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Jiya N, Ghosh R, Shede P, Sharma A. Comparative analysis of bacterial diversity in accumulated snow and exposed sediments across Antarctic Islands. Braz J Microbiol 2024; 55:2355-2362. [PMID: 38748395 PMCID: PMC11405587 DOI: 10.1007/s42770-024-01360-8] [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: 12/30/2023] [Accepted: 04/11/2024] [Indexed: 09/18/2024] Open
Abstract
The Antarctic continent hosts exceptional niches, making it an ideal environment for studying polyextremophilic microorganisms. These organisms are uniquely shaped by the geographic niches and variations in soil types. Here we present, a culture-independent approach using DNA metabarcoding to assess the bacterial communities associated with accumulated snow and exposed sediments across different Antarctic islands situated in the Larsemann Hills, Antarctica. The exposed sediments (ES) were found to be more diverse than the accumulated snow (AS) sediments as represented by the alpha diversity metrics. Out of the total 303 amplicon sequence variants (ASVs) found at the genus level, 93 were unique to accumulated snow sediments and 97 were unique to exposed sediments. The bacterial community composition in accumulated snow was dominated by the phylum Actinobacteriota (24.7%). However, Pseudonocardia (11.9%), Crossiella (11%), and Rhodanobacter (9.1%) were the predominant genera. In contrast, in the exposed sediments, Bacteroidota (24.6%) was the most prevalent phylum, with Crossiella (17.1%), Rhodanobacter (11.1%), and Blastocatella (10%) as the most abundant genera. Metagenomic imputations revealed the abundance of gene families responsible for carbon metabolism, coping with environmental stresses through DNA repair mechanisms, and carbon fixation.
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Affiliation(s)
- Namrata Jiya
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
- Department of Microbiology, MES' Abasaheb Garware College (Autonomous), Pune, India
| | - Rochita Ghosh
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Prafulla Shede
- Department of Microbiology, MES' Abasaheb Garware College (Autonomous), Pune, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India.
- School of Agriculture, Graphic Era Hill University, Dehradun, India.
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2
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Kosiorek K, Grzesiak J, Gawor J, Sałańska A, Aleksandrzak-Piekarczyk T. Polar-Region Soils as Novel Reservoir of Lactic Acid Bacteria from the Genus Carnobacterium. Int J Mol Sci 2024; 25:9444. [PMID: 39273391 PMCID: PMC11395011 DOI: 10.3390/ijms25179444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
Polar habitats offer excellent sites to isolate unique bacterial strains due to their diverse physical, geochemical, and biological factors. We hypothesize that the unique environmental conditions of polar regions select for distinct strains of lactic acid bacteria (LAB) with novel biochemical properties. In this study, we characterized ten strains of psychrotrophic LAB isolated from hitherto poorly described sources-High Arctic and maritime Antarctic soils and soil-like materials, including ornithogenic soils, cryoconites, elephant seal colonies, and postglacial moraines. We evaluated the physiological and biochemical properties of the isolates. Based on 16S rRNA and housekeeping genes, the four LAB strains were assigned to three Carnobacterium species: C. alterfunditum, C. maltaromaticum, and C. jeotgali. The remaining strains may represent three new species of the Carnobacterium genus. All isolates were neutrophilic and halophilic psychrotrophs capable of fermenting various carbohydrates, organic acids, and alcohols. The identified metabolic properties of the isolated Carnobacterium strains suggest possible syntrophic interactions with other microorganisms in polar habitats. Some showed antimicrobial activity against food pathogens such as Listeria monocytogenes and human pathogens like Staphylococcus spp. Several isolates exhibited unique metabolic traits with potential biotechnological applications that could be more effectively exploited under less stringent technological conditions compared to thermophilic LAB strains, such as lower temperatures and reduced nutrient concentrations. Analysis of extrachromosomal genetic elements revealed 13 plasmids ranging from 4.5 to 79.5 kb in five isolates, featuring unique genetic structures and high levels of previously uncharacterized genes. This work is the first comprehensive study of the biochemical properties of both known and new Carnobacterium species and enhances our understanding of bacterial communities in harsh and highly selective polar soil ecosystems.
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Affiliation(s)
- Katarzyna Kosiorek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Jakub Grzesiak
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Jan Gawor
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Agnieszka Sałańska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
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3
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Zhang Z, Bao Y, Fang X, Ruan Y, Rong Y, Yang G. A circumpolar study of surface zooplankton biodiversity of the Southern Ocean based on eDNA metabarcoding. ENVIRONMENTAL RESEARCH 2024; 255:119183. [PMID: 38768883 DOI: 10.1016/j.envres.2024.119183] [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: 03/03/2024] [Revised: 05/02/2024] [Accepted: 05/18/2024] [Indexed: 05/22/2024]
Abstract
Under pressure from climate change and fishing, the Southern Ocean ecosystems have been changing. Zooplankton plays a vital role in the food web of the Southern Ocean and is crucial for maintaining ecosystem stability. Investigating the circumpolar-scale species composition and biodiversity of zooplankton is crucial for ensuring ecosystem-based conservation and management of the Southern Ocean in a changing climate. Here, we utilized eDNA metabarcoding to assess the biodiversity of zooplankton in the surface seawater surrounding the Antarctica based on samples collected during two expeditions spanning from 2021 to 2022. The main purpose of this paper is to provide more baseline information about circumpolar zooplankton biodiversity based on the emerging eDNA metabarcoding tool. This comprehensive approach led to the identification of over 300 distinct zooplankton species, forming a diverse community dominated by Jellyfish, Mollusca and Polychaete. Surprisingly, common dominant taxonomic groups such as krill and copepods in the Southern Ocean did not show high relative abundance (reads) in surface seawater. The results of redundancy analysis (RDA) and correlation analysis highlighted that water temperature and chlorophyll a had the most significant impact on the reads and diversity of zooplankton. Notably, the influence of water temperature on zooplankton seemed to be primarily indirect, potentially mediated by its effects on primary productivity. Increasing in primary production might lead to lower zooplankton biodiversity in the Southern Ocean in future. This research underscores the effectiveness of eDNA metabarcoding as a valuable tool for monitoring zooplankton diversity in open seas. Given the ongoing changes in temperature, sea ice extent and their impact on primary production, our findings lay a crucial foundation for using eDNA techniques to establish long-term biodiversity monitoring programs across extensive marine ecosystems in the future.
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Affiliation(s)
- Zishang Zhang
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China; Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Yongchao Bao
- College of Environmental and Safety Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Xiaoyue Fang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao, 266590, China
| | - Yilin Ruan
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yue Rong
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Guang Yang
- Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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Savaglia V, Lambrechts S, Tytgat B, Vanhellemont Q, Elster J, Willems A, Wilmotte A, Verleyen E, Vyverman W. Geology defines microbiome structure and composition in nunataks and valleys of the Sør Rondane Mountains, East Antarctica. Front Microbiol 2024; 15:1316633. [PMID: 38380088 PMCID: PMC10877063 DOI: 10.3389/fmicb.2024.1316633] [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: 10/10/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024] Open
Abstract
Understanding the relation between terrestrial microorganisms and edaphic factors in the Antarctic can provide insights into their potential response to environmental changes. Here we examined the composition of bacterial and micro-eukaryotic communities using amplicon sequencing of rRNA genes in 105 soil samples from the Sør Rondane Mountains (East Antarctica), differing in bedrock or substrate type and associated physicochemical conditions. Although the two most widespread taxa (Acidobacteriota and Chlorophyta) were relatively abundant in each sample, multivariate analysis and co-occurrence networks revealed pronounced differences in community structure depending on substrate type. In moraine substrates, Actinomycetota and Cercozoa were the most abundant bacterial and eukaryotic phyla, whereas on gneiss, granite and marble substrates, Cyanobacteriota and Metazoa were the dominant bacterial and eukaryotic taxa. However, at lower taxonomic level, a distinct differentiation was observed within the Cyanobacteriota phylum depending on substrate type, with granite being dominated by the Nostocaceae family and marble by the Chroococcidiopsaceae family. Surprisingly, metazoans were relatively abundant according to the 18S rRNA dataset, even in samples from the most arid sites, such as moraines in Austkampane and Widerøefjellet ("Dry Valley"). Overall, our study shows that different substrate types support distinct microbial communities, and that mineral soil diversity is a major determinant of terrestrial microbial diversity in inland Antarctic nunataks and valleys.
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Affiliation(s)
- Valentina Savaglia
- InBioS Research Unit, Department of Life Sciences, University of Liège, Liège, Belgium
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Sam Lambrechts
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Bjorn Tytgat
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | | | - Josef Elster
- Faculty of Science, Centre for Polar Ecology, University of South Bohemia České Budějovice and Institute of Botany, Třeboň, Czechia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Annick Wilmotte
- InBioS Research Unit, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
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5
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Canini F, Borruso L, Newsham KK, D'Alò F, D'Acqui LP, Zucconi L. Wide divergence of fungal communities inhabiting rocks and soils in a hyper-arid Antarctic desert. Environ Microbiol 2023; 25:3671-3682. [PMID: 37964667 DOI: 10.1111/1462-2920.16534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
Highly simplified microbial communities colonise rocks and soils of continental Antarctica ice-free deserts. These two habitats impose different selection pressures on organisms, yet the possible filtering effects on the diversity and composition of microbial communities have not hitherto been fully characterised. We hence compared fungal communities in rocks and soils in three localities of inner Victoria Land. We found low fungal diversity in both substrates, with a mean species richness of 28 across all samples, and significantly lower diversity in rocks than in soils. Rock and soil communities were strongly differentiated, with a multinomial species classification method identifying just three out of 328 taxa as generalists with no affinity for either substrate. Rocks were characterised by a higher abundance of lichen-forming fungi (typically Buellia, Carbonea, Pleopsidium, Lecanora, and Lecidea), possibly owing to the more protected environment and the porosity of rocks permitting photosynthetic activity. In contrast, soils were dominated by obligate yeasts (typically Naganishia and Meyerozyma), the abundances of which were correlated with edaphic factors, and the black yeast Cryomyces. Our study suggests that strong differences in selection pressures may account for the wide divergences of fungal communities in rocks and soils of inner Victoria Land.
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Affiliation(s)
- Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Luigimaria Borruso
- Faculty of Agricultural, Environmental and Food Sciences, Free University of Bozen, Bozen-Bolzano, Italy
| | - Kevin K Newsham
- British Antarctic Survey (BAS), Natural Environment Research Council (NERC), Cambridge, UK
| | - Federica D'Alò
- Terrestrial Ecosystems Research Institute (IRET), National Research Council (CNR), Porano (TR), Italy
| | - Luigi P D'Acqui
- Institute of Polar Sciences (ISP), National Research Council (CNR), Messina, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Terrestrial Ecosystems Research Institute (IRET), National Research Council (CNR), Sesto Fiorentino (FI), Italy
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Mashamaite L, Lebre PH, Varliero G, Maphosa S, Ortiz M, Hogg ID, Cowan DA. Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient. Front Microbiol 2023; 14:1203216. [PMID: 37555066 PMCID: PMC10406297 DOI: 10.3389/fmicb.2023.1203216] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. METHODS We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. RESULTS AND DISCUSSION Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.
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Affiliation(s)
- Lefentse Mashamaite
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Pedro H. Lebre
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Gilda Varliero
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Silindile Maphosa
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
| | - Max Ortiz
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- Clemson University Genomics & Bioinformatics Facility, Clemson University, Clemson, SC, United States
| | - Ian D. Hogg
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, NU, Canada
| | - Don A. Cowan
- Department of Biochemistry, Genetics and Microbiology, Centre for Microbial Ecology and Genomics, University of Pretoria, Pretoria, South Africa
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Cowan DA, Cary SC, DiRuggiero J, Eckardt F, Ferrari B, Hopkins DW, Lebre PH, Maggs-Kölling G, Pointing SB, Ramond JB, Tribbia D, Warren-Rhodes K. 'Follow the Water': Microbial Water Acquisition in Desert Soils. Microorganisms 2023; 11:1670. [PMID: 37512843 PMCID: PMC10386458 DOI: 10.3390/microorganisms11071670] [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: 05/03/2023] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
Water availability is the dominant driver of microbial community structure and function in desert soils. However, these habitats typically only receive very infrequent large-scale water inputs (e.g., from precipitation and/or run-off). In light of recent studies, the paradigm that desert soil microorganisms are largely dormant under xeric conditions is questionable. Gene expression profiling of microbial communities in desert soils suggests that many microbial taxa retain some metabolic functionality, even under severely xeric conditions. It, therefore, follows that other, less obvious sources of water may sustain the microbial cellular and community functionality in desert soil niches. Such sources include a range of precipitation and condensation processes, including rainfall, snow, dew, fog, and nocturnal distillation, all of which may vary quantitatively depending on the location and geomorphological characteristics of the desert ecosystem. Other more obscure sources of bioavailable water may include groundwater-derived water vapour, hydrated minerals, and metabolic hydro-genesis. Here, we explore the possible sources of bioavailable water in the context of microbial survival and function in xeric desert soils. With global climate change projected to have profound effects on both hot and cold deserts, we also explore the potential impacts of climate-induced changes in water availability on soil microbiomes in these extreme environments.
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Affiliation(s)
- Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - S Craig Cary
- School of Biological Sciences, University of Waikato, Hamilton 3216, New Zealand
| | - Jocelyne DiRuggiero
- Departments of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
- Departments of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Frank Eckardt
- Department of Environmental and Geographical Science, University of Cape Town, Cape Town 7701, South Africa
| | - Belinda Ferrari
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - David W Hopkins
- Scotland's Rural College, West Mains Road, Edinburgh EH9 3JG, UK
| | - Pedro H Lebre
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | | | - Stephen B Pointing
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
- Departamento Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Dana Tribbia
- School of Biotechnology and Biological Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Egas C, Galbán-Malagón C, Castro-Nallar E, Molina-Montenegro MA. Role of Microbes in the degradation of organic semivolatile compounds in polar ecosystems: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163046. [PMID: 36965736 DOI: 10.1016/j.scitotenv.2023.163046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/09/2023] [Accepted: 03/20/2023] [Indexed: 05/17/2023]
Abstract
The Arctic and the Antarctic Continent correspond to two eco-regions with extreme climatic conditions. These regions are exposed to the presence of contaminants resulting from human activity (local and global), which, in turn, represent a challenge for life forms in these environments. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in polar ecosystems has been documented since the 1960s. Currently, various studies have shown the presence of SVOCs and their bioaccumulation and biomagnification in the polar regions with negative effects on biodiversity and the ecosystem. Although the production and use of these compounds has been regulated, their persistence continues to threaten biodiversity and the ecosystem. Here, we summarize the current literature regarding microbes and SVOCs in polar regions and pose that bioremediation by native microorganisms is a feasible strategy to mitigate the presence of SVOCs. Our systematic review revealed that microbial communities in polar environments represent a wide reservoir of biodiversity adapted to extreme conditions, found both in terrestrial and aquatic environments, freely or in association with vegetation. Microorganisms adapted to these environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes with the capacity to metabolize SVOCs. We suggest that a comprehensive approach at the molecular and ecological level is required to mitigate SVOCs presence in these regions. This is especially patent when considering that SVOCs degrade at slow rates and possess the ability to accumulate in polar ecosystems. The implications of SVOC degradation are relevant for the preservation of polar ecosystems with consequences at a global level.
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Affiliation(s)
- Claudia Egas
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Campus Lircay, Talca, Chile
| | - Cristóbal Galbán-Malagón
- Centro de Genómica, Ecología y Medio Ambiente (GEMA), Universidad Mayor, Campus Huechuraba, Santiago, Chile; Institute of Environment, Florida International University, University Park, Miami, FL 33199, USA
| | - Eduardo Castro-Nallar
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Departamento de Microbiología, Facultad de Ciencias de la Salud, Universidad de Talca, Campus Lircay, Talca, Chile
| | - Marco A Molina-Montenegro
- Centre for Integrative Ecology (CIE), Universidad de Talca, Campus Lircay, Talca, Chile; Instituto de Ciencias Biológicas (ICB), Universidad de Talca, Campus Lircay, Talca, Chile; Centro de Investigación en Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile.
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Liu Z, Jiang W, Kim C, Peng X, Fan C, Wu Y, Xie Z, Peng F. A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae. Int J Mol Sci 2023; 24:ijms24087662. [PMID: 37108829 PMCID: PMC10142737 DOI: 10.3390/ijms24087662] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4-40 °C) and pH (4-11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions.
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Affiliation(s)
- Zhenyu Liu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Wenhui Jiang
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Cholsong Kim
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoya Peng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Cong Fan
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yingliang Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhixiong Xie
- College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Fang Peng
- College of Life Sciences, Wuhan University, Wuhan 430072, China
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Identification of phenotypic and genotypic properties and cold adaptive mechanisms of novel freeze–thaw stress-resistant strain Pseudomonas mandelii from Antarctica. Polar Biol 2023. [DOI: 10.1007/s00300-023-03114-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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11
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Marcoleta AE, Arros P, Varas MA, Costa J, Rojas-Salgado J, Berríos-Pastén C, Tapia-Fuentes S, Silva D, Fierro J, Canales N, Chávez FP, Gaete A, González M, Allende ML, Lagos R. The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:152003. [PMID: 34856283 DOI: 10.1016/j.scitotenv.2021.152003] [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: 09/28/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The rise of multiresistant bacterial pathogens is currently one of the most critical threats to global health, encouraging a better understanding of the evolution and spread of antimicrobial resistance. In this regard, the role of the environment as a source of resistance mechanisms remains poorly understood. Moreover, we still know a minimal part of the microbial diversity and resistome present in remote and extreme environments, hosting microbes that evolved to resist harsh conditions and thus a potentially rich source of novel resistance genes. This work demonstrated that the Antarctic Peninsula soils host a remarkable microbial diversity and a widespread presence of autochthonous antibiotic-resistant bacteria and resistance genes. We observed resistance to a wide array of antibiotics among isolates, including Pseudomonas resisting ten or more different compounds, with an overall increased resistance in bacteria from non-intervened areas. In addition, genome analysis of selected isolates showed several genes encoding efflux pumps, as well as a lack of known resistance genes for some of the resisted antibiotics, including colistin, suggesting novel uncharacterized mechanisms. By combining metagenomic approaches based on analyzing raw reads, assembled contigs, and metagenome-assembled genomes, we found hundreds of widely distributed genes potentially conferring resistance to different antibiotics (including an outstanding variety of inactivation enzymes), metals, and biocides, hosted mainly by Polaromonas, Pseudomonas, Streptomyces, Variovorax, and Burkholderia. Furthermore, a proportion of these genes were found inside predicted plasmids and other mobile elements, including a putative OXA-like carbapenemase from Polaromonas harboring conserved key residues and predicted structural features. All this evidence indicates that the Antarctic Peninsula soil microbiota has a broad natural resistome, part of which could be transferred horizontally to pathogenic bacteria, acting as a potential source of novel resistance genes.
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Affiliation(s)
- Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Costa
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Johanna Rojas-Salgado
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sofía Tapia-Fuentes
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Daniel Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - José Fierro
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Nicolás Canales
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Alexis Gaete
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile; FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile, Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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12
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Life from a Snowflake: Diversity and Adaptation of Cold-Loving Bacteria among Ice Crystals. CRYSTALS 2022. [DOI: 10.3390/cryst12030312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Incredible as it is, researchers have now the awareness that even the most extreme environment includes special habitats that host several forms of life. Cold environments cover different compartments of the cryosphere, as sea and freshwater ice, glaciers, snow, and permafrost. Although these are very particular environmental compartments in which various stressors coexist (i.e., freeze–thaw cycles, scarce water availability, irradiance conditions, and poorness of nutrients), diverse specialized microbial communities are harbored. This raises many intriguing questions, many of which are still unresolved. For instance, a challenging focus is to understand if microorganisms survive trapped frozen among ice crystals for long periods of time or if they indeed remain metabolically active. Likewise, a look at their site-specific diversity and at their putative geochemical activity is demanded, as well as at the equally interesting microbial activity at subzero temperatures. The production of special molecules such as strategy of adaptations, cryoprotectants, and ice crystal-controlling molecules is even more intriguing. This paper aims at reviewing all these aspects with the intent of providing a thorough overview of the main contributors in investigating the microbial life in the cryosphere, touching on the themes of diversity, adaptation, and metabolic potential.
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Snopková K, Dufková K, Chamrád I, Lenobel R, Čejková D, Kosina M, Hrala M, Holá V, Sedláček I, Šmajs D. Pyocin-mediated antagonistic interactions in Pseudomonas spp. isolated in James Ross Island, Antarctica. Environ Microbiol 2021; 24:1294-1307. [PMID: 34735036 DOI: 10.1111/1462-2920.15809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/15/2021] [Accepted: 10/05/2021] [Indexed: 11/30/2022]
Abstract
Interactions within bacterial communities are frequently mediated by the production of antimicrobial agents. Despite the increasing interest in research of new antimicrobials, studies describing antagonistic interactions among cold-adapted microorganisms are still rare. Our study assessed the antimicrobial interactions of 36 Antarctic Pseudomonas spp. and described the genetic background of these interactions in selected strains. The overall bacteriocinogeny was greater compared to mesophilic Pseudomonas non-aeruginosa species. R-type tailocins were detected on transmission electron micrographs in 16 strains (44.4%); phylogenetic analysis of the corresponding gene clusters revealed that the P. prosekii CCM 8878 tailocin was related to the Rp3 group, whereas the tailocin in Pseudomonas sp. CCM 8880 to the Rp4 group. Soluble antimicrobials were produced by eight strains (22.-2%); gene mining found pyocin L homologues in the genomes of P. prosekii CCM 8881 and CCM 8879 and pyocin S9-like homologues in P. prosekii CCM 8881 and Pseudomonas sp. CCM 8880. Analysis of secretomes confirmed the production of all S- and L-type pyocin genes. Our results suggest that bacteriocin-based inhibition plays an important role in interactions among Antarctic soil bacteria, and these native, cold-adapted microorganisms could be a promising source of new antimicrobials.
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Affiliation(s)
- Kateřina Snopková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Kristýna Dufková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, Olomouc-Holice, 779 00, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, Olomouc-Holice, 779 00, Czech Republic
| | - Darina Čejková
- Veterinary Research Institute, Hudcova 296/70, Brno, 621 00, Czech Republic
| | - Marcel Kosina
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Matěj Hrala
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - Veronika Holá
- Faculty of Medicine, Institute for Microbiology, Masaryk University and St. Anne's University Hospital Brno, Pekařská 664/53, Brno, 656 91, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, Brno, 625 00, Czech Republic
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14
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Antarctica as a reservoir of planetary analogue environments. Extremophiles 2021; 25:437-458. [PMID: 34586500 DOI: 10.1007/s00792-021-01245-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
One of the main objectives of astrobiological research is the investigation of the habitability of other planetary bodies. Since space exploration missions are expensive and require long-term organization, the preliminary study of terrestrial environments is an essential step to prepare and support exploration missions. The Earth hosts a multitude of extreme environments whose characteristics resemble celestial bodies in our Solar System. In these environments, the physico-chemical properties partly match extraterrestrial environments and could clarify limits and adaptation mechanisms of life, the mineralogical or geochemical context, and support and interpret data sent back from planetary bodies. One of the best terrestrial analogues is Antarctica, whose conditions lie on the edge of habitability. It is characterized by a cold and dry climate (Onofri et al., Nova Hedwigia 68:175-182, 1999), low water availability, strong katabatic winds, salt concentration, desiccation, and high radiation. Thanks to the harsh conditions like those in other celestial bodies, Antarctica offers good terrestrial analogues for celestial body (Mars or icy moons; Léveillé, CR Palevol 8:637-648, https://doi.org/10.1016/j.crpv.2009.03.005 , 2009). The continent could be distinguished into several habitats, each with characteristics similar to those existing on other bodies. Here, we reported a description of each simulated parameter within the habitats, in relation to each of the simulated extraterrestrial environments.
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Algal Toxic Compounds and Their Aeroterrestrial, Airborne and other Extremophilic Producers with Attention to Soil and Plant Contamination: A Review. Toxins (Basel) 2021; 13:toxins13050322. [PMID: 33946968 PMCID: PMC8145420 DOI: 10.3390/toxins13050322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/27/2021] [Accepted: 04/27/2021] [Indexed: 12/16/2022] Open
Abstract
The review summarizes the available knowledge on toxins and their producers from rather disparate algal assemblages of aeroterrestrial, airborne and other versatile extreme environments (hot springs, deserts, ice, snow, caves, etc.) and on phycotoxins as contaminants of emergent concern in soil and plants. There is a growing body of evidence that algal toxins and their producers occur in all general types of extreme habitats, and cyanobacteria/cyanoprokaryotes dominate in most of them. Altogether, 55 toxigenic algal genera (47 cyanoprokaryotes) were enlisted, and our analysis showed that besides the “standard” toxins, routinely known from different waterbodies (microcystins, nodularins, anatoxins, saxitoxins, cylindrospermopsins, BMAA, etc.), they can produce some specific toxic compounds. Whether the toxic biomolecules are related with the harsh conditions on which algae have to thrive and what is their functional role may be answered by future studies. Therefore, we outline the gaps in knowledge and provide ideas for further research, considering, from one side, the health risk from phycotoxins on the background of the global warming and eutrophication and, from the other side, the current surge of interest which phycotoxins provoke due to their potential as novel compounds in medicine, pharmacy, cosmetics, bioremediation, agriculture and all aspects of biotechnological implications in human life.
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16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02843-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.
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Silva TRE, Silva LCF, de Queiroz AC, Alexandre Moreira MS, de Carvalho Fraga CA, de Menezes GCA, Rosa LH, Bicas J, de Oliveira VM, Duarte AWF. Pigments from Antarctic bacteria and their biotechnological applications. Crit Rev Biotechnol 2021; 41:809-826. [PMID: 33622142 DOI: 10.1080/07388551.2021.1888068] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pigments from microorganisms have triggered great interest in the market, mostly by their "natural" appeal, their favorable production conditions, in addition to the potential new chemical structures or naturally overproducing strains. They have been used in: food, feed, dairy, textile, pharmaceutical, and cosmetic industries. The high rate of pigment production in microorganisms recovered from Antarctica in response to selective pressures such as: high UV radiation, low temperatures, and freezing and thawing cycles makes this a unique biome which means that much of its biological heritage cannot be found elsewhere on the planet. This vast arsenal of pigmented molecules has different functions in bacteria and may exhibit different biotechnological activities, such as: extracellular sunscreens, photoprotective function, antimicrobial activity, biodegradability, etc. However, many challenges for the commercial use of these compounds have yet to be overcome, such as: the low stability of natural pigments in cosmetic formulations, the change in color when subjected to pH variations, the low yield and the high costs in their production. This review surveys the different types of natural pigments found in Antarctic bacteria, classifying them according to their chemical structure. Finally, we give an overview of the main pigments that are used commercially today.
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Affiliation(s)
- Tiago Rodrigues E Silva
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrárias, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil
| | | | | | | | | | | | - Luiz Henrique Rosa
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Juliano Bicas
- Departamento de Ciência de Alimentos, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil
| | - Valéria Maia de Oliveira
- Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrárias, Universidade Estadual de Campinas, UNICAMP, Campinas, Brazil
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Monaco P, Divino F, Naclerio G, Bucci A. Microbial community analysis with a specific statistical approach after a record breaking snowfall in Southern Italy. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01604-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Abstract
Purpose
Snow and ice ecosystems present unexpectedly high microbial abundance and diversity. Although arctic and alpine snow environments have been intensively investigated from a microbiological point of view, few studies have been conducted in the Apennines. Accordingly, the main purpose of this research was to analyze the microbial communities of the snow collected in two different locations of Capracotta municipality (Southern Italy) after a snowfall record occurred on March 2015 (256 cm of snow in less than 24 h).
Methods
Bacterial communities were analyzed by the Next-Generation Sequencing techniques. Furthermore, a specific statistical approach for taxonomic hierarchy data was introduced, both for the assessment of diversity within microbial communities and the comparison between different microbiotas. In general, diversity and similarity indices are more informative when computed at the lowest level of the taxonomic hierarchy, the species level. This is not the case with microbial data, for which the species level is not necessarily the most informative. Indeed, the possibility to detect a large number of unclassified records at every level of the hierarchy (even at the top) is very realistic due to both the partial knowledge about the cultivable fraction of microbial communities and limitations to taxonomic assignment connected to the quality and completeness of the 16S rRNA gene reference databases. Thus, a global approach considering information from the whole taxonomic hierarchy was adopted in order to obtain a more consistent assessment of the biodiversity.
Result
The main phyla retrieved in the investigated snow samples were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Interestingly, DNA from bacteria adapted to thrive at low temperatures, but also from microorganisms normally associated with other habitats, whose presence in the snow could be justified by wind-transport, was found. Biomolecular investigations and statistical data analysis showed relevant differences in terms of biodiversity, composition, and distribution of bacterial species between the studied snow samples.
Conclusion
The relevance of this research lies in the expansion of knowledge about microorganisms associated with cold environments in contexts poorly investigated such as the Italian Apennines, and in the development of a global statistical approach for the assessment of biological diversity and similarity of microbial communities as an additional tool to be usefully combined with the barcoding methods.
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Ortiz M, Bosch J, Coclet C, Johnson J, Lebre P, Salawu-Rotimi A, Vikram S, Makhalanyane T, Cowan D. Microbial Nitrogen Cycling in Antarctic Soils. Microorganisms 2020; 8:E1442. [PMID: 32967081 PMCID: PMC7564152 DOI: 10.3390/microorganisms8091442] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (M.O.); (J.B.); (C.C.); (J.J.); (P.L.); (A.S.-R.); (S.V.); (T.M.)
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Zhu C, Miller M, Lusskin N, Bergk Pinto B, Maccario L, Häggblom M, Vogel T, Larose C, Bromberg Y. Snow microbiome functional analyses reveal novel aspects of microbial metabolism of complex organic compounds. Microbiologyopen 2020; 9:e1100. [PMID: 32762019 PMCID: PMC7520998 DOI: 10.1002/mbo3.1100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/19/2020] [Accepted: 05/29/2020] [Indexed: 12/17/2022] Open
Abstract
Microbes active in extreme cold are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of 20 snow samples collected in early and late spring in Svalbard, Norway using mi-faser, our read-based computational microbiome function annotation tool. Our results reveal a more diverse microbiome functional capacity and activity in the early- vs. late-spring samples. We also find that functional dissimilarity between the same-sample metagenomes and metatranscriptomes is significantly higher in early than late spring samples. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant (or dead) organisms, while late spring samples reflect a new, metabolically active community. We further show that the abundance of sequencing reads mapping to the fatty acid synthesis-related microbial pathways in late spring metagenomes and metatranscriptomes is significantly correlated with the organic acid levels measured in these samples. Similarly, the organic acid levels correlate with the pathway read abundances of geraniol degradation and inversely correlate with those of styrene degradation, suggesting a possible nutrient change. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.
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Affiliation(s)
- Chengsheng Zhu
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Maximilian Miller
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Nicholas Lusskin
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Benoît Bergk Pinto
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
| | - Lorrie Maccario
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
- Section of MicrobiologyCopenhagen UniversityCopenhagen ØDenmark
| | - Max Häggblom
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
| | - Timothy Vogel
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
| | - Catherine Larose
- Environmental Microbial GenomicsLaboratoire AmpereEcole Centrale de LyonCNRS UMR 5005Université de LyonEcullyFrance
| | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNJUSA
- Department of GeneticsHuman Genetics InstituteRutgers UniversityPiscatawayNJUSA
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21
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Coleine C, Pombubpa N, Zucconi L, Onofri S, Turchetti B, Buzzini P, Stajich JE, Selbmann L. Uncovered Microbial Diversity in Antarctic Cryptoendolithic Communities Sampling three Representative Locations of the Victoria Land. Microorganisms 2020; 8:E942. [PMID: 32585947 PMCID: PMC7356261 DOI: 10.3390/microorganisms8060942] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/21/2020] [Accepted: 06/22/2020] [Indexed: 11/16/2022] Open
Abstract
The endolithic niche represents an ultimate refuge to microorganisms in the Mars-like environment of the Antarctic desert. In an era of rapid global change and desertification, the interest in these border ecosystems is increasing due to speculation on how they maintain balance and functionality at the dry limits of life. To assure a reliable estimation of microbial diversity, proper sampling must be planned in order to avoid the necessity of re-sampling as reaching these remote locations is risky and requires tremendous logistical and economical efforts. In this study, we seek to determine the minimum number of samples for uncovering comprehensive bacterial and fungal diversity, comparing communities in strict vicinity to each other. We selected three different locations of the Victoria Land (Continental Antarctica) at different altitudes and showing sandstone outcrops of a diverse nature and origin-Battleship promontory (834 m above sea level (a.s.l.), Southern VL), Trio Nunatak (1,470 m a.s.l., Northern VL) and Mt New Zealand (3,100 m a.s.l., Northern VL). Overall, we found that a wider sampling would be required to capture the whole amplitude of microbial diversity, particularly in Northern VL. We concluded that the inhomogeneity of the rock matrix and the stronger environmental pressure at higher altitudes may force the communities to a higher local diversification.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; (N.P.); (J.E.S.)
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
| | - Benedetta Turchetti
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (B.T.); (P.B.)
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy; (B.T.); (P.B.)
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA 92521, USA; (N.P.); (J.E.S.)
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, 01100 Viterbo, Italy; (L.Z.); (S.O.)
- Italian National Antarctic Museum (MNA), Mycological Section, 16166 Genoa, Italy
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22
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Gupta V, Singh I, Rasool S, Verma V. Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir, India. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Coleine C, Stajich JE, Pombubpa N, Zucconi L, Onofri S, Canini F, Selbmann L. Altitude and fungal diversity influence the structure of Antarctic cryptoendolithic Bacteria communities. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:718-726. [PMID: 31393667 PMCID: PMC8057506 DOI: 10.1111/1758-2229.12788] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 05/11/2023]
Abstract
Endolithic growth within rocks is a critical adaptation of microbes living in harsh environments where exposure to extreme temperature, radiation, and desiccation limits the predominant life forms, such as in the ice-free regions of Continental Antarctica. The microbial diversity of the endolithic communities in these areas has been sparsely examined. In this work, diversity and composition of bacterial assemblages in the cryptoendolithic lichen-dominated communities of Victoria Land (Continental Antarctica) were explored using a high-throughput metabarcoding approach, targeting the V4 region of 16S rDNA. Rocks were collected in 12 different localities (from 14 different sites), along a gradient ranging from 1000 to 3300 m a.s.l. and at a sea distance ranging from 29 to 96 km. The results indicate Actinobacteria and Proteobacteria are the dominant taxa in all samples and defined a 'core' group of bacterial taxa across all sites. The structure of bacteria communities is correlated with the fungal counterpart and among the environmental parameters considered, altitude was found to influence bacterial biodiversity, while distance from sea had no evident influence.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology and Institute of Integrative Genome Biology, University of California, Riverside, CA, USA
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Fabiana Canini
- 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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Lee J, Cho J, Cho YJ, Cho A, Woo J, Lee J, Hong SG, Sul WJ, Kim OS. The latitudinal gradient in rock-inhabiting bacterial community compositions in Victoria Land, Antarctica. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 657:731-738. [PMID: 30677938 DOI: 10.1016/j.scitotenv.2018.12.073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
The harsh conditions in Victoria Land, Antarctica have formed a simple ecosystem dominated by microbes that use rocks as shelters to avoid environmental stressors. The area is composed of basement rocks that illustrate the history of complex deformation, thus it is highly valuable not only in perspectives of geology but also in biological aspects. Because this region is inhospitable to higher-level organisms and receives least external influences, it can be an ideal environment to investigate the relationship between rock-inhabiting bacterial communities and environmental factors. In such conditions, inorganics dissolved from minerals can be considered as key factors influencing rock-inhabiting bacterial communities. Thus, the present study attempted to explore rock-inhabiting bacterial communities throughout Victoria Land, to identify environmental parameters that are more influential on bacterial community compositions, and to investigate latitudinal gradients in environmental parameters and rock-inhabiting bacterial communities. The results suggested that (i) rock-inhabiting bacterial communities in Victoria Land predominately consisted of either Actinobacteria or Proteobacteria; (ii) latitudinal gradients in rock-inhabiting bacterial community compositions and some environmental parameters were observed; (iii) latitude, pH, nitrate, and sulfate significantly correlated with the dominant phyla; and (iv) the Classification and Regression Tree (CART) analysis demonstrated that latitude, pH, and sulfate concentrations could explain the dominant phylum with 89% accuracy. These findings can provide important insight into the link between environmental factors and rock-inhabiting bacterial community compositions in conditions with extremely cold temperatures and high levels of radiation, which could also be of interest in astrobiology.
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Affiliation(s)
- Jaejin Lee
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Agricultural & Biosystems Engineering, Iowa State University, Ames, IA 50011, United States of America
| | - Junho Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea; Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Yong-Joon Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Ahnna Cho
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jusun Woo
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Jongik Lee
- Division of Polar Earth-System Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Soon Gyu Hong
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Ok-Sun Kim
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 21990, Republic of Korea.
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Maccario L, Carpenter SD, Deming JW, Vogel TM, Larose C. Sources and selection of snow-specific microbial communities in a Greenlandic sea ice snow cover. Sci Rep 2019; 9:2290. [PMID: 30783153 PMCID: PMC6381142 DOI: 10.1038/s41598-019-38744-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/14/2018] [Indexed: 11/09/2022] Open
Abstract
Sea ice and its snow cover are critical for global processes including climate regulation and biogeochemical cycles. Despite an increase in studies focused on snow microorganisms, the ecology of snow inhabitants remains unclear. In this study, we investigated sources and selection of a snowpack-specific microbial community by comparing metagenomes from samples collected in a Greenlandic fjord within a vertical profile including atmosphere, snowpack with four distinct layers of snow, sea ice brine and seawater. Microbial communities in all snow layers derived from mixed sources, both marine and terrestrial, and were more similar to atmospheric communities than to sea ice or seawater communities. The surface snow metagenomes were characterized by the occurrence of genes involved in photochemical stress resistance, primary production and metabolism of diverse carbon sources. The basal saline snow layer that was in direct contact with the sea ice surface harbored a higher abundance of cells than the overlying snow layers, with a predominance of Alteromonadales and a higher relative abundance of marine representatives. However, the overall taxonomic structure of the saline layer was more similar to that of other snow layers and the atmosphere than to underlying sea ice and seawater. The expulsion of relatively nutrient-rich sea ice brine into basal snow might have stimulated the growth of copiotrophic psychro- and halotolerant snow members. Our study indicates that the size, composition and function of snowpack microbial communities over sea ice were influenced primarily by atmospheric deposition and inflow of sea ice brine and that they form a snow-specific assemblage reflecting the particular environmental conditions of the snowpack habitat.
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Affiliation(s)
- Lorrie Maccario
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS, École Centrale de Lyon, Écully, France.
- Microbiology Section, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, USA
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS, École Centrale de Lyon, Écully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS, École Centrale de Lyon, Écully, France
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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28
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Hughes KA, Convey P, Pertierra LR, Vega GC, Aragón P, Olalla-Tárraga MÁ. Human-mediated dispersal of terrestrial species between Antarctic biogeographic regions: A preliminary risk assessment. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2019; 232:73-89. [PMID: 30468960 DOI: 10.1016/j.jenvman.2018.10.095] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 10/02/2018] [Accepted: 10/26/2018] [Indexed: 06/09/2023]
Abstract
The distribution of terrestrial biodiversity within Antarctica is complex, with 16 distinct biogeographic regions (Antarctic Conservation Biogeographic Regions) currently recognised within the Antarctic continent, Peninsula and Scotia Arc archipelagos of the Antarctic Treaty area. Much of this diversity is endemic not only to Antarctica as a whole, but to specific regions within it. Further complexity is added by inclusion of the biodiversity found on the islands located in the Southern Ocean north of the Treaty area. Within Antarctica, scientific, logistic and tourism activities may inadvertently move organisms over potentially long distances, far beyond natural dispersal ranges. Such translocation can disrupt natural species distribution patterns and biogeography through: (1) movement of spatially restricted indigenous species to other areas of Antarctica; (2) movement of distinct populations of more generally distributed species from one area of Antarctica to another, leading to genetic homogenisation and loss of assumed local patterns of adaptation; and (3) further dispersal of introduced non-native species from one area of Antarctica to another. Species can be moved between regions in association with people and cargo, by ship, aircraft and overland travel. Movement of cargo and personnel by ship between stations located in different biogeographic regions is likely to present one of the greatest risks, particularly as coastal stations may experience similar climatic conditions, making establishment more likely. Recognising that reducing the risk of inter-regional transfer of species is a priority issue for the Antarctic Treaty Consultative Meeting, we make practical recommendations aimed at reducing this risk, including the implementation of appropriate biosecurity procedures.
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Affiliation(s)
- Kevin A Hughes
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, United Kingdom.
| | - Peter Convey
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, United Kingdom
| | - Luis R Pertierra
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutierrez Abascal 2, Madrid 28006, Spain
| | - Greta C Vega
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Calle Tulipán s/n, Móstoles (Madrid) 28933, Spain
| | - Pedro Aragón
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (CSIC), Calle José Gutierrez Abascal 2, Madrid 28006, Spain
| | - Miguel Á Olalla-Tárraga
- Department of Biology and Geology, Physics and Inorganic Chemistry, Rey Juan Carlos University, Calle Tulipán s/n, Móstoles (Madrid) 28933, Spain
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29
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Amarelle V, Carrasco V, Fabiano E. The Hidden Life of Antarctic Rocks. SPRINGER POLAR SCIENCES 2019. [DOI: 10.1007/978-3-030-02786-5_10] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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30
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Antarctic Soil Microbial Communities in a Changing Environment: Their Contributions to the Sustainability of Antarctic Ecosystems and the Bioremediation of Anthropogenic Pollution. SPRINGER POLAR SCIENCES 2019. [DOI: 10.1007/978-3-030-02786-5_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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31
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Taxonomy and richness of yeasts associated with angiosperms, bryophytes, and meltwater biofilms collected in the Antarctic Peninsula. Extremophiles 2018; 23:151-159. [DOI: 10.1007/s00792-018-1069-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/20/2018] [Indexed: 10/27/2022]
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Lee KC, Caruso T, Archer SD, Gillman LN, Lau MC, Cary SC, Lee CK, Pointing SB. Stochastic and Deterministic Effects of a Moisture Gradient on Soil Microbial Communities in the McMurdo Dry Valleys of Antarctica. Front Microbiol 2018; 9:2619. [PMID: 30450087 PMCID: PMC6225844 DOI: 10.3389/fmicb.2018.02619] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/12/2018] [Indexed: 11/13/2022] Open
Abstract
Antarctic soil supports surface microbial communities that are dependent on ephemeral moisture. Understanding the response to availability of this resource is essential to predicting how the system will respond to climate change. The McMurdo Dry Valleys are the largest ice-free soil region in Antarctica. They are a hyper-arid polar desert with extremely limited moisture availability. Microbial colonization dominates this ecosystem but surprisingly little is known about how communities respond to changing moisture regimes. We utilized the natural model system provided by transiently wetted soil at lake margins in the Dry Valleys to interrogate microbial responses along a well-defined contiguous moisture gradient and disentangle responses between and within phyla. We identified a striking non-linear response among bacteria where at low moisture levels small changes resulted in a large impact on diversity. At higher moister levels community responses were less pronounced, resulting in diversity asymptotes. We postulate that whilst the main drivers of observed community diversity were deterministic, a switch in the major influence occurred from abiotic factors at low moisture levels to biotic interactions at higher moisture. Response between and within phyla was markedly different, highlighting the importance of taxonomic resolution in community analysis. Furthermore, we resolved apparent stochasticity at high taxonomic ranks as the result of deterministic interactions taking place at finer taxonomic and spatial scales. Overall the findings provide new insight on the response to moisture and this will be useful in advancing understanding of potential ecosystem responses in the threatened McMurdo Dry Valleys system.
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Affiliation(s)
- Kevin C. Lee
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Tancredi Caruso
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Institute for Global Food Security, Queen’s University Belfast, Belfast, United Kingdom
| | - Stephen D.J. Archer
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Len N. Gillman
- Institute for Applied Ecology New Zealand, Auckland University of Technology, Auckland, New Zealand
| | - Maggie C.Y. Lau
- Department of Geosciences, Princeton University, Princeton, NJ, United States
| | - S. Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Charles K. Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
| | - Stephen B. Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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33
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Coleine C, Stajich JE, Zucconi L, Onofri S, Pombubpa N, Egidi E, Franks A, Buzzini P, Selbmann L. Antarctic Cryptoendolithic Fungal Communities Are Highly Adapted and Dominated by Lecanoromycetes and Dothideomycetes. Front Microbiol 2018; 9:1392. [PMID: 30008702 PMCID: PMC6033990 DOI: 10.3389/fmicb.2018.01392] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/06/2018] [Indexed: 12/14/2022] Open
Abstract
Endolithic growth is one of the most spectacular microbial adaptations to extreme environmental constraints and the predominant life-form in the ice-free areas of Continental Antarctica. Although Antarctic endolithic microbial communities are known to host among the most resistant and extreme-adapted organisms, our knowledge on microbial diversity and composition in this peculiar niche is still limited. In this study, we investigated the diversity and structure of the fungal assemblage in the cryptoendolithic communities inhabiting sandstone using a meta-barcoding approach targeting the fungal Internal Transcribed Sequence region 1 (ITS1). Samples were collected from 14 sites in the Victoria Land, along an altitudinal gradient ranging from 1,000 to 3,300 m a.s.l. and from 29 to 96 km distance to coast. Our study revealed a clear dominance of a 'core' group of fungal taxa consistently present across all the samples, mainly composed of lichen-forming and Dothideomycetous fungi. Pareto-Lorenz curves indicated a very high degree of specialization (F0 approximately 95%), suggesting these communities are highly adapted but have limited ability to recover after perturbations. Overall, both fungal community biodiversity and composition did not show any correlation with the considered abiotic parameters, potentially due to strong fluctuations of environmental conditions at local scales.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Eleonora Egidi
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Ashley Franks
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC, Australia
- Centre for Future Landscapes, La Trobe University, Melbourne, VIC, Australia
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
- Section of Mycology, Italian National Antarctic Museum (MNA), Genoa, Italy
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Coleine C, Zucconi L, Onofri S, Pombubpa N, Stajich JE, Selbmann L. Sun Exposure Shapes Functional Grouping of Fungi in Cryptoendolithic Antarctic Communities. Life (Basel) 2018; 8:E19. [PMID: 29865244 PMCID: PMC6027399 DOI: 10.3390/life8020019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 05/30/2018] [Accepted: 05/31/2018] [Indexed: 11/16/2022] Open
Abstract
Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors. Sandstone rocks were collected in Victoria Land, Antarctica along an altitudinal gradient from 834 to 3100 m a.s.l.; differently sun-exposed rocks were selected to test the influence of this parameter on endolithic settlement. Metabarcoding targeting the fungal internal transcribed spacer region 1 (ITS1) was used to catalogue the species found in these communities. Functional profile of guilds found in the samples was associated to species using FUNGuild and variation in functional groups compared across sunlight exposure and altitude. Results revealed clear dominance of lichenized and stress-tolerant fungi in endolithic communities. The main variations in composition and abundance of functional groups among sites correlated to sun exposure, but not to altitude.
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Affiliation(s)
- Claudia Coleine
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
| | - Nuttapon Pombubpa
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, USA.
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo 01100, Italy.
- Italian National Antarctic Museum (MNA), Mycological Section, Genoa 16166, Italy.
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Vásquez-Ponce F, Higuera-Llantén S, Pavlov MS, Marshall SH, Olivares-Pacheco J. Phylogenetic MLSA and phenotypic analysis identification of three probable novel Pseudomonas species isolated on King George Island, South Shetland, Antarctica. Braz J Microbiol 2018; 49:695-702. [PMID: 29598976 PMCID: PMC6175711 DOI: 10.1016/j.bjm.2018.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Revised: 02/03/2018] [Accepted: 02/14/2018] [Indexed: 02/07/2023] Open
Abstract
Antarctica harbors a great diversity of microorganisms, including bacteria, archaea, microalgae and yeasts. The Pseudomonas genus is one of the most diverse and successful bacterial groups described to date, but only eight species isolated from Antarctica have been characterized. Here, we present three potentially novel species isolated on King George Island. The most abundant isolates from four different environments, were genotypically and phenotypically characterized. Multilocus sequence analysis and 16S rRNA gene analysis of a sequence concatenate for six genes (16S, aroE, glnS, gyrB, ileS and rpoD), determined one of the isolates to be a new Pseudomonas mandelii strain, while the other three are good candidates for new Pseudomonas species. Additionally, genotype analyses showed the three candidates to be part of a new subgroup within the Pseudomonas fluorescens complex, together with the Antarctic species Pseudomonas antarctica and Pseudomonas extremaustralis. We propose terming this new subgroup P. antarctica. Likewise, phenotypic analyses using API 20 NE and BIOLOG® corroborated the genotyping results, confirming that all presented isolates form part of the P. fluorescens complex. Pseudomonas genus research on the Antarctic continent is in its infancy. To understand these microorganisms’ role in this extreme environment, the characterization and description of new species is vital.
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Affiliation(s)
- Felipe Vásquez-Ponce
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Sebastián Higuera-Llantén
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - María S Pavlov
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Sergio H Marshall
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile
| | - Jorge Olivares-Pacheco
- Pontificia Universidad Católica de Valparaíso, Facultad de Ciencias, Instituto de Biología, Laboratorio de Genética e Inmunología Molecular, Valparaíso, Chile.
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Selbmann L, Onofri S, Coleine C, Buzzini P, Canini F, Zucconi L. Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities. Extremophiles 2017; 21:1069-1080. [PMID: 28993960 DOI: 10.1007/s00792-017-0967-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/21/2017] [Indexed: 11/29/2022]
Abstract
A wide sampling of rocks, colonized by microbial epi-endolithic communities, was performed along an altitudinal gradient from sea level to 3600 m asl and sea distance from the coast to 100 km inland along the Victoria Land Coast, Antarctica. Seventy-two rock samples of different typology, representative of the entire survey, were selected and studied using denaturing gradient gel electrophoresis to compare variation in fungal diversity according to environmental conditions along this altitudinal and sea distance transect. Lichenized fungi were largely predominant in all the samples studied and the biodiversity was heavily influenced even by minimal local variations. The n-MDS analysis showed that altitude and sea distance affect fungal biodiversity, while sandstone allows the communities to maintain high biodiversity indices. The Pareto-Lorenz curves indicate that all the communities analyzed are highly adapted to extreme conditions but scarcely resilient, so any external perturbation may have irreversible effects on these fragile ecosystems.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Claudia Coleine
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Pietro Buzzini
- Department of Agricultural, Food and Environmental Sciences, Industrial Yeasts Collection DBVPG, University of Perugia, Perugia, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Viterbo, Italy
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Higuera-Llantén S, Vásquez-Ponce F, Núñez-Gallegos M, Pavlov MS, Marshall S, Olivares-Pacheco J. Phenotypic and genotypic characterization of a novel multi-antibiotic-resistant, alginate hyperproducing strain of Pseudomonas mandelii isolated in Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2206-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Wang M, Tian J, Xiang M, Liu X. Living strategy of cold-adapted fungi with the reference to several representative species. Mycology 2017; 8:178-188. [PMID: 30123638 PMCID: PMC6059074 DOI: 10.1080/21501203.2017.1370429] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 08/16/2017] [Indexed: 12/25/2022] Open
Abstract
Our planet is dominant with cold environments that harbour enormously diverse cold-adapted fungi comprising representatives of all phyla. Investigation based on culture-dependent and independent methods has demonstrated that cold-adapted fungi are cosmopolitan and occur in diverse habitants and substrates. They live as saprobes, symbionts, plant and animal parasites and pathogens to perform crucial functions in different ecosystems. Pseudogymnoascus destructans caused bat white-nose syndrome and Ophiocordyceps sinensis as Chinese medicine are the representative species that have significantly ecological and economic significance. Adaptation to cold niches has made this group of fungi a fascinating resource for the discovery of novel enzymes and secondary metabolites for biotechnological and pharmaceutical uses. This review provides the current understanding of living strategy and ecological functions of cold-adapted fungi, with particular emphasis on how those fungi overcome the extreme low temperature and perform their ecological function.
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Affiliation(s)
- Manman Wang
- College of Life Science, Hebei University, Baoding, China
| | - Jianqing Tian
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, 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
| | - Xingzhong Liu
- 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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39
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Slattery M, Lesser MP. Allelopathy-mediated competition in microbial mats from Antarctic lakes. FEMS Microbiol Ecol 2017; 93:3003319. [PMID: 28334326 DOI: 10.1093/femsec/fix019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 02/15/2017] [Indexed: 11/14/2022] Open
Abstract
Microbial mats are vertically stratified communities that host a complex consortium of microorganisms, dominated by cyanobacteria, which compete for available nutrients and environmental niches, within these extreme habitats. The Antarctic Dry Valleys near McMurdo Sound include a series of lakes within the drainage basin that are bisected by glacial traverses. These lakes are traditionally independent, but recent increases in glacial melting have allowed two lakes (Chad and Hoare) to become connected by a meltwater stream. Microbial mats were collected from these lakes, and cultured under identical conditions at the McMurdo Station laboratory. Replicate pairings of the microbial mats exhibited consistent patterns of growth inhibition indicative of competitive dominance. Natural products were extracted from the microbial mats, and a disk diffusion assay was utilized to show that allelochemical compounds mediate competitive interactions. Both microscopy and 16S rRNA sequencing show that these mats contain significant populations of cyanobacteria known to produce allelochemicals. Two compounds were isolated from these microbial mats that might be important in the chemical ecology of these psychrophiles. In other disk:mat pairings, including extract versus mat of origin, the allelochemicals exhibited no effect. Taken together, these results indicate that Antarctic lake microbial mats can compete via allelopathy.
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Affiliation(s)
- Marc Slattery
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677, USA
| | - Michael P Lesser
- School of Marine Science and Ocean Engineering, University of New Hampshire, Durham, NH 03824, USA
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Wei STS, Lacap-Bugler DC, Lau MCY, Caruso T, Rao S, de Los Rios A, Archer SK, Chiu JMY, Higgins C, Van Nostrand JD, Zhou J, Hopkins DW, Pointing SB. Taxonomic and Functional Diversity of Soil and Hypolithic Microbial Communities in Miers Valley, McMurdo Dry Valleys, Antarctica. Front Microbiol 2016; 7:1642. [PMID: 27812351 PMCID: PMC5071352 DOI: 10.3389/fmicb.2016.01642] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/03/2016] [Indexed: 12/04/2022] Open
Abstract
The McMurdo Dry Valleys of Antarctica are an extreme polar desert. Mineral soils support subsurface microbial communities and translucent rocks support development of hypolithic communities on ventral surfaces in soil contact. Despite significant research attention, relatively little is known about taxonomic and functional diversity or their inter-relationships. Here we report a combined diversity and functional interrogation for soil and hypoliths of the Miers Valley in the McMurdo Dry Valleys of Antarctica. The study employed 16S rRNA fingerprinting and high throughput sequencing combined with the GeoChip functional microarray. The soil community was revealed as a highly diverse reservoir of bacterial diversity dominated by actinobacteria. Hypolithic communities were less diverse and dominated by cyanobacteria. Major differences in putative functionality were that soil communities displayed greater diversity in stress tolerance and recalcitrant substrate utilization pathways, whilst hypolithic communities supported greater diversity of nutrient limitation adaptation pathways. A relatively high level of functional redundancy in both soil and hypoliths may indicate adaptation of these communities to fluctuating environmental conditions.
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Affiliation(s)
- Sean T S Wei
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Donnabella C Lacap-Bugler
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Maggie C Y Lau
- Department of Geosciences, Princeton University Princeton, NJ, USA
| | - Tancredi Caruso
- School of Biological Sciences, Queen's University Belfast Belfast, Northern Ireland
| | - Subramanya Rao
- Department of Health Technology and Informatics, Hong Kong Polytechnic University Hong Kong, China
| | - Asunción de Los Rios
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales Madrid, Spain
| | - Stephen K Archer
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Jill M Y Chiu
- Department of Biology, Hong Kong Baptist University Hong Kong, China
| | - Colleen Higgins
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology Auckland, New Zealand
| | - Joy D Van Nostrand
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma Norman, OK, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of OklahomaNorman, OK, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China; Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - David W Hopkins
- School of Agriculture, Food and Environment, The Royal Agricultural University Gloucestershire, UK
| | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of TechnologyAuckland, New Zealand; Institute of Nature and Environmental Technology, Kanazawa UniversityKanazawa, Japan
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41
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Le PT, Makhalanyane TP, Guerrero LD, Vikram S, Van de Peer Y, Cowan DA. Comparative Metagenomic Analysis Reveals Mechanisms for Stress Response in Hypoliths from Extreme Hyperarid Deserts. Genome Biol Evol 2016; 8:2737-47. [PMID: 27503299 PMCID: PMC5630931 DOI: 10.1093/gbe/evw189] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding microbial adaptation to environmental stressors is crucial for interpreting broader ecological patterns. In the most extreme hot and cold deserts, cryptic niche communities are thought to play key roles in ecosystem processes and represent excellent model systems for investigating microbial responses to environmental stressors. However, relatively little is known about the genetic diversity underlying such functional processes in climatically extreme desert systems. This study presents the first comparative metagenome analysis of cyanobacteria-dominated hypolithic communities in hot (Namib Desert, Namibia) and cold (Miers Valley, Antarctica) hyperarid deserts. The most abundant phyla in both hypolith metagenomes were Actinobacteria, Proteobacteria, Cyanobacteria and Bacteroidetes with Cyanobacteria dominating in Antarctic hypoliths. However, no significant differences between the two metagenomes were identified. The Antarctic hypolithic metagenome displayed a high number of sequences assigned to sigma factors, replication, recombination and repair, translation, ribosomal structure, and biogenesis. In contrast, the Namib Desert metagenome showed a high abundance of sequences assigned to carbohydrate transport and metabolism. Metagenome data analysis also revealed significant divergence in the genetic determinants of amino acid and nucleotide metabolism between these two metagenomes and those of soil from other polar deserts, hot deserts, and non-desert soils. Our results suggest extensive niche differentiation in hypolithic microbial communities from these two extreme environments and a high genetic capacity for survival under environmental extremes.
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Affiliation(s)
- Phuong Thi Le
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Leandro D Guerrero
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Yves Van de Peer
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa Department of Plant Systems Biology, VIB, Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, Ghent Belgium
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics (CMEG), Department of Genetics, University of Pretoria, Pretoria, South Africa
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42
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Lopatina A, Medvedeva S, Shmakov S, Logacheva MD, Krylenkov V, Severinov K. Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow. Front Microbiol 2016; 7:398. [PMID: 27064693 PMCID: PMC4814470 DOI: 10.3389/fmicb.2016.00398] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/14/2016] [Indexed: 11/23/2022] Open
Abstract
The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.
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Affiliation(s)
- Anna Lopatina
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia
| | - Sofia Medvedeva
- Department of Molecular Genetics of Microorganisms, Institute of Gene Biology, Russian Academy of SciencesMoscow, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia
| | - Sergey Shmakov
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology Skolkovo, Russia
| | - Maria D Logacheva
- Belozersky Institute of Physico-Chemical Biology, Moscow State University Moscow, Russia
| | - Vjacheslav Krylenkov
- Department of Botany, Saint-Petersburg State University Saint-Petersburg, Russia
| | - Konstantin Severinov
- Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of SciencesMoscow, Russia; Research Complex of "Nanobiotechnology", Saint-Petersburg State Polytechnical UniversitySaint-Petersburg, Russia; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and TechnologySkolkovo, Russia
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43
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Van Goethem MW, Makhalanyane TP, Valverde A, Cary SC, Cowan DA. Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw051. [DOI: 10.1093/femsec/fiw051] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2016] [Indexed: 12/18/2022] Open
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44
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Makhalanyane TP, Van Goethem MW, Cowan DA. Microbial diversity and functional capacity in polar soils. Curr Opin Biotechnol 2016; 38:159-66. [PMID: 26921734 DOI: 10.1016/j.copbio.2016.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 11/18/2022]
Abstract
Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions.
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Affiliation(s)
- Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa
| | - Marc Warwick Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa
| | - Don Arthur Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa.
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45
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Archer SDJ, McDonald IR, Herbold CW, Lee CK, Niederberger TS, Cary C. Temporal, regional and geochemical drivers of microbial community variation in the melt ponds of the Ross Sea region, Antarctica. Polar Biol 2016. [DOI: 10.1007/s00300-015-1780-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Wang NF, Zhang T, Zhang F, Wang ET, He JF, Ding H, Zhang BT, Liu J, Ran XB, Zang JY. Diversity and structure of soil bacterial communities in the Fildes Region (maritime Antarctica) as revealed by 454 pyrosequencing. Front Microbiol 2015; 6:1188. [PMID: 26579095 PMCID: PMC4623505 DOI: 10.3389/fmicb.2015.01188] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/12/2015] [Indexed: 12/19/2022] Open
Abstract
This study assessed the diversity and composition of bacterial communities in four different soils (human-, penguin-, seal-colony impacted soils and pristine soil) in the Fildes Region (King George Island, Antarctica) using 454 pyrosequencing with bacterial-specific primers targeting the 16S rRNA gene. Proteobacteria, Actinobacteria, Acidobacteria, and Verrucomicrobia were abundant phyla in almost all the soil samples. The four types of soils were significantly different in geochemical properties and bacterial community structure. Thermotogae, Cyanobacteria, Fibrobacteres, Deinococcus-Thermus, and Chlorobi obviously varied in their abundance among the 4 soil types. Considering all the samples together, members of the genera Gaiella, Chloracidobacterium, Nitrospira, Polaromonas, Gemmatimonas, Sphingomonas, and Chthoniobacter were found to predominate, whereas members of the genera Chamaesiphon, Herbaspirillum, Hirschia, Nevskia, Nitrosococcus, Rhodococcus, Rhodomicrobium, and Xanthomonas varied obviously in their abundance among the four soil types. Distance-based redundancy analysis revealed that pH (p < 0.01), phosphate phosphorus (p < 0.01), organic carbon (p < 0.05), and organic nitrogen (p < 0.05) were the most significant factors that correlated with the community distribution of soil bacteria. To our knowledge, this is the first study to explore the soil bacterial communities in human-, penguin-, and seal- colony impacted soils from ice-free areas in maritime Antarctica using high-throughput pyrosequencing.
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Affiliation(s)
- Neng Fei Wang
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration Qingdao, China
| | - Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences Beijing, China
| | - Fang Zhang
- Polar Research Institute of China Shanghai, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional Mexico, Mexico
| | - Jian Feng He
- Polar Research Institute of China Shanghai, China
| | - Hui Ding
- Chemical Engineering Institute, Qingdao University Qingdao, China
| | - Bo Tao Zhang
- Chemical Engineering Institute, Qingdao University Qingdao, China
| | - Jie Liu
- Department of Bioengineering and Biotechnology, Qingdao University of Science and Technology Qingdao, China
| | - Xiang Bin Ran
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration Qingdao, China
| | - Jia Ye Zang
- Key Lab of Marine Bioactive Substances, The First Institute of Oceanography, State Oceanic Administration Qingdao, China
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47
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Ferrari BC, Bissett A, Snape I, van Dorst J, Palmer AS, Ji M, Siciliano SD, Stark JS, Winsley T, Brown MV. Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems. Environ Microbiol 2015; 18:1834-49. [DOI: 10.1111/1462-2920.13034] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/20/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
| | - Andrew Bissett
- CSIRO Agriculture Flagship; PO Box 1600 Canberra ACT 2601 Australia
| | - Ian Snape
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
| | - Anne S. Palmer
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
| | - Mukan Ji
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
| | - Steven D. Siciliano
- Department of Soil Science; University of Saskatchewan; Saskatoon Saskatchewan S7N 5A8 Canada
| | - Jonathon S. Stark
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
| | - Tristrom Winsley
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
- Australian Antarctic Division, Department of Sustainability; Environment, Water, Population and Communities; 203 Channel Highway Kingston Tasmania 7050 Australia
- Department of Soil Science; University of Saskatchewan; Saskatoon Saskatchewan S7N 5A8 Canada
| | - Mark V. Brown
- School of Biotechnology and Biomolecular Sciences; UNSW Australia; Randwick NSW 2052 Australia
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48
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49
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Maccario L, Sanguino L, Vogel TM, Larose C. Snow and ice ecosystems: not so extreme. Res Microbiol 2015; 166:782-95. [PMID: 26408452 DOI: 10.1016/j.resmic.2015.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/02/2015] [Accepted: 09/11/2015] [Indexed: 11/18/2022]
Abstract
Snow and ice environments cover up to 21% of the Earth's surface. They have been regarded as extreme environments because of their low temperatures, high UV irradiation, low nutrients and low water availability, and thus, their microbial activity has not been considered relevant from a global microbial ecology viewpoint. In this review, we focus on why snow and ice habitats might not be extreme from a microbiological perspective. Microorganisms interact closely with the abiotic conditions imposed by snow and ice habitats by having diverse adaptations, that include genetic resistance mechanisms, to different types of stresses in addition to inhabiting various niches where these potential stresses might be reduced. The microbial communities inhabiting snow and ice are not only abundant and taxonomically diverse, but complex in terms of their interactions. Altogether, snow and ice seem to be true ecosystems with a role in global biogeochemical cycles that has likely been underestimated. Future work should expand past resistance studies to understanding the function of these ecosystems.
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Affiliation(s)
- Lorrie Maccario
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Laura Sanguino
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS UMR 5005, Université de Lyon, Ecole Centrale de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
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50
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Stevenson A, Cray JA, Williams JP, Santos R, Sahay R, Neuenkirchen N, McClure CD, Grant IR, Houghton JDR, Quinn JP, Timson DJ, Patil SV, Singhal RS, Antón J, Dijksterhuis J, Hocking AD, Lievens B, Rangel DEN, Voytek MA, Gunde-Cimerman N, Oren A, Timmis KN, McGenity TJ, Hallsworth JE. Is there a common water-activity limit for the three domains of life? THE ISME JOURNAL 2015; 9:1333-51. [PMID: 25500507 PMCID: PMC4438321 DOI: 10.1038/ismej.2014.219] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/07/2014] [Accepted: 10/16/2014] [Indexed: 01/09/2023]
Abstract
Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a(w)) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a(w). Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a(w)). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 aw for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a(w) for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life.
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Affiliation(s)
- Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jonathan A Cray
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jim P Williams
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Ricardo Santos
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
- Laboratório de Análises, Instituto Superior Técnico, Lisboa, Portugal
| | - Richa Sahay
- University of Essex, School of Biological Sciences, Colchester, Essex, UK
| | - Nils Neuenkirchen
- University of Essex, School of Biological Sciences, Colchester, Essex, UK
| | - Colin D McClure
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Irene R Grant
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jonathan DR Houghton
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - John P Quinn
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - David J Timson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Satish V Patil
- School of Life Sciences, North Maharashtra University, Jalgaon, Maharashtra, India
| | - Rekha S Singhal
- Department of Food Engineering and Technology, Institute of Chemical Technology, Mumbai, India
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | | | - Ailsa D Hocking
- CSIRO Food and Nutrition, North Ryde, New South Wales, Australia
| | - Bart Lievens
- Microbial Ecology and Biorational Control, Scientia Terrae Research Institute, Sint-Katelijne-Waver, Belgium
| | - Drauzio E N Rangel
- Instituto de Pesquisa e Desenvolvimento, Universidade do Vale do Paraíba, São José dos Campos, São Paulo, Brazil
| | | | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Aharon Oren
- Hebrew University of Jerusalem, Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, Jerusalem, Israel
| | - Kenneth N Timmis
- University of Essex, School of Biological Sciences, Colchester, Essex, UK
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Terry J McGenity
- University of Essex, School of Biological Sciences, Colchester, Essex, UK
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, Northern Ireland, UK
- University of Essex, School of Biological Sciences, Colchester, Essex, UK
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