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Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. mSystems 2023; 8:e0068823. [PMID: 37942948 PMCID: PMC10734470 DOI: 10.1128/msystems.00688-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/02/2023] [Indexed: 11/10/2023] Open
Abstract
IMPORTANCE To our knowledge, IL-10-KO mice have not previously been used to investigate the interactions of host, microbiota, and broccoli, broccoli sprouts, or broccoli bioactives in resolving symptoms of CD. We showed that a diet containing 10% raw broccoli sprouts increased the plasma concentration of the anti-inflammatory compound sulforaphane and protected mice to varying degrees against disease symptoms, including weight loss or stagnation, fecal blood, and diarrhea. Younger mice responded more strongly to the diet, further reducing symptoms, as well as increased gut bacterial richness, increased bacterial community similarity to each other, and more location-specific communities than older mice on the diet intervention. Crohn's disease disrupts the lives of patients and requires people to alter dietary and lifestyle habits to manage symptoms. The current medical treatment is expensive with significant side effects, and a dietary intervention represents an affordable, accessible, and simple strategy to reduce the burden of symptoms.
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Affiliation(s)
- Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Brigitte Lavoie
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA
| | - Jahnavi Pathak
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Gary M. Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
- Finch Therapeutics, Somerville, Massachusetts, USA
| | - Emma Perry
- Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Suzanne L. Ishaq
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
| | - Yanyan Li
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA
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Tichy J, Waldherr M, Ortbauer M, Graf A, Sipek B, Jembrih-Simbuerger D, Sterflinger K, Piñar G. Pretty in pink? Complementary strategies for analysing pink biofilms on historical buildings. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166737. [PMID: 37659529 DOI: 10.1016/j.scitotenv.2023.166737] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/21/2023] [Accepted: 08/30/2023] [Indexed: 09/04/2023]
Abstract
Salt-weathering is a deterioration mechanism affecting building materials that results from repetitive cycles of salt crystallisation-dissolution in the porous mineral network under changing environmental conditions, causing damage to surfaces. However, an additional biodeterioration phenomenon frequently associated with salt efflorescence is the appearance of coloured biofilms, comprising halotolerant/halophilic microorganisms, containing carotenoid pigments that cause pinkish patinas. In this work, two Austrian historical salt-weathered buildings showing pink biofilms, the St. Virgil's Chapel and the Charterhouse Mauerbach, were investigated. Substrate chemistry (salt concentration/composition) was analysed by ion chromatography and X-ray diffraction to correlate these parameters with the associated microorganisms. Microbiomes were analysed by sequencing full-length 16S rRNA amplicons using Nanopore technology. Data demonstrates that microbiomes are not only influenced by salt concentration, but also by its chemical composition. The chapel showed a high overall halite (NaCl) concentration, but the factor influencing the microbiome was the presence/absence of K+. The K+ areas showed a dominance of Aliifodinibius and Salinisphaera species, capable of tolerating high salt concentrations through the "salt-in" strategy by transporting K+ into cells. Conversely, areas without K+ showed a community shift towards Halomonas species, which favour the synthesis of compatible solutes for salt tolerance. In the charterhouse, the main salts were sulphates. In areas with low concentrations, Rubrobacter species dominated, while in areas with high concentrations, Haloechinothrix species did. Among archaea, Haloccoccus species were dominant in all samples, except at high sulphate concentrations, where Halalkalicoccus prevailed. Finally, the biological pigments visible in both buildings were analysed by Raman spectroscopy, showing the same spectra in all areas investigated, regardless of the building and the microbiomes, demonstrating the presence of carotenoids in the pink biofilms. Comprehensive information on the factors affecting the microbiome associated with salt-weathered buildings should provide the basis for selecting the most appropriate desalination treatment to remove both salt efflorescence and associated biofilms.
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Affiliation(s)
- Johannes Tichy
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria.
| | - Monika Waldherr
- Department of Applied Life Sciences/Bioengineering/Bioinformatics, FH Campus Wien, Favoritenstrasse 226, A-1100 Vienna, Austria
| | - Martin Ortbauer
- Institute for Conservation - Restoration, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Alexandra Graf
- Department of Applied Life Sciences/Bioengineering/Bioinformatics, FH Campus Wien, Favoritenstrasse 226, A-1100 Vienna, Austria
| | - Beate Sipek
- Institute for Conservation - Restoration, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Dubravka Jembrih-Simbuerger
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Katja Sterflinger
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
| | - Guadalupe Piñar
- Institute for Natural Sciences and Technology in the Art, Academy of Fine Arts Vienna, Schillerplatz 3, A-1010 Vienna, Austria
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Villar-dePablo M, Ascaso C, Rodríguez-Pérez E, Urizal M, Wierzchos J, Pérez-Ortega S, de Los Ríos A. Innovative approaches to accurately assess the effectiveness of biocide-based treatments to fight biodeterioration of Cultural Heritage monuments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 897:165318. [PMID: 37422225 DOI: 10.1016/j.scitotenv.2023.165318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 07/10/2023]
Abstract
The development of diagnostic methods to accurately assess the effects of treatments on lithobiont colonization remains a challenge for the conservation of Cultural Heritage monuments. In this study, we tested the efficacy of biocide-based treatments on microbial colonization of a dolostone quarry, in the short and long-term, using a dual analytical strategy. We applied a metabarcoding approach to characterize fungal and bacterial communities over time, integrated with microscopy techniques to analyze the interactions of microorganisms with the substrate and evaluate the effectiveness. These communities were dominated by the bacterial phyla Actinobacteriota, Proteobacteria and Cyanobacteria, and the fungal order Verrucariales, which include taxa previously reported as biodeteriogenic agents and observed here associated with biodeterioration processes. Following the treatments, changes over time in the abundance profiles depend on taxa. While Cyanobacteriales, Cytophagales and Verrucariales decreased in abundance, other groups, such as Solirubrobacteriales, Thermomicrobiales and Pleosporales increased. These patterns could be related not only to the specific effects of the biocide on the different taxa, but also to different recolonization abilities of those organisms. The different susceptibility to treatments could be associated with the inherent cellular properties of different taxa, but differences in biocide penetration to endolithic microhabitats could be involved. Our results demonstrate the importance of both removing epilithic colonization and applying biocides to act against endolithic forms. Recolonization processes could also explain some of the taxon-dependent responses, especially in the long-term. Taxa showing resistance, and those benefiting from nutrient accumulation in the form of cellular debris following treatments, may have an advantage in colonizing treated areas, pointing to the need for long-term monitoring of a wide range of taxa. This study highlights the potential utility of combining metabarcoding and microscopy to analyze the effects of treatments and design appropriate strategies to combat biodeterioration and establish preventive conservation protocols.
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Affiliation(s)
- Mar Villar-dePablo
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (CSIC), Serrano 115 dpdo., E-28006 Madrid, Spain
| | - Carmen Ascaso
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (CSIC), Serrano 115 dpdo., E-28006 Madrid, Spain
| | - Esther Rodríguez-Pérez
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (CSIC), Serrano 115 dpdo., E-28006 Madrid, Spain
| | | | - Jacek Wierzchos
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (CSIC), Serrano 115 dpdo., E-28006 Madrid, Spain
| | - Sergio Pérez-Ortega
- Department of Mycology, Real Jardín Botánico (CSIC), Plaza Murillo 2, E-28014 Madrid, Spain
| | - Asunción de Los Ríos
- Biogeochemistry and Microbial Ecology Department, Museo Nacional de Ciencias Naturales (CSIC), Serrano 115 dpdo., E-28006 Madrid, Spain.
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Holcomb L, Holman JM, Hurd M, Lavoie B, Colucci L, Hunt B, Hunt T, Kinney M, Pathak J, Mawe GM, Moses PL, Perry E, Stratigakis A, Zhang T, Chen G, Ishaq SL, Li Y. Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525953. [PMID: 36747766 PMCID: PMC9900910 DOI: 10.1101/2023.01.27.525953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Crohn's Disease (CD) is a presentation of Inflammatory Bowel Disease (IBD) that manifests in childhood and adolescence, and involves chronic and severe enterocolitis, immune and gut microbiome dysregulation, and other complications. Diet and gut-microbiota-produced metabolites are sources of anti-inflammatories which could ameliorate symptoms. However, questions remain on how IBD influences biogeographic patterns of microbial location and function in the gut, how early life transitional gut communities are affected by IBD and diet interventions, and how disruption to biogeography alters disease mediation by diet components or microbial metabolites. Many studies on diet and IBD use a chemically induced ulcerative colitis model, despite the availability of an immune-modulated CD model. Interleukin-10-knockout (IL-10-KO) mice on a C57BL/6 background, beginning at age 4 or 7 weeks, were fed a control diet or one containing 10% (w/w) raw broccoli sprouts, which was high in the sprout-sourced anti-inflammatory sulforaphane. Diets began 7 days prior to, and for 2 weeks after inoculation with Helicobacter hepaticus, which triggers Crohn's-like symptoms in these immune-impaired mice. The broccoli sprout diet increased sulforaphane in plasma; decreased weight stagnation, fecal blood, and diarrhea associated; and increased microbiota richness in the gut, especially in younger mice. Sprout diets resulted in some anatomically specific bacteria in younger mice, and reduced the prevalence and abundance of pathobiont bacteria which trigger inflammation in the IL-10-KO mouse, for example; Escherichia coli and Helicobacter. Overall, the IL-10-KO mouse model is responsive to a raw broccoli sprout diet and represents an opportunity for more diet-host-microbiome research.
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Affiliation(s)
- Lola Holcomb
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Johanna M. Holman
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Molly Hurd
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Brigitte Lavoie
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Louisa Colucci
- Department of Biology, Husson University, Bangor, Maine, USA 04401
| | - Benjamin Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Timothy Hunt
- Department of Biology, University of Maine, Orono, Maine, USA 04469
| | - Marissa Kinney
- School of Food and Agriculture, University of Maine, Orono, Maine, USA 04469
| | - Jahnavi Pathak
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Gary M. Mawe
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
| | - Peter L. Moses
- Larner College of Medicine, University of Vermont, Burlington, Vermont, USA 05401
- Finch Therapeutics, Somerville, Massachusetts, USA 02143
| | - Emma Perry
- Electron Microscopy Laboratory, University of Maine, Orono, Maine, USA 04469
| | - Allesandra Stratigakis
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Tao Zhang
- School of Pharmacy and Pharmaceutical Sciences, SUNY Binghamton University, Johnson City, New York, USA 13790
| | - Grace Chen
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA 48109
| | - Suzanne L. Ishaq
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
| | - Yanyan Li
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, Maine, USA 04469
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Genomic microbiome analyses of surface sand samples from the Kyzyl-Kum Desert (Uzbekistan): characterization and comparative study. Arch Microbiol 2023; 205:90. [PMID: 36780035 DOI: 10.1007/s00203-023-03432-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
The Kyzyl-Kum Desert extends over an area of 300,000 Km2, in the region bordering Kazakhstan, Uzbekistan and Turkmenistan and is mainly covered by sand dunes. The Kyzyl-Kum desert is also known for its large deposits of minerals of economic interests, the exploitation of which is affecting the local ecosystem and increasing the desertification. We examined the bacterial biodiversity of surface sand samples from several sites from the Kyzyl-Kum desert using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. We also examined several physicochemical parameters of the sand samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant genera in our samples were found to belong to the Arthrobacter, Adhaeribacter and Roseomonas genera. We found that the relative abundance of members belonging to the Actinobacteria phylum, commonly found in desertic areas, increase in abundance in sites with higher content of organic matter and sulfur, whereas members of the Proteobacteria and Bacteroidetes phyla seems to diminish in abundance in coarse silt and fine-grained soils and those rich in magnesium, suggesting that those parameters might influence the bacterial community composition in this desertic area. This study is the first to provide new insights into the prokaryotic community composition from this unusual desert site.
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A Multi-Analytical Approach to Infer Mineral–Microbial Interactions Applied to Petroglyph Sites in the Negev Desert of Israel. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Petroglyph sites exist all over the world. They are one of the earliest forms of mankind’s expression and a precursor to art. Despite their outstanding value, comprehensive research on conservation and preservation of rock art is minimal, especially as related to biodeterioration. For this reason, the main objective of this study was to explore the factors involved in the degradation of petroglyph sites in the Negev desert of Israel, with a focus on biodegradation processes. Through the use of culture-independent microbiological methods (metagenomics), we characterized the microbiomes of the samples, finding they were dominated by bacterial communities, in particular taxa of Actinobacteria and Cyanobacteria, with resistance to radiation and desiccation. By means of XRF and Raman spectroscopies, we defined the composition of the stone (calcite and quartz) and the dark crust (clay minerals with Mn and Fe oxides), unveiling the presence of carotenoids, indicative of biological colonization. Optical microscopy and SEM–EDX analyses on thin sections highlighted patterns of weathering, possibly connected to the presence of biodeteriorative microorganisms that leach the calcareous matrix from the bedrock and mobilize metal cations from the black varnish for metabolic processes, slowly weathering it.
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Gonzalez-Pimentel JL, Hermosin B, Saiz-Jimenez C, Jurado V. Streptomyces benahoarensis sp. nov. Isolated From a Lava Tube of La Palma, Canary Islands, Spain. Front Microbiol 2022; 13:907816. [PMID: 35651486 PMCID: PMC9149447 DOI: 10.3389/fmicb.2022.907816] [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] [Received: 03/30/2022] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
Two Streptomyces strains, labeled as MZ03-37T and MZ03-48, were isolated from two different samples, a mucolite-type speleothem and a microbial mat on the walls of a lava tube from La Palma Island (Canary Islands). Phylogenetic analysis based on concatenated sequences of six housekeeping genes indicated that both strains belonged to the same species. The closest relatives for both strains were Streptomyces palmae CMU-AB204T (98.71%), Streptomyces catenulae NRRL B-2342T (98.35%), and Streptomyces ramulosus NRRL B-2714T (98.35%). Multi-locus sequence analysis (MLSA), based on five house-keeping gene alleles (i.e., atpD, gyrB, recA, rpoB, and trpB), indicated that both isolated strains were closely related to S. catenulae NRRL B-2342T. Whole-genome average nucleotide identity (ANI) scores of both strains were in the threshold value for species delineation with the closest species. Both strains presented a G+C content of 72.1 mol%. MZ03-37T was light brown in substrate and white in aerial mycelium, whereas MZ03-48 developed a black aerial and substrate mycelium. No pigment diffusion was observed in both strains. They grew at 10°C-37°C (optimum 28°C-32°C) and in the presence of up to 15% (w/v) NaCl. MZ03-37T grew at pH 5-10 (optimal 6-9), whereas MZ03-48 grew at pH 4-11 (optimal 5-10). LL-Diaminopimelic acid was the main diamino acid identified. The predominant fatty acids in both strains were iso-C16:0, anteiso-C15:0, C16:0, and iso-C14:0. The major isoprenoid quinones were MK-9(H6) and MK-9(H8), and the main polar lipids were aminolipid, phospholipid, and phosphoglycolipid. In silico analyses for functional annotation predicted the presence of gene clusters involved in resistome mechanisms and in the synthesis of described antimicrobials such as linocin-M18 and curamycin, as well as different genes likely involved in mechanisms for active compound synthesis, both already described and not discovered so far. On the basis of their phylogenetic relatedness and their phenotypic and genotypic features, the strains MZ03-37T and MZ03-48 represented a novel species within the genus Streptomyces, for which the name Streptomyces benahoarensis sp. nov. is proposed. The type strain is MZ03-37T (= CECT 9805 = DSMZ 8002); and MZ03-48 (= CECT 9806 = DSMZ 8011) is a reference strain.
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Affiliation(s)
| | - Bernardo Hermosin
- Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas (IRNAS-CSIC), Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas (IRNAS-CSIC), Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, Consejo Superior de Investigaciones Cientificas (IRNAS-CSIC), Sevilla, Spain
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Pavlović J, Bosch-Roig P, Rusková M, Planý M, Pangallo D, Sanmartín P. Long-amplicon MinION-based sequencing study in a salt-contaminated twelfth century granite-built chapel. Appl Microbiol Biotechnol 2022; 106:4297-4314. [PMID: 35596787 PMCID: PMC9200699 DOI: 10.1007/s00253-022-11961-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/14/2022] [Accepted: 05/02/2022] [Indexed: 11/30/2022]
Abstract
Abstract
The irregular damp dark staining on the stonework of a salt-contaminated twelfth century granite-built chapel is thought to be related to a non-homogeneous distribution of salts and microbial communities. To enhance understanding of the role of microorganisms in the presence of salt and damp stains, we determined the salt content and identified the microbial ecosystem in several paving slabs and inner wall slabs (untreated and previously bio-desalinated) and in the exterior surrounding soil. Soluble salt analysis and culture-dependent approaches combined with archaeal and bacterial 16S rRNA and fungal ITS fragment as well as with the functional genes nirK, dsr, and soxB long-amplicon MinION-based sequencing were performed. State-of-the-art technology was used for microbial identification, providing information about the microbial diversity and phylogenetic groups present and enabling us to gain some insight into the biological cycles occurring in the community key genes involved in the different geomicrobiological cycles. A well-defined relationship between microbial data and soluble salts was identified, suggesting that poorly soluble salts (CaSO4) could fill the pores in the stone and lead to condensation and dissolution of highly soluble salts (Ca(NO3)2 and Mg(NO3)2) in the thin layer of water formed on the stonework. By contrast, no direct relationship between the damp staining and the salt content or related microbiota was established. Further analysis regarding organic matter and recalcitrant elements in the stonework should be carried out. Key points
• Poorly (CaSO4) and highly (Ca(NO3)2, Mg(NO3)2) soluble salts were detected • Halophilic and mineral weathering microorganisms reveal ecological impacts of salts • Microbial communities involved in nitrate and sulfate cycles were detected Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11961-8.
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Affiliation(s)
- Jelena Pavlović
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Pilar Bosch-Roig
- Instituto Universitario de Restauración del Patrimonio, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Magdalena Rusková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Matej Planý
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia
| | - Domenico Pangallo
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51, Bratislava, Slovakia.,Caravella, s.r.o., Tupolevova 2, 851 01, Bratislava, Slovakia
| | - Patricia Sanmartín
- Departamento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain. .,CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain.
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Iquebal MA, Passari AK, Jagannadham J, Ahmad F, Leo VV, Singh G, Jaiswal S, Rai A, Kumar D, Singh BP. Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens. Genomics 2021; 113:4098-4108. [PMID: 34699904 DOI: 10.1016/j.ygeno.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
Pukzing cave, the largest cave of Mizoram, India was explored for bacterial diversity. Culture dependent method revealed 235 bacterial isolates using three different treatments. Identity of the microbial species was confirmed by 16S rDNA sequencing. The highest bacterial population was recovered from heat treatment (n = 97;41.2%) followed by normal (n = 79;33.6%) and cold treatment (n = 59;25.1%) indicating dominance of moderate thermophiles. Antimicrobial potential of isolates showed 20.4% isolates having antimicrobial ability against tested pathogens. Amplicon sequencing of PKSI, PKSII and NRP specific genes revealed presence of AMP genes in the microbial population. Six microbial pathogens were selected for screening as they are well known for different disease cause organism in various fields such as agriculture and human health. Cave environment harbors unique microbial flora and hypervariable region V4 is more informative. Higher activity of AMP assay against these microbes indicates that cave microbial communities could be potential source of future genomic resources.
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Affiliation(s)
- M A Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajit Kumar Passari
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India; Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico 04510, Mexico
| | - Jaisri Jagannadham
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Farzana Ahmad
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India
| | | | - Garima Singh
- Department of Botany, Pachhunga University College, Mizoram University, Aizawl 796001, Mizoram, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
| | - Bhim Pratap Singh
- Department of Biotechnology, Aizawl, Mizoram University, Mizoram, India; Department of Agriculture and Environmental Sciences, National Institute of Food Technology Entrepreneurship and Management (NIFTEM), Kundli, Sonipat 131028, Haryana, India.
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Huang T, Liu W, Long XE, Jia Y, Wang X, Chen Y. Different Responses of Soil Bacterial Communities to Nitrogen Addition in Moss Crust. Front Microbiol 2021; 12:665975. [PMID: 34566900 PMCID: PMC8460773 DOI: 10.3389/fmicb.2021.665975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/16/2021] [Indexed: 11/21/2022] Open
Abstract
Bacterial communities in soil serve an important role in controlling terrestrial biogeochemical cycles and ecosystem processes. Increased nitrogen (N) deposition in Northwest China is generating quantifiable changes in many elements of the desert environment, but the impacts of N deposition, as well as seasonal variations, on soil bacterial community composition and structure are poorly understood. We used high-throughput sequencing of bacterial 16S rRNA genes from Gurbantünggüt Desert moss crust soils to study the impacts of N addition on soil bacterial communities in March, May, and November. In November, we discovered that the OTU richness and diversity of soil bacterial community dropped linearly with increasing N input. In November and March, the diversity of the soil bacterial community decreased significantly in the medium-N and high-N treatments. In May, N addition caused a substantial change in the makeup of the soil bacterial composition, while the impacts were far less apparent in November and March. Furthermore, the relative abundance of major bacterial phyla reacted non-linearly to N addition, with high-N additions decreasing the relative richness of Proteobacteria, Bacteroidetes, and Acidobacteria while increasing the relative abundance of Actinobacteria and Chloroflexi. We also discovered that seasonality, as characterized by changes in soil moisture, pH, SOC, and AK content, had a significant impact on soil bacterial communities. Significant variations in the makeup of the community were discovered at the phylum and genus levels throughout the various months. In May, the variety of soil bacterial community was at its peak. Further investigation showed that the decrease in soil bacterial diversity was mostly attributed to a drop in soil pH. These results indicated that the impact of N deposition on the soil bacterial community was seasonally dependent, suggesting that future research should evaluate more than one sample season at the same time.
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Affiliation(s)
- Tingwen Huang
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Weiguo Liu
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Xi-En Long
- School of Geographic Sciences, Nantong University, Nantong, China
| | - Yangyang Jia
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Xiyuan Wang
- Ministry of Education, Key Laboratory of Oasis Ecology, College of Resources and Environment Science, Xinjiang University, Urumqi, China
| | - Yinguang Chen
- College of Environmental Science and Engineering, Tongji University, Shanghai, China
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11
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Role of Exposure on the Microbial Consortiums on Historical Rural Granite Buildings. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11093786] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Local granite has been used throughout history in Galicia (NW Spain), forming the basis of much of the region’s architecture. Like any other rock, granite provides an ecological niche for a multitude of organisms that form biofilms that can affect the physical integrity of the stone. In this study, for the first time, characterization of the microbial consortium forming biofilms that developed on historical rural granite buildings is carried out using a combination of culture-dependent and next generation sequencing (NGS) techniques. Results pointed to differences in biofilm composition on the studied rural granite buildings and that of previously analyzed urban granite buildings, especially in terms of abundance of cyanobacteria and lichenized fungi. Exposure was corroborated as an important factor, controlling both the diversity and abundance of microorganisms on walls, with environmental factors associated with a northern orientation favoring a higher diversity of fungi and green algae, and environmental factors associated with the west orientation determining the abundance of lichenized fungi. The orientation also affected the distribution of green algae, with one of the two most abundant species, Trentepohlia cf. umbrina, colonizing north-facing walls, while the other, Desmococcus olivaceus, predominated on west-facing walls.
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12
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Bacterial and Archaeal Structural Diversity in Several Biodeterioration Patterns on the Limestone Walls of the Old Cathedral of Coimbra. Microorganisms 2021; 9:microorganisms9040709. [PMID: 33808176 PMCID: PMC8065406 DOI: 10.3390/microorganisms9040709] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/24/2021] [Accepted: 03/26/2021] [Indexed: 11/25/2022] Open
Abstract
The “University of Coimbra-Alta and Sofia” area was awarded the UNESCO World Heritage Site distinction in 2013. The Old Cathedral of Coimbra, a 12th-century limestone monument located in this area, has been significantly impacted during the last 800 years by physical, chemical, and biological processes. This led to the significant deterioration of some of its structures and carvings, with loss of aesthetical, cultural, and historical values. For this work, deteriorated spots of the walls of three semi-open chapels from the cloister of the Cathedral were sampled to ascertain their bacterial and archaeal structural diversity. Based on Next-Generation Sequencing (NGS) result analysis, we report the presence of microbial populations that are well adapted to an ecosystem with harsh conditions and that can establish a diverse biofilm in most cases. While it was possible to determine dominant phylogenetic groups in Archaea and Bacteria domains, there was no clear connection between specific core microbiomes and the different deterioration patterns analyzed. The distribution of these archaeal and bacterial communities within the analyzed biodeterioration spots suggests they are more influenced by abiotic factors (i.e., water availability, salinity, etc.), although they influence (and are influenced by) the algal and fungal population composition in this ecosystem. This work provides valuable information that can assist in establishing future guidelines for the preservation and conservation of this kind of historic stone monuments.
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13
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Genderjahn S, Lewin S, Horn F, Schleicher AM, Mangelsdorf K, Wagner D. Living Lithic and Sublithic Bacterial Communities in Namibian Drylands. Microorganisms 2021; 9:235. [PMID: 33498742 PMCID: PMC7911874 DOI: 10.3390/microorganisms9020235] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/17/2021] [Accepted: 01/20/2021] [Indexed: 12/26/2022] Open
Abstract
Dryland xeric conditions exert a deterministic effect on microbial communities, forcing life into refuge niches. Deposited rocks can form a lithic niche for microorganisms in desert regions. Mineral weathering is a key process in soil formation and the importance of microbial-driven mineral weathering for nutrient extraction is increasingly accepted. Advances in geobiology provide insight into the interactions between microorganisms and minerals that play an important role in weathering processes. In this study, we present the examination of the microbial diversity in dryland rocks from the Tsauchab River banks in Namibia. We paired culture-independent 16S rRNA gene amplicon sequencing with culture-dependent (isolation of bacteria) techniques to assess the community structure and diversity patterns. Bacteria isolated from dryland rocks are typical of xeric environments and are described as being involved in rock weathering processes. For the first time, we extracted extra- and intracellular DNA from rocks to enhance our understanding of potentially rock-weathering microorganisms. We compared the microbial community structure in different rock types (limestone, quartz-rich sandstone and quartz-rich shale) with adjacent soils below the rocks. Our results indicate differences in the living lithic and sublithic microbial communities.
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Affiliation(s)
- Steffi Genderjahn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Simon Lewin
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Fabian Horn
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
| | - Anja M. Schleicher
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, Telegrafenberg, 14473 Potsdam, Germany;
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Anorganic Chemistry, Telegrafenberg, 14473 Potsdam, Germany;
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (S.L.); (F.H.); (D.W.)
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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14
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Jroundi F, Elert K, Ruiz-Agudo E, Gonzalez-Muñoz MT, Rodriguez-Navarro C. Bacterial Diversity Evolution in Maya Plaster and Stone Following a Bio-Conservation Treatment. Front Microbiol 2020; 11:599144. [PMID: 33240254 PMCID: PMC7680763 DOI: 10.3389/fmicb.2020.599144] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
To overcome the limitations of traditional conservation treatments used for protection and consolidation of stone and lime mortars and plasters, mostly based on polymers or alkoxysilanes, a novel treatment based on the activation of indigenous carbonatogenic bacteria has been recently proposed and applied both in the laboratory and in situ. Despite very positive results, little is known regarding its effect on the evolution of the indigenous bacterial communities, specially under hot and humid tropical conditions where proliferation of microorganisms is favored, as it is the case of the Maya area. Here, we studied changes in bacterial diversity of severely degraded tuff stone and lime plaster at the archeological Maya site of Copan (Honduras) after treatment with the patented sterile M-3P nutritional solution. High-throughput sequencing by Illumina MiSeq technology shows significant changes in the bacterial population of the treated stones, enhancing the development of Arthrobacter, Micrococcaceae, Nocardioides, Fictibacillus, and Streptomyces, and, in one case, Rubrobacter (carved stone blocks at Structure 18). In the lime plaster, Arthrobacter, Fictibacillus, Bacillus, Agrococcus, and Microbacterium dominated after treatment. Most of these detected genera have been shown to promote calcium carbonate biomineralization, thus implying that the novel bio-conservation treatment would be effective. Remarkably, the treatment induced the reduction or complete disappearance of deleterious acid-producing bacteria such as Marmoricola or the phylum Acidobacteria. The outcome of this study demonstrates that such a bio-conservation treatment can safely and effectively be applied on temples, sculptures and stuccos of the Maya area and, likely, in other hot and humid environments.
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Affiliation(s)
- Fadwa Jroundi
- Department of Microbiology, University of Granada, Granada, Spain
| | - Kerstin Elert
- Department of Mineralogy and Petrology, University of Granada, Granada, Spain
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15
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Schröer L, De Kock T, Cnudde V, Boon N. Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139339. [PMID: 32446079 DOI: 10.1016/j.scitotenv.2020.139339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 06/11/2023]
Abstract
Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.
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Affiliation(s)
- Laurenz Schröer
- PProGRess, Department of Geology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium; Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Tim De Kock
- PProGRess, Department of Geology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium; Antwerp Cultural Heritage Sciences (ARCHES), University of Antwerp, Mutsaardstraat 31, 2000 Antwerp, Belgium.
| | - Veerle Cnudde
- PProGRess, Department of Geology, Ghent University, Krijgslaan 281 S8, 9000 Ghent, Belgium; Environmental Hydrogeology, Department of Earth Sciences, Utrecht University, Princetonlaan 8a, 3584 Utrecht, the Netherlands.
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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16
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Li J, Zhang X, Xiao L, Liu K, Li Y, Zhang Z, Chen Q, Ao X, Liao D, Gu Y, Ma M, Yu X, Xiang Q, Chen J, Zhang X, Yang T, Penttinen P, Zhao K. Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration. BMC Microbiol 2020; 20:147. [PMID: 32503433 PMCID: PMC7275329 DOI: 10.1186/s12866-020-01836-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 06/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the microbial communities and their correlation with environmental factors, and to compare microbial community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa. RESULTS The relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-. CONCLUSION The microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.
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Affiliation(s)
- Jing Li
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Xiaoyue Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Lin Xiao
- Chengdu Institute of Cultural Relics and Archaeology, Chengdu, 610072, Sichuan, China
| | - Ke Liu
- Jinsha site museum, Chengdu, Sichuan, 610072, PR China
| | - Yue Li
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Ziwei Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Qiang Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Xiaolin Ao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Decong Liao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Yunfu Gu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Menggen Ma
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Xiumei Yu
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Quanju Xiang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Ji Chen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China
| | - Tao Yang
- Chengdu Institute of Cultural Relics and Archaeology, Chengdu, 610072, Sichuan, China
| | - Petri Penttinen
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China.
| | - Ke Zhao
- Department of Microbiology, College of Resources, Sichuan Agricultural University, Yaan, 625000, PR China.
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17
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Rosado T, Dias L, Lança M, Nogueira C, Santos R, Martins MR, Candeias A, Mirão J, Caldeira AT. Assessment of microbiota present on a Portuguese historical stone convent using high-throughput sequencing approaches. Microbiologyopen 2020; 9:1067-1084. [PMID: 32352657 PMCID: PMC7294311 DOI: 10.1002/mbo3.1030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/20/2022] Open
Abstract
The study performed on the stone materials from the Convent of Christ revealed the presence of a complex microbial ecosystem, emphasizing the determinant role of microorganisms on the biodecay of this built cultural heritage. In this case study, the presence of Rubrobacter sp., Arthrobacter sp., Roseomonas sp., and Marinobacter sp. seems to be responsible for colored stains and biofilm formation while Ulocladium sp., Cladosporium sp., and Dirina sp. may be related to structural damages. The implementation of high-throughput sequencing approaches on the Convent of Christ's biodecay assessment allowed us to explore, compare, and characterize the microbial communities, overcoming the limitations of culture-dependent techniques, which only identify the cultivable population. The application of these different tools and insights gave us a panoramic view of the microbiota thriving on the Convent of Christ and signalize the main biodeteriogenic agents acting on the biodecay of stone materials. This finding highlighted the importance of performing metagenomic studies due to the improvements and the reduced amount of sample DNA needed, promoting a deeper and more detailed knowledge of the microbiota present on these dynamic repositories that support microbial life. This will further enable us to perform prospective studies in quarry and applied stone context, monitoring biogenic and nonbiogenic agents, and also to define long-term mitigation strategies to prevent biodegradation/biodeterioration processes.
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Affiliation(s)
- Tânia Rosado
- HERCULES Laboratory, Évora University, Évora, Portugal
| | - Luís Dias
- HERCULES Laboratory, Évora University, Évora, Portugal.,Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - Mónica Lança
- Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - Carla Nogueira
- Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - Rita Santos
- Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - Maria Rosário Martins
- HERCULES Laboratory, Évora University, Évora, Portugal.,Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - António Candeias
- HERCULES Laboratory, Évora University, Évora, Portugal.,Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - José Mirão
- HERCULES Laboratory, Évora University, Évora, Portugal.,Geosciences Department, School of Sciences and Technology, Évora University, Évora, Portugal
| | - Ana Teresa Caldeira
- HERCULES Laboratory, Évora University, Évora, Portugal.,Chemistry Department, School of Sciences and Technology, Évora University, Évora, Portugal
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18
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Vilanova C, Porcar M. Art-omics: multi-omics meet archaeology and art conservation. Microb Biotechnol 2020; 13:435-441. [PMID: 31452355 PMCID: PMC7017809 DOI: 10.1111/1751-7915.13480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 08/10/2019] [Indexed: 11/30/2022] Open
Abstract
Multi-omics can informally be described as the combined use of high-throughput techniques allowing the characterization of complete microbial communities by the sequencing/identification of total pools of biomolecules including DNA, proteins or metabolites. These techniques have allowed an unprecedented level of knowledge on complex microbial ecosystems, which is having key implications in land and marine ecology, industrial biotechnology or biomedicine. Multi-omics have recently been applied to artistic or archaeological objects, with the goal of either contributing to shedding light on the original context of the pieces and/or to inform conservation approaches. In this minireview, we discuss the application of -omic techniques to the study of prehistoric artworks and ancient man-made objects in three main technical blocks: metagenomics, proteomics and metabolomics. In particular, we will focus on how proteomics and metabolomics can provide paradigm-breaking results by unambiguously identifying peptides associated with a given, palaeo-cultural context; and we will discuss how metagenomics can be central for the identification of the microbial keyplayers on artworks surfaces, whose conservation can then be approached by a range of techniques, including using selected microorganisms as 'probiotics' because of their direct or indirect effect in the stabilization and preservation of valuable art objects.
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Affiliation(s)
- Cristina Vilanova
- Darwin Bioprospecting Excellence SLCatedrático Agustín Escardino, 946980PaternaSpain
| | - Manuel Porcar
- Darwin Bioprospecting Excellence SLCatedrático Agustín Escardino, 946980PaternaSpain
- Institute for Integrative Systems BiologyISysBio (Universitat de València‐CSIC)Parc Científic de la Universitat de ValènciaC. Catedràtic José Beltrán 246980PaternaSpain
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19
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Mihajlovski A, Lepinay C, Mirval AL, Touron S, Bousta F, Di Martino P. Characterization of the archaeal and fungal diversity associated with gypsum efflorescences on the walls of the decorated Sorcerer’s prehistoric cave. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-019-01506-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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20
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Analysis of Soil Properties, Bacterial Community Composition, and Metabolic Diversity in Fluvisols of a Floodplain Area. SUSTAINABILITY 2019. [DOI: 10.3390/su11143929] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The quality of a soil environment affects the microbial community that inhabits it. We decided to examine whether soils formed from river sediments, located in an area of high biodiversity of organisms, are fertile and microbiologically diverse. Fluvisols are considered to be one of the most fertile soils. In this research, bacterial and metabolic diversity, as well as physico–chemical parameters, in three Fluvisols from the Vistula River Gorge of Lesser Poland was investigated. The analysis of physico–chemical and biological parameters demonstrated statistically significant differences between the three Fluvisols examined. While determining the metabolic potential of soil microbiomes with the use of the EcoPlate™ Biolog® technique, we also noted variation between the Fluvisols; however, they were arranged in a significantly different manner from other properties. The next generation sequencing method enabled us to determine the microorganisms common to three Fluvisols, and we identified bacteria specific to individual soils. These results corresponded with the data obtained through EcoPlate™, indicating that the structural diversity and metabolic potential of the microbiome does not always depend on soil quality parameters. Meanwhile, the increased structural diversity of the microbiome was found to improve the metabolic potential of soil microorganisms.
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21
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Cantisani E, Cuzman OA, Vettori S, Chelazzi L, Ciattini S, Ricci M, Manganelli Del Fá R, Chiarantini L, Garzonio CA. A multi-analytical approach for the study of red stains on heritage marble. Analyst 2019; 144:2375-2386. [PMID: 30801083 DOI: 10.1039/c8an02426j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Red stains are a common discolouration on stone cultural heritage all over the world. These are very difficult to remove and little is known about the reddish pigmentation. Numerous red stains were mapped on the Baptistery of San Giovanni in Florence, one of the most important monuments in Italy. This paper is focused on red stains on marble stone and the results of a detailed multidisciplinary approach are presented. Several analytical and investigation techniques (such as optical microscopy, X-ray fluorescence mapping, X-ray micro-tomography, micro-Raman spectroscopy, scanning electron microscopy with energy dispersive spectroscopy, microbial isolation, colorimetric measurements and isotopic analyses) were used to better understand the origin and processes involved in this kind of alteration. Analyses of the red stains led us to believe the presence of minium (lead tetroxide) and Pb are usually concentrated in the spaces between calcite grains. Red stains of Pb isotopic composition also overlap with data from Sardinian mines. These preliminary data seem to reinforce the suggestion of a source of lead from some metallic items (during restoration campaigns between 1938 and 1944, damaged parts were removed and replaced, and the new marble cladding was fixed with iron brackets treated with minium).
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Affiliation(s)
- Emma Cantisani
- Institute for Conservation and Valorization of Cultural Heritage (ICVBC) - National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino - Florence, Italy.
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22
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Arias D, Cisternas LA, Miranda C, Rivas M. Bioprospecting of Ureolytic Bacteria From Laguna Salada for Biomineralization Applications. Front Bioeng Biotechnol 2019; 6:209. [PMID: 30713841 PMCID: PMC6345690 DOI: 10.3389/fbioe.2018.00209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 12/18/2018] [Indexed: 11/22/2022] Open
Abstract
The processes of biomineralization, mediated by ureolytic bacteria, possess a wide range of technological applications, such as the formation of biocements and remediation of water and soil environments. For this reason, the bioprospecting of new ureolytic bacteria is interesting for its application to these technologies, particularly for water treatment. This study demonstrates the isolation, selection, and identification of halotolerant ureolytic bacteria from Laguna Salada (inland from Atacama Desert) and the evaluation of their ability to precipitate calcium carbonate crystals in freshwater in the presence of calcium ions, as well as the ability to induce the precipitation of crystals from different ions present in seawater. Twenty-four halotolerant ureolytic bacteria whose molecular identification gives between 99 and 100% identity with species of the genus Bacillus, Porphyrobacter, Pseudomonas, Salinivibrio, and Halomonas were isolated. When cultivated in freshwater, urea, and calcium chloride, all species are able to biomineralize calcium carbonate in different concentrations. In seawater, the strains that biomineralize the highest concentration of calcium carbonate correspond to Bacillus subtilis and Halomonas sp. SEM–EDX and XRD analyses determined that both bacteria induce the formation of 9–33% halite (NaCl), 31–66% monohydrocalcite (CaCO3 × H2O), and 24–27% struvite (MgNH4PO4 × 6H2O). Additionally, B.subtilis induces the formation of 7% anhydrite (CaSO4). In seawater, B.subtilis and Halomonas sp. were able to precipitate both calcium (96–97%) and magnesium (63–67%) ions over 14 days of testing. Ion removal assays with B.subtilis immobilized in beads indicate a direct relationship between the urea concentration and a greater removal of ions with similar rates to free cells. These results demonstrate that the biomineralization mediated by bacterial urea hydrolysis is feasible in both freshwater and seawater, and we propose its application as a new technology in improving water quality for industrial uses.
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Affiliation(s)
- Dayana Arias
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Antofagasta, Chile.,Laboratorio de Biotecnología Algal y Sustentabilidad (BIOAL), Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Luis A Cisternas
- Departamento de Ingeniería Química y Procesos de Minerales, Universidad de Antofagasta, Antofagasta, Chile.,Centro de Investigación Científico Tecnológico Para la Minería, Antofagasta, Chile
| | - Carol Miranda
- Laboratorio de Biotecnología Algal y Sustentabilidad (BIOAL), Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Mariella Rivas
- Laboratorio de Biotecnología Algal y Sustentabilidad (BIOAL), Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Centro de Investigación Científico Tecnológico Para la Minería, Antofagasta, Chile
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Dominguez-Moñino I, Jurado V, Gonzalez-Pimentel JL, Miller AZ, Hermosin B, Saiz-Jimenez C. Bacillus onubensis sp. nov., isolated from the air of two Andalusian caves. Syst Appl Microbiol 2018; 41:167-172. [DOI: 10.1016/j.syapm.2018.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/29/2017] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
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Adamiak J, Bonifay V, Otlewska A, Sunner JA, Beech IB, Stryszewska T, Kańka S, Oracz J, Żyżelewicz D, Gutarowska B. Untargeted Metabolomics Approach in Halophiles: Understanding the Biodeterioration Process of Building Materials. Front Microbiol 2017; 8:2448. [PMID: 29321766 PMCID: PMC5732225 DOI: 10.3389/fmicb.2017.02448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/24/2017] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to explore the halophile metabolome in building materials using untargeted metabolomics which allows for broad metabolome coverage. For this reason, we used high-performance liquid chromatography interfaced to high-resolution mass spectrometry (HPLC/HRMS). As an alternative to standard microscopy techniques, we introduced pioneering Coherent Anti-stokes Raman Scattering Microscopy (CARS) to non-invasively visualize microbial cells. Brick samples saturated with salt solution (KCl, NaCl (two salinity levels), MgSO4, Mg(NO3)2), were inoculated with the mixture of preselected halophilic microorganisms, i.e., bacteria: Halobacillus styriensis, Halobacillus naozhouensis, Halobacillus hunanensis, Staphylococcus succinus, Marinococcus halophilus, Virgibacillus halodenitryficans, and yeast: Sterigmatomyces halophilus and stored at 28°C and 80% relative humidity for a year. Metabolites were extracted directly from the brick samples and measured via HPLC/HRMS in both positive and negative ion modes. Overall, untargeted metabolomics allowed for discovering the interactions of halophilic microorganisms with buildings materials which together with CARS microscopy enabled us to elucidate the biodeterioration process caused by halophiles. We observed that halophile metabolome was differently affected by different salt solutions. Furthermore, we found indications for haloadaptive strategies and degradation of brick samples due to microbial pigment production as a salt stress response. Finally, we detected changes in lipid content related to changes in the structure of phospholipid bilayers and membrane fluidity.
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Affiliation(s)
- Justyna Adamiak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Jan A. Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Iwona B. Beech
- Center of Biofilm Engineering, Department of Chemical and Biochemical Engineering, Montana State University, Bozeman, MT, United States
| | - Teresa Stryszewska
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology, Cracow, Poland
| | - Stanisław Kańka
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology, Cracow, Poland
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Dorota Żyżelewicz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Beata Gutarowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
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Dominguez-Moñino I, Diaz-Herraiz M, Jurado V, Laiz L, Miller AZ, Santos JL, Alonso E, Saiz-Jimenez C. Nature and origin of the violet stains on the walls of a Roman tomb. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 598:889-899. [PMID: 28458206 DOI: 10.1016/j.scitotenv.2017.04.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/03/2017] [Accepted: 04/04/2017] [Indexed: 06/07/2023]
Abstract
The Circular Mausoleum tomb (Roman Necropolis of Carmona, Spain) dates back from the first century AD and is characterized by a dense microbial (phototrophic) colonization on the walls and ceiling. However, some walls exhibited an important number of violet stains of unknown origin. The microbial communities of these violet stains are mainly composed of cyanobacteria, streptomycetes and fungi. A strain of Streptomyces parvus, isolated from the walls, produces a violet pigment in culture media. High performance liquid chromatography-mass spectrometry of the culture extracts obtained from this Streptomyces revealed the presence of a few granaticins, pigments with a benzoisochromanequinone structure. When metabolically active in the tomb, S. parvus synthesizes the pigments that diffuse into the mortar. During rain and/or wetting periods, the pigments are solubilized by alkaline waters and elute from the starting position to the surrounding mortar, enlarging the pigmented area and thus contributing to this exceptional biodeterioration phenomenon.
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Affiliation(s)
- Irene Dominguez-Moñino
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Marta Diaz-Herraiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Ana Z Miller
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain
| | - Juan Luis Santos
- Escuela Politecnica Superior, Universidad de Sevilla, Virgen de Africa 7, 41011 Sevilla, Spain
| | - Esteban Alonso
- Escuela Politecnica Superior, Universidad de Sevilla, Virgen de Africa 7, 41011 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Avenida Reina Mercedes 10, 41012 Sevilla, Spain.
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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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Duan Y, Wu F, Wang W, He D, Gu JD, Feng H, Chen T, Liu G, An L. The microbial community characteristics of ancient painted sculptures in Maijishan Grottoes, China. PLoS One 2017; 12:e0179718. [PMID: 28678844 PMCID: PMC5497971 DOI: 10.1371/journal.pone.0179718] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/02/2017] [Indexed: 11/29/2022] Open
Abstract
In this study, a culture-independent Illumina MiSeq sequencing strategy was applied to investigate the microbial communities colonizing the ancient painted sculptures of the Maijishan Grottoes, a famous World Cultural Heritage site listed by UNESCO in China. Four mixed samples were collected from Cave 4–4 of the Maijishan Grottoes, the so-called Upper Seven Buddha Pavilion, which was built during the Northern Zhou Dynasty (557-581AD). The 16/18S rRNA gene-based sequences revealed a rich bacterial diversity and a relatively low fungal abundance, including the bacterial groups Actinobacteria, Acidobacteria, Bacteroidetes, Cyanobacteria, Chloroflexi, Firmicutes, Proteobacteria and Verrucomicrobia and the fungal groups Ascomycota, Basidiomycota and Chytridiomycota. Among them, the bacteria genera of Pseudonocardia and Rubrobacter and unclassified fungi in the order of Capnodiales were dominant. The relative abundance of Pseudonocardia in the painted layer samples was higher than that in the dust sample, while Cyanobacteria dominated in the dust sample. Many of them have been discovered at other cultural heritage sites and associated with the biodeterioration of cultural relics. The presence and activity of these pioneering microorganisms may lead to an unexpected deterioration of the painted sculptures that are preserved in this heritage site. Thus, proper management strategies and potential risk monitoring should be used in the Maijishan Grottoes to improve the conservation of these precious painted sculptures.
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Affiliation(s)
- Yulong Duan
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, P.R.China
| | - Fasi Wu
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, Gansu, P.R.China
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, P.R.China
| | - Wanfu Wang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, P.R.China
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, Gansu, P.R.China
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, P.R.China
- * E-mail: (WFW); (HYF)
| | - Dongpeng He
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Dunhuang Academy, Dunhuang, Gansu, P.R.China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Hong Kong SAR, P.R.China
| | - Huyuan Feng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, P.R.China
- * E-mail: (WFW); (HYF)
| | - Tuo Chen
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, P.R.China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, P.R.China
| | - Lizhe An
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, University of Chinese Academy of Sciences, Lanzhou, P.R.China
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, P.R.China
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Otlewska A, Adamiak J, Stryszewska T, Kańka S, Gutarowska B. Factors Determining the Biodiversity of Halophilic Microorganisms on Historic Masonry Buildings. Microbes Environ 2017; 32:164-173. [PMID: 28592721 PMCID: PMC5478540 DOI: 10.1264/jsme2.me16159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The aim of the present study was to obtain insights into the relationship between the chemical (salt content and pH) and physico-mechanical (humidity and compressive strength) properties of mineral-based materials from historic buildings with salt efflorescence and the growth and biodiversity of halophilic microorganisms. Samples were mainly characterized by pH 6.5–8.5 and a moisture content of between 0.12 and 3.3%. Significant variations were also found in the salt content (sulfates, chlorides, and nitrates) of the materials. An SEM/EDS analysis of material surfaces revealed the presence of halite, calcite, gypsum, sodium sulfate, and potassium-sodium sulfate. Culture-dependent and culture-independent (clone library construction) approaches were both applied to detect halophilic microorganisms. Results derived from culturable methods and the materials analysis revealed a correlation between the total halophile count and pH value as well as sulfate content. A correlation was not observed between the concentration of chlorides or nitrates and the number of halophilic microorganisms. The materials studied were inhabited by the culturable halophilic bacteria Halobacillus sp., Virgibacillus sp., and Marinococcus sp. as well as the yeast Sterigmatomyces sp., which was isolated for the first time from mineral materials. Culture-independent techniques revealed the following bacterial species: Salinibacterium, Salinisphaera, Rubrobacter, Rubricoccus, Halomonas, Halorhodospira, Solirubrobacter, Salinicoccus, and Salinibacter. Biodiversity was the highest in materials with high or moderate salinity.
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Affiliation(s)
- Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology
| | - Justyna Adamiak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology
| | - Teresa Stryszewska
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology
| | - Stanisław Kańka
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology
| | - Beata Gutarowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology
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Polysaccharide Degradation Capability of Actinomycetales Soil Isolates from a Semiarid Grassland of the Colorado Plateau. Appl Environ Microbiol 2017; 83:AEM.03020-16. [PMID: 28087533 DOI: 10.1128/aem.03020-16] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/10/2017] [Indexed: 02/03/2023] Open
Abstract
Among the bacteria, members of the order Actinomycetales are considered quintessential degraders of complex polysaccharides in soils. However, studies examining complex polysaccharide degradation by Actinomycetales (other than Streptomyces spp.) in soils are limited. Here, we examine the lignocellulolytic and chitinolytic potential of 112 Actinomycetales strains, encompassing 13 families, isolated from a semiarid grassland of the Colorado Plateau in Utah. Members of the Streptomycetaceae, Pseudonocardiaceae, Micromonosporaceae, and Promicromonosporaceae families exhibited robust activity against carboxymethyl cellulose, xylan, chitin, and pectin substrates (except for low/no pectinase activity by the Micromonosporaceae). When incubated in a hydrated mixture of blended Stipa and Hilaria grass biomass over a 5-week period, Streptomyces and Saccharothrix (a member of the Pseudonocardiaceae) isolates produced high levels of extracellular enzyme activity, such as endo- and exocellulase, glucosidase, endo- and exoxylosidase, and arabinofuranosidase. These characteristics make them well suited to degrade the cellulose and hemicellulose components of grass cell walls. On the basis of the polysaccharide degradation profiles of the isolates, relative abundance of Actinomycetales sequences in 16S rRNA gene surveys of Colorado Plateau soils, and analysis of genes coding for polysaccharide-degrading enzymes among 237 Actinomycetales genomes in the CAZy database and 5 genomes from our isolates, we posit that Streptomyces spp. and select members of the Pseudonocardiaceae and Micromonosporaceae likely play an important role in the degradation of hemicellulose, cellulose, and chitin substances in dryland soils.IMPORTANCE Shifts in the relative abundance of Actinomycetales taxa have been observed in soil microbial community surveys during large, manipulated climate change field studies. However, our limited understanding of the ecophysiology of diverse Actinomycetales taxa in soil systems undermines attempts to determine the underlying causes of the population shifts or their impact on carbon cycling in soil. This study combines a systematic analysis of the polysaccharide degradation potential of a diverse collection of Actinomycetales isolates from surface soils of a semiarid grassland with analysis of genomes from five of these isolates and publicly available Actinomycetales genomes for genes encoding polysaccharide-active enzymes. The results address an important gap in knowledge of Actinomycetales ecophysiology-identification of key taxa capable of facilitating lignocellulose degradation in dryland soils. Information from this study will benefit future metagenomic studies related to carbon cycling in dryland soils by providing a baseline linkage of Actinomycetales phylogeny with lignocellulolytic functional potential.
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Huang Z, Zhao F, Li Y, Zhang J, Feng Y. Variations in the bacterial community compositions at different sites in the tomb of Emperor Yang of the Sui Dynasty. Microbiol Res 2016; 196:26-33. [PMID: 28164788 DOI: 10.1016/j.micres.2016.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 11/29/2016] [Accepted: 12/07/2016] [Indexed: 11/28/2022]
Abstract
To fully understand the bacterial processes in tomb environments, it is necessary to investigate the details of the bacterial communities present under such oligotrophic conditions. Here, high-throughput sequencing based on partial 16S rRNA gene sequences was used to fully evaluate the bacterial communities at different sites in the tomb of Emperor Yang of the Sui Dynasty. We also aimed to identify the soil factors that were significant related to bacterial diversity and community composition. The results showed the presence of a broad taxonomic diversity that included nine major phyla. Actinobacteria, Firmicutes and Proteobacteria dominated the bacterial profiles in all tomb soil samples. However, significant differences between deposited soils (DS) and covering soils (CSA, CSB and CSC) were revealed by chemistry-based principal component analysis (PCA), the number of OTUs, and the Chao 1 and Shannon indexes. At the family level, hierarchically clustered heatmap and LefSe analyses showed differences in the bacterial community compositions at different sampling sites. Notably, CSA contained significant populations of Nocardioidaceae, Pseudonocardiaceae and Streptomycetaceae, which are often reported to be associated with biodeterioration in cave environments. Further, the most abundant group (>10%) in all soil samples was Streptococcaceae, whose abundance decreased from 34.66% to 13.43% with increasing soil depth. The results of redundancy analysis (RDA) and the Monte Carlo permutation test indicated that soil pH and Cu and Mn levels were significantly related to the bacterial communities in this tomb. This research offers new insight into bacterial communities in cave environments and also provides important information for the protection of this historically important tomb.
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Affiliation(s)
- Zhi Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fei Zhao
- Nanjing Institute for Comprehensive utilization of Wild Plants, China CO-OP, Nanjing 210042, China
| | - Yonghui Li
- Key Laboratory of Urban and Architectural Heritage Conservation of Ministry of Education, School of Architecture, Southeast University, Nanjing 210096, China
| | - Jianwei Zhang
- State Key Laboratory Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youzhi Feng
- State Key Laboratory Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.
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Dominguez-Moñino I, Jurado V, Hermosin B, Saiz-Jimenez C. Paracoccus cavernae sp. nov., isolated from a show cave. Int J Syst Evol Microbiol 2016; 66:2265-2270. [DOI: 10.1099/ijsem.0.001018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Irene Dominguez-Moñino
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Bernardo Hermosin
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Av. Reina Mercedes 10, 41012 Sevilla, Spain
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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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Villa F, Stewart PS, Klapper I, Jacob JM, Cappitelli F. Subaerial Biofilms on Outdoor Stone Monuments: Changing the Perspective Toward an Ecological Framework. Bioscience 2016. [DOI: 10.1093/biosci/biw006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms. PLoS One 2016; 11:e0148279. [PMID: 26885815 PMCID: PMC4757552 DOI: 10.1371/journal.pone.0148279] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 01/15/2016] [Indexed: 11/19/2022] Open
Abstract
Background The prosperity of Hallstatt (Salzkammergut region, Austria) is based on the richness of salt in the surrounding mountains and salt mining, which is documented as far back as 1500 years B.C. Substantial archaeological evidence of Bronze and Iron Age salt mining has been discovered, with a wooden staircase (1108 B.C.) being one of the most impressive and well preserved finds. However, after its discovery, fungal mycelia have been observed on the surface of the staircase, most probably due to airborne contamination after its find. Objective As a basis for the further preservation of this valuable object, the active micro-flora was examined to investigate the presence of potentially biodegradative microorganisms. Results Most of the strains isolated from the staircase showed to be halotolerant and halophilic microorganisms, due to the saline environment of the mine. Results derived from culture-dependent assays revealed a high fungal diversity, including both halotolerant and halophilic fungi, the most dominant strains being members of the genus Phialosimplex (synonym: Aspergillus). Additionally, some typical cellulose degraders, namely Stachybotrys sp. and Cladosporium sp. were detected. Numerous bacterial strains were isolated and identified as members of 12 different genera, most of them being moderately halophilic species. The most dominant isolates affiliated with species of the genera Halovibrio and Marinococcus. Halophilic archaea were also isolated and identified as species of the genera Halococcus and Halorubrum. Molecular analyses complemented the cultivation assays, enabling the identification of some uncultivable archaea of the genera Halolamina, Haloplanus and Halobacterium. Results derived from fungi and bacteria supported those obtained by cultivation methods, exhibiting the same dominant members in the communities. Conclusion The results clearly showed the presence of some cellulose degraders that may become active if the requirements for growth and the environmental conditions turn suitable; therefore, these microorganisms must be regarded as a threat to the wood.
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Adamiak J, Otlewska A, Gutarowska B. Halophilic microbial communities in deteriorated buildings. World J Microbiol Biotechnol 2015; 31:1489-99. [DOI: 10.1007/s11274-015-1913-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 07/29/2015] [Indexed: 11/29/2022]
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Otlewska A, Adamiak J, Gutarowska B. Clone-based comparative sequence analysis of 16S rRNA genes retrieved from biodeteriorating brick buildings of the former Auschwitz II–Birkenau concentration and extermination camp. Syst Appl Microbiol 2015; 38:48-55. [DOI: 10.1016/j.syapm.2014.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 09/04/2014] [Accepted: 09/23/2014] [Indexed: 10/24/2022]
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Halophilic microorganisms are responsible for the rosy discolouration of saline environments in three historical buildings with mural paintings. PLoS One 2014; 9:e103844. [PMID: 25084531 PMCID: PMC4118916 DOI: 10.1371/journal.pone.0103844] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 07/02/2014] [Indexed: 01/31/2023] Open
Abstract
A number of mural paintings and building materials from monuments located in central and south Europe are characterized by the presence of an intriguing rosy discolouration phenomenon. Although some similarities were observed among the bacterial and archaeal microbiota detected in these monuments, their origin and nature is still unknown. In order to get a complete overview of this biodeterioration process, we investigated the microbial communities in saline environments causing the rosy discolouration of mural paintings in three Austrian historical buildings using a combination of culture-dependent and -independent techniques as well as microscopic techniques. The bacterial communities were dominated by halophilic members of Actinobacteria, mainly of the genus Rubrobacter. Representatives of the Archaea were also detected with the predominating genera Halobacterium, Halococcus and Halalkalicoccus. Furthermore, halophilic bacterial strains, mainly of the phylum Firmicutes, could be retrieved from two monuments using special culture media. Inoculation of building materials (limestone and gypsum plaster) with selected isolates reproduced the unaesthetic rosy effect and biodeterioration in the laboratory.
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Piñar G, Kraková L, Pangallo D, Piombino-Mascali D, Maixner F, Zink A, Sterflinger K. Halophilic bacteria are colonizing the exhibition areas of the Capuchin Catacombs in Palermo, Italy. Extremophiles 2014; 18:677-91. [PMID: 24863363 PMCID: PMC4065341 DOI: 10.1007/s00792-014-0649-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/27/2014] [Indexed: 01/11/2023]
Abstract
The Capuchin Catacombs of Palermo, Italy, contain over 1800 mummies dating from the 16th to 20th centuries AD. Their environment is not conducive to the conservation of the remains due to, among other factors, water infiltration, which is producing salt efflorescences on the walls. A multiphasic approach was applied to investigate the halophilic microbiota present in the Catacombs. Enrichment cultures were conducted on media containing different NaCl concentrations, ranging from 3 to 20 %. For screening of the strains, the following two PCR-based methods were used and compared: fluorescence internal transcribed spacer PCR (f-ITS) and random amplification of polymorphic DNA (RAPD) analyses. Results derived from RAPD profiles were shown to be slightly more discriminative than those derived from f-ITS. In addition, the proteolytic and cellulolytic abilities were screened through the use of plate assays, gelatin agar and Ostazin Brilliant Red H-3B (OBR-HEC), respectively. Many of the strains isolated from the wall samples displayed proteolytic activities, such as all strains belonging to the genera Bacillus, Virgibacillus and Arthrobacter, as well as some strains related to the genera Oceanobacillus, Halobacillus and Idiomarina. In addition, many of the strains isolated from materials employed to stuff the mummies showed cellulolytic activities, such as those related to species of the genera Chromohalobacter and Nesterenkonia, as well as those identified as Staphylococcus equorum and Halomonas sp. Furthermore, many of the strains were pigmented ranging from yellow to a strong pink color, being directly related to the discoloration displayed by the materials.
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Affiliation(s)
- G Piñar
- VIBT-Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria,
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López-Moreno A, Sepúlveda-Sánchez JD, Mercedes Alonso Guzmán EM, Le Borgne S. Calcium carbonate precipitation by heterotrophic bacteria isolated from biofilms formed on deteriorated ignimbrite stones: influence of calcium on EPS production and biofilm formation by these isolates. BIOFOULING 2014; 30:547-560. [PMID: 24689777 DOI: 10.1080/08927014.2014.888715] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Heterotrophic CaCO3-precipitating bacteria were isolated from biofilms on deteriorated ignimbrites, siliceous acidic rocks, from Morelia Cathedral (Mexico) and identified as Enterobacter cancerogenus (22e), Bacillus sp. (32a) and Bacillus subtilis (52g). In solid medium, 22e and 32a precipitated calcite and vaterite while 52g produced calcite. Urease activity was detected in these isolates and CaCO3 precipitation increased in the presence of urea in the liquid medium. In the presence of calcium, EPS production decreased in 22e and 32a and increased in 52g. Under laboratory conditions, ignimbrite colonization by these isolates only occurred in the presence of calcium and no CaCO3 was precipitated. Calcium may therefore be important for biofilm formation on stones. The importance of the type of stone, here a siliceous stone, on biological colonization is emphasized. This calcium effect has not been reported on calcareous materials. The importance of the effect of calcium on EPS production and biofilm formation is discussed in relation to other applications of CaCO3 precipitation by bacteria.
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Key Words
- BG-11, Blue Green mineral medium
- BLAST, basic local alignment search tool
- CPS, capsular polysaccharides
- CR, Congo Red
- CaCO3 precipitation
- EPS production
- EPS, extracellular polymeric substances
- MEGA, molecular evolutionary genetics analysis
- NCBI, National Center for Biotechnology Information
- OD, optical density
- PBS, phosphate buffered saline
- PGY-BG11, BG-11 medium supplemented with peptone, glucose and yeast extract
- SEM, scanning electron microscopy
- XRD, X-ray diffraction
- biofilm formation
- calcium effect
- heterotrophic bacteria
- ignimbrite stones
- rRNA, ribosomal ribonucleic acid
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Affiliation(s)
- Angélica López-Moreno
- a Doctorado en Ciencias Biológicas y de la Salud , Universidad Autónoma Metropolitana , México D.F. , Mexico
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Deterioration of an Etruscan tomb by bacteria from the order Rhizobiales. Sci Rep 2014; 4:3610. [PMID: 24402302 PMCID: PMC3885883 DOI: 10.1038/srep03610] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 12/10/2013] [Indexed: 02/07/2023] Open
Abstract
The Etruscan civilisation originated in the Villanovan Iron Age in the ninth century BC and was absorbed by Rome in the first century BC. Etruscan tombs, many of which are subterranean, are one of the best representations of this culture. The principal importance of these tombs, however, lies in the wall paintings and in the tradition of rich burial, which was unique in the Mediterranean Basin, with the exception of Egypt. Relatively little information is available concerning the biodeterioration of Etruscan tombs, which is caused by a colonisation that covers the paintings with white, circular to irregular aggregates of bacteria or biofilms that tend to connect each other. Thus, these colonisations sometimes cover extensive surfaces. Here we show that the colonisation of paintings in Tomba del Colle is primarily due to bacteria of the order Rhizobiales (Alphaproteobacteria), which were likely influenced by the neighbouring rhizosphere community and the availability of nutrients from root exudates.
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Kusumi A, Li X, Osuga Y, Kawashima A, Gu JD, Nasu M, Katayama Y. Bacterial communities in pigmented biofilms formed on the sandstone bas-relief walls of the Bayon Temple, Angkor Thom, Cambodia. Microbes Environ 2013; 28:422-31. [PMID: 24334526 PMCID: PMC4070708 DOI: 10.1264/jsme2.me13033] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Bayon temple in Angkor Thom, Cambodia has shown serious deterioration and is subject to the formation of various pigmented biofilms. Because biofilms are damaging the bas-reliefs, low reliefs engraved on the surface of sandstone, information about the microbial community within them is indispensable to control biofilm colonization. PCR-denaturing gradient gel electrophoresis (DGGE) analysis of biofilm samples from the pigmented sandstone surfaces showed that the bacterial community members in the biofilms differed clearly from those in the air and had low sequence similarity to database sequences. Non-destructive sampling of biofilm revealed novel bacterial groups of predominantly Rubrobacter in salmon pink biofilm, Cyanobacteria in chrome green biofilm, Cyanobacteria and Chloroflexi in signal violet biofilm, Chloroflexi in black gray biofilm, and Deinococcus-Thermus, Cyanobacteria, and Rubrobacter in blue green biofilm. Serial peeling-off of a thick biofilm by layers with adhesive sheets revealed a stratified structure: the blue-green biofilm, around which there was serious deterioration, was very rich in Cyanobacteria near the surface and Chloroflexi in deep layer below. Nitrate ion concentrations were high in the blue-green biofilm. The characteristic distribution of bacteria at different biofilm depths provides valuable information on not only the biofilm formation process but also the sandstone weathering process in the tropics.
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Affiliation(s)
- Asako Kusumi
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology
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Sterflinger K, Piñar G. Microbial deterioration of cultural heritage and works of art--tilting at windmills? Appl Microbiol Biotechnol 2013; 97:9637-46. [PMID: 24100684 PMCID: PMC3825568 DOI: 10.1007/s00253-013-5283-1] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 11/02/2022]
Abstract
Microorganisms (bacteria, archaea and fungi), in addition to lichens and insect pests, cause problems in the conservation of cultural heritage because of their biodeteriorative potential. This holds true for all types of historic artefacts, and even for art made of modern materials, in public buildings, museums and private art collections. The variety of biodeterioration phenomena observed on materials of cultural heritage is determined by several factors, such as the chemical composition and nature of the material itself, the climate and exposure of the object, in addition to the manner and frequency of surface cleaning and housekeeping in museums. This study offers a review of a variety of well-known biodeterioration phenomena observed on different materials, such as stone and building materials, objects exhibited in museums and libraries, as well as human remains and burial-related materials. The decontamination of infected artefacts, exhibition rooms and depots incurs high expenditure for museums. Nevertheless, the question has to be raised: whether the process of biodeterioration of cultural heritage can or should be stopped under all circumstances, or whether we have to accept it as a natural and an implicit consecution of its creation. This study also highlights critically the pros and cons of biocide treatments and gives some prominent examples of successful and unsuccessful conservation treatments. Furthermore, an outlook on the future research needs and developments in this highly interesting field is given.
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Affiliation(s)
- Katja Sterflinger
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190, Vienna, Austria,
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43
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Piñar G, Piombino-Mascali D, Maixner F, Zink A, Sterflinger K. Microbial survey of the mummies from the Capuchin Catacombs of Palermo, Italy: biodeterioration risk and contamination of the indoor air. FEMS Microbiol Ecol 2013; 86:341-56. [PMID: 23772650 PMCID: PMC3916889 DOI: 10.1111/1574-6941.12165] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/06/2013] [Accepted: 06/06/2013] [Indexed: 12/19/2022] Open
Abstract
The Capuchin Catacombs of Palermo contain over 1800 preserved bodies dating from the 16th to 20th centuries AD and showing evidence of biodeterioration. An extensive microbiological and molecular investigation was recently performed. Samples were taken from skin, muscle, hair, bone, stuffing materials, clothes, and surrounding walls as well as from the indoor air. In this study, we witnessed that the different degradation phenomena observed on the variety of materials located at the Capuchin Catacombs of Palermo are biological in origin. Molecular techniques showed the dominance of halophilic species of the domains Bacteria and Archaea on the walls and – as a result of salt emanating from the walls – on the mummies themselves. Nevertheless, specialized microorganisms belonging to taxa well-known for their cellulolytic and proteolytic activities were detected on clothes and stuffing material, and on skin, muscle, hair, and bone, respectively. This specialized microbiota is threatening the conservation of the mummies themselves. Additionally, sequences related to the human skin microbiome and to some pathogenic Bacteria (order Clostridiales) and fungi (genus Phialosimplex) were identified on samples derived from the mummies. Furthermore, a phosphate-reducing fungus, Penicillium radicum, was detected on bone. Finally, the high concentration of airborne fungal spores is not conducive to the conservation of the human remains and is posing a potential health risk for visitors.
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Affiliation(s)
- Guadalupe Piñar
- Department of Biotechnology, VIBT-Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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Alias-Villegas C, Jurado V, Laiz L, Saiz-Jimenez C. Sphingopyxis
italica sp. nov., isolated from Roman catacombs. Int J Syst Evol Microbiol 2013; 63:2565-2569. [DOI: 10.1099/ijs.0.046573-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative, aerobic, motile, rod-shaped bacterium, strain SC13E-S71T, was isolated from tuff, volcanic rock, where the Roman catacombs of Saint Callixtus in Rome, Italy, was excavated. Analysis of 16S rRNA gene sequences revealed that strain SC13E-S71T belongs to the genus
Sphingopyxis
, and that it shows the greatest sequence similarity with
Sphingopyxis chilensis
DSM 14889T (98.72 %),
Sphingopyxis taejonensis
DSM 15583T (98.65 %),
Sphingopyxis ginsengisoli
LMG 23390T (98.16 %),
Sphingopyxis panaciterrae
KCTC 12580T (98.09 %),
Sphingopyxis alaskensis
DSM 13593T (98.09 %),
Sphingopyxis witflariensis
DSM 14551T (98.09 %),
Sphingopyxis bauzanensis
DSM 22271T (98.02 %),
Sphingopyxis granuli
KCTC 12209T (97.73 %),
Sphingopyxis macrogoltabida
KACC 10927T (97.49 %),
Sphingopyxis ummariensis
DSM 24316T (97.37 %) and
Sphingopyxis panaciterrulae
KCTC 22112T (97.09 %). The predominant fatty acids were C18 : 1ω7c, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), C14 : 0 2-OH and C16 : 0. The predominant menaquinone was MK-10. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and sphingoglycolipid. These chemotaxonomic data are common to members of the genus
Sphingopyxis
. However, a polyphasic approach using physiological tests, DNA base ratios, DNA–DNA hybridization and 16S rRNA gene sequence comparisons showed that the isolate SC13E-S71T belongs to a novel species within the genus
Sphingopyxis
, for which the name
Sphingopyxis
italica sp. nov. is proposed. The type strain is SC13E-S71T ( = DSM 25229T = CECT 8016T).
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Affiliation(s)
- Cynthia Alias-Villegas
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Apartado 1052, 41080 Sevilla, Spain
| | - Valme Jurado
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Apartado 1052, 41080 Sevilla, Spain
| | - Leonila Laiz
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Apartado 1052, 41080 Sevilla, Spain
| | - Cesareo Saiz-Jimenez
- Instituto de Recursos Naturales y Agrobiologia, IRNAS-CSIC, Apartado 1052, 41080 Sevilla, Spain
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Role of Mn2+ and compatible solutes in the radiation resistance of thermophilic bacteria and archaea. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2012; 2012:845756. [PMID: 23209374 PMCID: PMC3505630 DOI: 10.1155/2012/845756] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Revised: 09/18/2012] [Accepted: 10/13/2012] [Indexed: 01/28/2023]
Abstract
Radiation-resistant bacteria have garnered a great deal of attention from scientists seeking to expose the mechanisms underlying their incredible survival abilities. Recent analyses showed that the resistance to ionizing radiation (IR) in the archaeon Halobacterium salinarum is dependent upon Mn-antioxidant complexes responsible for the scavenging of reactive oxygen species (ROS) generated by radiation. Here we examined the role of the compatible solutes trehalose, mannosylglycerate, and di-myo-inositol phosphate in the radiation resistance of aerobic and anaerobic thermophiles. We found that the IR resistance of the thermophilic bacteria Rubrobacter xylanophilus and Rubrobacter radiotolerans was highly correlated to the accumulation of high intracellular concentration of trehalose in association with Mn, supporting the model of Mn2+-dependent ROS scavenging in the aerobes. In contrast, the hyperthermophilic archaea Thermococcus gammatolerans and Pyrococcus furiosus did not contain significant amounts of intracellular Mn, and we found no significant antioxidant activity from mannosylglycerate and di-myo-inositol phosphate in vitro. We therefore propose that the low levels of IR-generated ROS under anaerobic conditions combined with highly constitutively expressed detoxification systems in these anaerobes are key to their radiation resistance and circumvent the need for the accumulation of Mn-antioxidant complexes in the cell.
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Rubrobacter bracarensis sp. nov., a novel member of the genus Rubrobacter isolated from a biodeteriorated monument. Syst Appl Microbiol 2012; 35:306-9. [DOI: 10.1016/j.syapm.2012.04.007] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 04/24/2012] [Accepted: 04/27/2012] [Indexed: 11/18/2022]
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Fernandez-Cortes A, Cuezva S, Sanchez-Moral S, Cañaveras JC, Porca E, Jurado V, Martin-Sanchez PM, Saiz-Jimenez C. Detection of human-induced environmental disturbances in a show cave. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2011; 18:1037-1045. [PMID: 21553035 DOI: 10.1007/s11356-011-0513-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 04/14/2011] [Indexed: 05/30/2023]
Abstract
PURPOSE We investigated the effects of human-induced disruption in a subterranean stable environment containing valuable Palaeolithic paintings and engravings (Ardales Cave, Southern Spain) using a double analytical approach. METHODS An environmental monitoring system was installed in the cave to record temperature, relative humidity, carbon dioxide (CO(2)) and radon ((222)Rn) concentrations in air. In the same stations, an aerobiological sampling was conducted to quantify the level of airborne microorganisms. RESULTS The combination of different methods allowed us to detect the extent of human-induced changes, confirming that these can be very hazardous in certain cave areas that should be apparently outside the scope of human disturbances, either by their remoteness to the visitor entrance or by being briefly visited. CONCLUSIONS The detection of evident anomalies in the environmental parameters and airborne microorganism concentration in the cave area housing the high density of paintings and engravings helps to control human disturbances and supports the direct application of this double approach for cave management purposes.
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Affiliation(s)
- Angel Fernandez-Cortes
- Museo Nacional de Ciencias Naturales, MNCN-CSIC, Jose Gutierrez Abascal 2, 28006 Madrid, Spain
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Zammit G, Sánchez-Moral S, Albertano P. Bacterially mediated mineralisation processes lead to biodeterioration of artworks in Maltese catacombs. THE SCIENCE OF THE TOTAL ENVIRONMENT 2011; 409:2773-2782. [PMID: 21550635 DOI: 10.1016/j.scitotenv.2011.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2010] [Revised: 03/04/2011] [Accepted: 03/08/2011] [Indexed: 05/30/2023]
Abstract
Mineral structures formed by bacterial and microalgal biofilms growing on the archaeological surface in Maltese hypogea were studied using Energy Dispersive X-Ray Spectroscopy (EDS) coupled to Environmental Scanning Electron Microscopy (ESEM), X-ray micro-diffraction (XRD) and X-ray fluorescence (XRF). These techniques have shown that mineral structures having different morphologies and chemical composition were associated with the microorganisms in the subaerophytic biofilm. Salt efflorescences and mineral deposits on the archaeological surface were often formed from gypsum (CaSO(4)∙2H(2)O), halite (NaCl) and calcite (CaCO(3)). Biogenic carbonates produced by microbial activities were a common occurrence. These assumed different forms, such as the production of mineral coats around cyanobacterial sheaths and the occurrence of calcite fibres with different morphologies on the surface of the biofilms. Moreover, vaterite (CaCO(3)) spherulites which appeared hollow in cross-section were observed. The presence of struvite was recorded from one catacomb site. These investigations have facilitated the study of the neoformation of metastable minerals by microbially mediated processes, which potentially contribute to a better understanding of the biodeterioration of artworks in Maltese palaeo-Christian catacombs.
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Affiliation(s)
- Gabrielle Zammit
- Department of Physiology & Biochemistry, Faculty of Medicine & Surgery, University of Malta, Malta.
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49
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Empadinhas N, da Costa MS. Diversity, biological roles and biosynthetic pathways for sugar-glycerate containing compatible solutes in bacteria and archaea. Environ Microbiol 2010; 13:2056-77. [PMID: 21176052 DOI: 10.1111/j.1462-2920.2010.02390.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
A decade ago the compatible solutes mannosylglycerate (MG) and glucosylglycerate (GG) were considered to be rare in nature. Apart from two species of thermophilic bacteria, Thermus thermophilus and Rhodothermus marinus, and a restricted group of hyperthermophilic archaea, the Thermococcales, MG had only been identified in a few red algae. Glucosylglycerate was considered to be even rarer and had only been detected as an insignificant solute in two halophilic microorganisms, a cyanobacterium, as a component of a polysaccharide and of a glycolipid in two actinobacteria. Unlike the hyper/thermophilic MG-accumulating microorganisms, branching close to the root of the Tree of Life, those harbouring GG shared a mesophilic lifestyle. Exceptionally, the thermophilic bacterium Persephonella marina was reported to accumulate GG. However, and especially owing to the identification of the key-genes for MG and GG synthesis and to the escalating numbers of genomes available, a plethora of new organisms with the resources to synthesize these solutes has been recognized. The accumulation of GG as an 'emergency' compatible solute under combined salt stress and nitrogen-deficient conditions now seems to be a disseminated survival strategy from enterobacteria to marine cyanobacteria. In contrast, the thermophilic and extremely radiation-resistant bacterium Rubrobacter xylanophilus is the only actinobacterium known to accumulate MG, and under all growth conditions tested. This review addresses the environmental factors underlying the accumulation of MG, GG and derivatives in bacteria and archaea and their roles during stress adaptation or as precursors for more elaborated macromolecules. The diversity of pathways for MG and GG synthesis as well as those for some of their derivatives is also discussed. The importance of glycerate-derived organic solutes in the microbial world is only now being recognized. Their stress-dependent accumulation and the molecular aspects of their interactions with biomolecules have already fuelled several emerging applications in biotechnology and biomedicine.
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Affiliation(s)
- Nuno Empadinhas
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-517 Coimbra, Portugal.
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50
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Jurado V, Porca E, Pastrana MP, Cuezva S, Fernandez-Cortes A, Saiz-Jimenez C. Microbiological study of bulls of indulgence of the 15th-16th centuries. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:3711-5. [PMID: 20595060 DOI: 10.1016/j.scitotenv.2010.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 05/05/2010] [Accepted: 05/06/2010] [Indexed: 05/25/2023]
Abstract
During the restoration of the church of "San Esteban" in Cuéllar (Segovia, Spain) a few sepulchres were opened. Among them was that of Doña Isabel de Zuazo, from the 16th century. Together with the corpse was found a series of printed documents from the 15th-16th centuries, most of which were bulls of indulgence. A microbiological study of the documents was carried out using techniques of isolation and molecular microbiology, together with scanning electron microscopy. Most of the identified bacteria were highly suggestive of a human origin, particularly the predominance of Clostridium species consistent with the flora of the human intestinal tract. Our results demonstrate that appreciable post-mortem migration of bacteria has taken place from the corpse to the historic documents. This can be explained considering that the documents were found on pelvic region, and were contaminated by body fluids and putrefaction.
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Affiliation(s)
- V Jurado
- Instituto de Recursos Naturales y Agrobiología, CSIC, Apartado 1052, 41080 Sevilla, Spain
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