nearly complete genomes have been reconstructed spanning four phyla (Acidobacteria, Actinobacteria, Chloroflexi and TM7). The functional and taxonomic analyses presented in this study provide new insights into the ecosystem dynamics and survival strategies of microbial communities inhabiting varnish and non-varnish rock surfaces.
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Affiliation(s)
- Alfonso Esposito
- Department of Cellular, Computational and Integrative Biology – CIBIO – University of Trento, Via Sommarive 9, 38123 Trento, Italy
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen/Bolzano, piazza Università 5, 39100 Bolzano, Italy
| | - Jayne E Rattray
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen/Bolzano, piazza Università 5, 39100 Bolzano, Italy
| | - Engy Ahmed
- Institute of Soil Biology, Biology Centre, Czech Academy of Sciences, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
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Ren G, Yan Y, Nie Y, Lu A, Wu X, Li Y, Wang C, Ding H. Natural Extracellular Electron Transfer Between Semiconducting Minerals and Electroactive Bacterial Communities Occurred on the Rock Varnish. Front Microbiol 2019; 10:293. [PMID: 30886603 PMCID: PMC6410676 DOI: 10.3389/fmicb.2019.00293] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 02/04/2019] [Indexed: 11/13/2022] Open
Abstract
Rock varnish is a thin coating enriched with manganese (Mn) and iron (Fe) oxides. The mineral composition and formation of rock varnish elicit considerable attention from geologists and microbiologists. However, limited research has been devoted to the semiconducting properties of these Fe/Mn oxides in varnish and relatively little attention is paid to the mineral-microbe interaction under sunlight. In this study, the mineral composition and the bacterial communities on varnish from the Gobi Desert in Xinjiang, China were analyzed. Results of principal components analysis and t-test indicated that more electroactive genera such as Acinetobacter, Staphylococcus, Dietzia, and Pseudomonas gathered on varnish bacterial communities than on substrate rock and surrounding soils. We then explored the culture of varnish, substrate and soil samples in media and the extracellular electron transfer (EET) between bacterial communities and mineral electrodes under light/dark conditions for the first time. Orthogonal electrochemical experiments demonstrated that the most remarkable photocurrent density of 6.1 ± 0.4 μA/cm2 was observed between varnish electrode and varnish microflora. Finally, based on Raman and 16S rRNA gene-sequencing results, coculture system of birnessite and Pseudomonas (the major Mn oxide and a common electroactive bacterium in varnish) was established to study underlying mechanism. A steadily growing photocurrent (205 μA at 100 h) under light was observed with a stable birnessite after 110 h. However, only 47 μA was generated in the dark control and birnessite was reduced to Mn2+ in 13 h, suggesting that birnessite helped deliver electrons instead of serving as an electron acceptor under light. Our study demonstrated that electroactive bacterial communities were positively correlated with Fe/Mn semiconducting minerals in varnish, and diversified EET process occurred on varnish under sunlight. Overall, these phenomena may influence bacterial-community structure in natural environments over time.
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Affiliation(s)
- Guiping Ren
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Yingchun Yan
- College of Engineering, Peking University, Beijing, China
| | - Yong Nie
- College of Engineering, Peking University, Beijing, China
| | - Anhuai Lu
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Xiaolei Wu
- College of Engineering, Peking University, Beijing, China
| | - Yan Li
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Changqiu Wang
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing, China
| | - Hongrui Ding
- The Key Laboratory of Orogenic Belts and Crustal Evolution, Beijing Key Laboratory of Mineral Environmental Function, School of Earth and Space Sciences, Peking University, Beijing, China
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Lang-Yona N, Maier S, Macholdt DS, Müller-Germann I, Yordanova P, Rodriguez-Caballero E, Jochum KP, Al-Amri A, Andreae MO, Fröhlich-Nowoisky J, Weber B. Insights into microbial involvement in desert varnish formation retrieved from metagenomic analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:264-271. [PMID: 29488349 DOI: 10.1111/1758-2229.12634] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/19/2018] [Indexed: 06/08/2023]
Abstract
Desert varnishes are dark rock coatings observed in arid environments and might resemble Mn-rich coatings found on Martian rocks. Their formation mechanism is not fully understood and the possible microbial involvement is under debate. In this study, we applied DNA metagenomic Shotgun sequencing of varnish and surrounding soil to evaluate the composition of the microbial community and its potential metabolic function. We found that the α diversity was lower in varnish compared to soil samples (p value < 0.05), suggesting distinct populations with significantly higher abundance of Actinobacteria, Proteobacteria and Cyanobacteria within the varnish. Additionally, we observed increased levels of transition metal metabolic processes in varnish compared to soil samples. Nevertheless, potentially relevant enzymes for varnish formation were detected at low to insignificant levels in both niches, indicating no current direct microbial involvement in Mn oxidation. This finding is supported by quantitative genomic analysis, elemental analysis, fluorescence imaging and scanning transmission X-ray microscopy. We thus conclude that the distinct microbial communities detected in desert varnish originate from settled Aeolian microbes, which colonized this nutrient-enriched niche, and discuss possible indirect contributions of microorganisms to the formation of desert varnish.
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Affiliation(s)
- Naama Lang-Yona
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Stefanie Maier
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Dorothea S Macholdt
- Biogeochemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
- Climate Geochemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Isabell Müller-Germann
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Petya Yordanova
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Emilio Rodriguez-Caballero
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Klaus P Jochum
- Climate Geochemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Abdullah Al-Amri
- Geology and Geophysics Department, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Meinrat O Andreae
- Biogeochemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
- Geology and Geophysics Department, King Saud University, PO Box 2455, Riyadh 11451, Saudi Arabia
| | - Janine Fröhlich-Nowoisky
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
| | - Bettina Weber
- Multiphase Chemistry Department, Hahn-Meitner-Weg 1, Max Planck Institute for Chemistry, 55128 Mainz, Germany
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Profile of microbial communities on carbonate stones of the medieval church of San Leonardo di Siponto (Italy) by Illumina-based deep sequencing. Appl Microbiol Biotechnol 2016; 100:8537-48. [DOI: 10.1007/s00253-016-7656-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/25/2016] [Accepted: 05/27/2016] [Indexed: 10/21/2022]
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13
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Esposito A, Ahmed E, Ciccazzo S, Sikorski J, Overmann J, Holmström SJM, Brusetti L. Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description. MICROBIAL ECOLOGY 2015; 70:741-750. [PMID: 25921518 DOI: 10.1007/s00248-015-0617-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/16/2015] [Indexed: 06/04/2023]
Abstract
Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth's crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.
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Affiliation(s)
- Alfonso Esposito
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy
| | - Engy Ahmed
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Sonia Ciccazzo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy
| | - Johannes Sikorski
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, D-38124, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, D-38124, Braunschweig, Germany
| | - Sara J M Holmström
- Department of Geological Sciences, Stockholm University, SE-10691, Stockholm, Sweden
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 1, I-39100, Bozen-Bolzano, Italy.
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Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. ISME JOURNAL 2015; 10:21-9. [PMID: 26125681 DOI: 10.1038/ismej.2015.108] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/04/2015] [Accepted: 05/09/2015] [Indexed: 01/27/2023]
Abstract
The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including 'molecular tinkering/opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.
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15
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Marnocha CL, Dixon JC. Endolithic bacterial communities in rock coatings from Kärkevagge, Swedish Lapland. FEMS Microbiol Ecol 2014; 90:533-42. [DOI: 10.1111/1574-6941.12415] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 06/30/2014] [Accepted: 08/10/2014] [Indexed: 11/28/2022] Open
Affiliation(s)
| | - John C. Dixon
- Department of Geosciences; University of Arkansas; Fayetteville AR USA
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Karaevskaya ES, Demchenko LS, Demidov NE, Rivkina EM, Bulat SA, Gilichinsky DA. Archaeal diversity in permafrost deposits of Bunger Hills Oasis and King George Island (Antarctica) according to the 16S rRNA gene sequencing. Microbiology (Reading) 2014. [DOI: 10.1134/s0026261714040092] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Zhang T, Liu M, Sun J, Shi Y, Zeng J, Lou K. Bacterial diversity in rock varnish of extreme arid region of Turpan Basin. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.chnaes.2012.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Baskar S, Baskar R, Thorseth IH, Ovreås L, Pedersen RB. Microbially induced iron precipitation associated with a neutrophilic spring at Borra Caves, Vishakhapatnam, India. ASTROBIOLOGY 2012; 12:327-346. [PMID: 22519973 DOI: 10.1089/ast.2011.0672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The present investigation uncovers various pieces of evidence for the possible biologically induced mineralization in iron mats associated with a pH-neutral spring in the Borra caves, Vishakhapatnam, India. Electron microscopy [scanning electron microscopy (SEM) and transmission electron microscopy (TEM)] demonstrated large numbers of (i) hollow tubes (diameter ∼1 μm) resembling sheaths of the iron-oxidizing bacteria Leptothrix, (ii) thin (diameter <<1 μm) solid fibers of uncertain origin, (iii) nanoscale subspherical to irregularly shaped particles encrusting tubes and fibers, and (iv) aggregates of broken and partially disintegrated sheaths, fibers, and particles embedded in extracellular polymeric substances (EPS) occasionally including microbial cells. X-ray microanalyses by energy dispersive spectroscopy (EDS) revealed that the mat accumulated largely Fe but also smaller amounts of Si and traces of P and Ca. Particles rich in Si and Al (possibly kaolinite) and Ca (carbonate) were also observed. High-resolution TEM/EDS of unstained ultrathin sections suggests that microbial sheaths were highly mineralized by amorphous to cryptocrystalline Fe-rich phases and less frequently by other fine-grained and fibrous authigenic claylike minerals. Total number of microorganisms in the iron mats was 5.8×10(5) cells, g sed(-1) (wet weight). Analysis of the 16S rRNA gene diversity revealed microorganisms assigned to eight different phyla [Proteobacteria (62%), Chloroflexi (8%), Bacteroidetes (7%), Planctomycetes (1%), Actinobacteria (5%), Acidobacteria (6%), Nitrospira (1%), Firmicutes (5%)]. Within the Proteobacteria, Betaproteobacteria was the predominant class, which accounted for 28% of the sequences. Within this class some obvious similarities between the obtained sequences and sequences from other cave systems could be seen, especially sequences affiliated with Leptothrix, Siderooxidans, Crenothrix, Comamonadaceae, Dechloromonas, and many uncultured Betaproteobacteria. Four (4%) of the sequences could not be assigned to phylum level but were affiliating with the candidate division TM7 (2%), candidate division OP11 (1%), and candidate division WWE3 (1%). The results allow us to infer a possible relationship of microbial sheaths, EPS, and the iron precipitates to microbial community diversity in the Borra cave springs. Understanding biogenic iron oxides in caves has important astrobiological applications as it provides a potential tool for the detection of extraterrestrial life.
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Perfumo A, Cockell C, Elsaesser A, Marchant R, Kminek G. Microbial diversity in Calamita ferromagnetic sand. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:483-490. [PMID: 23761311 DOI: 10.1111/j.1758-2229.2011.00244.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Calamita is a black ferromagnetic sand from a marine iron ore on Elba Island (Italy). Its total iron content is approximately 80% and a major fraction (63% w/w) has magnetic properties. Desiccation, ultraviolet irradiation and the high temperature induced by the thermal conductivity of iron make Calamita sand an extreme biotope. We report, for the first time, the geomicrobiological characterization of Calamita sand, which showed a low bacterial biodiversity as determined by denaturing gradient gel electrophoresis and 16S rRNA gene clone library analysis. We retrieved sequences closely affiliated with uncultured bacteria inhabiting the harshest deserts on Earth. Radiation- and desiccation-tolerant bacteria from the phyla Proteobacteria, Actinobacteria and Deinococcus-Thermus dominated the community. Heavy metal-resistant organisms, for example Variovorax sp. were also abundant. Sequences of organisms with an inferred metabolism based on lithotrophic iron oxidation were detected. The sands also contained thermophilic bacilli, which were cultivated at 60°C. These data provided important insights also into the biogeographical distribution of these organisms in the Mediterranean region. In summary, this study on Calamita helps to expand our knowledge of the biodiversity in extreme, iron-rich, environments.
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Affiliation(s)
- Amedea Perfumo
- Planetary Protection, European Space Agency-ESA/ESTEC, Keplerlaan 1, 2201 AZ Noordwijk, The Netherlands School of Biomedical Sciences, University of Ulster, Coleraine, UK Planetary and Space Science Research Institute, Open University, Milton Keynes, UK
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21
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Evidence for a biogenic, microorganismal origin of rock varnish from the Gangdese Belt of Tibet. Micron 2011; 42:401-11. [DOI: 10.1016/j.micron.2010.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Revised: 12/02/2010] [Accepted: 12/02/2010] [Indexed: 11/22/2022]
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Abstract
PREMISE OF THE STUDY Fungi are major decomposers in certain ecosystems and essential associates of many organisms. They provide enzymes and drugs and serve as experimental organisms. In 1991, a landmark paper estimated that there are 1.5 million fungi on the Earth. Because only 70000 fungi had been described at that time, the estimate has been the impetus to search for previously unknown fungi. Fungal habitats include soil, water, and organisms that may harbor large numbers of understudied fungi, estimated to outnumber plants by at least 6 to 1. More recent estimates based on high-throughput sequencing methods suggest that as many as 5.1 million fungal species exist. METHODS Technological advances make it possible to apply molecular methods to develop a stable classification and to discover and identify fungal taxa. KEY RESULTS Molecular methods have dramatically increased our knowledge of Fungi in less than 20 years, revealing a monophyletic kingdom and increased diversity among early-diverging lineages. Mycologists are making significant advances in species discovery, but many fungi remain to be discovered. CONCLUSIONS Fungi are essential to the survival of many groups of organisms with which they form associations. They also attract attention as predators of invertebrate animals, pathogens of potatoes and rice and humans and bats, killers of frogs and crayfish, producers of secondary metabolites to lower cholesterol, and subjects of prize-winning research. Molecular tools in use and under development can be used to discover the world's unknown fungi in less than 1000 years predicted at current new species acquisition rates.
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Affiliation(s)
- Meredith Blackwell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.
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Kiss H, Cleland D, Lapidus A, Lucas S, Del Rio TG, Nolan M, Tice H, Han C, Goodwin L, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Lu M, Brettin T, Detter JC, Göker M, Tindall BJ, Beck B, McDermott TR, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, Cheng JF. Complete genome sequence of 'Thermobaculum terrenum' type strain (YNP1). Stand Genomic Sci 2010; 3:153-62. [PMID: 21304745 PMCID: PMC3035366 DOI: 10.4056/sigs.1153107] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
'Thermobaculum terrenum' Botero et al. 2004 is the sole species within the proposed genus 'Thermobaculum'. Strain YNP1(T) is the only cultivated member of an acid tolerant, extremely thermophilic species belonging to a phylogenetically isolated environmental clone group within the phylum Chloroflexi. At present, the name 'Thermobaculum terrenum' is not yet validly published as it contravenes Rule 30 (3a) of the Bacteriological Code. The bacterium was isolated from a slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is likely to be the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Chloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
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Proteomic and physiological responses of Kineococcus radiotolerans to copper. PLoS One 2010; 5:e12427. [PMID: 20865147 PMCID: PMC2928746 DOI: 10.1371/journal.pone.0012427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Accepted: 07/14/2010] [Indexed: 01/21/2023] Open
Abstract
Copper is a highly reactive, toxic metal; consequently, transport of this metal within the cell is tightly regulated. Intriguingly, the actinobacterium Kineococcus radiotolerans has been shown to not only accumulate soluble copper to high levels within the cytoplasm, but the phenotype also correlated with enhanced cell growth during chronic exposure to ionizing radiation. This study offers a first glimpse into the physiological and proteomic responses of K. radiotolerans to copper at increasing concentration and distinct growth phases. Aerobic growth rates and biomass yields were similar over a range of Cu(II) concentrations (0–1.5 mM) in complex medium. Copper uptake coincided with active cell growth and intracellular accumulation was positively correlated with Cu(II) concentration in the growth medium (R2 = 0.7). Approximately 40% of protein coding ORFs on the K. radiotolerans genome were differentially expressed in response to the copper treatments imposed. Copper accumulation coincided with increased abundance of proteins involved in oxidative stress and defense, DNA stabilization and repair, and protein turnover. Interestingly, the specific activity of superoxide dismutase was repressed by low to moderate concentrations of copper during exponential growth, and activity was unresponsive to perturbation with paraquot. The biochemical response pathways invoked by sub-lethal copper concentrations are exceptionally complex; though integral cellular functions are preserved, in part, through the coordination of defense enzymes, chaperones, antioxidants and protective osmolytes that likely help maintain cellular redox. This study extends our understanding of the ecology and physiology of this unique actinobacterium that could potentially inspire new biotechnologies in metal recovery and sequestration, and environmental restoration.
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Northup DE, Snider JR, Spilde MN, Porter ML, van de Kamp JL, Boston PJ, Nyberg AM, Bargar JR. Diversity of rock varnish bacterial communities from Black Canyon, New Mexico. ACTA ACUST UNITED AC 2010. [DOI: 10.1029/2009jg001107] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Diana E. Northup
- Department of Biology; University of New Mexico; Albuquerque New Mexico USA
| | - Jessica R. Snider
- Department of Biology; University of New Mexico; Albuquerque New Mexico USA
| | - Michael N. Spilde
- Institute of Meteoritics; University of New Mexico; Albuquerque New Mexico USA
| | - Megan L. Porter
- Department of Biological Sciences; University of Maryland Baltimore County; Baltimore Maryland USA
| | | | - Penelope J. Boston
- Earth and Environmental Science Department; New Mexico Institute of Mining and Technology; Socorro New Mexico USA
| | - April M. Nyberg
- National Clonal Germplasm Repository; USDA-ARS; Corvallis Oregon USA
| | - John R. Bargar
- Stanford Synchrotron Radiation Laboratory; Menlo Park California USA
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Horath T, Bachofen R. Molecular characterization of an endolithic microbial community in dolomite rock in the central Alps (Switzerland). MICROBIAL ECOLOGY 2009; 58:290-306. [PMID: 19172216 DOI: 10.1007/s00248-008-9483-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 12/19/2008] [Indexed: 05/21/2023]
Abstract
Endolithic microorganisms colonize the pores in exposed dolomite rocks in the Piora Valley in the Swiss Alps. They appear as distinct grayish-green bands about 1-8 mm below the rock surface. Based on environmental small subunit ribosomal RNA gene sequences, a diverse community driven by photosynthesis has been found. Cyanobacteria (57 clones), especially the genus Leptolyngbya, form the functional basis for an endolithic community which contains a wide spectrum of so far not characterized species of chemotrophic Bacteria (64 clones) with mainly Actinobacteria, Alpha-Proteobacteria, Bacteroidetes, and Acidobacteria, as well as a cluster within the Chloroflexaceae. Furthermore, a cluster within the Crenarchaeotes (40 clones) has been detected. Although the eukaryotic diversity was outside the scope of the study, an amoeba (39 clones), and several green algae (51 clones) have been observed. We conclude that the bacterial diversity in this endolithic habitat, especially of chemotrophic, nonpigmented organisms, is considerable and that Archaea are present as well.
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Affiliation(s)
- Thomas Horath
- Institute of Plant Biology/Microbiology, University of Zürich, Zollikerstr. 107, CH-8008 Zürich, Switzerland
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27
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Krinsley D, Dorn RI, DiGregorio B. Astrobiological implications of rock varnish in Tibet. ASTROBIOLOGY 2009; 9:551-562. [PMID: 19663762 DOI: 10.1089/ast.2008.0238] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The study of terrestrial geomicrobiology and its relationship to rock weathering processes is an essential tool in developing analogues for similar processes that may have occurred on Mars. Most studies of manganese-enhanced rock varnish have focused on samples taken from warm arid desert regions. Here, we examine samples obtained from eolian-abraded lava flows of the 4700-4800 m high Ashikule Basin in Tibet. Because it receives approximately 300 mm of precipitation annually, this site is nowhere near as dry as Atacama Desert locales. However, the dusty, sulfate-rich, high-altitude and high-UV flux environment of the Tibetan locale offers new insight into rock varnish formation processes in a terrestrial environment that displays some attributes similar to those expected on early Mars. Microprobe measurements reveal that Mn enhancements in varnish are two orders of magnitude above the dust source, but Fe is only enhanced by a factor of three. Manganese-enhancing bacterial forms are not abundant but are still approximately 3 times more common than in Mojave and Sonoran Desert varnishes. In addition to its occurrence in subaerial positions, Tibetan varnish also occurs in micron-scale "pods" enveloped by silica glaze and as remobilized constituents that have migrated into the underlying weathering rind. A lack of surficial Mn-rich varnish, therefore, might not imply the absence of varnish. In contrast to suggestions that silica glaze might be a good source of microbial fossils and a key to varnish formation, we did not observe any clear microfossil forms entombed in silica glaze; further, there is no gradation between varnish and silica glaze but only distinct contacts.
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Affiliation(s)
- David Krinsley
- Department of Geological Sciences, University of Oregon, Eugene, Oregon 97403-1272, USA.
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Kuhlman KR, Venkat P, La Duc MT, Kuhlman GM, McKay CP. Evidence of a microbial community associated with rock varnish at Yungay, Atacama Desert, Chile. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jg000677] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Parth Venkat
- California Institute of Technology; Pasadena California USA
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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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Life in extreme environments: survival strategy of the endolithic desert lichen Verrucaria rubrocincta. Naturwissenschaften 2008; 95:705-12. [DOI: 10.1007/s00114-008-0373-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Revised: 02/20/2008] [Accepted: 02/22/2008] [Indexed: 10/22/2022]
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Abstract
Biofilms are interface micro-habitats formed by microbes that differ markedly from those of the ambient environment. The term 'subaerial biofilm' (SAB) was coined for microbial communities that develop on solid mineral surfaces exposed to the atmosphere. Subaerial biofilms are ubiquitous, self-sufficient, miniature microbial ecosystems that are found on buildings, bare rocks in deserts, mountains, and at all latitudes where direct contact with the atmosphere and solar radiation occurs. Subaerial biofilms on exposed terrestrial surfaces are characterized by patchy growth that is dominated by associations of fungi, algae, cyanobacteria and heterotrophic bacteria. Inherent subaerial settlers include specialized actinobacteria (e.g. Geodermatophilus), cyanobacteria and microcolonial fungi. Individuals within SAB communities avoid sexual reproduction, but cooperate extensively with one another especially to avoid loss of energy and nutrients. Subaerial biofilm metabolic activity centres on retention of water, protecting the cells from fluctuating environmental conditions and solar radiation as well as prolonging their vegetative life. Atmospheric aerosols, gases and propagatory particles serve as sources of nutrients and inoculum for these open communities. Subaerial biofilms induce chemical and physical changes to rock materials, and they penetrate the mineral substrate contributing to rock and mineral decay, which manifests itself as bio-weathering of rock surfaces. Given their characteristic slow and sensitive growth, SAB may also serve as bioindicators of atmospheric and/or climate change.
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Affiliation(s)
- Anna A Gorbushina
- Geomicrobiology, ICBM, Carl von Ossietzky University, Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26111 Oldenburg, Germany.
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