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Rabelo NG, Gonçalves VN, Carvalho MA, Scheffler SM, Santiago G, Sucerquia PA, Oliveira FS, Campos LP, Lopes FAC, Santos KCR, Silva MC, Convey P, Câmara PEAS, Rosa LH. Endolithic Fungal Diversity in Antarctic Oligocene Rock Samples Explored Using DNA Metabarcoding. BIOLOGY 2024; 13:414. [PMID: 38927294 PMCID: PMC11200754 DOI: 10.3390/biology13060414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/15/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
In this study, we evaluated the fungal diversity present associated with cores of Oligocene rocks using a DNA metabarcoding approach. We detected 940,969 DNA reads grouped into 198 amplicon sequence variants (ASVs) representing the phyla Ascomycota, Basidiomycota, Mortierellomycota, Chytridiomycota, Mucoromycota, Rozellomycota, Blastocladiomycota, Monoblepharomycota, Zoopagomycota, Aphelidiomycota (Fungi) and the fungal-like Oomycota (Stramenopila), in rank abundance order. Pseudogymnoascus pannorum, Penicillium sp., Aspergillus sp., Cladosporium sp., Aspergillaceae sp. and Diaporthaceae sp. were assessed to be dominant taxa, with 22 fungal ASVs displaying intermediate abundance and 170 being minor components of the assigned fungal diversity. The data obtained displayed high diversity indices, while rarefaction indicated that the majority of the diversity was detected. However, the diversity indices varied between the cores analysed. The endolithic fungal community detected using a metabarcoding approach in the Oligocene rock samples examined contains a rich and complex mycobiome comprising taxa with different lifestyles, comparable with the diversity reported in recent studies of a range of Antarctic habitats. Due to the high fungal diversity detected, our results suggest the necessity of further research to develop strategies to isolate these fungi in culture for evolutionary, physiological, and biogeochemical studies, and to assess their potential role in biotechnological applications.
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Affiliation(s)
- Natana G. Rabelo
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (N.G.R.); (V.N.G.)
| | - Vívian N. Gonçalves
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (N.G.R.); (V.N.G.)
| | - Marcelo A. Carvalho
- Departamento de Geologia e Paleontologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil; (M.A.C.); (S.M.S.); (G.S.)
| | - Sandro M. Scheffler
- Departamento de Geologia e Paleontologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil; (M.A.C.); (S.M.S.); (G.S.)
| | - Gustavo Santiago
- Departamento de Geologia e Paleontologia, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro 20940-040, Brazil; (M.A.C.); (S.M.S.); (G.S.)
| | - Paula A. Sucerquia
- Departmento de Geologia, Universidade Federal de Pernambuco, Recife 50740-540, Brazil;
| | - Fabio S. Oliveira
- Departamento de Geografia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (F.S.O.); (L.P.C.)
| | - Larissa P. Campos
- Departamento de Geografia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (F.S.O.); (L.P.C.)
| | - Fabyano A. C. Lopes
- Laboratório de Microbiologia, Universidade Federal do Tocantins, Porto Nacional 77500-000, Brazil; (F.A.C.L.); (K.C.R.S.)
| | - Karita C. R. Santos
- Laboratório de Microbiologia, Universidade Federal do Tocantins, Porto Nacional 77500-000, Brazil; (F.A.C.L.); (K.C.R.S.)
| | - Micheline C. Silva
- Departamento de Botânica, Universidade de Brasília, Brasília 70297-400, Brazil; (M.C.S.)
| | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 0ET, UK;
- Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Las Palmeras 3425, Santiago 8320000, Chile
- Cape Horn International Center (CHIC), Puerto Williams 6350000, Chile
| | - Paulo E. A. S. Câmara
- Departamento de Botânica, Universidade de Brasília, Brasília 70297-400, Brazil; (M.C.S.)
- Programa de Pós-Graduação em Fungos, Algas e Plantas, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil
| | - Luiz H. Rosa
- Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (N.G.R.); (V.N.G.)
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2
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Williams TJ, Allen MA, Ray AE, Benaud N, Chelliah DS, Albanese D, Donati C, Selbmann L, Coleine C, Ferrari BC. Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert. Appl Environ Microbiol 2024; 90:e0226423. [PMID: 38372512 PMCID: PMC10952385 DOI: 10.1128/aem.02264-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024] Open
Abstract
The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota, and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment-including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.
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Affiliation(s)
- Timothy J. Williams
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Michelle A. Allen
- School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Nicole Benaud
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Devan S. Chelliah
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Davide Albanese
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Claudio Donati
- Research and Innovation Center, Fondazione Edmund Mach, San Michele all’Adige, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
- Mycological Section, Italian Antarctic National Museum (MNA), Genova, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
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3
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Varliero G, Lebre PH, Adams B, Chown SL, Convey P, Dennis PG, Fan D, Ferrari B, Frey B, Hogg ID, Hopkins DW, Kong W, Makhalanyane T, Matcher G, Newsham KK, Stevens MI, Weigh KV, Cowan DA. Biogeographic survey of soil bacterial communities across Antarctica. MICROBIOME 2024; 12:9. [PMID: 38212738 PMCID: PMC10785390 DOI: 10.1186/s40168-023-01719-3] [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: 07/07/2023] [Accepted: 11/11/2023] [Indexed: 01/13/2024]
Abstract
BACKGROUND Antarctica and its unique biodiversity are increasingly at risk from the effects of global climate change and other human influences. A significant recent element underpinning strategies for Antarctic conservation has been the development of a system of Antarctic Conservation Biogeographic Regions (ACBRs). The datasets supporting this classification are, however, dominated by eukaryotic taxa, with contributions from the bacterial domain restricted to Actinomycetota and Cyanobacteriota. Nevertheless, the ice-free areas of the Antarctic continent and the sub-Antarctic islands are dominated in terms of diversity by bacteria. Our study aims to generate a comprehensive phylogenetic dataset of Antarctic bacteria with wide geographical coverage on the continent and sub-Antarctic islands, to investigate whether bacterial diversity and distribution is reflected in the current ACBRs. RESULTS Soil bacterial diversity and community composition did not fully conform with the ACBR classification. Although 19% of the variability was explained by this classification, the largest differences in bacterial community composition were between the broader continental and maritime Antarctic regions, where a degree of structural overlapping within continental and maritime bacterial communities was apparent, not fully reflecting the division into separate ACBRs. Strong divergence in soil bacterial community composition was also apparent between the Antarctic/sub-Antarctic islands and the Antarctic mainland. Bacterial communities were partially shaped by bioclimatic conditions, with 28% of dominant genera showing habitat preferences connected to at least one of the bioclimatic variables included in our analyses. These genera were also reported as indicator taxa for the ACBRs. CONCLUSIONS Overall, our data indicate that the current ACBR subdivision of the Antarctic continent does not fully reflect bacterial distribution and diversity in Antarctica. We observed considerable overlap in the structure of soil bacterial communities within the maritime Antarctic region and within the continental Antarctic region. Our results also suggest that bacterial communities might be impacted by regional climatic and other environmental changes. The dataset developed in this study provides a comprehensive baseline that will provide a valuable tool for biodiversity conservation efforts on the continent. Further studies are clearly required, and we emphasize the need for more extensive campaigns to systematically sample and characterize Antarctic and sub-Antarctic soil microbial communities. Video Abstract.
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Affiliation(s)
- Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Pedro H Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa
| | - Byron Adams
- Department of Biology, Brigham Young University, Provo, UT, 84602, USA
- Monte L. Bean Life Science Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Steven L Chown
- Securing Antarctica's Environmental Future, School of Biological Sciences, Monash University, Clayton, VA, 3800, Australia
| | - Peter Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
- Department of Zoology, University of Johannesburg, PO Box 524, Auckland Park, 2006, South Africa
- Biodiversity of Antarctic and Sub-Antarctic Ecosystems (BASE), Santiago, Chile
| | - Paul G Dennis
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Dandan Fan
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Belinda Ferrari
- School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW, 2052, Australia
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, 8903, Birmensdorf, Switzerland
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - David W Hopkins
- SRUC - Scotland's Rural College, West Mains Road, Edinburgh, EH9 3JG, Scotland, UK
| | - Weidong Kong
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
| | - Thulani Makhalanyane
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Gwynneth Matcher
- Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kevin K Newsham
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Mark I Stevens
- Securing Antarctica's Environmental Future, Earth and Biological Sciences, South Australian Museum, Adelaide, SA, 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Katherine V Weigh
- School of the Environment, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Don A Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, 0002, South Africa.
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Coleine C, Delgado-Baquerizo M, Zerboni A, Turchetti B, Buzzini P, Franceschi P, Selbmann L. Rock Traits Drive Complex Microbial Communities at the Edge of Life. ASTROBIOLOGY 2023; 23:395-406. [PMID: 36812458 DOI: 10.1089/ast.2022.0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Antarctic deserts are among the driest and coldest ecosystems of the planet; there, some microbes survive under these extreme conditions inside porous rocks, forming the so-called endolithic communities. Yet the contribution of distinct rock traits to support complex microbial assemblies remains poorly determined. Here, we combined an extensive Antarctic rock survey with rock microbiome sequencing and ecological networks and found that contrasting combinations of microclimatic and rock traits such as thermal inertia, porosity, iron concentration, and quartz cement can help explain the multiple complex microbial assemblies found in Antarctic rocks. Our work highlights the pivotal role of rocky substrate heterogeneity in sustaining contrasting groups of microorganisms, which is essential to understand life at the edge on Earth and for the search for life on other rocky planets such as Mars.
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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, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun). Universidad Pablo de Olavide, Sevilla, Spain
| | - Andrea Zerboni
- Dipartimento di Scienze della Terra "A. Desio", Università degli Studi di Milano, Milano, Italy
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Pietro Franceschi
- Research and Innovation Center, Fondazione Edmund Mach, Trento, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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Si H, Wang Y, Liu Y, Li S, Bose T, Chang R. Fungal Diversity Associated with Thirty-Eight Lichen Species Revealed a New Genus of Endolichenic Fungi, Intumescentia gen. nov. (Teratosphaeriaceae). J Fungi (Basel) 2023; 9:jof9040423. [PMID: 37108878 PMCID: PMC10143819 DOI: 10.3390/jof9040423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Fungi from the Teratosphaeriaceae (Mycosphaerellales; Dothideomycetes; Ascomycota) have a wide range of lifestyles. Among these are a few species that are endolichenic fungi. However, the known diversity of endolichenic fungi from Teratosphaeriaceae is far less understood compared to other lineages of Ascomycota. We conducted five surveys from 2020 to 2021 in Yunnan Province of China, to explore the biodiversity of endolichenic fungi. During these surveys, we collected multiple samples of 38 lichen species. We recovered a total of 205 fungal isolates representing 127 species from the medullary tissues of these lichens. Most of these isolates were from Ascomycota (118 species), and the remaining were from Basidiomycota (8 species) and Mucoromycota (1 species). These endolichenic fungi represented a wide variety of guilds, including saprophytes, plant pathogens, human pathogens, as well as entomopathogenic, endolichenic, and symbiotic fungi. Morphological and molecular data indicated that 16 of the 206 fungal isolates belonged to the family Teratosphaeriaceae. Among these were six isolates that had a low sequence similarity with any of the previously described species of Teratosphaeriaceae. For these six isolates, we amplified additional gene regions and conducted phylogenetic analyses. In both single gene and multi-gene phylogenetic analyses using ITS, LSU, SSU, RPB2, TEF1, ACT, and CAL data, these six isolates emerged as a monophyletic lineage within the family Teratosphaeriaceae and sister to a clade that included fungi from the genera Acidiella and Xenopenidiella. The analyses also indicated that these six isolates represented four species. Therefore, we established a new genus, Intumescentia gen. nov., to describe these species as Intumescentia ceratinae, I. tinctorum, I. pseudolivetorum, and I. vitii. These four species are the first endolichenic fungi representing Teratosphaeriaceae from China.
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Affiliation(s)
- Hongli Si
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yichen Wang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Yanyu Liu
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Shiguo Li
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
| | - Tanay Bose
- Department of Biochemistry, Genetics & Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
- Correspondence: (T.B.); (R.C.)
| | - Runlei Chang
- College of Life Sciences, Shandong Normal University, Jinan 250014, China
- Correspondence: (T.B.); (R.C.)
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6
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Forecasting the number of species of asexually reproducing fungi (Ascomycota and Basidiomycota). FUNGAL DIVERS 2022. [DOI: 10.1007/s13225-022-00500-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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7
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Mezzasoma A, Coleine C, Sannino C, Selbmann L. Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica. MICROBIAL ECOLOGY 2022; 83:328-339. [PMID: 34081148 PMCID: PMC8891110 DOI: 10.1007/s00248-021-01769-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.
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Affiliation(s)
- Ambra Mezzasoma
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Ciro Sannino
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Italian Antarctic National Museum (MNA), Mycological Section, Genoa, Italy
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Culture-Dependent and Amplicon Sequencing Approaches Reveal Diversity and Distribution of Black Fungi in Antarctic Cryptoendolithic Communities. J Fungi (Basel) 2021; 7:jof7030213. [PMID: 33809619 PMCID: PMC8001563 DOI: 10.3390/jof7030213] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/14/2021] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
In the harshest environmental conditions of the Antarctic desert, normally incompatible with active life, microbes are adapted to exploit the cryptoendolithic habitat (i.e., pore spaces of rocks) and represent the predominant life-forms. In the rocky niche, microbes take advantage of the thermal buffering, physical stability, protection against UV radiation, excessive solar radiation, and water retention-of paramount importance in one of the driest environments on Earth. In this work, high-throughput sequencing and culture-dependent approaches have been combined, for the first time, to untangle the diversity and distribution of black fungi in the Antarctic cryptoendolithic microbial communities, hosting some of the most extreme-tolerant microorganisms. Rock samples were collected in a vast area, along an altitudinal gradient and opposite sun exposure-known to influence microbial diversity-with the aim to compare and integrate results gained with the two approaches. Among black fungi, Friedmanniomyces endolithicus was confirmed as the most abundant taxon. Despite the much stronger power of the high-throughput sequencing, several species were not retrieved with DNA sequencing and were detectable by cultivation only. We conclude that both culture-dependent and -independent analyses are needed for a complete overview of black fungi diversity. The reason why some species remain undetectable with molecular methods are speculated upon. The effect of environmental parameters such as sun exposure on relative abundance was clearer if based on the wider biodiversity detected with the molecular approach.
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de Menezes GCA, Câmara PEAS, Pinto OHB, Carvalho-Silva M, Oliveira FS, Souza CD, Reynaud Schaefer CEG, Convey P, Rosa CA, Rosa LH. Fungal diversity present on rocks from a polar desert in continental Antarctica assessed using DNA metabarcoding. Extremophiles 2021; 25:193-202. [PMID: 33651232 DOI: 10.1007/s00792-021-01221-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/11/2021] [Indexed: 01/04/2023]
Abstract
We evaluated the fungal diversity associated with carbonate veins and two types of salt encrustation in rocks in a polar desert region of continental Antarctica using DNA a metabarcoding approach. We detected 262,268 reads grouped into 517 amplicon sequence variants (ASVs) assigned to the phyla Ascomycota, Basidiomycota, Mortierellomycota and Mucoromycota. Fourteen ASVs belonging to the genera Trichosporon, Mortierella, Penicillium, Aspergillus, Cladosporium, Coprinellus, Pleurotus and Pseudogymnoascus were assessed to be dominant taxa. The fungal communities of the three habitats sampled displayed high diversity indices when compared with other habitats of Antarctica, although differing in detail, with the highest diversity indices in the gypsum crust type 2. Only 48 of the 517 ASVs (9.28%) were detected in all three habitats, including dominant, intermediate and minor components. In contrast with previous studies of fungal communities living in the ultra-extreme conditions of continental Antarctica, application of metabarcoding revealed the DNA of a rich and complex resident fungal community. The ASVs detected included fungi with different ecological roles, with xerophilic, human- and animal-associated, phytopathogenic, saprotrophic, mutualistic, psychrotolerant and cosmopolitan taxa. This sequence diversity may be the result of deposition of fungal propagules over time driven by air currents, precipitation or human activities in the region.
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Affiliation(s)
- Graciéle Cunha Alves de Menezes
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, PO Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil
| | | | | | | | - Fábio Soares Oliveira
- Departamento de Geografia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | - Peter Convey
- British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge, CB3 0ET, UK
| | - Carlos Augusto Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, PO Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - Luiz Henrique Rosa
- Laboratório de Microbiologia Polar e Conexões Tropicais, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, PO Box 486, Belo Horizonte, MG, CEP 31270-901, Brazil.
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10
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Coleine C, Biagioli F, de Vera JP, Onofri S, Selbmann L. Endolithic microbial composition in Helliwell Hills, a newly investigated Mars-like area in Antarctica. Environ Microbiol 2021; 23:4002-4016. [PMID: 33538384 DOI: 10.1111/1462-2920.15419] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 01/04/2023]
Abstract
The diversity and composition of Antarctic cryptoendolithic microbial communities in the Mars-analogue site of Helliwell Hills (Northern Victoria Land, Continental Antarctica) are investigated, for the first time, applying both culture-dependent and high-throughput sequencing approaches. The study includes all the domains of the tree of life: Eukaryotes, Bacteria and Archaea to give a complete overview of biodiversity and community structure. Furthermore, to explore the geographic distribution of endoliths throughout the Victoria Land (Continental Antarctica), we compared the fungal and bacterial community composition and structure of endolithically colonized rocks, collected in >30 sites in 10 years of Italian Antarctic Expeditions. Compared with the fungi and other eukaryotes, the prokaryotic communities were richer in species, more diverse and highly heterogeneous. Despite the diverse community compositions, shared populations were found and were dominant in all sites. Local diversification was observed and included prokaryotes as members of Alphaproteobacteria and Crenarchaeota (Archaea), the last detected for the first time in these cryptoendolithic communities. Few eukaryotes, namely lichen-forming fungal species as Lecidella grenii, were detected in Helliwell Hills only. These findings suggest that geographic distance and isolation in these remote areas may promote the establishment of peculiar locally diversified microorganisms.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Federico Biagioli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Jean Pierre de Vera
- German Aerospace Center (DLR), Institute of Planetary Research, Planetary Laboratories, Research Group Astrobiological Laboratories, Berlin, Germany
| | - Silvano Onofri
- 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
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Fanelli G, Coleine C, Gevi F, Onofri S, Selbmann L, Timperio AM. Metabolomics of Dry Versus Reanimated Antarctic Lichen-Dominated Endolithic Communities. Life (Basel) 2021; 11:96. [PMID: 33514042 PMCID: PMC7911838 DOI: 10.3390/life11020096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/25/2021] [Indexed: 12/31/2022] Open
Abstract
Cryptoendolithic communities are almost the sole life form in the ice-free areas of the Antarctic desert, encompassing among the most extreme-tolerant organisms known on Earth that still assure ecosystems functioning, regulating nutrient and biogeochemical cycles under conditions accounted as incompatible with active life. If high-throughput sequencing based studies are unravelling prokaryotic and eukaryotic diversity, they are not yet characterized in terms of stress adaptations and responses, despite their paramount ecological importance. In this study, we compared the responses of Antarctic endolithic communities, with special focus on fungi, both under dry conditions (i.e., when dormant), and after reanimation by wetting, light, and optimal temperature (15 °C). We found that several metabolites were differently expressed in reanimated opposite sun exposed communities, suggesting a critical role in their success. In particular, the saccharopine pathway was up-regulated in the north surface, while the spermine/spermidine pathway was significantly down-regulated in the shaded exposed communities. The carnitine-dependent pathway is up-regulated in south-exposed reanimated samples, indicating the preferential involvement of the B-oxidation for the functioning of TCA cycle. The role of these metabolites in the performance of the communities is discussed herein.
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Affiliation(s)
- Giuseppina Fanelli
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (C.C.); (F.G.); (S.O.)
| | - Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (C.C.); (F.G.); (S.O.)
| | - Federica Gevi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (C.C.); (F.G.); (S.O.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (C.C.); (F.G.); (S.O.)
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (C.C.); (F.G.); (S.O.)
- Italian National Antarctic Museum (MNA), Mycological Section, 16166 Genoa, Italy
| | - Anna Maria Timperio
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (G.F.); (C.C.); (F.G.); (S.O.)
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Microbial Communities in Permafrost Soils of Larsemann Hills, Eastern Antarctica: Environmental Controls and Effect of Human Impact. Microorganisms 2020; 8:microorganisms8081202. [PMID: 32784619 PMCID: PMC7464515 DOI: 10.3390/microorganisms8081202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022] Open
Abstract
Although ice-free areas cover only about 0.1% of Antarctica and are characterized by harsh environmental conditions, these regions provide quite diverse conditions for the soil-forming process, having various physical and geochemical properties, and also assuring different conditions for living organisms. This study is aimed to determine existing soil microbial communities, their relationship with soil parameters and the influence of anthropogenic activity in Larsemann Hills, Eastern Antarctica. The soil microbiome was investigated at different locations using 16S rRNA gene pyrosequencing. The taxonomic analysis of the soil microbiomes revealed 12 predominant bacterial and archaeal phyla—Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, Bacteroidetes, Armatimonadetes, Firmicutes, Cyanobacteria, Thaumarchaeota. Some specific phyla have been also found in sub-surface horizons of soils investigated, thus providing additional evidence of the crucial role of gravel pavement in saving the favorable conditions for both soil and microbiome development. Moreover, our study also revealed that some bacterial species might be introduced into Antarctic soils by human activities. We also assessed the effect of different soil parameters on microbial community in the harsh environmental conditions of Eastern Antarctica. pH, carbon and nitrogen, as well as fine earth content, were revealed as the most accurate predictors of soil bacterial community composition.
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