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Baptista MS, Lee CK, Monteiro MR, Torgo L, Cary SC, Magalhães C. Soils of two Antarctic Dry Valleys exhibit unique microbial community structures in response to similar environmental disturbances. ENVIRONMENTAL MICROBIOME 2024; 19:52. [PMID: 39060935 PMCID: PMC11282855 DOI: 10.1186/s40793-024-00587-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 06/30/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND Isolating the effects of deterministic variables (e.g., physicochemical conditions) on soil microbial communities from those of neutral processes (e.g., dispersal) remains a major challenge in microbial ecology. In this study, we disturbed soil microbial communities of two McMurdo Dry Valleys of Antarctica exhibiting distinct microbial biogeographic patterns, both devoid of aboveground biota and different in macro- and micro-physicochemical conditions. We modified the availability of water, nitrogen, carbon, copper ions, and sodium chloride salts in a laboratory-based experiment and monitored the microbial communities for up to two months. Our aim was to mimic a likely scenario in the near future, in which similar selective pressures will be applied to both valleys. We hypothesized that, given their unique microbial communities, the two valleys would select for different microbial populations when subjected to the same disturbances. RESULTS The two soil microbial communities, subjected to the same disturbances, did not respond similarly as reflected in both 16S rRNA genes and transcripts. Turnover of the two microbial communities showed a contrasting response to the same environmental disturbances and revealed different potentials for adaptation to change. These results suggest that the heterogeneity between these microbial communities, reflected in their strong biogeographic patterns, was maintained even when subjected to the same selective pressure and that the 'rare biosphere', at least in these samples, were deeply divergent and did not act as a reservoir for microbiota that enabled convergent responses to change in environmental conditions. CONCLUSIONS Our findings strongly support the occurrence of endemic microbial communities that show a structural resilience to environmental disturbances, spanning a wide range of physicochemical conditions. In the highly arid and nutrient-limited environment of the Dry Valleys, these results provide direct evidence of microbial biogeographic patterns that can shape the communities' response in the face of future environmental changes.
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Affiliation(s)
- Mafalda S Baptista
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- 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
- School of Science, University of Waikato, Hamilton, New Zealand
| | | | - Luís Torgo
- Faculty of Sciences, University of Porto, Porto, Portugal
- Ocean Frontier Institute, Dalhousie University, Halifax, NS, Canada
| | - S Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, New Zealand
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal.
- Faculty of Sciences, University of Porto, Porto, Portugal.
- Ocean Frontier Institute, Dalhousie University, Halifax, NS, Canada.
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Wang F, Sha Y, Liu X, He Y, Hu J, Wang J, Li S, Shao P, Chen X, Yang W, Chen Q, Gao M, Huang W. Study of the Interactions between Muscle Fatty Acid Composition, Meat Quality-Related Genes and the Ileum Microbiota in Tibetan Sheep at Different Ages. Foods 2024; 13:679. [PMID: 38472792 DOI: 10.3390/foods13050679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
The intestinal microbiota of ruminants is an important factor affecting animal production and health. Research on the association mechanism between the intestinal microbiota and meat quality of ruminants will play a positive role in understanding the formation mechanism of meat quality in ruminants and improving production efficiency. In this study, the fatty acid composition and content, expression of related genes, and structural characteristics of the ileum microbiota of ewes of Tibetan sheep at different ages (4 months, 1.5 years, 3.5 years, and 6 years) were detected and analyzed. The results revealed significant differences in fatty acid composition and content in the muscle of Tibetan sheep at different ages (p < 0.05); in addition, the content of MUFAs in the longissimus dorsi muscle and leg muscle was higher. Similarly, the expressions of muscle-related genes differed among the different age groups, and the expression of the LPL, SCD, and FABP4 genes was higher in the 1.5-year-old group. The ileum microbiota diversity was higher in the 1.5-year-old group, the Romboutsia abundance ratio was significantly higher in the 1.5-year-old group (p < 0.05), and there was a significant positive correlation with oleic acid (C18:1n9c) (p < 0.05). In conclusion, the content of beneficial fatty acids in the longissimus dorsi muscle and leg muscle of Tibetan sheep was higher at 1.5 years of age, and the best slaughter age was 1.5 years. This study provides a reference for in-depth research on the mechanism of the influence of the gut microbiota on meat quality and related regulation.
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Affiliation(s)
- Fanxiong Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuzhu Sha
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiu Liu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yanyu He
- School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiqing Wang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Shaobin Li
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengyang Shao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaowei Chen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wenxin Yang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Qianling Chen
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Min Gao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Wei Huang
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, 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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Silva JPD, Veloso TGR, Costa MD, Souza JJLLD, Soares EMB, Gomes LC, Schaefer CEGR. Microbial successional pattern along a glacier retreat gradient from Byers Peninsula, Maritime Antarctica. ENVIRONMENTAL RESEARCH 2024; 241:117548. [PMID: 37939803 DOI: 10.1016/j.envres.2023.117548] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/10/2023]
Abstract
The retreat of glaciers in Antarctica has increased in the last decades due to global climate change, influencing vegetation expansion, and soil physico-chemical and biological attributes. However, little is known about soil microbiology diversity in these periglacial landscapes. This study characterized and compared bacterial and fungal diversity using metabarcoding of soil samples from the Byers Peninsula, Maritime Antarctica. We identified bacterial and fungal communities by amplification of bacterial 16 S rRNA region V3-V4 and fungal internal transcribed spacer 1 (ITS1). We also applied 14C dating on soil organic matter (SOM) from six profiles. Physico-chemical analyses and attributes associated with SOM were evaluated. A total of 14,048 bacterial ASVs were obtained, and almost all samples had 50% of their sequences assigned to Actinobacteriota and Proteobacteria. Regarding the fungal community, Mortierellomycota, Ascomycota and Basidiomycota were the main phyla from 1619 ASVs. We found that soil age was more relevant than the distance from the glacier, with the oldest soil profile (late Holocene soil profile) hosting the highest bacterial and fungal diversity. The microbial indices of the fungal community were correlated with nutrient availability, soil reactivity and SOM composition, whereas the bacterial community was not correlated with any soil attribute. The bacterial diversity, richness, and evenness varied according to presence of permafrost and moisture regime. The fungal community richness in the surface horizon was not related to altitude, permafrost, or moisture regime. The soil moisture regime was crucial for the structure, high diversity and richness of the microbial community, specially to the bacterial community. Further studies should examine the relationship between microbial communities and environmental factors to better predict changes in this terrestrial ecosystem.
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Affiliation(s)
- Jônatas Pedro da Silva
- Graduate Program in Soils and Plant Nutrition, Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil
| | | | - Maurício Dutra Costa
- Microbiology Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Bolsista Pesquisador Do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
| | - José João Lelis Leal de Souza
- Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Bolsista Pesquisador Do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
| | | | | | - Carlos Ernesto G R Schaefer
- Soil Science Department, Universidade Federal de Viçosa - UFV, Viçosa, MG, Brazil; Bolsista Pesquisador Do Conselho Nacional de Desenvolvimento Científico e Tecnológico, CNPq, Brasília, DF, Brazil
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Cui S, Du J, Zhu L, Xin D, Xin Y, Zhang J. Analysis of Microbial Diversity in South Shetland Islands and Antarctic Peninsula Soils Based on Illumina High-Throughput Sequencing and Cultivation-Dependent Techniques. Microorganisms 2023; 11:2517. [PMID: 37894176 PMCID: PMC10609098 DOI: 10.3390/microorganisms11102517] [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: 09/12/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
To assess the diversity of bacterial taxa in Antarctic soils and obtain novel microbial resources, 15 samples from 3 sampling sites (DIS5, GWS7, FPS10) of South Shetland Islands and 2 sampling sites (APS18, CIS17) of Antarctic Peninsula were collected. High-throughput sequencing (HTS) of 16S rRNA genes within these samples was conducted on an Illumina Miseq platform. A total of 140,303 16S rRNA gene reads comprising 802 operational taxonomic units (OTUs) were obtained. After taxonomic classification, 25 phyla, 196 genera, and a high proportion of unidentified taxa were detected, among which seven phyla and 99 genera were firstly detected in Antarctica. The bacterial communities were dominated by Actinomycetota (40.40%), Pseudomonadota (17.14%), Bacteroidota (10.55%) and Chloroflexota (10.26%). Based on the HTS analyses, cultivation-dependent techniques were optimized to identify the cultivable members. A total of 30 different genera including 91 strains were obtained, the majority of which has previously been reported from Antarctica. However, for the genera Microterricola, Dyadobacter, Filibacter, Duganella, Ensifer, Antarcticirhabdus and Microvirga, this is the first report in Antarctica. In addition, seven strains represented novel taxa, two of which were psychropoilic and could be valuable resources for further research of cold-adaptability and their ecological significance in Antarctica.
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Affiliation(s)
- Siqi Cui
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Jie Du
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Lin Zhu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Di Xin
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
| | - Yuhua Xin
- China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Jianli Zhang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing 100081, China; (S.C.); (J.D.); (L.Z.); (D.X.)
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6
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Jiang X, Van Horn DJ, Okie JG, Buelow HN, Schwartz E, Colman DR, Feeser KL, Takacs-Vesbach CD. Limits to the three domains of life: lessons from community assembly along an Antarctic salinity gradient. Extremophiles 2022; 26:15. [PMID: 35296937 DOI: 10.1007/s00792-022-01262-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 02/10/2022] [Indexed: 02/01/2023]
Abstract
Extremophiles exist among all three domains of life; however, physiological mechanisms for surviving harsh environmental conditions differ among Bacteria, Archaea and Eukarya. Consequently, we expect that domain-specific variation of diversity and community assembly patterns exist along environmental gradients in extreme environments. We investigated inter-domain community compositional differences along a high-elevation salinity gradient in the McMurdo Dry Valleys, Antarctica. Conductivity for 24 soil samples collected along the gradient ranged widely from 50 to 8355 µS cm-1. Taxonomic richness varied among domains, with a total of 359 bacterial, 2 archaeal, 56 fungal, and 69 non-fungal eukaryotic operational taxonomic units (OTUs). Richness for bacteria, archaea, fungi, and non-fungal eukaryotes declined with increasing conductivity (all P < 0.05). Principal coordinate ordination analysis (PCoA) revealed significant (ANOSIM R = 0.97) groupings of low/high salinity bacterial OTUs, while OTUs from other domains were not significantly clustered. Bacterial beta diversity was unimodally distributed along the gradient and had a nested structure driven by species losses, whereas in fungi and non-fungal eukaryotes beta diversity declined monotonically without strong evidence of nestedness. Thus, while increased salinity acts as a stressor in all domains, the mechanisms driving community assembly along the gradient differ substantially between the domains.
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Affiliation(s)
- Xiaoben Jiang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - David J Van Horn
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jordan G Okie
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - Heather N Buelow
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Daniel R Colman
- Department of Biology, MSC03 2020 1UNM, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Kelli L Feeser
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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Mujakić I, Piwosz K, Koblížek M. Phylum Gemmatimonadota and Its Role in the Environment. Microorganisms 2022; 10:microorganisms10010151. [PMID: 35056600 PMCID: PMC8779627 DOI: 10.3390/microorganisms10010151] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 02/06/2023] Open
Abstract
Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.
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Affiliation(s)
- Izabela Mujakić
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
| | - Kasia Piwosz
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- National Marine Fisheries Research Institute, Kołłątaja 1, 81-332 Gdynia, Poland
| | - Michal Koblížek
- Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Novohradská 237, 379 81 Třeboň, Czech Republic; (I.M.); (K.P.)
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czech Republic
- Correspondence:
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KINASZ CAMILAT, KREUSCH MARIANNEG, BENDIA AMANDAG, PELLIZARI VIVIANH, DUARTE RUBENST. Taxonomic and functional diversity from Antarctic ice-tephra microbial community: ecological insights and potential for bioprospection. AN ACAD BRAS CIENC 2022; 94:e20210621. [DOI: 10.1590/0001-3765202220210621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
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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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Description and genome analysis of Microvirga antarctica sp. nov., a novel pink-pigmented psychrotolerant bacterium isolated from Antarctic soil. Antonie van Leeuwenhoek 2021; 114:2219-2228. [PMID: 34697697 DOI: 10.1007/s10482-021-01674-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
A novel pink-pigmented bacterium, designated strain 3D7T, was isolated during an investigation of potential psychrotolerant species from Antarctic soil. Cells of the isolate were observed to be rod-shaped (0.7-0.9 × 1.0-2.2 µm), Gram-stain negative and non-motile. It was able to grow at 4-32 °C, pH 7.0-10.0 and in the presence of 0-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 3D7T belongs to the genus Microvirga and was most closely related to 'Microvirga brassicacearum' CDVBN77T (98.3%), Microvirga subterranea DSM 14364 T (96.8%), Microvirga guangxiensis 25BT (96.5%) and Microvirga aerophila DSM 21344 T (96.5%). The predominant quinone was ubiquinone 10 (Q-10), and the major fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G + C content of strain 3D7T was 63.5 mol%. Its genome sequence showed genes encoding phosphatases and lipases. Genetic machinery related to carbohydrate-active enzymes and secondary metabolites were also observed. The average nucleotide identity and digital DNA-DNA hybridization values based on whole genome sequences of strain 3D7T and its closely related species were below the threshold range for species determination. Phenotypic, chemotaxonomic, phylogenetic and genomic analyses suggested that strain 3D7T represents a novel species of the genus Microvirga, for which the name Microvirga antarctica sp. nov. is proposed. The type strain is 3D7T (= CGMCC 1.13821T = KCTC 72465T).
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Borsodi AK, Mucsi M, Krett G, Szabó A, Felföldi T, Szili-Kovács T. Variation in Sodic Soil Bacterial Communities Associated with Different Alkali Vegetation Types. Microorganisms 2021; 9:microorganisms9081673. [PMID: 34442752 PMCID: PMC8402138 DOI: 10.3390/microorganisms9081673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 11/22/2022] Open
Abstract
In this study, we examined the effect of salinity and alkalinity on the metabolic potential and taxonomic composition of microbiota inhabiting the sodic soils in different plant communities. The soil samples were collected in the Pannonian steppe (Hungary, Central Europe) under extreme dry and wet weather conditions. The metabolic profiles of microorganisms were analyzed using the MicroResp method, the bacterial diversity was assessed by cultivation and next-generation amplicon sequencing based on the 16S rRNA gene. Catabolic profiles of microbial communities varied primarily according to the alkali vegetation types. Most members of the strain collection were identified as plant associated and halophilic/alkaliphilic species of Micrococcus, Nesterenkonia, Nocardiopsis, Streptomyces (Actinobacteria) and Bacillus, Paenibacillus (Firmicutes) genera. Based on the pyrosequencing data, the relative abundance of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes and Bacteroidetes also changed mainly with the sample types, indicating distinctions within the compositions of bacterial communities according to the sodic soil alkalinity-salinity gradient. The effect of weather extremes was the most pronounced in the relative abundance of the phyla Actinobacteria and Acidobacteria. The type of alkali vegetation caused greater shifts in both the diversity and activity of sodic soil microbial communities than the extreme aridity and moisture.
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Affiliation(s)
- Andrea K. Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary;
- Correspondence: (A.K.B.); (T.S.-K.); Tel.: +36-13812177 (A.K.B.); +36-309617452 (T.S.-K.)
| | - Márton Mucsi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
- Institute for Soil Sciences, Centre for Agricultural Research, Herman Ottó út 15, H-1022 Budapest, Hungary
| | - Gergely Krett
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary;
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. Sétány 1/C, H-1117 Budapest, Hungary; (M.M.); (G.K.); (T.F.)
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, H-1113 Budapest, Hungary;
| | - Tibor Szili-Kovács
- Institute for Soil Sciences, Centre for Agricultural Research, Herman Ottó út 15, H-1022 Budapest, Hungary
- Correspondence: (A.K.B.); (T.S.-K.); Tel.: +36-13812177 (A.K.B.); +36-309617452 (T.S.-K.)
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12
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Severgnini M, Canini F, Consolandi C, Camboni T, Paolo D'Acqui L, Mascalchi C, Ventura S, Zucconi L. Highly differentiated soil bacterial communities in Victoria Land macro-areas (Antarctica). FEMS Microbiol Ecol 2021; 97:6307020. [PMID: 34151349 DOI: 10.1093/femsec/fiab087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/17/2021] [Indexed: 11/13/2022] Open
Abstract
Ice-free areas of Victoria Land, in Antarctica, are characterized by different terrestrial ecosystems, that are dominated by microorganisms supporting highly adapted communities. Despite the unique conditions of these ecosystems, reports on their bacterial diversity are still fragmentary. From this perspective, 60 samples from 14 localities were analyzed. These localities were distributed in coastal sites with differently developed biological soil crusts, inner sites in the McMurdo Dry Valleys with soils lacking of plant coverage, and a site called Icarus Camp, with a crust developed on a thin locally weathered substrate of the underlying parent granitic-rock. Bacterial diversity was studied through 16S rRNA metabarcoding sequencing. Communities diversity, composition and the abundance and composition of different taxonomic groups were correlated to soil physicochemical characteristics. Firmicutes, Bacteroidetes, Cyanobacteria and Proteobacteria dominated these communities. Most phyla were mainly driven by soil granulometry, an often disregarded parameter and other abiotic parameters. Bacterial composition differed greatly among the three macrohabitats, each having a distinct bacterial profile. Communities within the two main habitats (coastal and inner ones) were well differentiated from each other as well, therefore depending on site-specific physicochemical characteristics. A core community of the whole samples was observed, mainly represented by Firmicutes and Bacteroidetes.
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Affiliation(s)
- Marco Severgnini
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), via f.lli Cervi, 93, 20054, Segrate, Italy
| | - Fabiana Canini
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università s.n.c., 01100, Viterbo, Italy
| | - Clarissa Consolandi
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), via f.lli Cervi, 93, 20054, Segrate, Italy
| | - Tania Camboni
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), via f.lli Cervi, 93, 20054, Segrate, Italy
| | - Luigi Paolo D'Acqui
- Terrestria Ecosystems Research Institute, National Research Council (IRET-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Cristina Mascalchi
- Terrestria Ecosystems Research Institute, National Research Council (IRET-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy
| | - Stefano Ventura
- Terrestria Ecosystems Research Institute, National Research Council (IRET-CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy.,The Italian Embassy in Israel, Trade Tower, 25 Hamered Street, 68125, Tel Aviv, Israel
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università s.n.c., 01100, Viterbo, Italy
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13
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Almela P, Justel A, Quesada A. Heterogeneity of Microbial Communities in Soils From the Antarctic Peninsula Region. Front Microbiol 2021; 12:628792. [PMID: 33664717 PMCID: PMC7920962 DOI: 10.3389/fmicb.2021.628792] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/28/2021] [Indexed: 01/04/2023] Open
Abstract
Ice-free areas represent less than 1% of the Antarctic surface. However, climate change models predict a significant increase in temperatures in the coming decades, triggering a relevant reduction of the ice-covered surface. Microorganisms, adapted to the extreme and fluctuating conditions, are the dominant biota. In this article we analyze the diversity and composition of soil bacterial communities in 52 soil samples on three scales: (i) fine scale, where we compare the differences in the microbial community between top-stratum soils (0-2 cm) and deeper-stratum soils (5-10 cm) at the same sampling point; (ii) medium scale, in which we compare the composition of the microbial community of top-stratum soils from different sampling points within the same sampling location; and (iii) coarse scale, where we compare communities between comparable ecosystems located hundreds of kilometers apart along the Antarctic Peninsula. The results suggest that in ice-free soils exposed for longer periods of time (millennia) microbial communities are significantly different along the soil profiles. However, in recently (decades) deglaciated soils the communities are not different along the soil profile. Furthermore, the microbial communities found in soils at the different sampling locations show a high degree of heterogeneity, with a relevant proportion of unique amplicon sequence variants (ASV) that appeared mainly in low abundance, and only at a single sampling location. The Core90 community, defined as the ASVs shared by 90% of the soils from the 4 sampling locations, was composed of 26 ASVs, representing a small percentage of the total sequences. Nevertheless, the taxonomic composition of the Core80 (ASVs shared by 80% of sampling points per location) of the different sampling locations, was very similar, as they were mostly defined by 20 common taxa, representing up to 75.7% of the sequences of the Core80 communities, suggesting a greater homogeneity of soil bacterial taxa among distant locations.
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Affiliation(s)
- Pablo Almela
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ana Justel
- Department of Mathematics, Universidad Autónoma de Madrid, Madrid, Spain
| | - Antonio Quesada
- Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
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14
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Bottos EM, Laughlin DC, Herbold CW, Lee CK, McDonald IR, Cary SC. Abiotic factors influence patterns of bacterial diversity and community composition in the Dry Valleys of Antarctica. FEMS Microbiol Ecol 2020; 96:5815075. [PMID: 32239205 DOI: 10.1093/femsec/fiaa042] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 03/23/2020] [Indexed: 11/13/2022] Open
Abstract
The Dry Valleys of Antarctica are a unique ecosystem of simple trophic structure, where the abiotic factors that influence soil bacterial communities can be resolved in the absence of extensive biotic interactions. This study evaluated the degree to which aspects of topographic, physicochemical and spatial variation explain patterns of bacterial richness and community composition in 471 soil samples collected across a 220 square kilometer landscape in Southern Victoria Land. Richness was most strongly influenced by physicochemical soil properties, particularly soil conductivity, though significant trends with several topographic and spatial variables were also observed. Structural equation modeling (SEM) supported a final model in which variation in community composition was best explained by physicochemical variables, particularly soil water content, and where the effects of topographic variation were largely mediated through their influence on physicochemical variables. Community dissimilarity increased with distance between samples, and though most of this variation was explained by topographic and physicochemical variation, a small but significant relationship remained after controlling for this environmental variation. As the largest survey of terrestrial bacterial communities of Antarctica completed to date, this work provides fundamental knowledge of the Dry Valleys ecosystem, and has implications globally for understanding environmental factors that influence bacterial distributions.
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Affiliation(s)
- Eric M Bottos
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Daniel C Laughlin
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Craig W Herbold
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Charles K Lee
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Ian R McDonald
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - S Craig Cary
- School of Science, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand.,The International Centre for Terrestrial Antarctic Research, The University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
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15
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Lario LD, Pillaca-Pullo OS, Durães Sette L, Converti A, Casati P, Spampinato C, Pessoa A. Optimization of protease production and sequence analysis of the purified enzyme from the cold adapted yeast Rhodotorula mucilaginosa CBMAI 1528. ACTA ACUST UNITED AC 2020; 28:e00546. [PMID: 33204658 PMCID: PMC7653053 DOI: 10.1016/j.btre.2020.e00546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/21/2020] [Indexed: 11/29/2022]
Abstract
A protease from a psychrotolerant yeast was characterized. Protease production was dependent on temperature and medium composition. Mass spectrometry analysis indicated that the protein belongs to the pepsin family. We propose that the enzyme reported here could be Rodothorulapepsin.
Enzymes from cold-adapted microorganisms are of high interest to industries due to their high activity at low and mild temperatures, which makes them suitable for their use in several processes that either require a supply of exogenous energy or involve the use of heat labile products. In this work, the protease production by the strain Rhodotorula mucilaginosa CBMAI 1528, previously isolated from the Antarctic continent, was optimized, and the purified enzyme analyzed. It was found that protease production was dependent on culture medium composition and growth temperature, being 20 °C and a culture medium containing both glucose and casein peptone (20 and 10 g/L, respectively) the optimal growing conditions in batch as well as in bioreactor. Moreover, mass spectrometry analysis revealed that the enzyme under study has a 100 % sequence identity with the deduced amino acid sequence of a putative aspartic protease from Rhodotorula sp. JG-1b (protein ID: KWU42276.1). This result was confirmed by the decrease of 95 % proteolytic activity by pepstatin A, a specific inhibitor of aspartic proteases. We propose that the enzyme reported here could be Rodothorulapepsin, a protein characterized in 1972 that did not have an associated sequence to date and has been classified as an orphan enzyme.
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Affiliation(s)
- Luciana Daniela Lario
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, 05508-000, Sao Paulo, SP, Brazil
- Instituto de Ingeniería Ambiental, Química y Biotecnología Aplicada (INGEBIO), Facultad de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, 2000, Rosario, Argentina
- Corresponding author at: Fac. de Química e Ingeniería del Rosario, Pontificia Universidad Católica Argentina (UCA), Av. Pellegrini 3314, 2000, Rosario, Argentina.
| | - Omar Santiago Pillaca-Pullo
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, 05508-000, Sao Paulo, SP, Brazil
| | - Lara Durães Sette
- Department of General and Applied Biology, Institute of Biosciences, Sao Paulo State University (UNESP), Av. 24A, 1515, 13506-900, Rio Claro, SP, Brazil
| | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Pole of Chemical Engineering, University of Genoa, Via Opera Pia 15, 16145, Genoa, Italy
| | - Paula Casati
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Claudia Spampinato
- Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, 2000, Rosario, Argentina
| | - Adalberto Pessoa
- Department of Biochemical and Pharmaceutical Technology, School of Pharmaceutical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 580, 05508-000, Sao Paulo, SP, Brazil
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16
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Zhang W, Bahadur A, Zhang G, Zhang B, Wu X, Chen T, Liu G. Diverse Bacterial Communities From Qaidam Basin of the Qinghai-Tibet Plateau: Insights Into Variations in Bacterial Diversity Across Different Regions. Front Microbiol 2020; 11:554105. [PMID: 33042062 PMCID: PMC7530167 DOI: 10.3389/fmicb.2020.554105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 08/17/2020] [Indexed: 12/20/2022] Open
Abstract
The Qaidam Basin of the Qinghai–Tibet Plateau is a cold, hyper-arid desert that presents extreme challenges to microbial communities. As little is known about variations between surface and subsurface microbial communities, high-throughput DNA sequencing was used in this study to profile bacterial communities of the soil samples collected at different depths in three regions in the Qaidam Basin. The α-diversity indices (Chao, Shannon, and Simpson) indicated that bacterial abundance and diversity were higher in the east and the high-elevation regions compared to the west region. In general, Firmicutes was dominant in the west region, while Proteobacteria and Acidobacteria were dominant in the east and the high-elevation regions. The structure of the bacterial communities differed greatly across regions, being strongly correlated with total organic carbon (TOC) and total nitrogen (TN) content. The differences in bacterial communities between the surface and the subsurface soil samples were smaller than the differences across the regions. Network analyses of environmental factors and bacterial genera indicated significant positive correlations in all regions. Overall, our study provides evidence that TOC and TN are the best predictors of both surface and subsurface bacterial communities across the Qaidam Basin. This study concludes that the bacterial community structure is influenced by both the spatial distance and the local environment, but environmental factors are the primary drivers of bacterial spatial patterns in the Qaidam Basin.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Ali Bahadur
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Binglin Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China.,State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Xiukun Wu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Guangxiu Liu
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
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17
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Microbial Communities in Permafrost Soils of Larsemann Hills, Eastern Antarctica: Environmental Controls and Effect of Human Impact. Microorganisms 2020; 8:microorganisms8081202. [PMID: 32784619 PMCID: PMC7464515 DOI: 10.3390/microorganisms8081202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 11/16/2022] Open
Abstract
Although ice-free areas cover only about 0.1% of Antarctica and are characterized by harsh environmental conditions, these regions provide quite diverse conditions for the soil-forming process, having various physical and geochemical properties, and also assuring different conditions for living organisms. This study is aimed to determine existing soil microbial communities, their relationship with soil parameters and the influence of anthropogenic activity in Larsemann Hills, Eastern Antarctica. The soil microbiome was investigated at different locations using 16S rRNA gene pyrosequencing. The taxonomic analysis of the soil microbiomes revealed 12 predominant bacterial and archaeal phyla—Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, Bacteroidetes, Armatimonadetes, Firmicutes, Cyanobacteria, Thaumarchaeota. Some specific phyla have been also found in sub-surface horizons of soils investigated, thus providing additional evidence of the crucial role of gravel pavement in saving the favorable conditions for both soil and microbiome development. Moreover, our study also revealed that some bacterial species might be introduced into Antarctic soils by human activities. We also assessed the effect of different soil parameters on microbial community in the harsh environmental conditions of Eastern Antarctica. pH, carbon and nitrogen, as well as fine earth content, were revealed as the most accurate predictors of soil bacterial community composition.
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18
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Garrido-Benavent I, Pérez-Ortega S, Durán J, Ascaso C, Pointing SB, Rodríguez-Cielos R, Navarro F, de los Ríos A. Differential Colonization and Succession of Microbial Communities in Rock and Soil Substrates on a Maritime Antarctic Glacier Forefield. Front Microbiol 2020; 11:126. [PMID: 32117148 PMCID: PMC7018881 DOI: 10.3389/fmicb.2020.00126] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/20/2020] [Indexed: 12/20/2022] Open
Abstract
Glacier forefields provide a unique chronosequence to assess microbial or plant colonization and ecological succession on previously uncolonized substrates. Patterns of microbial succession in soils of alpine and subpolar glacier forefields are well documented but those affecting high polar systems, including moraine rocks, remain largely unexplored. In this study, we examine succession patterns in pioneering bacterial, fungal and algal communities developing on moraine rocks and soil at the Hurd Glacier forefield (Livingston Island, Antarctica). Over time, changes were produced in the microbial community structure of rocks and soils (ice-free for different lengths of time), which differed between both substrates across the entire chronosequence, especially for bacteria and fungi. In addition, fungal and bacterial communities showed more compositional consistency in soils than rocks, suggesting community assembly in each niche could be controlled by processes operating at different temporal and spatial scales. Microscopy revealed a patchy distribution of epilithic and endolithic lithobionts, and increasing endolithic colonization and microbial community complexity along the chronosequence. We conclude that, within relatively short time intervals, primary succession processes at polar latitudes involve significant and distinct changes in edaphic and lithic microbial communities associated with soil development and cryptogamic colonization.
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Affiliation(s)
- Isaac Garrido-Benavent
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | | | - Jorge Durán
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Carmen Ascaso
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Stephen B. Pointing
- Yale-NUS College, National University of Singapore, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Ricardo Rodríguez-Cielos
- ETSI de Telecomunicación, Departamento de Señales, Sistemas y Radiocomunicaciones, Universidad Politécnica de Madrid, Madrid, Spain
| | - Francisco Navarro
- ETSI de Telecomunicación, Departamento de Matemática Aplicada a las TIC, Universidad Politécnica de Madrid, Madrid, Spain
| | - Asunción de los Ríos
- Departamento de Biogeoquímica y Ecología Microbiana, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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19
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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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20
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Oh HN, Park D, Seong HJ, Kim D, Sul WJ. Antarctic tundra soil metagenome as useful natural resources of cold-active lignocelluolytic enzymes. J Microbiol 2019; 57:865-873. [PMID: 31571125 DOI: 10.1007/s12275-019-9217-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/03/2019] [Accepted: 07/04/2019] [Indexed: 11/25/2022]
Abstract
Lignocellulose composed of complex carbohydrates and aromatic heteropolymers is one of the principal materials for the production of renewable biofuels. Lignocellulose-degrading genes from cold-adapted bacteria have a potential to increase the productivity of biological treatment of lignocellulose biomass by providing a broad range of treatment temperatures. Antarctic soil metagenomes allow to access novel genes encoding for the cold-active lignocellulose-degrading enzymes, for biotechnological and industrial applications. Here, we investigated the metagenome targeting cold-adapted microbes in Antarctic organic matter-rich soil (KS 2-1) to mine lignolytic and celluloytic enzymes by performing single molecule, real-time metagenomic (SMRT) sequencing. In the assembled Antarctic metagenomic contigs with relative long reads, we found that 162 (1.42%) of total 11,436 genes were annotated as carbohydrate-active enzymes (CAZy). Actinobacteria, the dominant phylum in this soil's metagenome, possessed most of candidates of lignocellulose catabolic genes like glycoside hydrolase families (GH13, GH26, and GH5) and auxiliary activity families (AA7 and AA3). The predicted lignocellulose degradation pathways in Antarctic soil metagenome showed synergistic role of various CAZyme harboring bacterial genera including Streptomyces, Streptosporangium, and Amycolatopsis. From phylogenetic relationships with cellular and environmental enzymes, several genes having potential for participating in overall lignocellulose degradation were also found. The results indicated the presence of lignocellulose-degrading bacteria in Antarctic tundra soil and the potential benefits of the lignocelluolytic enzymes as candidates for cold-active enzymes which will be used for the future biofuel-production industry.
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Affiliation(s)
- Han Na Oh
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Doyoung Park
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Dockyu Kim
- 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.
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The disappearing periglacial ecosystem atop Mt. Kilimanjaro supports both cosmopolitan and endemic microbial communities. Sci Rep 2019; 9:10676. [PMID: 31337772 PMCID: PMC6650471 DOI: 10.1038/s41598-019-46521-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 06/18/2019] [Indexed: 11/08/2022] Open
Abstract
Microbial communities have not been studied using molecular approaches at high elevations on the African continent. Here we describe the diversity of microbial communities from ice and periglacial soils from near the summit of Mt. Kilimanjaro by using both Illumina and Sanger sequencing of 16S and 18S rRNA genes. Ice and periglacial soils contain unexpectedly diverse and rich assemblages of Bacteria and Eukarya indicating that there may be high rates of dispersal to the top of this tropical mountain and/or that the habitat is more conducive to microbial life than was previously thought. Most bacterial OTUs are cosmopolitan and an analysis of isolation by geographic distance patterns of the genus Polaromonas emphasized the importance of global Aeolian transport in the assembly of bacterial communities on Kilimanjaro. The eukaryotic communities were less diverse than the bacterial communities and showed more evidence of dispersal limitations and apparent endemism. Cercozoa dominated the 18S communities, including a high abundance of testate amoebae and a high diversity of endemic OTUs within the Vampyrellida. These results argue for more intense study of this unique high-elevation "island of the cryosphere" before the glaciers of Kilimanjaro disappear forever.
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22
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Staebe K, Meiklejohn KI, Singh SM, Matcher GF. Biogeography of soil bacterial populations in the Jutulsessen and Ahlmannryggen of Western Dronning Maud Land, Antarctica. Polar Biol 2019. [DOI: 10.1007/s00300-019-02532-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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23
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Niederberger TD, Bottos EM, Sohm JA, Gunderson T, Parker A, Coyne KJ, Capone DG, Carpenter EJ, Cary SC. Rapid Microbial Dynamics in Response to an Induced Wetting Event in Antarctic Dry Valley Soils. Front Microbiol 2019; 10:621. [PMID: 31019494 PMCID: PMC6458288 DOI: 10.3389/fmicb.2019.00621] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/12/2019] [Indexed: 11/13/2022] Open
Abstract
The cold deserts of the McMurdo Dry Valleys (MDV), Antarctica, host a high level of microbial diversity. Microbial composition and biomass in arid vs. ephemerally wetted regions are distinctly different, with wetted communities representing hot spots of microbial activity that are important zones for biogeochemical cycling. While climatic change is likely to cause wetting in areas not historically subject to wetting events, the responses of microorganisms inhabiting arid soils to water addition is unknown. The purpose of this study was to observe how an associated, yet non-wetted microbial community responds to an extended addition of water. Water from a stream was diverted to an adjacent area of arid soil with changes in microbial composition and activities monitored via molecular and biochemical methods over 7 weeks. The frequency of genetic signatures related to both prokaryotic and eukaryotic organisms adapted to MDV aquatic conditions increased during the limited 7 week period, indicating that the soil community was transitioning into a typical "high-productivity" MDV community. This work is consistent with current predictions that MDV microbial communities in arid regions are highly sensitive to climate change, and further supports the notion that changes in community structure and associated biogeochemical cycling may occur much more rapidly than predicted.
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Affiliation(s)
- Thomas D Niederberger
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Eric M Bottos
- International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand.,Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jill A Sohm
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Troy Gunderson
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Alex Parker
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Kathryn J Coyne
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States
| | - Douglas G Capone
- Department of Biological Sciences, Wrigley Institute for Environmental Studies, University of Southern California, Los Angeles, CA, United States
| | - Edward J Carpenter
- Romberg Tiburon Center, San Francisco State University, Tiburon, CA, United States
| | - Stephen Craig Cary
- College Earth, Ocean, and Environment, University of Delaware, Lewes, DE, United States.,International Centre for Terrestrial Antarctic Research, School of Science, University of Waikato, Hamilton, New Zealand
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24
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Rajawat MVS, Singh R, Singh D, Saxena AK. Psychrotrophs of the genus Janthinobacterium with potential to weather potassium aluminosilicate mineral. 3 Biotech 2019; 9:142. [PMID: 30944789 DOI: 10.1007/s13205-019-1672-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 03/09/2019] [Indexed: 11/28/2022] Open
Abstract
In the present investigation, five strains of Janthinobacterium obtained from Rohtang Pass, Himachal Pradesh, India along with one strain of Bacillus decolorationis (IARI-SL-13) were screened qualitatively and quantitatively for their ability to solubilize K at different temperatures ranging from 5 to 30 °C. All the selected strains do not produce violet colonies, instead produced pink or red coloured colonies. In a plate assay, among all the strains tested, Janthinobacterium sp. IARI-R-81 was most efficient in solubilization of K at lower temperatures of 5 and 10 °C and was closely followed by Janthinobacterium lividum (IARI-R-71). Janthinobacterium sp. IARI-R-70 did not produce any detectable halo zones at all temperatures except 10 and 25 °C. Quantitative analysis revealed that all the selected pigment-producing strains could solubilize potassium-bearing mineral at low temperature (5 °C). J. lividum IARI-R-50 strain was most efficient in solubilizing K (29.87 ± 1.22 µg K/mL) from its mineral at 5 °C. This strain was typical as it solubilized almost the same amount of K both at 5 and 30 °C indicating its capability to adapt to different temperatures. All other strains showed a significantly higher concentration of solubilized K at 30 °C as compared to other temperatures tested. The non-pigmented B. decolorationis showed solubilization only at 25 and 30 °C and the concentration of K solubilized at 30 °C was significantly higher than at 25 °C. There was no correlation between pigment production and solubilization of potassium. This is the first report depicting solubilization trait of members of genus Janthinobacterium and confirms its evolutionary relatedness to Collimonads.
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Affiliation(s)
- Mahendra Vikram Singh Rajawat
- 1ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, Uttar Pradesh 275103 India
- 2Amity Institute of Microbial Biotechnology, Amity University, Noida, Uttar Pradesh 201303 India
| | - Rajni Singh
- 2Amity Institute of Microbial Biotechnology, Amity University, Noida, Uttar Pradesh 201303 India
| | - Devendra Singh
- Dr. Rajendra Prasad Central Agricultural University Pusa, Samastipur, Bihar 848125 India
| | - Anil Kumar Saxena
- 1ICAR-National Bureau of Agriculturally Important Microorganisms, Kushmaur, Maunath Bhanjan, Uttar Pradesh 275103 India
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Ramírez-Fernández L, Trefault N, Carú M, Orlando J. Seabird and pinniped shape soil bacterial communities of their settlements in Cape Shirreff, Antarctica. PLoS One 2019; 14:e0209887. [PMID: 30625192 PMCID: PMC6326729 DOI: 10.1371/journal.pone.0209887] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/13/2018] [Indexed: 01/24/2023] Open
Abstract
Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems.
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Affiliation(s)
- Lía Ramírez-Fernández
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Nicole Trefault
- Centre for Genomics, Ecology and Environment (GEMA), Faculty of Sciences, Universidad Mayor, Santiago, Chile
| | - Margarita Carú
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Julieta Orlando
- Laboratory of Microbial Ecology, Department of Ecological Sciences, Faculty of Sciences, Universidad de Chile, Santiago, Chile
- * E-mail:
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26
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Zhang Y, Lu L, Chang X, Jiang F, Gao X, Yao Y, Li C, Cao S, Zhou Q, Peng F. Small-Scale Soil Microbial Community Heterogeneity Linked to Landform Historical Events on King George Island, Maritime Antarctica. Front Microbiol 2018; 9:3065. [PMID: 30619151 PMCID: PMC6296293 DOI: 10.3389/fmicb.2018.03065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 11/28/2018] [Indexed: 11/13/2022] Open
Abstract
Although research on microbial biogeography has made great progress in the past decade, distributions of terrestrial microbial communities in extreme environments such as Antarctica are not well understood. In addition, knowledge of whether and how historical contingencies affect microbial distributions at small spatial scales is lacking. Here, we analyzed soil-borne microbial (bacterial, archaeal, and fungal) communities in 12 quadrat plots around the Fildes Region of King George Island, maritime Antarctica, and the communities were divided into two groups according to the soil elemental compositions and environmental attributes of Holocene raised beach and Tertiary volcanic stratigraphy. Prokaryotic communities of the two groups were well separated; the prokaryotic data were primarily correlated with soil elemental compositions and were secondly correlated with environmental attributes (e.g., soil pH, total organic carbon, NO3 -, and vegetation coverage; Pearson test, r = 0.59 vs. 0.52, both P < 0.01). The relatively high abundance of P, S, Cl, and Br in Group 1 (Holocene raised beach site) was likely due to landform uplift. Lithophile-elements (Si, Al, Ca, Sr, Ti, V, and Fe) correlated with prokaryotic communities in Group 2 may have originated from weathering of Tertiary volcanic rock. No significant correlations were found between the fungal community distribution and both the soil elemental composition and environmental attributes in this study; however, Monte Carlo tests revealed that elements Sr and Ti, soil pH, sampling altitude, and moss and lichen species numbers had significant impacts on fungal communities. The elements and nutrients accumulated during the formation of different landforms influenced the development of soils, plant growth, and microbial communities, and this resulted in small-scale spatially heterogeneous biological distributions. These findings provide new evidence that geological evolutionary processes in the Fildes Region were crucial to its microbial community development, and the results highlight that microbial distribution patterns are the legacies of historical events at this small spatial scale. Based on this study, the ice-free regions in maritime Antarctica represent suitable research sites for studying the influence of geomorphological features on microbial distributions, and we envision the possibility of a site-specific landform assignment through the analysis of the soil prokaryotic community structure.
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Affiliation(s)
- Yumin Zhang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Lu Lu
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Xulu Chang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Fan Jiang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiangdong Gao
- College of Life Sciences, Wuhan University, Wuhan, China
| | - Yifeng Yao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chengsen Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shunan Cao
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Qiming Zhou
- ChosenMed Technology (Beijing) Company Limited, Jinghai Industrial Park, Economic and Technological Development Area, Beijing, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, China
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27
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Malard LA, Pearce DA. Microbial diversity and biogeography in Arctic soils. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:611-625. [PMID: 30028082 DOI: 10.1111/1758-2229.12680] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 06/08/2023]
Abstract
Microorganisms dominate terrestrial environments in the polar regions and Arctic soils are known to harbour significant microbial diversity, far more diverse and numerous in the region than was once thought. Furthermore, the geographic distribution and structure of Arctic microbial communities remains elusive, despite their important roles in both biogeochemical cycling and in the generation and decomposition of climate active gases. Critically, Arctic soils are estimated to store over 1500 Pg of carbon and, thus, have the potential to generate positive feedback within the climate system. As the Arctic region is currently undergoing rapid change, the likelihood of faster release of greenhouse gases such as CO2 , CH4 and N2 O is increasing. Understanding the microbial communities in the region, in terms of their diversity, abundance and functional activity, is key to producing accurate models of greenhouse gas release. This review brings together existing data to determine what we know about microbial diversity and biogeography in Arctic soils.
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Affiliation(s)
- Lucie A Malard
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
| | - David A Pearce
- Faculty of Health and Life Sciences, Northumbria University, Newcastle-upon-Tyne, NE1 8ST, UK
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28
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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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29
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Feeser KL, Van Horn DJ, Buelow HN, Colman DR, McHugh TA, Okie JG, Schwartz E, Takacs-Vesbach CD. Local and Regional Scale Heterogeneity Drive Bacterial Community Diversity and Composition in a Polar Desert. Front Microbiol 2018; 9:1928. [PMID: 30186257 PMCID: PMC6110917 DOI: 10.3389/fmicb.2018.01928] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023] Open
Abstract
The distribution of organisms in an environment is neither uniform nor random but is instead spatially patterned. The factors that control this patterning are complex and the underlying mechanisms are poorly understood. Soil microbes are critical to ecosystem function but exhibit highly complex distributions and community dynamics due in large part to the scale-dependent effects of environmental heterogeneity. To better understand the impact of environmental heterogeneity on the distribution of soil microbes, we sequenced the 16S rRNA gene from bacterial communities in the microbe-dominated polar desert ecosystem of the McMurdo Dry Valleys (MDV), Antarctica. Significant differences in key edaphic variables and alpha diversity were observed among the three lake basins of the Taylor Valley (Kruskal-Wallis; pH: χ2 = 68.89, P < 0.001, conductivity: χ2 = 35.03, P < 0.001, observed species: χ2 = 7.98, P = 0.019 and inverse Simpson: χ2 = 18.52, P < 0.001) and each basin supported distinctive microbial communities (ANOSIM R = 0.466, P = 0.001, random forest ratio of 14.1). However, relationships between community structure and edaphic characteristics were highly variable and contextual, ranging in magnitude and direction across regional, basin, and local scales. Correlations among edaphic factors (pH and soil conductivity) and the relative abundance of specific phyla were most pronounced along local environmental gradients in the Lake Fryxell basin where Acidobacteria, Bacteroidetes, and Proteobacteria declined while Deinococcus-Thermus and Gemmatimonadetes increased with soil conductivity (all P < 0.1). Species richness was most strongly related to the soil conductivity gradient present within this study system. We suggest that the relative importance of pH versus soil conductivity in structuring microbial communities is related to the length of edaphic gradients and the spatial scale of sampling. These results highlight the importance of conducting studies over large ranges of key environmental gradients and across multiple spatial scales to assess the influence of environmental heterogeneity on the composition and diversity of microbial communities.
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Affiliation(s)
- Kelli L. Feeser
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - David J. Van Horn
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Heather N. Buelow
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Daniel R. Colman
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Theresa A. McHugh
- Department of Biological Sciences, Colorado Mesa University, Grand Junction, CO, United States
| | - Jordan G. Okie
- School of Life Sciences, School of Earth and Space Exploration, Arizona State University, Tempe, AZ, United States
| | - Egbert Schwartz
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, United States
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30
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Delgado-Baquerizo M, Reith F, Dennis PG, Hamonts K, Powell JR, Young A, Singh BK, Bissett A. Ecological drivers of soil microbial diversity and soil biological networks in the Southern Hemisphere. Ecology 2018; 99:583-596. [PMID: 29315530 DOI: 10.1002/ecy.2137] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 12/08/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
The ecological drivers of soil biodiversity in the Southern Hemisphere remain underexplored. Here, in a continental survey comprising 647 sites, across 58 degrees of latitude between tropical Australia and Antarctica, we evaluated the major ecological patterns in soil biodiversity and relative abundance of ecological clusters within a co-occurrence network of soil bacteria, archaea and eukaryotes. Six major ecological clusters (modules) of co-occurring soil taxa were identified. These clusters exhibited strong shifts in their relative abundances with increasing distance from the equator. Temperature was the major environmental driver of the relative abundance of ecological clusters when Australia and Antarctica are analyzed together. Temperature, aridity, soil properties and vegetation types were the major drivers of the relative abundance of different ecological clusters within Australia. Our data supports significant reductions in the diversity of bacteria, archaea and eukaryotes in Antarctica vs. Australia linked to strong reductions in temperature. However, we only detected small latitudinal variations in soil biodiversity within Australia. Different environmental drivers regulate the diversity of soil archaea (temperature and soil carbon), bacteria (aridity, vegetation attributes and pH) and eukaryotes (vegetation type and soil carbon) across Australia. Together, our findings provide new insights into the mechanisms driving soil biodiversity in the Southern Hemisphere.
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Affiliation(s)
- Manuel Delgado-Baquerizo
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA.,Departamento de Biología, Geología, Física y Química Inorgánica, Escuela Superior de Ciencias Experimentales y Tecnología, Universidad Rey Juan Carlos, c/ Tulipán s/n, Móstoles, 28933, Spain
| | - Frank Reith
- Department of Molecular and Cellular Biology, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,Land and Water, Environmental Contaminant Mitigation and Technologies, PMB2, Glen Osmond, South Australia, 5064, Australia
| | - Paul G Dennis
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Kelly Hamonts
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Jeff R Powell
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia
| | - Andrew Young
- National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, 2601, Australia
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, 2751, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith South DC, New South Wales, 2751, Australia
| | - Andrew Bissett
- CSIRO, Oceans and Atmosphere, Hobart, Tasmania, 7000, Australia
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31
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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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32
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Adriaenssens EM, Kramer R, Van Goethem MW, Makhalanyane TP, Hogg I, Cowan DA. Environmental drivers of viral community composition in Antarctic soils identified by viromics. MICROBIOME 2017; 5:83. [PMID: 28724405 PMCID: PMC5518109 DOI: 10.1186/s40168-017-0301-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/06/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND The Antarctic continent is considered the coldest and driest place on earth with simple ecosystems, devoid of higher plants. Soils in the ice-free regions of Antarctica are known to harbor a wide range of microorganisms from primary producers to grazers, yet their ecology and particularly the role of viruses is poorly understood. In this study, we examined the virus community structures of 14 soil samples from the Mackay Glacier region. METHODS Viral communities were extracted from soil and the dsDNA was extracted, amplified using single-primer amplification, and sequenced using the Ion Torrent Proton platform. Metadata on soil physico-chemistry was collected from all sites. Both read and contig datasets were analyzed with reference-independent and reference-dependent methods to assess viral community structures and the influence of environmental parameters on their distribution. RESULTS We observed a high heterogeneity in virus signatures, independent of geographical proximity. Tailed bacteriophages were dominant in all samples, but the incidences of the affiliated families Siphoviridae and Myoviridae were inversely correlated, suggesting direct competition for hosts. Viruses of the families Phycodnaviridae and Mimiviridae were present at significant levels in high-diversity soil samples and were found to co-occur, implying little competition between them. Combinations of soil factors, including pH, calcium content, and site altitude, were found to be the main drivers of viral community structure. CONCLUSIONS The pattern of viral community structure with higher levels of diversity at lower altitude and pH, and co-occurring viral families, suggests that these cold desert soil viruses interact with each other, the host, and the environment in an intricate manner, playing a potentially crucial role in maintaining host diversity and functioning of the microbial ecosystem in the extreme environments of Antarctic soil.
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Affiliation(s)
- Evelien M. Adriaenssens
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Rolf Kramer
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Marc W. Van Goethem
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Thulani P. Makhalanyane
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
| | - Ian Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Polar Knowledge Canada, 170 Laurier Avenue West, Ottawa, Ontario K1P 5V5 Canada
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, University of Pretoria, Natural Sciences Building II, Private Bag X20, Hatfield, 0028 South Africa
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Archer SDJ, de los Ríos A, Lee KC, Niederberger TS, Cary SC, Coyne KJ, Douglas S, Lacap-Bugler DC, Pointing SB. Endolithic microbial diversity in sandstone and granite from the McMurdo Dry Valleys, Antarctica. Polar Biol 2016. [DOI: 10.1007/s00300-016-2024-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Baweja M, Tiwari R, Singh PK, Nain L, Shukla P. An Alkaline Protease from Bacillus pumilus MP 27: Functional Analysis of Its Binding Model toward Its Applications As Detergent Additive. Front Microbiol 2016; 7:1195. [PMID: 27536284 PMCID: PMC4971029 DOI: 10.3389/fmicb.2016.01195] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/19/2016] [Indexed: 01/27/2023] Open
Abstract
A proteolytic strain of Bacillus pumilus MP 27 was isolated from water samples of Southern ocean produced alkaline protease. Since protease production need expensive ingredients, an economically viable process was developed by using low cost carbon source, wheat straw, supplemented with peptone. This protease was active within temperature ranges 10–70°C at pH 9. This process was optimized by response surface methodology using a Box Bekhman design by Design Expert 7.0 software that increased the protease activity to 776.5 U/ml. Moreover, the enzyme was extremely stable at a broad range of temperature and pH retaining 69% of its activity at 50°C and 70% at pH 11. The enzyme exhibited excellent compatibility with surfactants and commercial detergents, showing 87% stability with triton X-100 and 100% stability with Tide commercial detergent. The results of the wash performance analysis demonstrated considerably good de-staining at 50 and 4°C with low supplementation (109 U/ml). Molecular modeling of the protease revealed the presence of serine proteases, subtilase family and serine active site and further docking supported the association of catalytic site with the various substrates. Certainly, such protease can be considered as a good detergent additive in detergent industry with a possibility to remove the stains effectively even in a cold wash.
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Affiliation(s)
- Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
| | - Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India; Division of Microbiology, Indian Agricultural Research InstituteNew Delhi, India
| | - Puneet K Singh
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
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Tytgat B, Verleyen E, Sweetlove M, D'hondt S, Clercx P, Van Ranst E, Peeters K, Roberts S, Namsaraev Z, Wilmotte A, Vyverman W, Willems A. Bacterial community composition in relation to bedrock type and macrobiota in soils from the Sør Rondane Mountains, East Antarctica. FEMS Microbiol Ecol 2016; 92:fiw126. [PMID: 27402710 DOI: 10.1093/femsec/fiw126] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 01/06/2023] Open
Abstract
Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high-altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analyzed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica), using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km(2) Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP-dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock.
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Affiliation(s)
- Bjorn Tytgat
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elie Verleyen
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Maxime Sweetlove
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Sofie D'hondt
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Pia Clercx
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Eric Van Ranst
- Laboratory of Soil Science, Department of Geology and Soil Science, Ghent University, 9000 Ghent, Belgium
| | - Karolien Peeters
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Stephen Roberts
- British Antarctic Survey, Natural Environment Research, Cambridge, CB3 0ET, UK
| | - Zorigto Namsaraev
- Department of Biotechnology and Bioenergy, NRC 'Kurchatov Institute', Moscow, 123182, Russia Winogradsky Institute of Microbiology RAS, Moscow, 117312, Russia
| | - Annick Wilmotte
- Centre for Protein Engineering, Department of Life Sciences, Liège University, 4000 Liège, Belgium
| | - Wim Vyverman
- Laboratory of Protistology and Aquatic Ecology, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Microbiology and Biochemistry, Ghent University, 9000 Ghent, Belgium
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McCann CM, Wade MJ, Gray ND, Roberts JA, Hubert CRJ, Graham DW. Microbial Communities in a High Arctic Polar Desert Landscape. Front Microbiol 2016; 7:419. [PMID: 27065980 PMCID: PMC4814466 DOI: 10.3389/fmicb.2016.00419] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022] Open
Abstract
The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accounted for 95% of all sequences, with the Proteobacteria, Actinobacteria, and Chloroflexi being the major lineages. In contrast to previous investigations of Arctic soils, relative Acidobacterial abundances were found to be very low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to characteristic circumneutral soil pHs in this region, which has resulted from the weathering of underlying carbonate bedrock. In addition, we compared previously measured geochemical conditions as possible controls on soil microbial communities. Phosphorus, pH, nitrogen, and calcium levels all significantly correlated with β-diversity, indicating landscape-scale lithological control of available nutrients, which in turn, significantly influenced soil community composition. In addition, soil phosphorus and pH significantly correlated with α-diversity, particularly with the Shannon diversity and Chao 1 richness indices.
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Affiliation(s)
- Clare M McCann
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
| | - Matthew J Wade
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
| | - Neil D Gray
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
| | | | - Casey R J Hubert
- School of Civil Engineering and Geosciences, Newcastle UniversityNewcastle upon Tyne, UK; Energy Bioengineering and Geomicrobiology, University of Calgary, CalgaryAB, Canada
| | - David W Graham
- School of Civil Engineering and Geosciences, Newcastle University Newcastle upon Tyne, UK
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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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Gugliandolo C, Michaud L, Lo Giudice A, Lentini V, Rochera C, Camacho A, Maugeri TL. Prokaryotic Community in Lacustrine Sediments of Byers Peninsula (Livingston Island, Maritime Antarctica). MICROBIAL ECOLOGY 2016; 71:387-400. [PMID: 26337826 DOI: 10.1007/s00248-015-0666-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 08/18/2015] [Indexed: 06/05/2023]
Abstract
Byers Peninsula (Livingston Island, Antarctica), the largest seasonally ice-free region of the Maritime Antarctica, holds a large number of lakes, ponds, and streams. The prokaryotic structure and bacterial diversity in sediment samples collected during the 2008-2009 austral summer from five inland lakes, two coastal lakes, and an estuarine site were analyzed by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) and 16S rRNA 454 tag pyrosequencing techniques, respectively. Differently from inland lakes, which range around the oligotrophic status, coastal lakes are eutrophic environments, enriched by nutrient inputs from marine animals. Although the prokaryotic abundances (estimated as DAPI stained cells) in sediment samples were quite similar among inland and coastal lakes, Bacteria always far dominated over Archaea. Despite the phylogenetic analysis indicated that most of sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria, Bacteroidetes, and Actinobacteria, their relative abundances greatly differed from each site. Differences in bacterial composition showed that lacustrine sediments were more phyla rich than the estuarine sediment. Proteobacterial classes in lacustrine samples were dominated by Betaproteobacteria (followed by Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria), while in the estuarine sample, they were mainly related to Gammaproteobacteria (followed by Deltaproteobacteria, Epsilonproteobacteria, Alphaproteobacteria, and Betaproteobacteria). Higher number of sequences of Alphaproteobacteria, Cyanobacteria, Verrucomicrobia, and Planctomycetes were observed in sediments of inland lakes compared to those of coastal lakes, whereas Chloroflexi were relatively more abundant in the sediments of coastal eutrophic lakes. As demonstrated by the great number of dominant bacterial genera, bacterial diversity was higher in the sediments of inland lakes than that in coastal lakes. Ilumatobacter (Actinobacteria), Gp16 (Acidobacteria), and Gemmatimonas (Gemmatimonadetes) were recovered as dominant genera in both inland and coastal lakes, but not in the estuarine sample, indicating that they may be useful markers of Antarctic lakes. The proximity to the sea, the different lake depths and the external or internal origin of the nutrient sources shape the bacterial communities composition in lacustrine sediments of Byers Peninsula.
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Affiliation(s)
- Concetta Gugliandolo
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy.
| | - Luigi Michaud
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Angelina Lo Giudice
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
- Institute for Coastal Marine Environment, National Research Council (IAMC-CNR), Spianata San Raineri 86, 98122, Messina, Italy
| | - Valeria Lentini
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
| | - Carlos Rochera
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Campus de Burjassot, University of Valencia, E-46100, Burjassot, Spain
| | - Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology and Department of Microbiology and Ecology, Campus de Burjassot, University of Valencia, E-46100, Burjassot, Spain
| | - Teresa Luciana Maugeri
- Research Centre for Extreme Environments and Extremophiles, Department of Biological and Environmental Sciences, University of Messina, V.le F. Stagno d'Alcontres 31, 98166, Messina, Italy
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Niederberger TD, Sohm JA, Gunderson T, Tirindelli J, Capone DG, Carpenter EJ, Cary SC. Carbon-Fixation Rates and Associated Microbial Communities Residing in Arid and Ephemerally Wet Antarctic Dry Valley Soils. Front Microbiol 2015; 6:1347. [PMID: 26696969 PMCID: PMC4673872 DOI: 10.3389/fmicb.2015.01347] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 11/16/2015] [Indexed: 11/13/2022] Open
Abstract
Carbon-fixation is a critical process in severely oligotrophic Antarctic Dry Valley (DV) soils and may represent the major source of carbon in these arid environments. However, rates of C-fixation in DVs are currently unknown and the microorganisms responsible for these activities unidentified. In this study, C-fixation rates measured in the bulk arid soils (<5% moisture) ranged from below detection limits to ∼12 nmol C/cc/h. Rates in ephemerally wet soils ranged from ∼20 to 750 nmol C/cc/h, equating to turnover rates of ∼7-140 days, with lower rates in stream-associated soils as compared to lake-associated soils. Sequencing of the large subunit of RuBisCO (cbbL) in these soils identified green-type sequences dominated by the 1B cyanobacterial phylotype in both arid and wet soils including the RNA fraction of the wet soil. Red-type cbbL genes were dominated by 1C actinobacterial phylotypes in arid soils, with wetted soils containing nearly equal proportions of 1C (actinobacterial and proteobacterial signatures) and 1D (algal) phylotypes. Complementary 16S rRNA and 18S rRNA gene sequencing also revealed distinct differences in community structure between biotopes. This study is the first of its kind to examine C-fixation rates in DV soils and the microorganisms potentially responsible for these activities.
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Affiliation(s)
| | - Jill A. Sohm
- Wrigley Institute of Environmental Studies and Department of Biological Science, University of Southern CaliforniaLos Angeles, CA, USA
| | - Troy Gunderson
- Wrigley Institute of Environmental Studies and Department of Biological Science, University of Southern CaliforniaLos Angeles, CA, USA
| | - Joëlle Tirindelli
- Romberg Tiburon Center, San Francisco State UniversityTiburon, CA, USA
| | - Douglas G. Capone
- Wrigley Institute of Environmental Studies and Department of Biological Science, University of Southern CaliforniaLos Angeles, CA, USA
| | | | - S. Craig Cary
- College of Marine and Earth Sciences, University of DelawareLewes, DE, USA
- International Centre for Terrestrial Antarctic Research, University of WaikatoHamilton, New Zealand
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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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Chauhan A, Bharti PK, Goyal P, Varma A, Jindal T. Psychrophilic pseudomonas in antarctic freshwater lake at stornes peninsula, larsemann hills over east Antarctica. SPRINGERPLUS 2015; 4:582. [PMID: 26543717 PMCID: PMC4627980 DOI: 10.1186/s40064-015-1354-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 09/18/2015] [Indexed: 11/10/2022]
Abstract
The Larsemann Hills is an ice-free area of approximately 50 km(2), located halfway between the Vestfold Hills and the Amery Ice Shelf on the south-eastern coast of Prydz Bay, Princess Elizabeth Land, East Antarctica (69º30'S, 76º19'58″E). The ice-free area consists of two major peninsulas (Stornes and Broknes), four minor peninsulas, and approximately 130 islands. The Larsemann Hills area contains more than 150 lakes at different Islands and Peninsulas. Nine lake water samples were collected in a gamma sterilized bottles and were kept in an ice pack to prevent any changes in the microbial flora of the samples during the transportation. The water samples were transported to the lab in vertical position maintaining the temperature 1-4 °C with ice pack enveloped conditions. Samples were studied for Psychrophilic bacterial count, Pseudomonas spp., Staphylococcus aureus, Salmonella and Total MPN Coliform per 100 ml. Psychrophillic counts were found in the range of 12 cfu to 1.6 × 10(2) cfu in all the samples. MPN Coliform per 100 ml was found to be absent in all the samples. No growth and characteristics colonies observed when tested for Salmonella and S.aureus. Pseudomonas sp. was found in ST-2 lake water sample as characteristics colonies (Optimum Growth) were observed on selective media at 22 and 25 °C. Further several biochemical tests were also performed to confirm the presence of this Potential Psychrophilic Pseudomonas sp. for its further application in Science and Technology.
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Affiliation(s)
- Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Sector-125, Noida, Uttar Pradesh India
| | - Pawan K Bharti
- Antarctica Laboratory, R & D Division, Shriram Institute for Industrial Research, 19, University Road, Delhi, 110007 India
| | - Pankaj Goyal
- Amity Institute of Microbial Technology, Amity University, Sector-125, Noida, Uttar Pradesh India
| | - Ajit Varma
- Amity Institute of Microbial Technology, Amity University, Sector-125, Noida, Uttar Pradesh India
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Sector-125, Noida, Uttar Pradesh India
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Rampelotto PH, Barboza ADM, Pereira AB, Triplett EW, Schaefer CEGR, de Oliveira Camargo FA, Roesch LFW. Distribution and interaction patterns of bacterial communities in an ornithogenic soil of Seymour Island, Antarctica. MICROBIAL ECOLOGY 2015; 69:684-694. [PMID: 25342537 DOI: 10.1007/s00248-014-0510-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 10/08/2014] [Indexed: 06/04/2023]
Abstract
Next-generation, culture-independent sequencing offers an excellent opportunity to examine network interactions among different microbial species. In this study, soil bacterial communities from a penguin rookery site at Seymour Island were analyzed for abundance, structure, diversity, and interaction networks to identify interaction patterns among the various taxa at three soil depths. The analysis revealed the presence of eight phyla distributed in different proportions among the surface layer (0-8 cm), middle layer (20-25 cm), and bottom (35-40 cm). The bottom layer presented the highest values of bacterial richness, diversity, and evenness when compared to surface and middle layers. The network analysis revealed the existence of a unique pattern of interactions in which the soil microbial network formed a clustered topology, rather than a modular structure as is usually found in biological communities. In addition, specific taxa were identified as important players in microbial community structure. Furthermore, simulation analyses indicated that the loss of potential keystone groups of microorganisms might alter the patterns of interactions within the microbial community. These findings provide new insights for assessing the consequences of environmental disturbances at the whole-community level in Antarctica.
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Affiliation(s)
- Pabulo Henrique Rampelotto
- Universidade Federal do Pampa, Campus São Gabriel, Av. Antonio Trilha, 1847, 97300-000, São Gabriel, Rio Grande do Sul, Brazil
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Kim M, Cho A, Lim HS, Hong SG, Kim JH, Lee J, Choi T, Ahn TS, Kim OS. Highly heterogeneous soil bacterial communities around Terra Nova Bay of Northern Victoria Land, Antarctica. PLoS One 2015; 10:e0119966. [PMID: 25799273 PMCID: PMC4370865 DOI: 10.1371/journal.pone.0119966] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/18/2015] [Indexed: 11/19/2022] Open
Abstract
Given the diminished role of biotic interactions in soils of continental Antarctica, abiotic factors are believed to play a dominant role in structuring of microbial communities. However, many ice-free regions remain unexplored, and it is unclear which environmental gradients are primarily responsible for the variations among bacterial communities. In this study, we investigated the soil bacterial community around Terra Nova Bay of Victoria Land by pyrosequencing and determined which environmental variables govern the bacterial community structure at the local scale. Six bacterial phyla, Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, Cyanobacteria, and Bacteroidetes, were dominant, but their relative abundance varied greatly across locations. Bacterial community structures were affected little by spatial distance, but structured more strongly by site, which was in accordance with the soil physicochemical compositions. At both the phylum and species levels, bacterial community structure was explained primarily by pH and water content, while certain earth elements and trace metals also played important roles in shaping community variation. The higher heterogeneity of the bacterial community structure found at this site indicates how soil bacterial communities have adapted to different compositions of edaphic variables under extreme environmental conditions. Taken together, these findings greatly advance our understanding of the adaption of soil bacterial populations to this harsh environment.
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Affiliation(s)
- Mincheol Kim
- Arctic Research Center, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Ahnna Cho
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- Department of Environmental Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Hyoun Soo Lim
- Department of Geological Sciences, Pusan National University, Busan, Republic of Korea
| | - Soon Gyu Hong
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Ji Hee Kim
- Department of New Antarctic Station, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Joohan Lee
- Department of New Antarctic Station, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Taejin Choi
- Division of Climate Change, Korea Polar Research Institute, Incheon, Republic of Korea
| | - Tae Seok Ahn
- Department of Environmental Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ok-Sun Kim
- Division of Life Sciences, Korea Polar Research Institute, Incheon, Republic of Korea
- * E-mail:
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Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils. BMC Genomics 2015; 16:36. [PMID: 25649291 PMCID: PMC4326396 DOI: 10.1186/s12864-015-1220-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 01/02/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Members of the bacterial genus Arthrobacter are both readily cultured and commonly identified in Antarctic soil communities. Currently, relatively little is known about the physiological traits that allow these bacteria to survive in the harsh Antarctic soil environment. The aim of this study is to investigate if Antarctic strains of Arthrobacter owe their resilience to substantial genomic changes compared to Arthrobacter spp. isolated from temperate soil environments. RESULTS Quantitative PCR-based analysis revealed that up to 4% of the soil bacterial communities were comprised of Arthrobacter spp. at four locations in the Ross Sea Region. Genome analysis of the seven Antarctic Arthrobacter isolates revealed several features that are commonly observed in psychrophilic/psychrotolerant bacteria. These include genes primarily associated with sigma factors, signal transduction pathways, the carotenoid biosynthesis pathway and genes induced by cold-shock, oxidative and osmotic stresses. However, these genes were also identified in genomes of seven temperate Arthrobacter spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. Phenotypic characterisation revealed that Antarctic Arthrobacter isolates demonstrate significantly lower metabolic versatility and a narrower salinity tolerance range compared to temperate Arthrobacter species. Comparative analyses also revealed fewer protein-coding sequences and a significant decrease in genes associated with transcription and carbohydrate transport and metabolism in four of the seven Antarctic Arthrobacter isolates. Notwithstanding genome incompleteness, these differences together with the decreased metabolic versatility are indicative of genome content scaling. CONCLUSIONS The genomes of the seven Antarctic Arthrobacter isolates contained several features that may be beneficial for growth and survival in the Antarctic soil environment, although these features were not unique to the Antarctic isolates. These genome sequences allow further investigations into the expression of physiological traits that enable survival under extreme conditions and, more importantly, into the ability of these bacteria to respond to future perturbations including climate change and human impacts.
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Affiliation(s)
- Melissa Dsouza
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Michael W Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Susan J Turner
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
- BioDiscovery New Zealand Limited, Parnell, Auckland, New Zealand.
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Niederberger TD, Sohm JA, Gunderson TE, Parker AE, Tirindelli J, Capone DG, Carpenter EJ, Cary SC. Microbial community composition of transiently wetted Antarctic Dry Valley soils. Front Microbiol 2015; 6:9. [PMID: 25674080 PMCID: PMC4309182 DOI: 10.3389/fmicb.2015.00009] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 11/13/2022] Open
Abstract
During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm3 for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas.
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Affiliation(s)
| | - Jill A Sohm
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | - Troy E Gunderson
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | - Alexander E Parker
- Romberg Tiburon Center for Environmental Studies, San Francisco State University Tiburon, CA, USA
| | - Joëlle Tirindelli
- Romberg Tiburon Center for Environmental Studies, San Francisco State University Tiburon, CA, USA
| | - Douglas G Capone
- Wrigley Institute for Environmental Studies and Department of Biological Sciences, University of Southern California Los Angeles, CA, USA
| | - Edward J Carpenter
- Romberg Tiburon Center for Environmental Studies, San Francisco State University Tiburon, CA, USA
| | - Stephen C Cary
- College of Marine and Earth Sciences, University of Delaware Lewes, DE, USA ; School of Science, University of Waikato Hamilton, New Zealand
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46
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Youssef NH, Couger MB, McCully AL, Criado AEG, Elshahed MS. Assessing the global phylum level diversity within the bacterial domain: A review. J Adv Res 2014; 6:269-82. [PMID: 26257925 PMCID: PMC4522544 DOI: 10.1016/j.jare.2014.10.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 10/06/2014] [Accepted: 10/23/2014] [Indexed: 12/11/2022] Open
Abstract
Microbial ecology is the study of microbes in the natural environment and their interactions with each other. Investigating the nature of microorganisms residing within a specific habitat is an extremely important component of microbial ecology. Such microbial diversity surveys aim to determine the identity, physiological preferences, metabolic capabilities, and genomic features of microbial taxa within a specific ecosystem. A comprehensive review of various aspects of microbial diversity (phylogenetic, functional, and genomic diversities) in the microbial (bacterial, archaeal, and microeukaryotic) world is clearly a daunting task that could not be aptly summarized in a single review. Here, we focus on one aspect of diversity (phylogenetic diversity) in one microbial domain (the Bacteria). We restrict our analysis to the highest taxonomic rank (phylum) and attempt to investigate the extent of global phylum level diversity within the Bacteria. We present a brief historical perspective on the subject and highlight how the adaptation of molecular biological and phylogenetic approaches has greatly expanded our view of global bacterial diversity. We also summarize recent progress toward the discovery of novel bacterial phyla, present evidences that the scope of phylum level diversity in nature has hardly been exhausted, and propose novel approaches that could greatly facilitate the discovery process of novel bacterial phyla within various ecosystems.
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Affiliation(s)
- Noha H Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - M B Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Alexandra L McCully
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | | | - Mostafa S Elshahed
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
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47
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Dsouza M, Taylor MW, Turner SJ, Aislabie J. Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus. PLoS One 2014; 9:e108009. [PMID: 25285990 PMCID: PMC4186907 DOI: 10.1371/journal.pone.0108009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 08/21/2014] [Indexed: 12/02/2022] Open
Abstract
Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR). However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs), primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further investigations into the expression of physiological attributes that enable survival under extreme conditions and selection processes that affect prokaryotic genome evolution.
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Affiliation(s)
- Melissa Dsouza
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan J. Turner
- Centre for Microbial Innovation, School of Biological Sciences, University of Auckland, Auckland, New Zealand
- BioDiscovery New Zealand Limited, Parnell, Auckland, New Zealand
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48
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Magalhães CM, Machado A, Frank-Fahle B, Lee CK, Cary SC. The ecological dichotomy of ammonia-oxidizing archaea and bacteria in the hyper-arid soils of the Antarctic Dry Valleys. Front Microbiol 2014; 5:515. [PMID: 25324835 PMCID: PMC4179728 DOI: 10.3389/fmicb.2014.00515] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/12/2014] [Indexed: 12/03/2022] Open
Abstract
The McMurdo Dry Valleys of Antarctica are considered to be one of the most physically and chemically extreme terrestrial environments on the Earth. However, little is known about the organisms involved in nitrogen transformations in these environments. In this study, we investigated the diversity and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in four McMurdo Dry Valleys with highly variable soil geochemical properties and climatic conditions: Miers Valley, Upper Wright Valley, Beacon Valley and Battleship Promontory. The bacterial communities of these four Dry Valleys have been examined previously, and the results suggested that the extremely localized bacterial diversities are likely driven by the disparate physicochemical conditions associated with these locations. Here we showed that AOB and AOA amoA gene diversity was generally low; only four AOA and three AOB operational taxonomic units (OTUs) were identified from a total of 420 AOA and AOB amoA clones. Quantitative PCR analysis of amoA genes revealed clear differences in the relative abundances of AOA and AOB amoA genes among samples from the four dry valleys. Although AOB amoA gene dominated the ammonia-oxidizing community in soils from Miers Valley and Battleship Promontory, AOA amoA gene were more abundant in samples from Upper Wright and Beacon Valleys, where the environmental conditions are considerably harsher (e.g., extremely low soil C/N ratios and much higher soil electrical conductivity). Correlations between environmental variables and amoA genes copy numbers, as examined by redundancy analysis (RDA), revealed that higher AOA/AOB ratios were closely related to soils with high salts and Cu contents and low pH. Our findings hint at a dichotomized distribution of AOA and AOB within the Dry Valleys, potentially driven by environmental constraints.
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Affiliation(s)
- Catarina M Magalhães
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto Porto, Portugal
| | - Ana Machado
- Institute of Biomedical Sciences University of Porto Porto, Portugal
| | - Béatrice Frank-Fahle
- Institute of Groundwater Ecology, Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg, Germany
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato Hamilton, New Zealand
| | - S Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato Hamilton, New Zealand ; College of Earth, Ocean and Environment, University of Delaware Lewes, DE, USA
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49
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Yung CCM, Chan Y, Lacap DC, Pérez-Ortega S, de Los Rios-Murillo A, Lee CK, Cary SC, Pointing SB. Characterization of chasmoendolithic community in Miers Valley, McMurdo Dry Valleys, Antarctica. MICROBIAL ECOLOGY 2014; 68:351-359. [PMID: 24671755 DOI: 10.1007/s00248-014-0412-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/11/2014] [Indexed: 05/28/2023]
Abstract
The Antarctic Dry Valleys are unable to support higher plant and animal life and so microbial communities dominate biotic ecosystem processes. Soil communities are well characterized, but rocky surfaces have also emerged as a significant microbial habitat. Here, we identify extensive colonization of weathered granite on a landscape scale by chasmoendolithic microbial communities. A transect across north-facing and south-facing slopes plus valley floor moraines revealed 30-100 % of available substrate was colonized up to an altitude of 800 m. Communities were assessed at a multidomain level and were clearly distinct from those in surrounding soils and other rock-inhabiting cryptoendolithic and hypolithic communities. All colonized rocks were dominated by the cyanobacterial genus Leptolyngbya (Oscillatoriales), with heterotrophic bacteria, archaea, algae, and fungi also identified. Striking patterns in community distribution were evident with regard to microclimate as determined by aspect. Notably, a shift in cyanobacterial assemblages from Chroococcidiopsis-like phylotypes (Pleurocapsales) on colder-drier slopes, to Synechococcus-like phylotypes (Chroococcales) on warmer-wetter slopes. Greater relative abundance of known desiccation-tolerant bacterial taxa occurred on colder-drier slopes. Archaeal phylotypes indicated halotolerant taxa and also taxa possibly derived from nearby volcanic sources. Among the eukaryotes, the lichen photobiont Trebouxia (Chlorophyta) was ubiquitous, but known lichen-forming fungi were not recovered. Instead, fungal assemblages were dominated by ascomycetous yeasts. We conclude that chasmoendoliths likely constitute a significant geobiological phenomenon at lower elevations in granite-dominated Antarctic Dry Valley systems.
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Affiliation(s)
- Charmaine C M Yung
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
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50
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Dreesens LL, Lee CK, Cary SC. The Distribution and Identity of Edaphic Fungi in the McMurdo Dry Valleys. BIOLOGY 2014; 3:466-83. [PMID: 25079129 PMCID: PMC4192622 DOI: 10.3390/biology3030466] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/14/2014] [Accepted: 07/16/2014] [Indexed: 11/30/2022]
Abstract
Contrary to earlier assumptions, molecular evidence has demonstrated the presence of diverse and localized soil bacterial communities in the McMurdo Dry Valleys of Antarctica. Meanwhile, it remains unclear whether fungal signals so far detected in Dry Valley soils using both culture-based and molecular techniques represent adapted and ecologically active biomass or spores transported by wind. Through a systematic and quantitative molecular survey, we identified significant heterogeneities in soil fungal communities across the Dry Valleys that robustly correlate with heterogeneities in soil physicochemical properties. Community fingerprinting analysis and 454 pyrosequencing of the fungal ribosomal intergenic spacer region revealed different levels of heterogeneity in fungal diversity within individual Dry Valleys and a surprising abundance of Chytridiomycota species, whereas previous studies suggested that Dry Valley soils were dominated by Ascomycota and Basidiomycota. Critically, we identified significant differences in fungal community composition and structure of adjacent sites with no obvious barrier to aeolian transport between them. These findings suggest that edaphic fungi of the Antarctic Dry Valleys are adapted to local environments and represent an ecologically relevant (and possibly important) heterotrophic component of the ecosystem.
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Affiliation(s)
- Lisa L Dreesens
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton 3216, New Zealand.
| | - Charles K Lee
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton 3216, New Zealand.
| | - S Craig Cary
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton 3216, New Zealand.
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