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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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Gadd GM, Fomina M, Pinzari F. Fungal biodeterioration and preservation of cultural heritage, artwork, and historical artifacts: extremophily and adaptation. Microbiol Mol Biol Rev 2024; 88:e0020022. [PMID: 38179930 PMCID: PMC10966957 DOI: 10.1128/mmbr.00200-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/11/2023] [Indexed: 01/06/2024] Open
Abstract
SUMMARYFungi are ubiquitous and important biosphere inhabitants, and their abilities to decompose, degrade, and otherwise transform a massive range of organic and inorganic substances, including plant organic matter, rocks, and minerals, underpin their major significance as biodeteriogens in the built environment and of cultural heritage. Fungi are often the most obvious agents of cultural heritage biodeterioration with effects ranging from discoloration, staining, and biofouling to destruction of building components, historical artifacts, and artwork. Sporulation, morphological adaptations, and the explorative penetrative lifestyle of filamentous fungi enable efficient dispersal and colonization of solid substrates, while many species are able to withstand environmental stress factors such as desiccation, ultra-violet radiation, salinity, and potentially toxic organic and inorganic substances. Many can grow under nutrient-limited conditions, and many produce resistant cell forms that can survive through long periods of adverse conditions. The fungal lifestyle and chemoorganotrophic metabolism therefore enable adaptation and success in the frequently encountered extremophilic conditions that are associated with indoor and outdoor cultural heritage. Apart from free-living fungi, lichens are a fungal growth form and ubiquitous pioneer colonizers and biodeteriogens of outdoor materials, especially stone- and mineral-based building components. This article surveys the roles and significance of fungi in the biodeterioration of cultural heritage, with reference to the mechanisms involved and in relation to the range of substances encountered, as well as the methods by which fungal biodeterioration can be assessed and combated, and how certain fungal processes may be utilized in bioprotection.
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Affiliation(s)
- Geoffrey Michael Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- State Key Laboratory of Heavy Oil Processing, Beijing Key Laboratory of Oil and Gas Pollution Control, College of Chemical Engineering and Environment, China University of Petroleum, Beijing, China
| | - Marina Fomina
- Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National Reserve “Sophia of Kyiv”, Kyiv, Ukraine
| | - Flavia Pinzari
- Institute for Biological Systems (ISB), Council of National Research of Italy (CNR), Monterotondo (RM), Italy
- Natural History Museum, London, United Kingdom
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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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Toreno G, Zucconi L, Caneva G, Meloni P, Isola D. Recolonization dynamics of marble monuments after cleaning treatments: A nine-year follow-up study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169350. [PMID: 38103606 DOI: 10.1016/j.scitotenv.2023.169350] [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: 06/30/2023] [Revised: 11/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
The prevention and control of biological patinas on outdoor stone monuments represent a demanding challenge for the conservation of cultural heritage also due to some microorganisms, particularly resistant to treatments, such as black meristematic fungi, an eco-physiological group well known for its tolerance to extreme conditions. Even if several methods and eco-friendly products have been proposed as new alternatives, traditional biocides are still far from being completely replaced. Recolonization is a natural process that occurs sooner or later after cleaning. The time that elapses until its occurrence can vary considerably depending on environmental conditions and the used products; unfortunately, the papers describing the effect of treatments over time are rare. This work aims to shed light on the recolonization process of marble surfaces in the ancient monumental cemetery of Bonaria (Cagliari) after nine years from treatments, evaluating the long-term efficiency of two different cleaning methods, namely dimethyl sulfoxide-based gel (DMSO-based gel) and Biotin T (a didecyldimethylammonium chloride-based product-). In this context, the microflora present before treatments and in the following years was assessed by culture-based methods and identified by molecular techniques, with attention on black meristematic fungi, which were used as reference for the most resistant lithobiontic organisms. Different environmental parameters, such as temperature, exposition, dominant winds, and rainfall, were considered, and infrared thermography, portable light microscopy, and image analysis were used. This research evidenced the influence of water availability and lightning in recolonization processes, the transition from the pioneer fungal community versus more resistant black fungal species after Biotin T treatment, and the long-lasting efficiency of the DMSO-based gel. These findings prove that this low-impact method deserves more attention in the conservation of outdoor marble monuments, emphasizing the importance of long-term studies.
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Affiliation(s)
- Georgia Toreno
- Superintendency of Archaeology, Fine Arts and Landscape for the metropolitan city of Cagliari and the Provinces of Oristano and South Sardinia, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, 01100 Viterbo, Italy.
| | - Giulia Caneva
- Department of Sciences, Roma Tre University, 00146 Rome, Italy.
| | - Paola Meloni
- Department of Mechanical, Chemical and Materials Engineering (DIMCM), University of Cagliari, 09123 Cagliari, Italy; Laboratorio Colle di Bonaria, University of Cagliari, 09125 Cagliari, Italy.
| | - Daniela Isola
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; Department of Economics, Engineering, Society and Business Organization (DEIM), University of Tuscia, 01100 Viterbo, Italy.
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5
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Bartoli F, Corradi L, Hosseini Z, Privitera A, Zuena M, Kumbaric A, Graziani V, Tortora L, Sodo A, Caneva G. In Vitro Viability Tests of New Ecofriendly Nanosystems Incorporating Essential Oils for Long-Lasting Conservation of Stone Artworks. Gels 2024; 10:132. [PMID: 38391462 PMCID: PMC10888044 DOI: 10.3390/gels10020132] [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: 01/16/2024] [Revised: 02/02/2024] [Accepted: 02/04/2024] [Indexed: 02/24/2024] Open
Abstract
The study explores the application of natural biocides (oregano essential oil and eugenol, directly applied in solutions or encapsulated within silica nanocapsules) for safeguarding stone cultural heritage from biodeterioration, using green algae (Chlorococcum sp.) and cyanobacteria (Leptolyngbya sp.) as common pioneer biodeteriogens. Core-shell nanocontainers were built for a controlled release of microbicidal agents, a safe application of chemicals and a prolonged efficacy. The qualitative and quantitative evaluations of biocide efficiency at different doses were periodically performed in vitro, after six scheduled intervals of time (until 100 days). The release kinetics of composite biocide-embedding silica nanocapsules were characterized by the UV-Vis spectroscopy technique. Data showed both promising potential and some limitations. The comparative tests of different biocidal systems shed light on their variable efficacy against microorganisms, highlighting how encapsulation influences the release dynamics and the overall effectiveness. Both the essential oils showed a potential efficacy in protective antifouling coatings for stone artifacts. Ensuring compatibility with materials, understanding their differences in biocidal activity and their release rates becomes essential in tailoring gel, microemulsion or coating products for direct on-site application.
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Affiliation(s)
- Flavia Bartoli
- Institute of Heritage Science, National Research Council, ISPC-CNR, 00010 Rome, Italy
- Department of Science, University of Roma Tre, 00146 Rome, Italy
| | - Leonora Corradi
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, Ravenna Campus, Bologna University, 48121 Ravenna, Italy
| | - Zohreh Hosseini
- Department of Science, University of Roma Tre, 00146 Rome, Italy
| | | | - Martina Zuena
- Department of Science, University of Roma Tre, 00146 Rome, Italy
| | - Alma Kumbaric
- Department of Science, University of Roma Tre, 00146 Rome, Italy
| | - Valerio Graziani
- National Institute of Nuclear Physics (INFN), Roma Tre Section, 00146 Rome, Italy
| | - Luca Tortora
- National Institute of Nuclear Physics (INFN), Roma Tre Section, 00146 Rome, Italy
| | - Armida Sodo
- Department of Science, University of Roma Tre, 00146 Rome, Italy
| | - Giulia Caneva
- Department of Science, University of Roma Tre, 00146 Rome, Italy
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6
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Fu R, Sun W, Liu B, Sun J, Wu Q, Liu X, Xiang M. Genome and transcriptome reveal lithophilic adaptation of Cladophialophora brunneola, a new rock-inhabiting fungus. Mycology 2024; 14:326-343. [PMID: 38187882 PMCID: PMC10769131 DOI: 10.1080/21501203.2023.2256764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/04/2023] [Indexed: 01/09/2024] Open
Abstract
Rock-inhabiting fungi (RIF) are slow-growing microorganisms that inhabit rocks and exhibit exceptional stress tolerance owing to their thick melanised cell walls. This study reports the identification of a novel rock-inhabiting fungus, Cladophialophora brunneola sp. nov. which was isolated from a karst landform in Guizhou, China, using a combination of morphological and phylogenetic analyses. The genome of C. brunneola was sequenced and assembled, with a total size of approximately 33.8 Mb, encoding 14,168 proteins and yielding an N50 length of 1.88 Mb. C. brunneola possessed a larger proportion of species-specific genes, and phylogenomic analysis positioned it in an early diverged lineage within Chaetothyriales. In comparison to non-RIF, C. brunneola displayed reduction in carbohydrate-active enzyme families (CAZymes) and secondary metabolite biosynthetic gene clusters (BGCs). Transcriptome analysis conducted under PEG-induced drought stress revealed elevated expression levels of genes associated with melanin synthesis pathways, cell wall biosynthesis, and lipid metabolism. This study contributes to our understanding of the genomic evolution and polyextremotolerance exhibited by rock-inhabiting fungi.
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Affiliation(s)
- Rong Fu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wei Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Bingjie Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jingzu Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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7
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Irit N, Hana B, Laura R, Arielle K, Mariela P, Esti KW, Guadalupe P, Katja S, Ariel K. Trichocoleus desertorum isolated from Negev desert petroglyphs: Characterization, adaptation and bioerosion potential. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166739. [PMID: 37673239 DOI: 10.1016/j.scitotenv.2023.166739] [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: 02/01/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.
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Affiliation(s)
- Nir Irit
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Barak Hana
- Department of Civil and Environmental Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rabbachin Laura
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kahn Arielle
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Pavan Mariela
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Kramarsky-Winter Esti
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Piñar Guadalupe
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Sterflinger Katja
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kushmaro Ariel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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8
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Tenore A, Wu Y, Jacob J, Bittermann D, Villa F, Buttaro B, Klapper I. Water activity in subaerial microbial biofilms on stone monuments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165790. [PMID: 37517730 DOI: 10.1016/j.scitotenv.2023.165790] [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: 03/27/2023] [Revised: 06/30/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023]
Abstract
Stone monuments can be difficult environments for life, particularly with respect to liquid water access. Nevertheless, microbial communities are found on them with apparent ubiquity. A variety of strategies for access to liquid water have been proposed. Regardless of their water-retention mechanisms details, though, we argue that water activity (a key indicator for cell viability) is constrained by environmental conditions, largely independently of community structure, and is predicted by the local temperature and relative humidity. However, direct measurement of water activity in SABs, particularly those growing on stone surfaces, is difficult. A method for estimating water activity within SABs is presented that uses a minimally invasive combination of conservative sampling, weather data, confocal imaging, and mathematical modeling. Applying the methodology to measurements from the marble roofs of the Federal Hall National Memorial and of the Thomas Jefferson Memorial, estimations are made for water activity in their subaerial stone communities over the course of an approximately one year period.
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Affiliation(s)
- A Tenore
- Department of Mathematics, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Y Wu
- Department of Mathematics, Temple University, Philadelphia, PA, United States of America
| | - J Jacob
- U.S. National Park Service, North Atlantic-Appalachian Region, Historic Architecture, Conservation, and Engineering Program, United States of America
| | - D Bittermann
- U.S. National Park Service, North Atlantic-Appalachian Region, Historic Architecture, Conservation, and Engineering Program, United States of America
| | - F Villa
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, Milan, Italy
| | - B Buttaro
- Sol Sherry Thrombosis Research Center, Katz School of Medicine, Temple University, Philadelphia, PA, United States of America
| | - I Klapper
- Department of Mathematics, Temple University, Philadelphia, PA, United States of America.
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Paiva DS, Trovão J, Fernandes L, Mesquita N, Tiago I, Portugal A. Expanding the Microcolonial Black Fungi Aeminiaceae Family: Saxispiralis lemnorum gen. et sp. nov. ( Mycosphaerellales), Isolated from Deteriorated Limestone in the Lemos Pantheon, Portugal. J Fungi (Basel) 2023; 9:916. [PMID: 37755024 PMCID: PMC10533162 DOI: 10.3390/jof9090916] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023] Open
Abstract
With an impressive ability to survive in harsh environments, black fungi are an ecological group of melanized fungi that are widely recognized as a major contributor to the biodeterioration of stone cultural heritage materials. As part of the ongoing efforts to study the fungal diversity thriving in a deteriorated limestone funerary art piece at the Lemos Pantheon, a national monument located in Águeda, Portugal, two isolates of an unknown microcolonial black fungus were retrieved. These isolates were thoroughly studied through a comprehensive analysis based on a multi-locus phylogeny of a combined dataset of ITS rDNA, LSU, and rpb2, along with morphological, physiological, and ecological characteristics. Based on the data obtained from this integrative analysis, we propose a new genus, Saxispiralis gen. nov., and a new species, Saxispiralis lemnorum sp. nov., in the recently described Aeminiaceae family (order Mycosphaerellales). Prior to this discovery, this family only had one known genus and species, Aeminium ludgeri, also isolated from deteriorated limestone. Additionally, considering the isolation source of the fungus and to better understand its potential contribution to the overall stone monument biodeterioration, its in vitro biodeteriorative potential was also evaluated. This work represents a significant contribution to the understanding of the fungal diversity involved in the biodeterioration of limestone heritage.
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Affiliation(s)
- Diana S. Paiva
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - João Trovão
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís Fernandes
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Nuno Mesquita
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Igor Tiago
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - António Portugal
- Centre for Functional Ecology (CFE)—Science for People & the Planet, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
- FitoLab—Laboratory for Phytopathology, Instituto Pedro Nunes (IPN), Rua Pedro Nunes, 3030-199 Coimbra, Portugal
- TERRA—Associate Laboratory for Sustainable Land Use and Ecosystem Services, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
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Thitla T, Kumla J, Hongsanan S, Senwanna C, Khuna S, Lumyong S, Suwannarach N. Exploring diversity rock-inhabiting fungi from northern Thailand: a new genus and three new species belonged to the family Herpotrichiellaceae. Front Cell Infect Microbiol 2023; 13:1252482. [PMID: 37692164 PMCID: PMC10485699 DOI: 10.3389/fcimb.2023.1252482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/01/2023] [Indexed: 09/12/2023] Open
Abstract
Members of the family Herpotrichiellaceae are distributed worldwide and can be found in various habitats including on insects, plants, rocks, and in the soil. They are also known to be opportunistic human pathogens. In this study, 12 strains of rock-inhabiting fungi that belong to Herpotrichiellaceae were isolated from rock samples collected from forests located in Lamphun and Sukhothai provinces of northern Thailand during the period from 2021 to 2022. On the basis of the morphological characteristics, growth temperature, and multi-gene phylogenetic analyses of a combination of the internal transcribed spacer, the large subunit, and the small subunit of ribosomal RNA, beta tubulin and the translation elongation factor 1-a genes, the new genus, Petriomyces gen. nov., has been established to accommodate the single species, Pe. obovoidisporus sp. nov. In addition, three new species of Cladophialophora have also been introduced, namely, Cl. rupestricola, Cl. sribuabanensis, and Cl. thailandensis. Descriptions, illustrations, and a phylogenetic trees indicating the placement of these new taxa are provided. Here, we provide updates and discussions on the phylogenetic placement of other fungal genera within Herpotrichiellaceae.
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Affiliation(s)
- Tanapol Thitla
- Master of Science Program in Applied Microbiology (International Program), Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jaturong Kumla
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Sinang Hongsanan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Chanokned Senwanna
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Surapong Khuna
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Saisamorn Lumyong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok, Thailand
| | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Center of Excellence in Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
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11
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Carr EC, Barton Q, Grambo S, Sullivan M, Renfro CM, Kuo A, Pangilinan J, Lipzen A, Keymanesh K, Savage E, Barry K, Grigoriev IV, Riekhof WR, Harris SD. Characterization of a novel polyextremotolerant fungus, Exophiala viscosa, with insights into its melanin regulation and ecological niche. G3 (BETHESDA, MD.) 2023; 13:jkad110. [PMID: 37221014 PMCID: PMC10411609 DOI: 10.1093/g3journal/jkad110] [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: 02/22/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/25/2023]
Abstract
Black yeasts are polyextremotolerant fungi that contain high amounts of melanin in their cell wall and maintain a primar yeast form. These fungi grow in xeric, nutrient depletes environments which implies that they require highly flexible metabolisms and have been suggested to contain the ability to form lichen-like mutualisms with nearby algae and bacteria. However, the exact ecological niche and interactions between these fungi and their surrounding community are not well understood. We have isolated 2 novel black yeasts from the genus Exophiala that were recovered from dryland biological soil crusts. Despite notable differences in colony and cellular morphology, both fungi appear to be members of the same species, which has been named Exophiala viscosa (i.e. E. viscosa JF 03-3 Goopy and E. viscosa JF 03-4F Slimy). A combination of whole genome sequencing, phenotypic experiments, and melanin regulation experiments have been performed on these isolates to fully characterize these fungi and help decipher their fundamental niche within the biological soil crust consortium. Our results reveal that E. viscosa is capable of utilizing a wide variety of carbon and nitrogen sources potentially derived from symbiotic microbes, can withstand many forms of abiotic stresses, and excretes melanin which can potentially provide ultraviolet resistance to the biological soil crust community. Besides the identification of a novel species within the genus Exophiala, our study also provides new insight into the regulation of melanin production in polyextremotolerant fungi.
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Affiliation(s)
- Erin C Carr
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Quin Barton
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Sarah Grambo
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Mitchell Sullivan
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Cecile M Renfro
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Keykhosrow Keymanesh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Wayne R Riekhof
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Steven D Harris
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50011, USA
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12
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Němečková K, Mareš J, Procházková L, Culka A, Košek F, Wierzchos J, Nedbalová L, Dudák J, Tymlová V, Žemlička J, Kust A, Zima J, Nováková E, Jehlička J. Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition. Front Microbiol 2023; 14:1175066. [PMID: 37485515 PMCID: PMC10359912 DOI: 10.3389/fmicb.2023.1175066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/15/2023] [Indexed: 07/25/2023] Open
Abstract
In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.
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Affiliation(s)
- Kateřina Němečková
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Mareš
- Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czechia
- Center Algatech, Institute of Microbiology, The Czech Academy of Sciences, Třeboň, Czechia
| | - Lenka Procházková
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Adam Culka
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Filip Košek
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
| | - Jacek Wierzchos
- Department of Biochemistry and Microbial Ecology, Museo Nacional de Ciencias Naturales - Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Linda Nedbalová
- Department of Ecology, Faculty of Science, Charles University, Prague, Czechia
| | - Jan Dudák
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Veronika Tymlová
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Jan Žemlička
- Institute of Experimental and Applied Physics, Czech Technical University in Prague, Prague, Czechia
| | - Andreja Kust
- Department of Earth and Planetary Science, University of Berkeley, Berkeley, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jan Zima
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Eva Nováková
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Jan Jehlička
- Institute of Geochemistry, Mineralogy and Mineral Resources, Faculty of Science, Charles University, Prague, Czechia
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13
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Berti L, Marvasi M, Perito B. Characterization of the Community of Black Meristematic Fungi Inhabiting the External White Marble of the Florence Cathedral. J Fungi (Basel) 2023; 9:665. [PMID: 37367601 DOI: 10.3390/jof9060665] [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: 05/22/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/28/2023] Open
Abstract
Meristematic black fungi are a highly damaging group of microorganisms responsible for the deterioration of outdoor exposed monuments. Their resilience to various stresses poses significant challenges for removal efforts. This study focuses on the community of meristematic fungi inhabiting the external white marble of the Cathedral of Santa Maria del Fiore, where they contribute to its darkening. Twenty-four strains were isolated from two differently exposed sites of the Cathedral, and their characterization was conducted. Phylogenetic analysis using ITS and LSU rDNA regions revealed a wide diversity of rock-inhabiting fungal strains within the sampled areas. Eight strains, belonging to different genera, were also tested for thermal preferences, salt tolerance, and acid production to investigate their tolerance to environmental stressors and their interaction with stone. All tested strains were able to grow in the range of 5-30 °C, in the presence 5% NaCl, and seven out of eight strains were positive for the production of acid. Their sensitivities to essential oils of thyme and oregano and to the commercial biocide Biotin T were also tested. The essential oils were found to be the most effective against black fungi growth, indicating the possibility of developing a treatment with a low environmental impact.
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Affiliation(s)
- Letizia Berti
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
- Department of Sciences of Antiquity, "La Sapienza" University of Rome, Piazzale Aldo Moro 5, 00186 Rome, Italy
| | - Massimiliano Marvasi
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
| | - Brunella Perito
- Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy
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14
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Chen J, Zhao Q, Li F, Zhao X, Wang Y, Zhang L, Liu J, Yan L, Yu L. Nutrient availability and acid erosion determine the early colonization of limestone by lithobiontic microorganisms. Front Microbiol 2023; 14:1194871. [PMID: 37362915 PMCID: PMC10289080 DOI: 10.3389/fmicb.2023.1194871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Microorganisms, including the pioneer microorganisms that play a role in the early colonization of rock, are extremely important biological factors in rock deterioration. The interaction of microorganisms with limestone leads to biodeterioration, accelerates soil formation, and plays an important role in the restoration of degraded ecosystems that cannot be ignored. However, the process of microbial colonization of sterile limestone in the early stages of ecological succession is unclear, as are the factors that affect the colonization. Acid erosion (both organic and inorganic), nutrient availability, and water availability are thought to be key factors affecting the colonization of lithobiontic microorganisms. Methods In this study, organic acid (Oa), inorganic acid (Ia), inorganic acid + nutrient solution (Ia + Nut), nutrient solution (Nut), and rain shade (RS) treatments were applied to sterilized limestone, and the interaction between microorganisms and limestone was investigated using high-throughput sequencing techniques to assess the microorganisms on the limestone after 60 days of natural placement. Results The results were as follows: (1) The abundance of fungi was higher than that of bacteria in the early colonization of limestone, and the dominant bacterial phyla were Proteobacteria, Bacteroidota, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Chytridiomycota. (2) Acid erosion and nutrient availability shaped different microbial communities in different ways, with bacteria being more sensitive to the environmental stresses than fungi, and the higher the acidity (Ia and Oa)/nutrient concentration, the greater the differences in microbial communities compared to the control (based on principal coordinate analysis). (3) Fungal communities were highly resistant to environmental stress and competitive, while bacterial communities were highly resilient to environmental stress and stable. Discussion In conclusion, our results indicate that limestone exhibits high bioreceptivity and can be rapidly colonized by microorganisms within 60 days in its natural environment, and both nutrient availability and acid erosion of limestone are important determinants of early microbial colonization.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Qing Zhao
- School of Mathematical Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Fangbing Li
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Xiangwei Zhao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Yang Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Limin Zhang
- Institute of Guizhou Mountain Resources, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Jinan Liu
- Garden Greening Center of Logistics Management Office, Guizhou University, Guiyang, Guizhou, China
| | - Lingbin Yan
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
| | - Lifei Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou, China
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15
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Rizk SM, Magdy M, De Leo F, Werner O, Rashed MAS, Ros RM, Urzì C. Culturable and unculturable potential heterotrophic microbiological threats to the oldest pyramids of the Memphis necropolis, Egypt. Front Microbiol 2023; 14:1167083. [PMID: 37275160 PMCID: PMC10232867 DOI: 10.3389/fmicb.2023.1167083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/27/2023] [Indexed: 06/07/2023] Open
Abstract
A large percentage of the world's tangible cultural heritage is made from stone; thus, it deteriorates due to physical, chemical, and/or biological factors. The current study explored the microbial community inhabiting two prehistoric sites with high cultural value in the Memphis necropolis of Egypt (Djoser and Lahun Pyramids) using amplicon-based metabarcoding and culture-dependent isolation methods. Samples were examined by epifluorescent microscopy for biological signs before environmental DNA extraction and in vitro cultivation. The metabarcoding analysis identified 644 bacterial species (452 genera) using the 16S rRNA and 204 fungal species (146 genera) using ITS. In comparison with the isolation approach, an additional 28 bacterial species (13 genera) and 34 fungal species (20 genera) were identified. A total of 19 bacterial and 16 fungal species were exclusively culture-dependent, while 92 bacterial and 122 fungal species were culture-independent. The most abundant stone-inhabiting bacteria in the current study were Blastococcus aggregatus, Blastococcus saxobsidens, and Blastococcus sp., among others. The most abundant rock-inhabiting fungi were Knufia karalitana and Pseudotaeniolina globosa, besides abundant unknown Sporormiaceae species. Based on previous reports, microorganisms associated with biodeterioration were detected on color-altered sites at both pyramids. These microorganisms are potentially dangerous as physical and chemical deterioration factors and require proper conservation plans from a microbiological perspective.
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Affiliation(s)
- Samah Mohamed Rizk
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| | - Filomena De Leo
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
| | - Olaf Werner
- Department of Plant Biology, Faculty of Biology, Murcia University, Murcia, Spain
| | | | - Rosa M. Ros
- Department of Plant Biology, Faculty of Biology, Murcia University, Murcia, Spain
| | - Clara Urzì
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
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16
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McCourt RM, Lewis LA, Strother PK, Delwiche CF, Wickett NJ, de Vries J, Bowman JL. Green land: Multiple perspectives on green algal evolution and the earliest land plants. AMERICAN JOURNAL OF BOTANY 2023; 110:e16175. [PMID: 37247371 DOI: 10.1002/ajb2.16175] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/10/2023] [Accepted: 03/10/2023] [Indexed: 05/31/2023]
Abstract
Green plants, broadly defined as green algae and the land plants (together, Viridiplantae), constitute the primary eukaryotic lineage that successfully colonized Earth's emergent landscape. Members of various clades of green plants have independently made the transition from fully aquatic to subaerial habitats many times throughout Earth's history. The transition, from unicells or simple filaments to complex multicellular plant bodies with functionally differentiated tissues and organs, was accompanied by innovations built upon a genetic and phenotypic toolkit that have served aquatic green phototrophs successfully for at least a billion years. These innovations opened an enormous array of new, drier places to live on the planet and resulted in a huge diversity of land plants that have dominated terrestrial ecosystems over the past 500 million years. This review examines the greening of the land from several perspectives, from paleontology to phylogenomics, to water stress responses and the genetic toolkit shared by green algae and plants, to the genomic evolution of the sporophyte generation. We summarize advances on disparate fronts in elucidating this important event in the evolution of the biosphere and the lacunae in our understanding of it. We present the process not as a step-by-step advancement from primitive green cells to an inevitable success of embryophytes, but rather as a process of adaptations and exaptations that allowed multiple clades of green plants, with various combinations of morphological and physiological terrestrialized traits, to become diverse and successful inhabitants of the land habitats of Earth.
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Affiliation(s)
- Richard M McCourt
- Department of Biodiversity, Earth, and Environmental Sciences, Drexel University, Philadelphia, PA, 19118, USA
| | - Louise A Lewis
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Paul K Strother
- Department of Earth and Environmental Sciences, Boston College Weston Observatory, 381 Concord Road, Weston, MA, 02493, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Norman J Wickett
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
| | - Jan de Vries
- Göttingen Center for Molecular Biosciences, Department of Applied Bioinformatics, University of Göttingen Goldschmidtstr. 1, Göttingen, 37077, Germany
| | - John L Bowman
- School of Biological Sciences, Monash University, Clayton Campus, Melbourne, Victoria, 3800, Australia
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17
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Bontemps Z, Prigent-Combaret C, Guillmot A, Hugoni M, Moënne-Loccoz Y. Dark-zone alterations expand throughout Paleolithic Lascaux Cave despite spatial heterogeneity of the cave microbiome. ENVIRONMENTAL MICROBIOME 2023; 18:31. [PMID: 37032363 PMCID: PMC10084675 DOI: 10.1186/s40793-023-00488-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Cave anthropization related to rock art tourism can lead to cave microbiota imbalance and microbial alterations threatening Paleolithic artwork, but the underpinning microbial changes are poorly understood. Caves can be microbiologically heterogeneous and certain rock wall alterations may develop in different rooms despite probable spatial heterogeneity of the cave microbiome, suggesting that a same surface alteration might involve a subset of cosmopolitan taxa widespread in each cave room. We tested this hypothesis in Lascaux, by comparing recent alterations (dark zones) and nearby unmarked surfaces in nine locations within the cave. RESULTS Illumina MiSeq metabarcoding of unmarked surfaces confirmed microbiome heterogeneity of the cave. Against this background, the microbial communities of unmarked and altered surfaces differed at each location. The use of a decision matrix showed that microbiota changes in relation to dark zone formation could differ according to location, but dark zones from different locations displayed microbial similarities. Thus, dark zones harbor bacterial and fungal taxa that are cosmopolitan at the scale of Lascaux, as well as dark zone-specific taxa present (i) at all locations in the cave (i.e. the six bacterial genera Microbacterium, Actinophytocola, Lactobacillus, Bosea, Neochlamydia and Tsukamurella) or (ii) only at particular locations within Lascaux. Scanning electron microscopy observations and most qPCR data evidenced microbial proliferation in dark zones. CONCLUSION Findings point to the proliferation of different types of taxa in dark zones, i.e. Lascaux-cosmopolitan bacteria and fungi, dark zone-specific bacteria present at all locations, and dark zone-specific bacteria and fungi present at certain locations only. This probably explains why dark zones could form in various areas of the cave and suggests that the spread of these alterations might continue according to the area of distribution of key widespread taxa.
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Affiliation(s)
- Zélia Bontemps
- CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, University of Lyon, Université Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne, France
| | - Claire Prigent-Combaret
- CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, University of Lyon, Université Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne, France
| | - Alice Guillmot
- CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, University of Lyon, Université Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne, France
| | - Mylène Hugoni
- CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, University of Lyon, Université Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne, France
- CNRS, INSA de Lyon, UMR Microbiologie Adaptation et Pathogénie, University of Lyon, Université Claude Bernard Lyon 1, 69622, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
| | - Yvan Moënne-Loccoz
- CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, University of Lyon, Université Claude Bernard Lyon 1, 43 Bd du 11 Novembre 1918, 69622, Villeurbanne, France.
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18
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Villa F, Ludwig N, Mazzini S, Scaglioni L, Fuchs AL, Tripet B, Copié V, Stewart PS, Cappitelli F. A desiccated dual-species subaerial biofilm reprograms its metabolism and affects water dynamics in limestone. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161666. [PMID: 36669662 DOI: 10.1016/j.scitotenv.2023.161666] [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: 10/23/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
Understanding the impact of sessile communities on underlying materials is of paramount importance in stone conservation. Up until now, the critical role of subaerial biofilms (SABs) whether they are protective or deteriorative remains unclear, especially under desiccation. The interest in desiccated SABs is raised by the prediction of an increase in drought events in the next decades that will affect the Mediterranean regions' rich stone heritage as never before. Thus, the main goal of this research is to study the effects of desiccation on both the biofilms' eco-physiology and its impacts on the lithic substrate. To this end, we used a dual-species model system composed of a phototroph and a chemotroph to simulate biofilm behavior on stone heritage. We found that drought altered the phototroph-chemotroph balance and enriched the biofilm matrix with proteins and DNA. Desiccated SABs underwent a shift in metabolism to fermentation and a decrease in oxidative stress. Additionally, desiccated SABs changed the water-related dynamics (adsorption, evaporation, and wetting properties) in limestone. Water absorption experiments showed that desiccated SABs protected the stone from rapid water uptake, while a thermographic survey indicated a delay in water evaporation. Spilling-drop tests revealed a change in the wettability of the stone-SAB interface, which affected the water transport properties of the stone. Finally, desiccated SABs reduced stone swelling in the presence of water vapor. The biodeteriorative and bioprotective implications of desiccated SABs on the stone were ultimately assessed.
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Affiliation(s)
- F Villa
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - N Ludwig
- Dipartimento di Fisica Aldo Pontremoli, Università degli Studi di Milano, 20133 Milan, Italy.
| | - S Mazzini
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - L Scaglioni
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
| | - A L Fuchs
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, USA
| | - B Tripet
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, USA.
| | - V Copié
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, USA.
| | - P S Stewart
- Center for Biofilm Engineering, Montana State University, Bozeman 59717, USA.
| | - F Cappitelli
- Dipartimento di Scienze per gli Alimenti, la Nutrizione e l'Ambiente, Università degli Studi di Milano, 20133 Milan, Italy.
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19
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Sanmartín P, Bosch-Roig P, Pangallo D, Kraková L, Serrano M. Unraveling disparate roles of organisms, from plants to bacteria, and viruses on built cultural heritage. Appl Microbiol Biotechnol 2023; 107:2027-2037. [PMID: 36820899 PMCID: PMC9947938 DOI: 10.1007/s00253-023-12423-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/19/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023]
Abstract
The different organisms, ranging from plants to bacteria, and viruses that dwell on built cultural heritage can be passive or active participants in conservation processes. For the active participants, particular attention is generally given to organisms that play a positive role in bioprotection, bioprecipitation, bioconsolidation, bioremediation, biocleaning, and biological control and to those involved in providing ecosystem services, such as reducing temperature, pollution, and noise in urban areas. The organisms can also evolve or mutate in response to changes, becoming tolerant and resistant to biocidal treatments or acquiring certain capacities, such as water repellency or resistance to ultraviolet radiation. Our understanding of the capacities and roles of these active organisms is constantly evolving as bioprotection/biodeterioration, and biotreatment studies are conducted and new techniques for characterizing species are developed. This brief review article aims to shed light on interesting research that has been abandoned as well as on recent (some ongoing) studies opening up new scopes of research involving a wide variety of organisms and viruses, which are likely to receive more attention in the coming years. KEY POINTS: • Organisms and viruses can be active or passive players in heritage conservation • Biotreatment and ecosystem service studies involving organisms and viruses are shown • Green deal, health, ecosystem services, and global change may shape future research.
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Affiliation(s)
- Patricia Sanmartín
- grid.11794.3a0000000109410645GEMAP (GI-1243), Departamento de Edafoloxía e Química Agrícola, Facultade de Farmacia, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
- grid.11794.3a0000000109410645CRETUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pilar Bosch-Roig
- grid.157927.f0000 0004 1770 5832Instituto Universitario de Restauración del Patrimonio, Dpto. Conservación y Restauración del Patrimonio, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Domenico Pangallo
- grid.419303.c0000 0001 2180 9405Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
- Caravella, s.r.o., Tupolevova 2, 851 01 Bratislava, Slovakia
| | - Lucia Kraková
- grid.419303.c0000 0001 2180 9405Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Miguel Serrano
- grid.11794.3a0000000109410645Department of Botany, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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20
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Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland. Microorganisms 2023; 11:microorganisms11030665. [PMID: 36985243 PMCID: PMC10057085 DOI: 10.3390/microorganisms11030665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey’s air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site’s nature and location.
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21
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Sazanova KV, Ponizovskaya VB. Metabolite Profile of the Micromycete Lecanicillium gracile Isolated from Plaster and Limestone. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 507:456-462. [PMID: 36781540 DOI: 10.1134/s0012496622060205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 02/15/2023]
Abstract
Lecanicillium gracile is a recently described micromycete species isolated from mineral-based building materials (plaster and limestone) in interiors of cultural heritage sites in Russia. In this work, the composition of L. gracile metabolites, as well as of the culture liquid, have been characterized. The results suggest that L. gracile is a promising candidate for the search for novel biologically active compounds. During the exponential growth phase, the diversity of metabolites in the mycelium was low; the metabolome profile demonstrated predominant accumulation of monosaccharides and polyols. In the stationary phase, the metabolite diversity in the L. gracile mycelium was high; apparently, at this stage biosynthesis dominated over energy-producing processes. L. gracile synthesized extracellular polymer compounds and shifted medium рН to the alkaline range. When fungi are developing on rock substrates, their extracellular polymer matrix not only serves to facilitate the formation of biofilms with other microorganisms of lithobiont communities, but also, at alkaline pH values, it promotes the formation of secondary calcite on calcium-containing substrates, such as limestone and marble. That is, L. gracile possesses certain biochemical traits that facilitate its long-term growth on rock substrates and reflect the specific character of interactions between the fungus and the substrate materials.
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Affiliation(s)
- K V Sazanova
- Komarov Botanical Institute, Russian Academy of Sciences, 197376, St. Petersburg, Russia. .,St. Petersburg Branch of the Archive of the Russian Academy of Sciences, 196084, St. Petersburg, Russia.
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22
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Three New Plectolyngbya Species (Leptolyngbyaceae, Cyanobacteria) Isolated from Rocks and Saltern of the Republic of Korea. DIVERSITY 2022. [DOI: 10.3390/d14121013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Thin filamentous cyanobacteria isolated from three collection sites in the Republic of Korea were suggested as three new species belonging to the genus Plectolyngbya, mainly according to their molecular characteristics. The species of Plectolyngbya, including the type species of P. hodgsonii, were cryptic species that were difficult to distinguish morphologically from each other, and had appeared in ecologically diverse habitats. P. terrestris and P. koreana were subaerophytes collected from certain black spots and soils between stone walls in Seoul, Republic of Korea. In addition, hypersaline species collected from a saltern, P. salina, shared the same halophytic feature as the P. hodgsonii from the littoral zone of a coastal lake in the Antarctic. The 16S rRNA gene phylogeny supported the monophyly of Plectolyngbya with solid support, 99% Maximum Likelihood, 98% Neighbor-Joining bootstrap support values, and 1.0 Bayesian posterior probability. The ITS sequences of P. terrestris, P. koreana, and P. salina were unique in length and nucleotide composition, with different secondary structures of D1–D1ʹ and Box-B helices, compared with those of P. hodgsonii. These results demonstrate that the proposed new Plectolyngbya species were unique in their molecular traits. Therefore, we suggest them as new species belonging to the genus Plectolyngbya with the names P. terrestris sp. nov., P. koreana sp. nov., and P. salina sp. nov.
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23
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Chen J, Li F, Zhao X, Wang Y, Zhang L, Yan L, Yu L. Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times. Front Microbiol 2022; 13:1024672. [PMID: 36386643 PMCID: PMC9663929 DOI: 10.3389/fmicb.2022.1024672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/04/2022] [Indexed: 11/26/2022] Open
Abstract
Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Fangbing Li
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Xiangwei Zhao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Yang Wang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Limin Zhang
- Institute of Guizhou Mountain Resources, Guizhou Academy of Sciences, Guiyang, Guizhou, China
| | - Lingbin Yan
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China
| | - Lifei Yu
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences and Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou,China,*Correspondence: Lifei Yu,
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24
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Raya D, Shreya A, Kumar A, Giri SK, Salem DR, Gnimpieba EZ, Gadhamshetty V, Dhiman SS. Molecular regulation of conditioning film formation and quorum quenching in sulfate reducing bacteria. Front Microbiol 2022; 13:1008536. [PMID: 36386676 PMCID: PMC9659907 DOI: 10.3389/fmicb.2022.1008536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/26/2022] [Indexed: 09/19/2023] Open
Abstract
Sensing surface topography, an upsurge of signaling biomolecules, and upholding cellular homeostasis are the rate-limiting spatio-temporal events in microbial attachment and biofilm formation. Initially, a set of highly specialized proteins, viz. conditioning protein, directs the irreversible attachment of the microbes. Later signaling molecules, viz. autoinducer, take over the cellular communication phenomenon, resulting in a mature microbial biofilm. The mandatory release of conditioning proteins and autoinducers corroborated the existence of two independent mechanisms operating sequentially for biofilm development. However, both these mechanisms are significantly affected by the availability of the cofactor, e.g., Copper (Cu). Generally, the Cu concentration beyond threshold levels is detrimental to the anaerobes except for a few species of sulfate-reducing bacteria (SRB). Remarkably SRB has developed intricate ways to resist and thrive in the presence of Cu by activating numerous genes responsible for modifying the presence of more toxic Cu(I) to Cu(II) within the periplasm, followed by their export through the outer membrane. Therefore, the determinants of Cu toxicity, sequestration, and transportation are reconnoitered for their contribution towards microbial adaptations and biofilm formation. The mechanistic details revealing Cu as a quorum quencher (QQ) are provided in addition to the three pathways involved in the dissolution of cellular communications. This review articulates the Machine Learning based data curing and data processing for designing novel anti-biofilm peptides and for an in-depth understanding of QQ mechanisms. A pioneering data set has been mined and presented on the functional properties of the QQ homolog in Oleidesulfovibrio alaskensis G20 and residues regulating the multicopper oxidase properties in SRB.
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Affiliation(s)
- Dheeraj Raya
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Aritree Shreya
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Anil Kumar
- Centre for Medical Biotechnology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Shiv Kumar Giri
- Department of Biotechnology, Maharaja Agrasen University, Baddi, Himachal Pradesh, India
| | - David R. Salem
- Chemical and Biological Engineering, South Dakota Mines, Rapid City, SD, United States
| | - Etienne Z. Gnimpieba
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
- Department of Biomedical Engineering, University of South Dakota, Vermillion, SD, United States
| | - Venkataramana Gadhamshetty
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
| | - Saurabh Sudha Dhiman
- Department of Civil and Environmental Engineering, South Dakota Mines, Rapid City, SD, United States
- 2DBEST Research Center, South Dakota Mines, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Sciences, South Dakota Mines, Rapid City, SD, United States
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25
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Villa F, Wu YL, Zerboni A, Cappitelli F. In Living Color: Pigment-Based Microbial Ecology At the Mineral-Air Interface. Bioscience 2022; 72:1156-1175. [PMID: 36451971 PMCID: PMC9699719 DOI: 10.1093/biosci/biac091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pigment-based color is one of the most important phenotypic traits of biofilms at the mineral-air interface (subaerial biofilms, SABs), because it reflects the physiology of the microbial community. Because color is the hallmark of all SABs, we argue that pigment-based color could convey the mechanisms that drive microbial adaptation and coexistence across different terrestrial environments and link phenotypic traits to community fitness and ecological dynamics. Within this framework, we present the most relevant microbial pigments at the mineral-air interface and discuss some of the evolutionary landscapes that necessitate pigments as adaptive strategies for resource allocation and survivability. We report several pigment features that reflect SAB communities' structure and function, as well as pigment ecology in the context of microbial life-history strategies and coexistence theory. Finally, we conclude the study of pigment-based ecology by presenting its potential application and some of the key challenges in the research.
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26
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Wu F, Zhang Y, Gu JD, He D, Zhang G, Liu X, Guo Q, Cui H, Zhao J, Feng H. Community assembly, potential functions and interactions between fungi and microalgae associated with biodeterioration of sandstone at the Beishiku Temple in Northwest China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 835:155372. [PMID: 35489512 DOI: 10.1016/j.scitotenv.2022.155372] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 05/11/2023]
Abstract
Fungi, cyanobacteria and algae are specific microbial groups associated with the deterioration and safety of stone monuments. In this study, high-throughput sequencing analysis was used to investigate the diversity, distributions, ecological functions, and interaction patterns of both the fungal and microalgal (including cyanobacteria and algae) communities on sandstone in the Beishiku Temple, located on the ancient Silk Road. The results showed that the core phyla of fungi were affiliated with unclassified Lecanoromycetes, Engyodontium, Knufia, Epicoccum, Endocarpon, and Cladosporium of Ascomycota whereas the phyla of microalgae were dominated by prokaryotic Cyanobacteria and eukaryotic Chlorophyta. The environmental factors of temperature, relative humidity, and light intensity were monitored simultaneously. The structure of the microbial communities was much more strongly shaped by soluble Cl-, Na+, NO3- ions than by the light intensity, moisture content or temperature, especially for the weathered sandstone located outside the caves. The co-occurrence network analysis suggested that a more stable community structure was evident outside the caves than inside. The stronger positive connections and coexistence patterns that were detected indicate a strong adaptability of fungi and microalgae to the distinct oligotrophic microhabitats on sandstone. The metacommunity co-occurrence network exhibited the ecological predominance of fungi, and most of the functional fungi in the biofilms outside the caves belonged to the Lichenized group, based on the FUNGuild prediction. These findings highlight the ecology and functions of stone-inhabiting microorganisms to further advance the current understanding and knowledge of sandstone biodeterioration for protection and management.
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Affiliation(s)
- Fasi Wu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Center of Grassland Microbiome, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China; National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Yong Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Center of Grassland Microbiome, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China
| | - Ji-Dong Gu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, PR China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, PR China
| | - Dongpeng He
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, Gansu 730000, PR China
| | - Xiaobo Liu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong 515063, PR China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, Jiangsu, PR China
| | - Qinglin Guo
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Huiping Cui
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu 736200, PR China
| | - Jianhua Zhao
- Shanghai Majorbio Bio-pharm Technology Co., Ltd., Shanghai 200120, PR China
| | - Huyuan Feng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, Center of Grassland Microbiome, School of Life Sciences, Lanzhou University, Lanzhou, Gansu 730000, PR China.
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27
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Vidović K, Hočevar S, Menart E, Drventić I, Grgić I, Kroflič A. Impact of air pollution on outdoor cultural heritage objects and decoding the role of particulate matter: a critical review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:46405-46437. [PMID: 35501442 DOI: 10.1007/s11356-022-20309-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/13/2022] [Indexed: 05/27/2023]
Abstract
Atmospheric gases and particulate matter (PM) in contact with the material's surface lead to chemical and physical changes, which in most cases cause degradation of the cultural heritage material. Atmospheric damage and soiling are recognized as two pivotal forms of deterioration of cultural heritage materials caused by air pollution. However, the atmospheric damage effect of PM is rather complicated; its variable composition accelerates the deterioration process. Considering this, one of the important contributions of this work is to review the existing knowledge on PM influence on atmospheric damage, further recognize, and critically evaluate the main gaps in current understanding. The second phenomenon related to cultural heritage material and PM pollution is soiling. Even if soiling was recognized long ago, its definition and knowledge have not changed much for several decades. In the past, it was believed that black carbon (BC) was the primary soiling agent and that the change of the lightness could effectively measure the soiling. With the change of pollution situation, the lightness measurements do not represent the degree of soiling correctly. The additional contribution of this work is thus, the critical evaluation of soiling measurements, and accordingly, due to the change of pollution situation, redefinition of soiling is proposed. Even though numerous studies have treated soiling and atmospheric damage separately, there is an overlap between these two processes. No systematic studies exist on the synergy between soiling and atmospheric damage caused by atmospheric PM.
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Affiliation(s)
- Kristijan Vidović
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.
| | - Samo Hočevar
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Eva Menart
- National Museum of Slovenia, Muzejska ulica 1, 1000, Ljubljana, Slovenia
- Jožef Stefan Institute, Jamova 39, 1000, Ljubljana, Slovenia
| | - Ivana Drventić
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Irena Grgić
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
| | - Ana Kroflič
- Department of Analytical Chemistry, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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Anglés A, He Q, Sánchez García L, Carrizo D, Rodriguez N, Huang T, Shen Y, Amils R, Fernández-Remolar DC. Biospeleothems Formed by Fungal Activity During the Early Holocene in the “Salar de Uyuni”. Front Microbiol 2022; 13:913452. [PMID: 35814676 PMCID: PMC9260512 DOI: 10.3389/fmicb.2022.913452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/28/2022] [Indexed: 11/28/2022] Open
Abstract
The Chiquini and Galaxias caves contain speleothems that are templated by long fungal structures. They have been associated with the carbonate lacustrine deposits in the margins of the Coipasa and Uyuni Salar basins. During a wetter episode, such carbonates formed at the end of the last glaciation raising the lake level to more than 100 m in the Tauca events (15–12 ky). Such an event flooded the caves that eventually became a cryptic habitat in the lake. The caves show bizarre speleothems framed by large (>1 m) fungal buildings covering the older algal mineralized structures. Although the origin of the caves is not fully understood, the occurrence of two carbonatic units with very distinctive fabric suggests that they formed in two separated humid events. In this regard, the mineralized algal structures, showing the same features as the lacustrine carbonates, likely formed during the Tauca flooding events in the terminal Pleistocene that inundated older caves. The different caves were exposed to the atmosphere after a drop in the lake level that promoted alluvial erosion by <12–10 ky (Ticaña episode) under arid conditions. A last humid episode rising the lake surface 10 m above the Salar level, which was not enough to inundate the caves a second time, drove the formation of the biospeleothems by fungi biomineralization. The abundance and size of the preserved fungal structures suggest that they were sustained by a stable hydrological activity plus a constant organic supply. While nutrients could have been primarily sourced from the vegetal communities that occupied the exhumated lake margins, they might have also been released from the lacustrine carbonatic unit. The combination of hydrology and biological activities were likely determinants for a fast rock dissolution and mineralization ending in the construction of the fungal biospeleothems.
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Affiliation(s)
- Angélica Anglés
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
- Blue Marble Space Institute of Science, Seattle, WA, United States
- *Correspondence: Angélica Anglés
| | - Qitao He
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
| | - Laura Sánchez García
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - Daniel Carrizo
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - Nuria Rodriguez
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - Ting Huang
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
| | - Yan Shen
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
| | - Ricardo Amils
- Centro de Astrobiología Instituto Nacional de Tecnica Aeroespacial - Consejo Superior de Investigaciones Científicas (INTA-CSIC), Madrid, Spain
| | - David C. Fernández-Remolar
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Macau, China
- China National Space Administration (CNSA) Macau Center for Space Exploration and Science, Macau, China
- Carl Sagan Center, The SETI Institute, Mountain View, CA, United States
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29
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Holistic Approach to the Restoration of a Vandalized Monument: The Cross of the Inquisition, Seville City Hall, Spain. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12126222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The Cross of the Inquisition, sculpted in 1903 and raised on a column with a fluted shaft and ornamented with vegetable garlands, is located in a corner of the Plateresque façade of the Seville City Hall. The Cross was vandalized in September 2019 and the restoration concluded in September 2021. A geological and microbiological study was carried out in a few small fragments. The data are consistent with the exposure of the Cross of the Inquisition to an urban environment for more than 100 years. During that time, a lichen community colonized the Cross and the nearby City Hall façades. The lichens, bryophytes and fungi colonizing the limestone surface composed an urban community, regenerated from the remains of the original communities, after superficial cleaning of the limestone between 2008 and 2010. This biological activity was detrimental to the integrity of the limestone, as showed by the pitting and channels, which evidence the lytic activity of organisms on the stone surface. Stone consolidation was achieved with Estel 1000. Preventol RI80, a biocide able to penetrate the porous limestone and active against bacteria, fungi, lichens, and bryophytes, was applied in the restoration.
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Kminek G, Benardini JN, Brenker FE, Brooks T, Burton AS, Dhaniyala S, Dworkin JP, Fortman JL, Glamoclija M, Grady MM, Graham HV, Haruyama J, Kieft TL, Koopmans M, McCubbin FM, Meyer MA, Mustin C, Onstott TC, Pearce N, Pratt LM, Sephton MA, Siljeström S, Sugahara H, Suzuki S, Suzuki Y, van Zuilen M, Viso M. COSPAR Sample Safety Assessment Framework (SSAF). ASTROBIOLOGY 2022; 22:S186-S216. [PMID: 35653292 DOI: 10.1089/ast.2022.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The Committee on Space Research (COSPAR) Sample Safety Assessment Framework (SSAF) has been developed by a COSPAR appointed Working Group. The objective of the sample safety assessment would be to evaluate whether samples returned from Mars could be harmful for Earth's systems (e.g., environment, biosphere, geochemical cycles). During the Working Group's deliberations, it became clear that a comprehensive assessment to predict the effects of introducing life in new environments or ecologies is difficult and practically impossible, even for terrestrial life and certainly more so for unknown extraterrestrial life. To manage expectations, the scope of the SSAF was adjusted to evaluate only whether the presence of martian life can be excluded in samples returned from Mars. If the presence of martian life cannot be excluded, a Hold & Critical Review must be established to evaluate the risk management measures and decide on the next steps. The SSAF starts from a positive hypothesis (there is martian life in the samples), which is complementary to the null-hypothesis (there is no martian life in the samples) typically used for science. Testing the positive hypothesis includes four elements: (1) Bayesian statistics, (2) subsampling strategy, (3) test sequence, and (4) decision criteria. The test sequence capability covers self-replicating and non-self-replicating biology and biologically active molecules. Most of the investigations associated with the SSAF would need to be carried out within biological containment. The SSAF is described in sufficient detail to support planning activities for a Sample Receiving Facility (SRF) and for preparing science announcements, while at the same time acknowledging that further work is required before a detailed Sample Safety Assessment Protocol (SSAP) can be developed. The three major open issues to be addressed to optimize and implement the SSAF are (1) setting a value for the level of assurance to effectively exclude the presence of martian life in the samples, (2) carrying out an analogue test program, and (3) acquiring relevant contamination knowledge from all Mars Sample Return (MSR) flight and ground elements. Although the SSAF was developed specifically for assessing samples from Mars in the context of the currently planned NASA-ESA MSR Campaign, this framework and the basic safety approach are applicable to any other Mars sample return mission concept, with minor adjustments in the execution part related to the specific nature of the samples to be returned. The SSAF is also considered a sound basis for other COSPAR Planetary Protection Category V, restricted Earth return missions beyond Mars. It is anticipated that the SSAF will be subject to future review by the various MSR stakeholders.
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Affiliation(s)
- Gerhard Kminek
- European Space Agency, Mars Exploration Group, Noordwijk, The Netherlands
| | - James N Benardini
- NASA Headquarters, Office of Planetary Protection, Washington, DC, USA
| | - Frank E Brenker
- Goethe University, Department of Geoscience, Frankfurt, Germany
| | - Timothy Brooks
- UK Health Security Agency, Rare & Imported Pathogens Laboratory, Salisbury, UK
| | - Aaron S Burton
- NASA Johnson Space Center, Astromaterials Research and Exploration Science Division, Houston, Texas, USA
| | - Suresh Dhaniyala
- Clarkson University, Department of Mechanical and Aeronautical Engineering, Potsdam, New York, USA
| | - Jason P Dworkin
- NASA Goddard Space Flight Center, Solar System Exploration Division, Greenbelt, Maryland, USA
| | - Jeffrey L Fortman
- Security Programs, Engineering Biology Research Consortium, Emeryville, USA
| | - Mihaela Glamoclija
- Rutgers University, Department of Earth and Environmental Sciences, Newark, New Jersey, USA
| | - Monica M Grady
- The Open University, Faculty of Science, Technology, Engineering & Mathematics, Milton Keynes, UK
| | - Heather V Graham
- NASA Goddard Space Flight Center, Astrochemistry Laboratory, Greenbelt, Maryland, USA
| | - Junichi Haruyama
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science (ISAS), Chofu, Tokyo, Japan
| | - Thomas L Kieft
- New Mexico Institute of Mining and Technology, Biology Department, Socorro, New Mexico, USA
| | - Marion Koopmans
- Erasmus University Medical Centre, Department of Viroscience, Rotterdam, The Netherlands
| | - Francis M McCubbin
- NASA Johnson Space Center, Astromaterials Research and Exploration Science Division, Houston, Texas, USA
| | - Michael A Meyer
- NASA Headquarters, Planetary Science Division, Washington, DC, USA
| | | | - Tullis C Onstott
- Princeton University, Department of Geosciences, Princeton, New Jersey, USA
| | - Neil Pearce
- London School of Hygiene & Tropical Medicine, Department of Medical Statistics, London, UK
| | - Lisa M Pratt
- Indiana University Bloomington, Earth and Atmospheric Sciences, Emeritus, Bloomington, Indiana, USA
| | - Mark A Sephton
- Imperial College London, Department of Earth Science & Engineering, London, UK
| | - Sandra Siljeström
- RISE, Research Institutes of Sweden, Department of Methodology, Textiles and Medical Technology, Stockholm, Sweden
| | - Haruna Sugahara
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science, Sagamihara Kanagawa, Japan
| | - Shino Suzuki
- Japan Aerospace Exploration Agency (JAXA), Institute of Space and Astronautical Science, Sagamihara Kanagawa, Japan
| | - Yohey Suzuki
- University of Tokyo, Graduate School of Science, Tokyo, Japan
| | - Mark van Zuilen
- Université de Paris, Institut de Physique du Globe de Paris, Paris, France
- European Institute for Marine Studies (IUEM), CNRS-UMR6538 Laboratoire Geo-Ocean, Plouzané, France
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Sazanova KV, Vlasov DY, Zelenskaya MS, Panova EG, Rodina OA, Miklashevich EA. Lithobiotic Communities on the Surface of Rock Art Monuments in the Minusinsk Basin (South Siberia): Conditions for Formation and Biomineral Interactions. CONTEMP PROBL ECOL+ 2022. [DOI: 10.1134/s1995425522030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gaylarde C, Little B. Biodeterioration of stone and metal - Fundamental microbial cycling processes with spatial and temporal scale differences. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 823:153193. [PMID: 35122860 DOI: 10.1016/j.scitotenv.2022.153193] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Fundamental processes for the biodeterioration of stone and metal involve many of the same microbially mediated reactions - oxidation, reduction, acid dissolution and elemental cycling - resulting from the activities of many of the same groups of environmental microorganisms. Differences depend on the nature of the substratum - stone vs. metal - and the composition of the surroundings, whether terrestrial (stone) or aquatic (stone and metal). Reactions within surface-related biofilms dominate the biodeterioration of metals and contribute greatly to the biodeterioration of stone. In the latter, phototrophic organisms, and especially cyanobacteria, are important first participants, while metal biodeterioration is almost entirely associated with bacteria, archaea and fungi. Biofilms on metal surfaces can produce chemical and electrochemical responses. While electrochemical responses are absent in stone, extracellular electron transfer can be a biodeterioration mechanism in some iron-rich rocks. Microorganisms in biofilms can penetrate and create fissures or cracks in stone and metals. However, the most obvious differences in the reactions of built stone and metal structures are related to the definition of failure, length of time required for a defined failure of the substratum, the area over which the failure occurs and the consequences of failure. Time and space are, similarly, quite distinct for biological breakdown and mineral cycling of metal and stone, with stone/rock cycling potentially occurring over thousands of years and kilometers.
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Affiliation(s)
- Christine Gaylarde
- Department of Microbiology and Plant Biology, Oklahoma University, 770 Van Vleet Oval, Norman, OK 73019, USA
| | - Brenda Little
- BJ Little Corrosion Consulting, LLC, 6528 Alakoko Drive, Diamondhead, MS 39525, USA.
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Dawiec-Liśniewska A, Podstawczyk D, Bastrzyk A, Czuba K, Pacyna-Iwanicka K, Okoro OV, Shavandi A. aNew trends in biotechnological applications of photosynthetic microorganisms. Biotechnol Adv 2022; 59:107988. [DOI: 10.1016/j.biotechadv.2022.107988] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 05/17/2022] [Accepted: 05/17/2022] [Indexed: 12/20/2022]
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Black Fungi on Stone-Built Heritage: Current Knowledge and Future Outlook. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12083969] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Black fungi are considered as one of the main group of microorganisms responsible for the biodeterioration of stone cultural heritage artifacts. In this paper, we provide a critical analysis and review of more than 30 years of studies on black fungi isolated from stone-built heritage from 1990 to date. More than 109 papers concerning the fungal biodeterioration activity of stone were analysed. The main findings were a check list of the black fungal taxa involved in the biodeterioration of stone-built heritage, with a particular reference to meristematic black fungi, the main biodeterioration pattern attributed to them, and the methods of study including the new molecular advances. A particular focus was to discuss the current approaches to control black fungi from stone-built heritage and future perspectives. Black fungi are notoriously hard to remove or mitigate, so new methods of study and of control are needed, but it is also important to combine classical methods with new approaches to improve current knowledge to implement future conservation strategies.
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35
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Bontemps Z, Alonso L, Pommier T, Hugoni M, Moënne-Loccoz Y. Microbial ecology of tourist Paleolithic caves. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151492. [PMID: 34793801 DOI: 10.1016/j.scitotenv.2021.151492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/19/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms colonize caves extensively, and in caves open for tourism they may cause alterations on wall surfaces. This is a major concern in caves displaying Paleolithic art, which is usually fragile and may be irremediably damaged by microbial alterations. Therefore, many caves were closed for preservation purposes, e.g. Lascaux (France), Altamira (Spain), while others were never opened to the public to avoid microbial contamination, e.g. Chauvet Cave (France), etc. The recent development of high-throughput sequencing technologies allowed several descriptions of cave microbial diversity and prompted the writing of this review, which focuses on the cave microbiome for the three domains of life (Bacteria, Archaea, microeukaryotes), the impact of tourism-related anthropization on microorganisms in Paleolithic caves, and the development of microbial alterations on the walls of these caves. This review shows that the microbial phyla prevalent in pristine caves are similar to those evidenced in water, soil, plant and metazoan microbiomes, but specificities at lower taxonomic levels remain to be clarified. Most of the data relates to Bacteria and Fungi, while other microeukaryotes and Archaea are poorly documented. Tourism may cause shifts in the microbiota of Paleolithic caves, but larger-scale investigation are required as these shifts may differ from one cave to the next. Finally, different types of alterations can occur in caves, especially in Paleolithic caves. Many microorganisms potentially involved have been identified, but diversity analyses of these alterations have not always included a comparison with neighboring unaltered zones as controls, making such associations uncertain. It is expected that omics technologies will also allow a better understanding of the functional diversities of the cave microbiome. This will be needed to decipher microbiome dynamics in response to touristic frequentation, to guide cave management, and to identify the most appropriate reclamation approaches to mitigate microbial alterations in tourist Paleolithic caves.
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Affiliation(s)
- Zélia Bontemps
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Lise Alonso
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Thomas Pommier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, F-69622 Villeurbanne, France.
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36
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Suban S, Sendersky E, Golden SS, Schwarz R. Impairment of a cyanobacterial glycosyltransferase that modifies a pilin results in biofilm development. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:218-229. [PMID: 35172394 PMCID: PMC9306852 DOI: 10.1111/1758-2229.13050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 02/03/2022] [Indexed: 05/03/2023]
Abstract
A biofilm inhibiting mechanism operates in the cyanobacterium Synechococcus elongatus. Here, we demonstrate that the glycosyltransferase homologue, Ogt, participates in the inhibitory process - inactivation of ogt results in robust biofilm formation. Furthermore, a mutational approach shows requirement of the glycosyltransferase activity for biofilm inhibition. This enzyme is necessary for glycosylation of the pilus subunit and for adequate pilus formation. In contrast to wild-type culture in which most cells exhibit several pili, only 25% of the mutant cells are piliated, half of which possess a single pilus. In spite of this poor piliation, natural DNA competence was similar to that of wild-type; therefore, we propose that the unglycosylated pili facilitate DNA transformation. Additionally, conditioned medium from wild-type culture, which contains a biofilm inhibiting substance(s), only partially blocks biofilm development by the ogt-mutant. Thus, we suggest that inactivation of ogt affects multiple processes including production or secretion of the inhibitor as well as the ability to sense or respond to it.
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Affiliation(s)
- Shiran Suban
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
| | - Eleonora Sendersky
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
| | - Susan S. Golden
- Division of Biological SciencesUniversity of California, San DiegoLa JollaCA92093USA
- Center for Circadian BiologyUniversity of California, San DiegoLa JollaCA92093USA
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life SciencesBar‐Ilan UniversityRamat‐Gan5290002Israel
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Coleine C, Selbmann L, Singh BK, Delgado-Baquerizo M. The poly-extreme tolerant black yeasts are prevalent under high ultraviolet light and climatic seasonality across soils of global biomes. Environ Microbiol 2022; 24:1988-1999. [PMID: 35324062 PMCID: PMC9311647 DOI: 10.1111/1462-2920.15969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 11/29/2022]
Abstract
Black yeasts are among the most stress‐tolerant organisms of the planet, thriving under all types of terrestrial habitats and extreme environments. Yet, their global patterns and ecology remain far less studied, limiting our capacity to identify the main environmental drivers of these important organisms across biomes. To fill this knowledge gap, we analysed topsoils from 235 terrestrial ecosystems across and within globally distributed climate groups (i.e. dry, temperate and continental). We found that soils are important repositories of black yeasts, and that ultraviolet light, fine soil texture, and precipitation seasonality are the most consistent environmental factors associated with their diversity across biomes. Finally, we identified Exophiala and Cladophialophora as the most dominant black yeasts genera in soils across the globe. These findings provide novel evidence of global distribution of black yeasts and their key environmental predictors, giving new insights for speculating the evolution and spreading of these extreme‐tolerant organisms throughout both natural and human associated extreme environments.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, 41013, Spain
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38
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Nuppunen-Puputti M, Kietäväinen R, Raulio M, Soro A, Purkamo L, Kukkonen I, Bomberg M. Epilithic Microbial Community Functionality in Deep Oligotrophic Continental Bedrock. Front Microbiol 2022; 13:826048. [PMID: 35300483 PMCID: PMC8921683 DOI: 10.3389/fmicb.2022.826048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/12/2022] [Indexed: 01/03/2023] Open
Abstract
The deep terrestrial biosphere hosts vast sessile rock surface communities and biofilms, but thus far, mostly planktic communities have been studied. We enriched deep subsurface microbial communities on mica schist in microcosms containing bedrock groundwater from the depth of 500 m from Outokumpu, Finland. The biofilms were visualized using scanning electron microscopy, revealing numerous different microbial cell morphologies and attachment strategies on the mica schist surface, e.g., bacteria with outer membrane vesicle-like structures, hair-like extracellular extensions, and long tubular cell structures expanding over hundreds of micrometers over mica schist surfaces. Bacterial communities were analyzed with amplicon sequencing showing that Pseudomonas, Desulfosporosinus, Hydrogenophaga, and Brevundimonas genera dominated communities after 8–40 months of incubation. A total of 21 metagenome assembled genomes from sessile rock surface metagenomes identified genes involved in biofilm formation, as well as a wide variety of metabolic traits indicating a high degree of environmental adaptivity to oligotrophic environment and potential for shifting between multiple energy or carbon sources. In addition, we detected ubiquitous organic carbon oxidation and capacity for arsenate and selenate reduction within our rocky MAGs. Our results agree with the previously suggested interaction between the deep subsurface microbial communities and the rock surfaces, and that this interaction could be crucial for sustaining life in the harsh anoxic and oligotrophic deep subsurface of crystalline bedrock environment.
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Affiliation(s)
| | | | - Mari Raulio
- European Chemicals Agency (ECHA), Helsinki, Finland
| | - Aino Soro
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
| | | | - Ilmo Kukkonen
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Malin Bomberg
- VTT Technical Research Centre of Finland Ltd., Espoo, Finland
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Coleine C, Delgado-Baquerizo M, Albanese D, Singh BK, Stajich JE, Selbmann L, Egidi E. Rocks support a distinctive and consistent mycobiome across contrasting dry regions of Earth. FEMS Microbiol Ecol 2022; 98:6550019. [PMID: 35298630 DOI: 10.1093/femsec/fiac030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/05/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Rock-dwelling fungi play critical ecological roles in drylands, including soil formation and nutrient cycling; however, we know very little about the identity, function and environmental preferences of these important organisms, and the mere existence of a consistent rock mycobiome across diverse arid regions of the planet remains undetermined. To address this knowledge gap, we conducted a meta-analysis of rock fungi and spatially associated soil communities, surveyed across 28 unique sites spanning four major biogeographic regions (North America, Arctic, Maritime and Continental Antarctica) including contrasting climates, from cold and hot deserts to semi-arid drylands. We show that rocks support a consistent and unique mycobiome that was different to that found in surrounding soils. Lichenized fungi from class Lecanoromycetes were consistently indicative of rocks across contrasting regions, together with ascomycetous representatives of black fungi in Arthoniomycetes, Dothideomycetes, and Eurotiomycetes. In addition, comparing to soil, rocks had a lower proportion of saprobes and plant symbiotic fungi. The main drivers structuring rock fungi distribution were spatial distance and, to a larger extent, climatic factors regulating moisture and temperature (i.e. mean annual temperature and mean annual precipitation), suggesting that these paramount and unique communities might be particularly sensitive to increases in temperature and desertification.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico. Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Av. Reina Mercedes 10, E-41012, Sevilla, Spain.,Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Davide Albanese
- Research and Innovation Centre, Fondazione Edmund Mach (FEM), Via E. Mach, 1, 38098 S. Michele all'Adige (TN), Italy
| | - Brajesh K Singh
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California-Riverside, Riverside, CA, 92521, USA
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
| | - Eleonora Egidi
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
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Examining the Potential of Enzyme-Based Detergents to Remove Biofouling from Limestone Heritage. COATINGS 2022. [DOI: 10.3390/coatings12030375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Commonwealth war cemeteries commemorate the fallen of both world wars. Every casualty is remembered with a memorial or on a headstone. However, the headstones need to be maintained extensively, as microorganisms easily colonise them, affecting legibility and the stone substrate in the longer term. In the past, pesticides and other chemicals were popular to clean headstones, but due to raised environmental concerns, new treatment strategies are necessary. Within conservation science, enzymes have emerged as a popular tool for restoration. However, studies related to the use of enzymes for stone conservation are limited. Within this preliminary study, we applied commercially available enzyme-based treatments on biofouled natural building stones in the laboratory and in situ. Photography and spectrophotometry were used to monitor the effect of the treatment. The application of enzymes resulted in rapid disintegration of biological pigments, whereas visual improvement occurred more gradually. The successful application of enzymes suggests their potential to replace pesticides as the principal cleaning agent for headstones and natural building stones in a more general fashion.
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Liu B, Fu R, Wu B, Liu X, Xiang M. Rock-inhabiting fungi: terminology, diversity, evolution and adaptation mechanisms. Mycology 2022; 13:1-31. [PMID: 35186410 PMCID: PMC8856086 DOI: 10.1080/21501203.2021.2002452] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rock-inhabiting fungi (RIF) constitute an ecological group associated with terrestrial rocks. This association is generally restricted to the persistent colonisation of rocks and peculiar morphological features based on melanisation and slow growth, which endow RIF with significance in eukaryotic biology, special status in ecology, and exotic potential in biotechnology. There is a need to achieve a better understanding of the hidden biodiversity, antistress biology, origin and convergent evolution of RIF, which will facilitate cultural relic preservation, exploitation of the biogeochemical cycle of rock elements and biotechnology applications. This review focuses on summarising the current knowledge of rock-inhabiting fungi, with particular reference to terminology, biodiversity and geographic distribution, origin and evolution, and stress adaptation mechanisms. We especially teased out the definition through summing up the terms related to rock-inhabting fungi, and also provided a checklist of rock-inhabiting fungal taxa recorded following updated classification schemes.
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Affiliation(s)
- Bingjie Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Fu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Bing Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xingzhong Liu
- Department of Microbiology, College of Life Science, Nankai University, Tianjin, China
| | - Meichun Xiang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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42
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Microorganisms in Superficial Deposits on the Stone Monuments in Saint Petersburg. Microorganisms 2022; 10:microorganisms10020316. [PMID: 35208771 PMCID: PMC8879635 DOI: 10.3390/microorganisms10020316] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
The composition of superficial deposits in urban environment and their importance in the development of the lithobiotic community of microorganisms has been investigated. Polyols, organic acids, mono- and disaccharides, as well as some amino acids, are the predominant low molecular weight organic components in superficial deposits, although the conditions on the stone surface are undoubtedly oligotrophic. Superficial deposits accumulate heavy metals, including Fe, Mn, Zn, Cu, Pb, and Cd, in surface sediments, among which the potentially toxic elements Zn, Cu, and Pb are accumulated in rather high concentrations. On model of Aspergillus niger as an example, it was shown micromycetes are resistant to heavy metals and retain their physiological activity when grown on this substrate. According to cultural studies, as well as metagenomic analysis, stress-resistant fungi and dark organotrophic bacteria are the main inhabitants of surface sediments. Probably, in the conditions of accumulation of superficial deposits on the stone, these organisms are the main inhabitants of the surface of the stone. With the development of more multi-species lithobiotic communities, they form the core of these communities. In the urban environment this type of primary colonization of the stone is likely realized.
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Jimenez-Martinez J, Nguyen J, Or D. Controlling pore-scale processes to tame subsurface biomineralization. RE/VIEWS IN ENVIRONMENTAL SCIENCE AND BIO/TECHNOLOGY 2022; 21:27-52. [PMID: 35221831 PMCID: PMC8831379 DOI: 10.1007/s11157-021-09603-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Microorganisms capable of biomineralization can catalyze mineral precipitation by modifying local physical and chemical conditions. In porous media, such as soil and rock, these microorganisms live and function in highly heterogeneous physical, chemical and ecological microenvironments, with strong local gradients created by both microbial activity and the pore-scale structure of the subsurface. Here, we focus on extracellular bacterial biomineralization, which is sensitive to external heterogeneity, and review the pore-scale processes controlling microbial biomineralization in natural and engineered porous media. We discuss how individual physical, chemical and ecological factors integrate to affect the spatial and temporal control of biomineralization, and how each of these factors contributes to a quantitative understanding of biomineralization in porous media. We find that an improved understanding of microbial behavior in heterogeneous microenvironments would promote understanding of natural systems and output in diverse technological applications, including improved representation and control of fluid mixing from pore to field scales. We suggest a range of directions by which future work can build from existing tools to advance each of these areas to improve understanding and predictability of biomineralization science and technology.
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Affiliation(s)
- Joaquin Jimenez-Martinez
- Department of Water Resources and Drinking Water, Eawag, Dübendorf, Switzerland
- Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zürich, Switzerland
| | - Jen Nguyen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC V6T 1Z3 Canada
| | - Dani Or
- Division of Hydrologic Sciences, Desert Research Institute, Reno, NV USA
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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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Ren W, Guo Y, Han X, Sun Y, Li Q, Wu B, Xia T, Shen K, Wu P, He Y. Indigenous Microorganisms Offset Arbuscular Mycorrhizal Fungi-Induced Plant Growth and Nutrient Acquisition Through Negatively Modulating the Genes of Phosphorus Transport and Nitrogen Assimilation. FRONTIERS IN PLANT SCIENCE 2022; 13:880181. [PMID: 35615141 PMCID: PMC9125159 DOI: 10.3389/fpls.2022.880181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/18/2022] [Indexed: 05/06/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi that promote plant growth and nutrient acquisition are essential for nutrient-deficient karst areas, while they inevitably regulate host plants jointly with indigenous microorganisms in natural soil. However, how indigenous microorganisms regulate AM-induced benefits on plant growth and nutrient acquisition remains unclear. In this study, the Bidens tripartita as the common plant species in the karst region was cultivated into three soil substrates treated by AM fungi inoculation (AMF), AM fungi inoculation combining with indigenous microorganisms (AMI), and the control without AM fungi and indigenous microorganisms (CK). The plant biomass and concentration of nitrogen (N) and phosphorus (P) were measured, and the transcriptomic analysis was carried out using root tissues. The results showed that AM fungi significantly enhanced the plant biomass, N, and P accumulation with the reduction of plants' N/P ratio; however, the indigenous microorganisms offset the AM-induced benefits in biomass and N and P acquisition. In addition, there are 819 genes in differentially expressed genes (DEGs) of AMF vs. AMI ∩ AMF vs. CK, meaning that AM fungi induced these genes that were simultaneously regulated by indigenous microorganisms. Furthermore, the enrichment analysis suggested that these genes were significantly associated with the metabolic processes of organophosphate, P, sulfur, N, and arginine biosynthesis. Notably, 34 and 17 genes of DEGs were related to P and N metabolism, respectively. Moreover, the indigenous microorganisms significantly downregulated these DEGs, especially those encoding the PHO1 P transporters and the glnA, glutamate dehydrogenase 2 (GDH2), and urease as key enzymes in N assimilation; however, the indigenous microorganisms significantly upregulated genes encoding PHO84 inducing cellular response to phosphate (Pi) starvation. These regulations indicated that indigenous microorganisms restrained the N and P metabolism induced by AM fungi. In conclusion, we suggested that indigenous microorganisms offset nutrient benefits of AM fungi for host plants through regulating these genes related to P transport and N assimilation.
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Affiliation(s)
- Wenda Ren
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Yun Guo
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Xu Han
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Yan Sun
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Qing Li
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Bangli Wu
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Tingting Xia
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Kaiping Shen
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
| | - Pan Wu
- Key Laboratory of Karst Georesources and Environment, Ministry of Education, Guizhou University, Guiyang, China
| | - Yuejun He
- Forestry College, Research Center of Forest Ecology, Guizhou University, Guiyang, China
- *Correspondence: Yuejun He,
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Analysis of Biodeteriogens on Architectural Heritage. An Approach of Applied Botany on a Gothic Building in Southern Italy. SUSTAINABILITY 2021. [DOI: 10.3390/su14010034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The degradation of stone materials depends on several interlinked factors. The effects caused by biodeteriogens on mineral-based substrates are now increasingly considered in the field of cultural heritage conservation from different experimental approaches. In this study, biodeteriogenic micro- and macroflora within the gothic building of Santa Maria della Pietà, Squillace, Calabria, have been analyzed using multiple approaches, such as optical microscopy and molecular techniques. All 17 plant species detected are usually widespread in Mediterranean regions and some of these, such as Ailanthus altissima and Ficus carica, showed a very high hazard index, which is potentially dangerous for masonry stability. Fungi, cyanobacteria, and green algae were identified within biofilm compositions in a total of 23 different taxa, showing many similarities with microbial associations commonly found in cave and hypogean environments. All of the 11 fungal taxa detected belong to Ascomycota phylum, with Penicillium as the most represented genus. Photoautotrophic organisms are mostly represented by filamentous genera, with widespread presence of Leptolyngbya as the most abundant genus. The results highlighted how the singular environmental conditions of the study site, combined with the architectural features and the building materials, determined all the degradation phenomena affecting the building’s internal surfaces, compromising over time the structural integrity.
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Boada E, Santos-Clotas E, Cabrera-Codony A, Martín MJ, Bañeras L, Gich F. The core microbiome is responsible for volatile silicon and organic compounds degradation during anoxic lab scale biotrickling filter performance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149162. [PMID: 34333428 DOI: 10.1016/j.scitotenv.2021.149162] [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: 06/02/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Volatile silicon compounds present in the biogas of anaerobic digesters can cause severe problems in the energy recovery systems, inducing costly damages. Herein, the microbial community of a lab-scale biotrickling filter (BTF) was studied while testing its biodegradation capacity on octamethylcyclotetrasiloxane (D4) and decamethylcyclopentasiloxane (D5), in the presence of toluene, limonene and hexane. The reactor performance was tested at different empty bed residence times (EBRT) and packing materials. Community structure was analysed by bar-coded amplicon sequencing of the 16S rRNA gene. Microbial diversity and richness were higher in the inoculum and progressively decreased during BTF operation (Simpson's diversity index changing from 0.98-0.90 and Richness from 900 to 200 OTUs). Minimum diversity was found when reactor was operated at relatively low EBRT (7.3 min) using a multicomponent feed. The core community was composed of 36 OTUs (accounting for 55% of total sequences). Packing material played a key role in the community structure. Betaproteobacteriales were dominant in the presence of lava rock and were partially substituted by Corynebacteriales and Rhizobiales when activated carbon was added to the BTF. Despite these changes, a stable and resilient core microbiome was selected defining a set of potentially degrading bacteria for siloxane bioremoval as a complementary alternative to non-regenerative adsorption onto activated carbon.
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Affiliation(s)
- Ellana Boada
- Molecular Microbial Ecology Group (gEMM), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, 17003 Girona, Spain.
| | - Eric Santos-Clotas
- LEQUIA, Institute of the Environment, University of Girona, 17003 Girona, Spain.
| | - Alba Cabrera-Codony
- LEQUIA, Institute of the Environment, University of Girona, 17003 Girona, Spain.
| | - Maria J Martín
- LEQUIA, Institute of the Environment, University of Girona, 17003 Girona, Spain.
| | - Lluís Bañeras
- Molecular Microbial Ecology Group (gEMM), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, 17003 Girona, Spain.
| | - Frederic Gich
- Molecular Microbial Ecology Group (gEMM), Institute of Aquatic Ecology, Faculty of Sciences, University of Girona, 17003 Girona, Spain.
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Gat D, Reicher N, Schechter S, Alayof M, Tarn MD, Wyld BV, Zimmermann R, Rudich Y. Size-Resolved Community Structure of Bacteria and Fungi Transported by Dust in the Middle East. Front Microbiol 2021; 12:744117. [PMID: 34858365 PMCID: PMC8631519 DOI: 10.3389/fmicb.2021.744117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/01/2021] [Indexed: 11/13/2022] Open
Abstract
The atmosphere plays an important role in transporting microorganisms on a global scale, yet the processes affecting the composition of the airborne microbiome, the aerobiome, are not fully outlined. Here we present the community compositions of bacteria and fungi obtained by DNA amplicon-sequencing of aerosol samples collected in a size-resolved manner during nine consecutive days in central Israel. The campaign captured dust events originating from the Sahara and the Arabian deserts, as well as days without dust ("clear days"). We found that the source of the aerosol was the main variable contributing to the composition of both fungal and bacterial communities. Significant differences were also observed between communities representing particles of different sizes. We show evidence for the significant transport of bacteria as cell-aggregates and/or via bacterial attachment to particles during dust events. Our findings further point to the mixing of local and transported bacterial communities, observed mostly in particles smaller than 0.6 μm in diameter, representing bacterial single cells. Fungal communities showed the highest dependence on the source of the aerosols, along with significant daily variability, and without significant mixing between sources, possibly due to their larger aerodynamic size and shorter atmospheric residence times. These results, obtained under highly varied atmospheric conditions, provide significant assurances to previously raised hypotheses and could set the course for future studies on aerobiome composition.
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Affiliation(s)
- Daniella Gat
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
- Joint Mass Spectrometry Centre (JMSC), Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Munich, Germany
| | - Naama Reicher
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Shai Schechter
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Matan Alayof
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Mark D. Tarn
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Bethany V. Wyld
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, Leeds, United Kingdom
| | - Ralf Zimmermann
- Joint Mass Spectrometry Centre (JMSC), Comprehensive Molecular Analytics (CMA), Helmholtz Zentrum München – German Research Center for Environmental Health (GmbH), Munich, Germany
- Joint Mass Spectrometry Centre, Chair of Analytical Chemistry, Institute of Chemistry, University of Rostock, Rostock, Germany
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, Rehovot, Israel
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Cockell CS. Are microorganisms everywhere they can be? Environ Microbiol 2021; 23:6355-6363. [PMID: 34693610 DOI: 10.1111/1462-2920.15825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 10/15/2021] [Indexed: 11/27/2022]
Abstract
Baas-Becking is famously attributed with the conjecture that 'everything is everywhere, but the environment selects'. Although this aphorism is largely challenged by microbial biogeographical data, even weak versions of the claim leave unanswered the question about whether all environments that could theoretically support life contain life. In the last decade, the discovery of thermally sterilized habitable environments disconnected from inhabited regions, and habitats within organisms such as the sterile, but habitable human fetal gut, suggest the existence of a diversity of macroscopic habitable environments apparently devoid of actively metabolizing or reproducing life. Less clear is the status of such environments at the micron scale, for example, between colonies of organisms within rock interstices or on and within other substrates. I discuss recent evidence for these types of environments. These environments have practical uses in: (i) being negative controls for understanding the role of microbial processes in geochemical cycles and geological processes, (ii) yielding insights into the extent to which the biosphere extends into all spaces it theoretically can, (iii) suggesting caution in interpreting the results of life detection instrumentation, and (iv) being useful for establishing the conditions for the origin of life and its prevalence on other planetary bodies.
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Affiliation(s)
- Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, James Clerk Maxwell Building, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3JZ, UK
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50
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Řeháková K, Čapková K, Altman J, Dančák M, Majeský Ľ, Doležal J. Contrasting Patterns of Soil Chemistry and Vegetation Cover Determine Diversity Changes of Soil Phototrophs Along an Afrotropical Elevation Gradient. Ecosystems 2021. [DOI: 10.1007/s10021-021-00698-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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