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Ljaljević Grbić M, Dimkić I, Janakiev T, Kosel J, Tavzes Č, Popović S, Knežević A, Legan L, Retko K, Ropret P, Unković N. Uncovering the Role of Autochthonous Deteriogenic Biofilm Community: Rožanec Mithraeum Monument (Slovenia). MICROBIAL ECOLOGY 2024; 87:87. [PMID: 38940862 PMCID: PMC11213730 DOI: 10.1007/s00248-024-02404-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 06/21/2024] [Indexed: 06/29/2024]
Abstract
The primary purpose of the study, as part of the planned conservation work, was to uncover all aspects of autochthonous biofilm pertaining to the formation of numerous deterioration symptoms occurring on the limestone Rožanec Mithraeum monument in Slovenia. Using state-of-the-art sequencing technologies combining mycobiome data with observations made via numerous light and spectroscopic (FTIR and Raman) microscopy analyses pointed out to epilithic lichen Gyalecta jenensis and its photobiont, carotenoid-rich Trentepohlia aurea, as the origin of salmon-hued pigmented alterations of limestone surface. Furthermore, the development of the main deterioration symptom on the monument, i.e., biopitting, was instigated by the formation of typical endolithic thalli and ascomata of representative Verrucariaceae family (Verrucaria sp.) in conjunction with the oxalic acid-mediated dissolution of limestone. The domination of lichenized fungi, as the main deterioration agents, both on the relief and surrounding limestone, was additionally supported by the high relative abundance of lichenized and symbiotroph groups in FUNGuild analysis. Obtained results not only upgraded knowledge of this frequently occurring but often overlooked group of extremophilic stone heritage deteriogens but also provided a necessary groundwork for the development of efficient biocontrol formulation applicable in situ for the preservation of similarly affected limestone monuments.
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Grants
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- 451-03-47/2023-01/200178 Ministry of Education, Science, and Technological Development of the Republic of Serbia
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
- BI-RS/20-21-013 and J7-3147 Slovenian Research Agency (ARRS)
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Affiliation(s)
- M Ljaljević Grbić
- University of Belgrade-Faculty of Biology, Studentski Trg 16, 11 000, Belgrade, Serbia
| | - Ivica Dimkić
- University of Belgrade-Faculty of Biology, Studentski Trg 16, 11 000, Belgrade, Serbia
| | - Tamara Janakiev
- University of Belgrade-Faculty of Biology, Studentski Trg 16, 11 000, Belgrade, Serbia
| | - Janez Kosel
- The Institute for the Protection of Cultural Heritage of Slovenia, Poljanska Cesta 40, 1000, Ljubljana, Slovenia
| | - Črtomir Tavzes
- The Institute for the Protection of Cultural Heritage of Slovenia, Poljanska Cesta 40, 1000, Ljubljana, Slovenia
| | - Slađana Popović
- University of Belgrade-Faculty of Biology, Studentski Trg 16, 11 000, Belgrade, Serbia
| | - Aleksandar Knežević
- University of Belgrade-Faculty of Biology, Studentski Trg 16, 11 000, Belgrade, Serbia
| | - Lea Legan
- The Institute for the Protection of Cultural Heritage of Slovenia, Poljanska Cesta 40, 1000, Ljubljana, Slovenia
| | - Klara Retko
- The Institute for the Protection of Cultural Heritage of Slovenia, Poljanska Cesta 40, 1000, Ljubljana, Slovenia
| | - Polonca Ropret
- The Institute for the Protection of Cultural Heritage of Slovenia, Poljanska Cesta 40, 1000, Ljubljana, Slovenia
| | - Nikola Unković
- University of Belgrade-Faculty of Biology, Studentski Trg 16, 11 000, Belgrade, Serbia.
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2
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Wang S, He JN, Wang YJ, Zhao WY, Yang QX, Wang YN, Zhang Y, Zhang LP, Liu HW. Metabolome and Genome Analysis of a Novel Endophytic Fungus Aureobasidium pullulans KB3: Discovery of Polyketones and Polyketone Biosynthesis Pathway. Biochem Genet 2024:10.1007/s10528-024-10866-7. [PMID: 38877158 DOI: 10.1007/s10528-024-10866-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 06/09/2024] [Indexed: 06/16/2024]
Abstract
Endophytic fungi associated with plants may contain undiscovered bioactive compounds. Under standard laboratory conditions, most undiscovered compounds are inactive, whereas their production could be stimulated under different cultivation conditions. In this study, six endophytic fungi were isolated from the bark of Koelreuteria paniculata in Quancheng Park, Jinan City, Shandong Province, one of which was identified as a new subspecies of Aureobasidium pullulans, named A. pullulans KB3. Additionally, metabolomic tools were used to screen suitable media for A. pullulans KB3 fermentation, and the results showed that peptone dextrose medium (PDM) was more beneficial to culture A. pullulans KB3 for isolation of novel compounds. Sphaerolone, a polyketone compound, was initially isolated from A. pullulans KB3 via scaled up fermentation utilizing PDM. Additionally, the whole-genome DNA of A. pullulans KB3 was sequenced to facilitate compound isolation and identify the biosynthesis gene clusters (BGCs). This study reports the multi-omics (metabolome and genome) analysis of A. pullulans KB3, laying the foundation for discovering novel compounds of silent BGCs and identifying their biosynthesis pathway.
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Affiliation(s)
- Shuai Wang
- School of Pharmaceutical Sciences, Liaocheng University, Liaocheng, 252000, Shandong, People's Republic of China
| | - Jia-Nuo He
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Ying-Jie Wang
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Wen-Ya Zhao
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Qing-Xia Yang
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Ya-Na Wang
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Yang Zhang
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Li-Ping Zhang
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China
| | - Hong-Wei Liu
- Laboratory of Microbiology, Institute of Biology, Hebei Academy of Sciences, 15, Shijiazhuang, 050081, Hebei, People's Republic of China.
- Laboratory of Microbiology, Main Crops Disease of Microbial Control Engineering Technology Research Center in Hebei Province, 15, Shijiazhuang, 050081, Hebei, People's Republic of China.
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3
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Sanjurjo-Sánchez J, Alves C, Freire-Lista DM. Biomineral deposits and coatings on stone monuments as biodeterioration fingerprints. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168846. [PMID: 38036142 DOI: 10.1016/j.scitotenv.2023.168846] [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: 07/27/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Biominerals deposition processes, also called biomineralisation, are intimately related to biodeterioration on stone surfaces. They include complex processes not always completely well understood. The study of biominerals implies the identification of organisms, their molecular mechanisms, and organism/rock/atmosphere interactions. Sampling restrictions of monument stones difficult the biominerals study and the in situ demonstrating of biodeterioration processes. Multidisciplinary works are required to understand the whole process. Thus, studies in heritage buildings have taken advantage of previous knowledge acquired thanks to laboratory experiments, investigations carried out on rock outcrops and within caves from some years ago. With the extrapolation of such knowledge to heritage buildings and the advances in laboratory techniques, there has been a huge increase of knowledge regarding biomineralisation and biodeterioration processes in stone monuments during the last 20 years. These advances have opened new debates about the implications on conservation interventions, and the organism's role in stone conservation and decay. This is a review of the existing studies of biominerals formation, biodeterioration on laboratory experiments, rocks, caves, and their application to building stones of monuments.
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Affiliation(s)
| | - Carlos Alves
- LandS/Lab2PT-Landscapes, Heritage and Territory Laboratory (FCT-UIDB/04509/2020) and Earth Sciences Department/School of Sciences, University of Minho, 4710-057 Braga, Portugal
| | - David M Freire-Lista
- Universidade de Trás-os-Montes e Alto Douro, UTAD, Escola de Ciências da Vida e do Ambiente, Quinta dos Prados, 5000-801 Vila Real, Portugal; Centro de Geociências, Universidade de Coimbra, Portugal
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4
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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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5
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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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Cattò C, Mu A, Moreau JW, Wang N, Cappitelli F, Strugnell R. Biofilm colonization of stone materials from an Australian outdoor sculpture: Importance of geometry and exposure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 339:117948. [PMID: 37080094 DOI: 10.1016/j.jenvman.2023.117948] [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: 01/13/2023] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 05/04/2023]
Abstract
The safeguarding of Australian outdoor stone heritage is currently limited by a lack of information concerning mechanisms responsible for the degradation of the built heritage. In this study, the bacterial community colonizing the stone surface of an outdoor sculpture located at the Church of St. John the Evangelist in Melbourne was analysed, providing an overview of the patterns of microbial composition associated with stone in an anthropogenic context. Illumina MiSeq 16S rRNA gene sequencing together with confocal laser microscope investigations highlighted the bacterial community was composed of both phototrophic and chemotrophic microorganisms characteristic of stone and soil, and typical of arid, salty and urban environments. Cardinal exposure, position and surface geometry were the most important factors in determining the structure of the microbial community. The North-West exposed areas on the top of the sculpture with high light exposure gave back the highest number of sequences and were dominated by Cyanobacteria. The South and West facing in middle and lower parts of the sculpture received significantly lower levels of radiation and were dominated by Actinobacteria. Proteobacteria were observed as widespread on the sculpture. This pioneer research provided an in-depth investigation of the microbial community structure on a deteriorated artistic stone in the Australian continent and provides information for the identification of deterioration-associated microorganisms and/or bacteria beneficial for stone preservation.
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Affiliation(s)
- Cristina Cattò
- Department of Food Environmental and Nutritional Sciences, Università Degli Studi di Milano, Milano, Italy; Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Andre Mu
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, Glasgow, United Kingdom; School of Geographical, Atmospheric and Earth Sciences, The University of Melbourne, Parkville, VIC, Australia.
| | - Nancy Wang
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Sciences, Università Degli Studi di Milano, Milano, Italy.
| | - Richard Strugnell
- Department of Microbiology and Immunology, At the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia.
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Dobretsov S, Rittschof D. "Omics" Techniques Used in Marine Biofouling Studies. Int J Mol Sci 2023; 24:10518. [PMID: 37445696 DOI: 10.3390/ijms241310518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern "omic" techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different "omics" techniques. Finally, this review presents the future outlook for the use of "omics" techniques in marine biofouling studies. Like all trans-disciplinary research, environmental "omics" is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology.
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Affiliation(s)
- Sergey Dobretsov
- Department of Marine Science and Fisheries, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoud 123, Muscat P.O. Box 34, Oman
| | - Daniel Rittschof
- Nicholas School of the Environment, Duke University, Beaufort, NC 28516, USA
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Bacha SAS, Li Y, Nie J, Xu G, Han L, Farooq S. Comprehensive review on patulin and Alternaria toxins in fruit and derived products. FRONTIERS IN PLANT SCIENCE 2023; 14:1139757. [PMID: 37077634 PMCID: PMC10108681 DOI: 10.3389/fpls.2023.1139757] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Mycotoxins are toxic secondary metabolites produced by certain fungi, which can contaminate various food commodities, including fruits and their derived products. Patulin and Alternaria toxins are among the most commonly encountered mycotoxins in fruit and their derived products. In this review, the sources, toxicity, and regulations related to these mycotoxins, as well as their detection and mitigation strategies are widely discussed. Patulin is a mycotoxin produced mainly by the fungal genera Penicillium, Aspergillus, and Byssochlamys. Alternaria toxins, produced by fungi in the Alternaria genus, are another common group of mycotoxins found in fruits and fruit products. The most prevalent Alternaria toxins are alternariol (AOH) and alternariol monomethyl ether (AME). These mycotoxins are of concern due to their potential negative effects on human health. Ingesting fruits contaminated with these mycotoxins can cause acute and chronic health problems. Detection of patulin and Alternaria toxins in fruit and their derived products can be challenging due to their low concentrations and the complexity of the food matrices. Common analytical methods, good agricultural practices, and contamination monitoring of these mycotoxins are important for safe consumption of fruits and derived products. And Future research will continue to explore new methods for detecting and managing these mycotoxins, with the ultimate goal of ensuring the safety and quality of fruits and derived product supply.
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Affiliation(s)
- Syed Asim Shah Bacha
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Yinping Li
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Jiyun Nie, ; Yinping Li,
| | - Jiyun Nie
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, China
- *Correspondence: Jiyun Nie, ; Yinping Li,
| | - Guofeng Xu
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Lingxi Han
- College of Horticulture, Qingdao Agricultural University/Laboratory of Quality & Safety Risk Assessment for Fruit (Qingdao), Ministry of Agriculture and Rural Affairs/National Technology Centre for Whole Process Quality Control of FSEN Horticultural Products (Qingdao)/Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao, China
| | - Saqib Farooq
- Laboratory of Quality & Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
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Zhgun A, Avdanina D, Shagdarova B, Nuraeva G, Shumikhin K, Zhuikova Y, Il’ina A, Troyan E, Shitov M, Varlamov V. The Application of Chitosan for Protection of Cultural Heritage Objects of the 15-16th Centuries in the State Tretyakov Gallery. MATERIALS (BASEL, SWITZERLAND) 2022; 15:7773. [PMID: 36363375 PMCID: PMC9658413 DOI: 10.3390/ma15217773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/19/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Microorganisms are one of the main factors in the deterioration of cultural heritage, in particular art paintings. The antiseptics currently used in painting have significant limitations due to insufficient effectiveness or increased toxicity and interaction with art materials. In this regard, the actual challenge is the search for novel materials that effectively work against microorganisms in the composition with painting materials and do not change their properties. Chitosan has pronounced antimicrobial properties but was not used previously as an antiseptic for paintings. In our study we developed a number of mock layers based on sturgeon glue, supplemented which chitosan (molecular weight 25 kDa or 45 kDa), standard antiseptics for paintings (positive controls) or without additives (negative control). According to Fourier transform infrared spectroscopy and atomic force microscopy, the addition of chitosan did not significantly affect the optical and surface properties of this material. The ability of chitosan to effectively protect paintings was shown after inoculation on the created mock-up layers of 10 fungi-destructors of tempera painting, previously isolated from cultural heritage of the of the 15-16th centuries in the State Tretyakov Gallery, on the created mock layers. Our study demonstrated the principled opportunity of using chitosan in the composition of painting materials to prevent biodeterioration for the first time.
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Affiliation(s)
- Alexander Zhgun
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Darya Avdanina
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Balzhima Shagdarova
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Gulgina Nuraeva
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | | | - Yuliya Zhuikova
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Alla Il’ina
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - Egor Troyan
- State Tretyakov Gallery, 119017 Moscow, Russia
| | | | - Valery Varlamov
- Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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10
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Liu X, Qian Y, Wang Y, Wu F, Wang W, Gu JD. Innovative approaches for the processes involved in microbial biodeterioration of cultural heritage materials. Curr Opin Biotechnol 2022; 75:102716. [DOI: 10.1016/j.copbio.2022.102716] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/13/2022] [Accepted: 03/01/2022] [Indexed: 12/30/2022]
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11
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Katemauswa M, Hossain E, Liu Z, Lesani M, Parab AR, Dean DA, McCall LI. Enabling Quantitative Analysis of Surface Small Molecules for Exposomics and Behavioral Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:412-419. [PMID: 35084848 DOI: 10.1021/jasms.1c00263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Workplace chemical exposures are a major source of occupational injury. Although over half of these are skin exposures, exposomics research often focuses on chemical levels in the air or in worker biofluids such as blood and urine. Until now, one limitation has been the lack of methods to quantitatively measure surface chemical transfer. Outside the realm of harmful chemicals, the small molecules we leave behind on surfaces can also reveal important aspects of human behavior. In this study, we developed a swab-based quantitative approach to determine small molecule concentrations across common surfaces. We demonstrate its utility using one drug, cyclobenzaprine, on metal surfaces, and two human-derived metabolites, carnitine and phenylacetylglutamine, on four common surfaces: linoleum flooring, plastified laboratory workbench, metal, and Plexiglas. We observed peak areas proportional to surface analyte concentrations at 45 min and 1 week after deposition, enabling quantification of molecule abundance on workplace built environment surfaces. In contrast, this method was unsuitable for analysis of oleanolic acid, for which we did not observe a strong linear proportional relationship following swab-based recovery from surfaces. Overall, this method paves the way for future quantitative exposomics studies in analyte-specific and surface-specific frameworks.
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Affiliation(s)
- Mitchelle Katemauswa
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Ekram Hossain
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Zongyuan Liu
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Mahbobeh Lesani
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Adwaita R Parab
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Danya A Dean
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
| | - Laura-Isobel McCall
- University of Oklahoma, Department of Chemistry and Biochemistry, Norman, Oklahoma 73019, United States
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, Oklahoma 73019, United States
- University of Oklahoma, Laboratories of Molecular Anthropology and Microbiome Research, Norman, Oklahoma 73019, United States
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12
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Ding X, Lan W, Yan A, Li Y, Katayama Y, Gu JD. Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 302:114041. [PMID: 34741944 DOI: 10.1016/j.jenvman.2021.114041] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/11/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
The surfaces of historical stone monuments are visibly covered with a layer of colonizing microorganisms and their degradation products. In this study, a metadata analysis was conducted using the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential and functionality of the stone microbiome on important world cultural heritage sites under four different climatic conditions. The retrieved stone microbial community composition in these metagenomes shows a clear association between climate types of the historical monuments and the diversity and taxonomic composition of the stone microbiomes. Shannon diversity values showed that microbial communities on stone monuments exposed to dry climate were more diverse than those under humid ones. In particular, functions associated with photosynthesis and UV resistance were identified from geographical locations under different climate types. The distribution of key microbial determinants responsible for stone deterioration was linked to survival under extreme environmental conditions and biochemical capabilities and reactions. Among them, biochemical reactions of the microbial nitrogen and sulfur cycles were most predominant. These stone-dwelling microbiomes on historical stone monuments were highly diverse and self-sustaining driven by energy metabolism and biomass accumulation. And metabolic products of the internal geomicrobiological nitrogen cycling on these ancient monuments play a unique role in the biodeterioration of stone monuments. These results highlight the significance of identifying the essential microbial biochemical reactions to advance the understanding of stone biodeterioration for protection management.
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Affiliation(s)
- Xinghua Ding
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Wensheng Lan
- Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, The Shenzhen Academy of Inspection and Quarantine, Food Inspection and Quarantine Center of Shenzhen Custom, 1011 Fuqiang Road, Shenzhen, 518045, People's Republic of China
| | - Aixin Yan
- School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Yiliang Li
- Department of Earth Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Yoko Katayama
- Institute of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, 183-8509, Japan; Tokyo National Research Institute for Cultural Properties, 13-43 Ueno Park, Taito-ku, Tokyo, 110-8713, Japan
| | - Ji-Dong Gu
- Environmental Science and Engineering Research Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, People's Republic of China.
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13
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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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14
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Current Knowledge on the Fungal Degradation Abilities Profiled through Biodeteriorative Plate Essays. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11094196] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fungi are known to contribute to the development of drastic biodeterioration of historical and valuable cultural heritage materials. Understandably, studies in this area are increasingly reliant on modern molecular biology techniques due to the enormous benefits they offer. However, classical culture dependent methodologies still offer the advantage of allowing fungal species biodeteriorative profiles to be studied in great detail. Both the essays available and the results concerning distinct fungal species biodeteriorative profiles obtained by amended plate essays, remain scattered and in need of a deep summarization. As such, the present work attempts to provide an overview of available options for this profiling, while also providing a summary of currently known fungal species putative biodeteriorative abilities solely obtained by the application of these methodologies. Consequently, this work also provides a series of checklists that can be helpful to microbiologists, restorers and conservation workers when attempting to safeguard cultural heritage materials worldwide from biodeterioration.
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15
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Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11020620] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.
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Pyzik A, Ciuchcinski K, Dziurzynski M, Dziewit L. The Bad and the Good-Microorganisms in Cultural Heritage Environments-An Update on Biodeterioration and Biotreatment Approaches. MATERIALS (BASEL, SWITZERLAND) 2021; 14:E177. [PMID: 33401448 PMCID: PMC7795576 DOI: 10.3390/ma14010177] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022]
Abstract
Cultural heritage objects constitute a very diverse environment, inhabited by various bacteria and fungi. The impact of these microorganisms on the degradation of artworks is undeniable, but at the same time, some of them may be applied for the efficient biotreatment of cultural heritage assets. Interventions with microorganisms have been proven to be useful in restoration of artworks, when classical chemical and mechanical methods fail or produce poor or short-term effects. The path to understanding the impact of microbes on historical objects relies mostly on multidisciplinary approaches, combining novel meta-omic technologies with classical cultivation experiments, and physico-chemical characterization of artworks. In particular, the development of metabolomic- and metatranscriptomic-based analyses associated with metagenomic studies may significantly increase our understanding of the microbial processes occurring on different materials and under various environmental conditions. Moreover, the progress in environmental microbiology and biotechnology may enable more effective application of microorganisms in the biotreatment of historical objects, creating an alternative to highly invasive chemical and mechanical methods.
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Affiliation(s)
- Adam Pyzik
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.C.); (M.D.); (L.D.)
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17
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Perini N, Mercuri F, Orlanducci S, Thaller MC, Migliore L. The Integration of Metagenomics and Chemical Physical Techniques Biodecoded the Buried Traces of the Biodeteriogens of Parchment Purple Spots. Front Microbiol 2020; 11:598945. [PMID: 33408706 PMCID: PMC7779469 DOI: 10.3389/fmicb.2020.598945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/02/2020] [Indexed: 11/13/2022] Open
Abstract
Ancient parchments record an immense part of our cultural heritage, having been used as the main written support material for centuries. Parchment easily undergoes biodeterioration, whose main signs are the so-called purple spots, which often lead to detachment of the superficial written layer. Up to recent years, several studies have been analyzing damaged parchments from different world’s archives, trying to trace back the culprit of the purple spots. However, standard cultivation and early molecular techniques have been demonstrated to be unsuccessful, leading the parchment damage issue remaining unsolved for many years. Nowadays, some studies have explored the parchment biodeterioration dynamics by adopting a multidisciplinary approach combining standard microbiological methods with high-throughput molecular, chemical and physical techniques. This approach allowed an unprecedented level of knowledge on the complex dynamics of parchment biodeterioration. This mini review discusses the application of the combination of basic and high-throughput techniques to study historical parchments, highlighting the strengths and weaknesses of this approach. In particular, it focuses on how metagenomics has been paramount for the unequivocal identification of the microbial main actors of parchment biodeterioration and their dynamics, but also on how metagenomics may suffer the distortion inflict by the historical perspective on the analysis of ancient specimens. As a whole, this mini review aims to describe the scenario of information on parchment biodeterioration obtained so far by using the integration of metagenomic with recent chemical (Raman spectroscopy) and physical (Light Transmission Analysis) approaches, which might have key implications in the preservation of many ancient documents.
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Affiliation(s)
| | - Fulvio Mercuri
- Department of Industrial Engineering, Tor Vergata University, Rome, Italy
| | - Silvia Orlanducci
- Department of Chemical Science and Technology, Tor Vergata University, Rome, Italy
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Microbiologically Induced Carbonate Precipitation in the Restoration and Conservation of Cultural Heritage Materials. Molecules 2020; 25:molecules25235499. [PMID: 33255349 PMCID: PMC7727839 DOI: 10.3390/molecules25235499] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/17/2020] [Accepted: 07/19/2020] [Indexed: 11/30/2022] Open
Abstract
Microbiologically induced carbonate precipitation (MICP) is a well-known biogeochemical process that allows the formation of calcium carbonate deposits in the extracellular environment. The high concentration of carbonate and calcium ions on the bacterial surface, which serves as nucleation sites, promotes the calcium carbonate precipitation filling and binding deteriorated materials. Historic buildings and artwork, especially those present in open sites, are susceptible to enhanced weathering resulting from environmental agents, interaction with physical-chemical pollutants, and living organisms, among others. In this work, some published variations of a novel and ecological surface treatment of heritage structures based on MICP are presented and compared. This method has shown to be successful as a restoration, consolidation, and conservation tool for improvement of mechanical properties and prevention of unwanted gas and fluid migration from historical materials. The treatment has revealed best results on porous media matrixes; nevertheless, it can also be applied on soil, marble, concrete, clay, rocks, and limestone. MICP is proposed as a potentially safe and powerful procedure for efficient conservation of worldwide heritage structures.
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19
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A Review on Sampling Techniques and Analytical Methods for Microbiota of Cultural Properties and Historical Architecture. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10228099] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
World cultural heritage suffers from deterioration caused by both natural and anthropogenic processes, among which microorganisms are significantly involved. Among the key issues of this topic, sampling techniques and analytical methods for revealing the microbiome are fundamental to obtaining useful results for understanding the key players and processes involved, and also for effective protection and management of the cultural heritage for humanity. A non-invasive and non-destructive sampling method is required for sampling of cultural properties prior to further analysis of the microbiome. One example is illustrated in this article. For many years, culture-dependent methods had been used before the invention of polymerase-chain reaction (PCR) methods and, more recently, specifically high-throughput next generation sequencing (NGS). NGS reveals the whole microbial community composition and the active microorganisms from genomic DNA and RNA, respectively. The recovered environmental DNA and RNA from samples provide the information on microbial community and composition, and the active members and biochemical processes of the microbial attributes. It should be emphasized that the metabolically-active members of functional microflora in the biofilm or microbiome on cultural heritage must be determined and identified from the RNA-based analysis to gain a substantially important insight of the active biodeterioration processes and also the effectiveness of the conservation strategies. The importance of the culture-independent technique, based on NGS, is that it can be used in combination with the conventional culturing methods to guide the isolation and enrichment of new microorganisms to gain further biochemical insights to advance the role of the specific microbial groups for biodeterioration of cultural heritage. At the same time, effective restoration and maintenance strategies can be formulated for the protection of world cultural heritage.
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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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21
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Preliminary Studies on Fungal Contamination of Two Rupestrian Churches from Matera (Southern Italy). SUSTAINABILITY 2020. [DOI: 10.3390/su12176988] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The Sassi, a UNESCO World Heritage Site and its rupestrian churches, are richly decorated and visited by thousands of visitors every year. It is important to preserve this heritage which shows signs of deterioration due to abiotic and/or biotic factors. Aiming to carry out in the future an environmental-friendly restoration, a screening of the fungi present on walls and frescoes of two rupestrian churches “Santa Lucia alle Malve” and “La Madonna dei derelitti” located, respectively, in the “Sasso Caveoso” and in the “Sasso Barisano” was performed. Isolation and characterization of fungal species from investigated sites was carried out. Total genomic DNA (gDNA) was extracted from pure fungal cultures and subsequently utilized in PCRs using primers that amplify a portion of the ribosomal DNA (ITS5/ITS4) or the β-tubulin gene (Bt2a/Bt2b). The amplicons were directly sequenced. Obtained nucleotide sequences were compared to those present in the GenBank (NCBI) showing a very high similarity (99–100%) with the following species: Parengyodontium album, Alternaria alternata, Cladosporium cladosporioides, Lecanicillium psalliotae, Meyerozyma guilliermondii and Botryotrichum atrogriseum. All sequences from this study were deposited in the EMBL database. Detailed knowledge about fungi isolated from stone is indispensable not only to counter/reduce the structural and aesthetic damage but also to protect the health of both guardians and visitors who may develop different pathologies due to the spores diffused in the environment.
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Yang S, Wu L, Wu B, Zhang Y, Wang H, Tan X. Diversity and structure of soil microbiota of the Jinsha earthen relic. PLoS One 2020; 15:e0236165. [PMID: 32697804 PMCID: PMC7375591 DOI: 10.1371/journal.pone.0236165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/30/2020] [Indexed: 12/02/2022] Open
Abstract
In order to define the diversity and composition of the microbial communities colonizing of the soil microbiome of the Jinsha earthen relic, we used high-throughput sequencing technology to identify and characterize the microbiota in 22 samples collected from the Jinsha earthen relic in China during 2017 and 2018. We compared the taxonomy of the microbial communities from samples taken at different times and different sites. Our results showed that the identity of the dominant bacterial phyla differed among the samples. Proteobacteria (23–86.2%) were the predominant bacterial phylum in all samples taken from site A in both 2017 and 2018. However, Actinobacteria (21–92.3%) were the most popular bacterial phylum in samples from sites B and C in 2017 and 2018. Ascomycota were identified as the only fungal phyla in samples in 2017. However, the group varied drastically in relative abundance between 2017 and 2018. Functional analysis of the soil bacterial community suggested that abundant members of the microbiota may be associated with metabolism and the specific environment. This report was the first high-throughput sequencing study of the soil of the Jinsha earthen relic microbiome. Since soil microbiota can damage soil and archeological structures, comprehensive analyses of the microbiomes at archeological sites may contribute to the understand of the influence of microorganisms on the degradation of soil, as well as to the identification of potentially beneficial or undesirable members of these microbial communities in archeological sites. The study will be helpful to provide effective data and guidance for the prevention and control of microbial corrosion of the Jinsha earthen relic.
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Affiliation(s)
- Sheng Yang
- Chengdu Institute of Cultural Relics, Chengdu, PR China
| | - Linfeng Wu
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Bin Wu
- Jinsha Site Museum, Chengdu, PR China
| | - Yizheng Zhang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Haiyan Wang
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
| | - Xuemei Tan
- College of Life Sciences, Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, Sichuan University, Chengdu, PR China
- * E-mail:
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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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24
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Lima JY, Moreira C, Nunes Freitas PN, Olchanheski LR, Veiga Pileggi SA, Etto RM, Staley C, Sadowsky MJ, Pileggi M. Structuring biofilm communities living in pesticide contaminated water. Heliyon 2020; 6:e03996. [PMID: 32462094 PMCID: PMC7240113 DOI: 10.1016/j.heliyon.2020.e03996] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/07/2020] [Accepted: 05/12/2020] [Indexed: 12/12/2022] Open
Abstract
The wide use of pesticides in agriculture expose microbiota to stressful conditions that require the development of survival strategies. The bacterial response to many pollutants has not been elucidated in detail, as well as the evolutionary processes that occur to build adapted communities. The purpose of this study was to evaluate the bacterial population structure and adaptation strategies in planktonic and biofilm communities in limited environments, as tanks containing water used for washing herbicide containers. This biodiversity, with high percentage of nonculturable microorganisms, was characterized based on habitat and abiotic parameters using molecular and bioinformatics tools. According to water and wastewater standards, the physicochemical conditions of the tank water were inadequate for survival of the identified bacteria, which had to develop survival strategies in this hostile environment. The biodiversity decreased in the transition from planktonic to biofilm samples, indicating a possible association between genetic drift and selection of individuals that survive under stressful conditions, such as heating in water and the presence of chlorine, fluorine and agrochemicals over a six-month period. The abundance of Enterobacter, Acinetobacter and Pseudomonas in biofilms from water tanks was linked to essential processes, deduced from the genes attributed to these taxonomic units, and related to biofilm formation, structure and membrane transport, quorum sensing and xenobiotic degradation. These characteristics were randomly combined and fixed in the biofilm community. Thus, communities of biofilm bacteria obtained under these environmental conditions serve as interesting models for studying herbicide biodegradation kinetics and the prospects of consortia suitable for use in bioremediation in reservoirs containing herbicide-contaminated wastewater, as biofilters containing biofilm communities capable of degrading herbicides.
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Affiliation(s)
- Jhenifer Yonara Lima
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Cassiano Moreira
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Paloma Nathane Nunes Freitas
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | | | - Sonia Alvim Veiga Pileggi
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Rafael Mazer Etto
- Department of Chemistry, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
| | - Christopher Staley
- The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States
| | - Michael Jay Sadowsky
- Department of Soil, Water, and Climate, The Biotechnology Institute, University of Minnesota, St. Paul, Minnesota, United States
| | - Marcos Pileggi
- Department of Structural and Molecular Biology and Genetics, Ponta Grossa State University, Ponta Grossa, Paraná, Brazil
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25
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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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26
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Samuels T, Bryce C, Landenmark H, Marie‐Loudon C, Nicholson N, Stevens AH, Cockell C. Microbial Weathering of Minerals and Rocks in Natural Environments. ACTA ACUST UNITED AC 2020. [DOI: 10.1002/9781119413332.ch3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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27
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Antibacterial Effect of Zinc Oxide-Based Nanomaterials on Environmental Biodeteriogens Affecting Historical Buildings. NANOMATERIALS 2020; 10:nano10020335. [PMID: 32079073 PMCID: PMC7075178 DOI: 10.3390/nano10020335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 11/17/2022]
Abstract
The colonization of microorganisms and their subsequent interaction with stone substrates under different environmental conditions encourage deterioration of materials by multiple mechanisms resulting in changes in the original color, appearance and durability. One of the emerging alternatives to remedy biodeterioration is nanotechnology, thanks to nanoparticle properties such as small size, no-toxicity, high photo-reactivity, and low impact on the environment. This study highlighted the effects of ZnO-based nanomaterials of two bacteria genera isolated from the Temple of Concordia (Agrigento’s Valley of the Temples in Sicily, Italy) that are involved in biodeterioration processes. The antimicrobial activities of ZnO-nanorods (Zn-NRs) and graphene nanoplatelets decorated with Zn-NRs (ZNGs) were evaluated against the Gram positive Arthrobacter aurescens and two isolates of the Gram negative Achromobacter spanius. ZNGs demonstrated high antibacterial and antibiofilm activities on several substrates such as stones with different porosity. In the case of ZNGs, a marked time- and dose-dependent bactericidal effect was highlighted against all bacterial species. Therefore, these nanomaterials represent a promising tool for developing biocompatible materials that can be exploited for the conservation of cultural heritage. These nanostructures can be successfully applied without releasing toxic compounds, thus spreading their usability.
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28
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Kobetičová K, Černý R. Terrestrial eutrophication of building materials and buildings: An emerging topic in environmental studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 689:1316-1328. [PMID: 31466168 DOI: 10.1016/j.scitotenv.2019.06.423] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 05/27/2019] [Accepted: 06/25/2019] [Indexed: 06/10/2023]
Abstract
Eutrophication has been analyzed mostly in aquatic or soil environments to date. Direct terrestrial eutrophication of building materials and buildings, contrary e.g. to their biodeterioration or biodegradation, was studied so rarely that even its exact definition does not exist yet. In this paper, eutrophication of building materials and buildings as an emerging topic in environmental studies is analyzed in detail and future developments in the field are contemplated. The analysis includes a survey of directly and indirectly related research studies, identification of basic mechanisms and principal factors, and a critical assessment of current methodologies potentially applicable for recognition and classification of eutrophication of building materials and buildings. A definition of direct terrestrial eutrophication of building materials and buildings is proposed afterwards and an alternative method for the calculation of their eutrophication potential is suggested. Finally, recommendations for solving the most urgent problems in future research are formulated.
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Affiliation(s)
- Klára Kobetičová
- Department of Materials Engineering and Chemistry, Faculty of Civil Engineering, Czech Technical University in Prague, Thákurova 7, CZ-166 29 Prague, Czech Republic.
| | - Robert Černý
- Department of Materials Engineering and Chemistry, Faculty of Civil Engineering, Czech Technical University in Prague, Thákurova 7, CZ-166 29 Prague, Czech Republic
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29
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Negi A, Sarethy IP. Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses. MICROBIAL ECOLOGY 2019; 78:1014-1029. [PMID: 31025063 DOI: 10.1007/s00248-019-01366-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 03/18/2019] [Indexed: 06/09/2023]
Abstract
Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the "omics" technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.
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Affiliation(s)
- Abhishek Negi
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sec 62, Noida, 201309, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sec 62, Noida, 201309, India.
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30
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Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland). Microorganisms 2019; 7:microorganisms7100416. [PMID: 31623322 PMCID: PMC6843168 DOI: 10.3390/microorganisms7100416] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/29/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Biodeterioration is a serious threat to cultural heritage objects and buildings. The deterioration of a given material often incurs irreparable losses in terms of uniqueness and historical value. Hence preventive actions should be taken. One important challenge is to identify microbes involved in the biodeterioration process. In this study, we analyzed the microbial diversity of an ancient architectonical structure of the Rotunda of Sts. Felix and Adauctus, which is a part of the Wawel Royal Castle located in Krakow, Poland. The Rotunda is unavailable to tourists and could be treated as an extreme habitat due to the low content of nutrients coming either from sandstone plates bound with lime mortar or air movement. Microbial diversity was analyzed with the use of the high-throughput sequencing of marker genes corresponding to fragments of 16S rDNA (for Bacteria) and ITS2 (internal transcribed spacer 2) (for Fungi). The results showed that the microbial community adhered to wall surfaces is, to a large extent, endemic. Furthermore, alongside many microorganisms that could be destructive to masonry and mortar (e.g., Pseudomonas, Aspergillus), there were also bacteria, such as species of genera Bacillus, Paenisporosarcina, and Amycolatopsis, that can positively affect wall surface properties by reducing the damage caused by the presence of other microorganisms. We also showed that airborne microorganisms probably have little impact on the biodeterioration process as their abundance in the microbial community adhered to the ancient walls was very low.
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31
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Zanardini E, May E, Purdy KJ, Murrell JC. Nutrient cycling potential within microbial communities on culturally important stoneworks. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:147-154. [PMID: 30346661 PMCID: PMC7379959 DOI: 10.1111/1758-2229.12707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 09/24/2018] [Accepted: 10/10/2018] [Indexed: 06/08/2023]
Abstract
Previous studies on microbes associated with deterioration of cultural heritage (CH) stoneworks have revealed a diverse microbiota adapted to stresses such as low nutrients, aridity and high salinity, temperatures and radiation. However, the function of these pioneer microbial communities is still unclear. This study examines bacterial and archaeal diversity in exfoliated and dark encrustation sandstone from Portchester Castle (UK) by 16S rRNA and functional gene analyses. Bacterial and archaeal communities from the exfoliated sites were distinctly different from the dark encrustation. Detected genera were linked to extreme environmental conditions, various potential functional roles and degradation abilities. From these data it was possible to reconstruct almost complete nitrogen and sulfur cycles, as well as autotrophic carbon fixation and mineral transformation processes. Analysis of RNA showed that many of the detected genera in these nutrient cycles were probably active in situ. Thus, CH stonework microbial communities are highly diverse and potentially self-sustaining ecosystems capable of cycling carbon, nitrogen and sulfur as well as the stone biodeterioration processes that lead to alterations such as exfoliation and corrosion. These results highlight the importance of diversity and internal recycling capacity in the development of microbial communities in harsh and low energy systems.
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Affiliation(s)
- Elisabetta Zanardini
- School of Life SciencesUniversity of WarwickCoventryUK
- Department of Science and High TechnologyUniversity of InsubriaComoItaly
| | - Eric May
- School of Biological SciencesUniversity of PortsmouthPortsmouthUK
| | | | - J. Colin Murrell
- School of Environmental SciencesUniversity of East AngliaNorwichUK
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32
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Nowicka-Krawczyk P, Żelazna-Wieczorek J, Koziróg A, Otlewska A, Rajkowska K, Piotrowska M, Gutarowska B, Brycki B. Multistep approach to control microbial fouling of historic building materials by aerial phototrophs. BIOFOULING 2019; 35:284-298. [PMID: 31014110 DOI: 10.1080/08927014.2019.1598396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/13/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023]
Abstract
The scientific multistep approach described herein is a result of two years of research into a control method against microbial fouling and biodeterioration of historic building materials by phototrophs. A series of tests were conducted to select the best antifouling agent for eliminating 'green' coatings and protecting surfaces against biofouling. Of the seven active compounds, two with the best penetration abilities were subjected to a photosynthetic activity inhibition test using confocal microscopy. Of the two, a quaternary ammonium salt (QAC) - didecyldimethylammonium chloride (DDAC) - was found to be the most effective. Ten biocides containing QACs at different concentrations were then tested against 'green' coatings on wood, brick and plaster, with the best four being selected for further research in model conditions. As a result, biocides containing >14% (v v-1) DDAC were found to be successful antifouling agents for protecting historical materials against biodeterioration by phototrophs.
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Affiliation(s)
- Paulina Nowicka-Krawczyk
- a Department of Algology and Mycology, Faculty of Biology and Environmental Protection , University of Łódź , Łódź , Poland
| | - Joanna Żelazna-Wieczorek
- a Department of Algology and Mycology, Faculty of Biology and Environmental Protection , University of Łódź , Łódź , Poland
| | - Anna Koziróg
- b Institute of Fermentation Technology and Microbiology , Łódź University of Technology , Łódź , Poland
| | - Anna Otlewska
- b Institute of Fermentation Technology and Microbiology , Łódź University of Technology , Łódź , Poland
| | - Katarzyna Rajkowska
- b Institute of Fermentation Technology and Microbiology , Łódź University of Technology , Łódź , Poland
| | - Małgorzata Piotrowska
- b Institute of Fermentation Technology and Microbiology , Łódź University of Technology , Łódź , Poland
| | - Beata Gutarowska
- b Institute of Fermentation Technology and Microbiology , Łódź University of Technology , Łódź , Poland
| | - Bogumił Brycki
- c Laboratory of Microbiocides Chemistry, Faculty of Chemistry , Adam Mickiewicz University , Poznań , Poland
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33
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Kannan P, Su SS, Mannan MS, Castaneda H, Vaddiraju S. A Review of Characterization and Quantification Tools for Microbiologically Influenced Corrosion in the Oil and Gas Industry: Current and Future Trends. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.8b02211] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pranav Kannan
- Mary Kay O’Connor Process Safety Center, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
| | - Shei Sia Su
- National Corrosion and Materials Reliability Laboratory, Texas A&M University, College Station, Texas 77843-3003, United States
- Materials Science and Engineering Department, Texas A&M University, College Station, Texas 77843-3003, United States
| | - M. Sam Mannan
- Mary Kay O’Connor Process Safety Center, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
| | - Homero Castaneda
- National Corrosion and Materials Reliability Laboratory, Texas A&M University, College Station, Texas 77843-3003, United States
- Materials Science and Engineering Department, Texas A&M University, College Station, Texas 77843-3003, United States
| | - Sreeram Vaddiraju
- Mary Kay O’Connor Process Safety Center, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
- Artie McFerrin Department of Chemical Engineering, Texas A&M University System, 3122 TAMU, College Station, Texas 77843-3122, United States
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34
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Liu Z, Zhang Y, Zhang F, Hu C, Liu G, Pan J. Microbial Community Analyses of the Deteriorated Storeroom Objects in the Tianjin Museum Using Culture-Independent and Culture-Dependent Approaches. Front Microbiol 2018; 9:802. [PMID: 29780363 PMCID: PMC5946025 DOI: 10.3389/fmicb.2018.00802] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022] Open
Abstract
In the storeroom C7 of the Tianjin Museum, one wooden desk and two leather luggages dated back to Qing dynasty (1644-1912 AD) presented viable microbial contamination. The aim of the present study was to investigate microbial communities responsible for the biodeterioration of storeroom objects using a combination of culture-independent and culture-dependent methods as well microscopic techniques. Scanning electron microscopy (SEM) revealed that the microflora on three storeroom objects were characterized by a marked presence of Eurotium halophilicum. Real-time quantitative polymerase chain reaction (qPCR) analysis proved that fungi were the main causative agents behind the biodeterioration in this case. Fungal internal transcribed spacer (ITS) amplicon sequencing documented the presence of two main fungi — Eurotium halophilicum and Aspergillus penicillioides. Molecular identification of fungal strains isolated from the surfaces and the air of the storeroom were most closely related to Chaetomium, Aspergillus, Penicillium, and Fusarium, showing discrepancies in fungal taxa compared to ITS amplicon sequencing. The most isolated bacterial phylum was Firmicutes, mostly Bacillus members. In addition, four biocide products — Preventol® D 7, P 91, 20 N and Euxyl® K 100 were selected to test their capability against fungal strains isolated from the surfaces. According to the susceptibility assay, Preventol® D 7 based on isothiazolinones was the most effective against fungal isolates. Findings from this study provided a knowledge about storeroom fungi, and exemplify a type of preliminary test that may be conducted before planning any biocide treatment, which may be useful to mitigate the fungal deterioration for further conservation of the museum.
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Affiliation(s)
- Zijun Liu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Fengyu Zhang
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cuiting Hu
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | | | - Jiao Pan
- Key Laboratory of Molecular Microbiology and Technology of the Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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35
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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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Antolak H, Oracz J, Otlewska A, Żyżelewicz D, Kręgiel D. Identification of Carotenoids and Isoprenoid Quinones from Asaia lannensis and Asaia bogorensis. Molecules 2017; 22:molecules22101608. [PMID: 28946700 PMCID: PMC6151773 DOI: 10.3390/molecules22101608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 09/24/2017] [Accepted: 09/24/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of the study was to identify and quantitatively assess of carotenoids and isoprenoid quinones biosynthesized by six different strains of acetic acid bacteria, belonging to genus Asaia, that are common beverage-spoiling bacteria in Europe. Bacterial cultures were conducted in a laboratory liquid culture minimal medium with 2% sucrose. Carotenoids and isoprenoid quinones were investigated using UHPLC-DAD-ESI-MS analysis. In general, tested strains of Asaia spp. were able to produce 10 carotenoids and 3 isoprenoid quinones: menaquinone-7, menaquinone-8, and ubiquinone-10. The main identified carotenoids in Asaia lannensis strains were phytofluene, neurosporene, α-carotene, while for Asaia bogorensis, neurosporene, canthaxanthin, and zeaxanthin were noted. What is more, tested Asaia spp. were able to produce myxoxanthophyll, which has so far been identified primarily in cyanobacteria. The results show that A. lannensis are characterized by statistically higher concentrations of produced carotenoids, as well as a greater variety of these compounds. We have noted that carotenoids were not only accumulated by bacterial cells, but also some strains of A. lannensis produced extracellular carotenoids.
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Affiliation(s)
- Hubert Antolak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Science, Lodz University of Technology, 4/10 Stefanowskiego, 90-924 Lodz, Poland.
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
| | - Dorota Żyżelewicz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Science, Lodz University of Technology, 4/10 Stefanowskiego, 90-924 Lodz, Poland.
| | - Dorota Kręgiel
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Lodz University of Technology, 171/173 Wólczańska, 90-924 Lodz, Poland.
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Liu Z, Wang Y, Pan X, Ge Q, Ma Q, Li Q, Fu T, Hu C, Zhu X, Pan J. Identification of Fungal Communities Associated with the Biodeterioration of Waterlogged Archeological Wood in a Han Dynasty Tomb in China. Front Microbiol 2017; 8:1633. [PMID: 28890715 PMCID: PMC5575450 DOI: 10.3389/fmicb.2017.01633] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/11/2017] [Indexed: 12/12/2022] Open
Abstract
The Mausoleum of the Dingtao King (termed ‘M2’) is a large-scale huangchang ticou tomb that dates to the Western Han Dynasty (206 B.C.–25 A.D.). It is the highest-ranking Han Dynasty tomb discovered to date. However, biodeterioration on the surface of the tomb M2 is causing severe damage to its wooden materials. The aim of the present study was to give insight into the fungal communities colonized the wooden tomb. For this purpose, seven samples were collected from different sections of the tomb M2 which exhibited obvious biodeterioration in the form of white spots. Microbial structures associated with the white spots were observed with scanning electron microscopy. Fungal community structures were assessed for seven samples via a combination of high-throughput sequencing and culture-dependent techniques. Sequencing analyses identified 114 total genera that belonged to five fungal phyla. Hypochnicium was the most abundant genus across all samples and accounted for 98.61–99.45% of the total community composition. Further, Hypochnicium sp. and Mortierella sp. cultures were successfully isolated from the tomb samples, and were distinguished as Hypochnicium sp. WY-DT1 and Mortierella sp. NK-DT1, respectively. Cultivation-dependent experiments indicated that the dominant member, Hypochnicium sp. WY- DT1, could grow at low temperatures and significantly degraded cellulose and lignin. Thus, our results taken together suggest that this fungal strain must be regarded as a serious threat to the preservation of the wooden tomb M2. The results reported here are useful for informing future contamination mitigation efforts for the tomb M2 as well as other similar cultural artifacts.
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Affiliation(s)
- Zijun Liu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Yu Wang
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Xiaoxuan Pan
- Chinese Academy of Cultural HeritageBeijing, China
| | - Qinya Ge
- Chinese Academy of Cultural HeritageBeijing, China
| | - Qinglin Ma
- Chinese Academy of Cultural HeritageBeijing, China
| | - Qiang Li
- Laboratory of Cultural Relics Conservation Materials, Department of Chemistry, Zhejiang UniversityHangzhou, China
| | - Tongtong Fu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Cuiting Hu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Xudong Zhu
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
| | - Jiao Pan
- Key Laboratory of Molecular Microbiology and Technology for Ministry of Education, Department of Microbiology, College of Life Sciences, Nankai UniversityTianjin, China
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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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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Ogawa A, Celikkol-Aydin S, Gaylarde C, Baptista-Neto JA, Beech I. Microbiomes of Biofilms on Decorative Siliceous Stone: Drawbacks and Advantages of Next Generation Sequencing. Curr Microbiol 2017; 74:848-853. [PMID: 28466090 DOI: 10.1007/s00284-017-1257-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 04/25/2017] [Indexed: 11/30/2022]
Abstract
Next Generation Sequencing (NGS), using the Illumina® metabarcoding system, showed differences between biofilm communities on three degraded siliceous stone church façades in central Rio de Janeiro. Two church biofilms (on granite and augen gneiss) were dominated by Actinobacteria; the third (granite), surrounded by trees and further from intense vehicular traffic, by Gammaproteobacteria. Yeast-like forms of Basidiomycetes and Ascomycetes were major fungi on all facades, but 22.8% of Operational Taxonomic Units could not be assigned to any fungal taxon after DNA amplification with ITS primers and analysis with the UNITE database, indicating the need for more fungal NGS studies. The pipeline used in analysis of the V4 region of rRNA bacterial gene sequences influenced the taxa detected, with two major classes and many genera identified only by the pipeline using the Greengenes, and not the Silva, database. Principal Components Analysis separated façade biofilms into the appropriate three groups and indicated greater dissimilarity of the tree-surrounded church biofilm from the others, confirmed by Jaccard Similarity coefficients, suggesting that local environment influences community composition more than stone type. NGS allows rapid and detailed analysis of microbiomes, but results must be carefully assessed and must not be used as the sole indication of community composition.
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Affiliation(s)
- Akiko Ogawa
- Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA
- Department Chemistry and Biochemistry, Suzuka College, National Institute of Technology, Suzuka, Japan
| | | | - Christine Gaylarde
- Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA.
| | | | - Iwona Beech
- Department Microbiology and Plant Biology, University of Oklahoma, Norman, USA
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41
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Geomicrobiology of the built environment. Nat Microbiol 2017; 2:16275. [DOI: 10.1038/nmicrobiol.2016.275] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 12/21/2016] [Indexed: 01/28/2023]
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Gaylarde C, Baptista-Neto JA, Ogawa A, Kowalski M, Celikkol-Aydin S, Beech I. Epilithic and endolithic microorganisms and deterioration on stone church facades subject to urban pollution in a sub-tropical climate. BIOFOULING 2017; 33:113-127. [PMID: 28054493 DOI: 10.1080/08927014.2016.1269893] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
Weathering of two church facades in Rio de Janeiro was caused substantially by salts, mainly halite and gypsum, detected by SEM and chemical analyses, which cause physical stresses by deposition within the rock. Biofilm populations, determined by SEM and as operational taxonomic units (OTUs), degraded stone by penetration, solubilization and redeposition of minerals on their surfaces. Endolithic cyanobacteria were associated with gypsum deposits. Microbiomes were typical for high-stress environments, high salt, intense insolation, low water and low nutrients (eg halophilic Rubrobacter, Salinicola, Sterigmatomyces). The main colonizers on the church most affected by traffic (Nossa Senhora da Candelária - CA) were Actinobacteria; Gammaproteobacteria (chiefly Pseudomonas) were predominant on the site situated in a leafy square (São Francisco de Paula - SF). Major Gammaproteobacteria on CA were halophilic Halomonas and Rhodobacteriaceae. Fungal OTUs on both churches were principally dimorphic, yeast-like basidiomycetes. Many OTUs of thermophilic microorganisms (eg the Thermomicrobia class, Chloroflexi) were present. This is the first use of next generation sequencing (NGS) to study microbial biofilm interactions with metamorphic and granite buildings in an intensely urban, sub-tropical climate.
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Affiliation(s)
- Christine Gaylarde
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | | | - Akiko Ogawa
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | - Matthew Kowalski
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | - Sukriye Celikkol-Aydin
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
| | - Iwona Beech
- a Department of Microbiology and Plant Biology, University of Oklahoma , Norman , OK , USA
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Microbiological Contamination at Workplaces in a Combined Heat and Power (CHP) Station Processing Plant Biomass. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14010099. [PMID: 28117709 PMCID: PMC5295349 DOI: 10.3390/ijerph14010099] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/06/2017] [Accepted: 01/17/2017] [Indexed: 01/30/2023]
Abstract
The aim of the study was to evaluate the microbial contamination at a plant biomass processing thermal power station (CHP). We found 2.42 × 103 CFU/m3 of bacteria and 1.37 × 104 CFU/m3 of fungi in the air; 2.30 × 107 CFU/g of bacteria and 4.46 × 105 CFU/g of fungi in the biomass; and 1.61 × 102 CFU/cm2 bacteria and 2.39 × 101 CFU/cm2 fungi in filtering facepiece respirators (FFRs). Using culture methods, we found 8 genera of mesophilic bacteria and 7 of fungi in the air; 10 genera each of bacteria and fungi in the biomass; and 2 and 5, respectively, on the FFRs. Metagenomic analysis (Illumina MiSeq) revealed the presence of 46 bacterial and 5 fungal genera on the FFRs, including potential pathogens Candida tropicalis, Escherichia coli, Prevotella sp., Aspergillus sp., Penicillium sp.). The ability of microorganisms to create a biofilm on the FFRs was confirmed using scanning electron microscopy (SEM). We also identified secondary metabolites in the biomass and FFRs, including fumigaclavines, quinocitrinines, sterigmatocistin, and 3-nitropropionic acid, which may be toxic to humans. Due to the presence of potential pathogens and mycotoxins, the level of microbiological contamination at workplaces in CHPs should be monitored.
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Oldham AL, Steinberg MK, Duncan KE, Makama Z, Beech I. Molecular methods resolve the bacterial composition of natural marine biofilms on galvanically coupled stainless steel cathodes. J Ind Microbiol Biotechnol 2016; 44:167-180. [PMID: 28013395 DOI: 10.1007/s10295-016-1887-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/14/2016] [Indexed: 11/25/2022]
Abstract
Navy vessels consist of various metal alloys and biofilm accumulation at the metal surface is thought to play a role in influencing metal deterioration. To develop better strategies to monitor and control metallic biofilms, it is necessary to resolve the bacterial composition within the biofilm. This study aimed to determine if differences in electrochemical current could influence the composition of dominant bacteria in a metallic biofilm, and if so, determine the level of resolution using metagenomic amplicon sequencing. Current was generated by creating galvanic couples between cathodes made from stainless steel and anodes made from carbon steel, aluminum, or copper nickel and exposing them in the Delaware Bay. Stainless steel cathodes (SSCs) coupled to aluminum or carbon steel generated a higher mean current (0.39 mA) than that coupled to copper nickel (0.17 mA). Following 3 months of exposure, the bacterial composition of biofilms collected from the SSCs was determined and compared. Dominant bacterial taxa from the two higher current SSCs were different from that of the low-current SSC as determined by DGGE and verified by Illumina DNA-seq analysis. These results demonstrate that electrochemical current could influence the composition of dominant bacteria in metallic biofilms and that amplicon sequencing is sufficient to complement current methods used to study metallic biofilms in marine environments.
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Affiliation(s)
- Athenia L Oldham
- Department of Biology, University of Texas of the Permian Basin, 4901 E University, Odessa, TX, 79762, USA.
| | - Mia K Steinberg
- Naval Surface Warfare Center Carderock Division, 9500 Macarthur Blvd, West Bethesda, MD, 20817, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH #136, Norman, OK, 73019, USA
| | - Zakari Makama
- Department of Microbiology and Plant Biology, University of Oklahoma, 100 E Boyd, Norman, OK, 73019, USA
| | - Iwona Beech
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, GLCH #136, Norman, OK, 73019, USA
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Celikkol-Aydin S, Gaylarde CC, Lee T, Melchers RE, Witt DL, Beech IB. 16S rRNA gene profiling of planktonic and biofilm microbial populations in the Gulf of Guinea using Illumina NGS. MARINE ENVIRONMENTAL RESEARCH 2016; 122:105-112. [PMID: 27742449 DOI: 10.1016/j.marenvres.2016.10.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 09/24/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
16S rRNA gene profiling using a pipeline involving the Greengenes database revealed that bacterial populations in innermost (proximal to the steel surface) and outer regions of biofilms on carbon steel exposed 3 m below the surface at an offshore site in the Gulf of Guinea differed from one another and from seawater. There was a preponderance of gammaproteobacterial sequences, representing organisms known for hydrocarbon degradation. Total DNA from the innermost layer was 1500 times that recovered from the outermost. Stramenopiles (diatom) sequences were prevalent in the former. Rhodobacteriaceae, key biofilm formers, comprised 14.9% and 4.22% OTUs of inner and outer layers, respectively. Photosynthetic anaerobic sulfur oxidizer sequences were also prominent in the biofilms. Analysis of data using a different pipeline with Silva111 allowed detection of 0.3-0.4% SRB in the biofilms. The high abundance of aerobic micro-algal sequences in inner biofilm suggests they are initial colonizers of carbon steel surfaces in a marine environment. This is the first time that the microbial population of the strongly attached inner layer of the biofilm on steel has been differentiated from the outer, readily removed layer. The accepted scraping removal method is obviously inadequate and the resulting microbial analysis does not offer complete information on the biofilm community structure.
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Affiliation(s)
| | - Christine C Gaylarde
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, USA.
| | - Tim Lee
- AMOG Consulting Inc., Houston, USA.
| | | | - Devin L Witt
- Chevron Energy Technology Company, Houston, USA.
| | - Iwona B Beech
- University of Oklahoma, Department of Microbiology and Plant Biology, Norman, USA.
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Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing. PLoS One 2016; 11:e0163287. [PMID: 27658256 PMCID: PMC5033376 DOI: 10.1371/journal.pone.0163287] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/05/2016] [Indexed: 11/19/2022] Open
Abstract
The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960-1219 A.D.) and Qing dynasties (1636-1912 A.D.) and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities' diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.
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Koziróg A, Rajkowska K, Otlewska A, Piotrowska M, Kunicka-Styczyńska A, Brycki B, Nowicka-Krawczyk P, Kościelniak M, Gutarowska B. Protection of Historical Wood against Microbial Degradation-Selection and Application of Microbiocides. Int J Mol Sci 2016; 17:ijms17081364. [PMID: 27556450 PMCID: PMC5000759 DOI: 10.3390/ijms17081364] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/10/2016] [Accepted: 08/11/2016] [Indexed: 12/01/2022] Open
Abstract
The aim of this study was to select effective and safe microbiocides for the disinfection and protection of historical wooden surfaces at the former Auschwitz II-Birkenau concentration and extermination camp. We tested seven active compounds against bacteria and moulds, of which didecyldimethylammonium chloride and N-(3-aminopropyl)-N-dodecylpropane-1,3-diamine were effective even at 0.02%–2%. Subsequently, eight microbiocides containing the selected active ingredients were chosen and applied three times on the surface of wood samples colonized by bacteria and moulds. ABM-1 and ABM-2—6% solution; Rocima 101—8%; Preventol R 80—12%; Acticide 706 LV—15% and Boramon—30% were the most effective disinfectants. Under laboratory conditions, ABM-1, Boramon and Rocima 101 ensured antimicrobial protection of new wood samples for six months. In situ, 30% Boramon and 8% Rocima 101 applied by spraying effectively protected the historical wood from bacterial and mould growth for 12 and 3 months, respectively. Colour and luminance of the new wood were not altered after exposure to the biocides. Boramon and Rocima 101, applied by the spraying method, caused no significant change in the colour of the historical wood. Results from this study were used to develop a procedure for the protection of wood in historical buildings against biodeterioration.
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Affiliation(s)
- Anna Koziróg
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, 90-924 Łódź, Poland.
| | - Katarzyna Rajkowska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, 90-924 Łódź, Poland.
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, 90-924 Łódź, Poland.
| | - Małgorzata Piotrowska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, 90-924 Łódź, Poland.
| | - Alina Kunicka-Styczyńska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, 90-924 Łódź, Poland.
| | - Bogumił Brycki
- Laboratory of Microbiocide Chemistry, Faculty of Chemistry, Adam Mickiewicz University, 60-780 Poznań, Poland.
| | | | | | - Beata Gutarowska
- Institute of Fermentation Technology and Microbiology, Lodz University of Technology, 90-924 Łódź, Poland.
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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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