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Gao X, Wang S, Kong W, Li G, Zhang L, Yin X. Floristic changes and environmental drivers of soil fungi and archaea in different salt-tolerant plant communities in the intertidal habitat of coastal wetlands. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2024; 46:167. [PMID: 38592380 DOI: 10.1007/s10653-024-01951-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 03/08/2024] [Indexed: 04/10/2024]
Abstract
Microorganisms are crucial elements of terrestrial ecosystems, which play significant roles in improving soil physicochemical properties, providing plant growth nutrients, degrading toxic and harmful chemicals, and biogeochemical cycling. Variations in the types and quantities of root exudates among different plants greatly alter soil physicochemical properties and result in variations in the diversity, structure, and function of soil microorganisms. Not much is understood about the differences of soil fungi and archaea communities for different plant communities in coastal wetlands, and their response mechanisms to environmental changes. In this study, fungal and archaea communities in soils of Suaeda salsa, Phragmites australis, and Spartina alterniflora in the intertidal habitat of coastal wetlands were selected for research. Soil fungi and archaea were analyzed for diversity, community structure, and function using high throughput ITS and 16S rRNA gene sequencing. The study revealed significant differences in fungi and archaea's diversity and community structure in the rhizosphere soil of three plant communities. At the same time, there is no significant difference in the functional groups. SOM, TP, AP, MC, EC and SOM, TN, TP, AP, MC, EC are the primary environmental determinants affecting changes in soil fungal and archaeal communities, respectively. Variations in the diversity, community structure, and ecological functions of fungi and archaea can be used as indicators characterizing the impact of external disturbances on the soil environment, providing a theoretical foundation for the effective utilization of soil microbial resources, thereby achieving the goal of environmental protection and health promotion.
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Affiliation(s)
- Xin Gao
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shuping Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Weijing Kong
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Guowen Li
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Lieyu Zhang
- Institute of Water Ecology and Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xuwang Yin
- Liaoning Provincial Key Laboratory for Hydrobiology, College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023, China
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2
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Ray AE, Zaugg J, Benaud N, Chelliah DS, Bay S, Wong HL, Leung PM, Ji M, Terauds A, Montgomery K, Greening C, Cowan DA, Kong W, Williams TJ, Hugenholtz P, Ferrari BC. Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts. THE ISME JOURNAL 2022; 16:2547-2560. [PMID: 35933499 PMCID: PMC9561532 DOI: 10.1038/s41396-022-01298-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022]
Abstract
Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.
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3
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Doytchinov VV, Dimov SG. Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060916. [PMID: 35743947 PMCID: PMC9228076 DOI: 10.3390/life12060916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/09/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.
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4
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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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5
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Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems from James Ross Archipelago (West Antarctica). Polar Biol 2022. [DOI: 10.1007/s00300-021-02997-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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6
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Antarctica as a reservoir of planetary analogue environments. Extremophiles 2021; 25:437-458. [PMID: 34586500 DOI: 10.1007/s00792-021-01245-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
One of the main objectives of astrobiological research is the investigation of the habitability of other planetary bodies. Since space exploration missions are expensive and require long-term organization, the preliminary study of terrestrial environments is an essential step to prepare and support exploration missions. The Earth hosts a multitude of extreme environments whose characteristics resemble celestial bodies in our Solar System. In these environments, the physico-chemical properties partly match extraterrestrial environments and could clarify limits and adaptation mechanisms of life, the mineralogical or geochemical context, and support and interpret data sent back from planetary bodies. One of the best terrestrial analogues is Antarctica, whose conditions lie on the edge of habitability. It is characterized by a cold and dry climate (Onofri et al., Nova Hedwigia 68:175-182, 1999), low water availability, strong katabatic winds, salt concentration, desiccation, and high radiation. Thanks to the harsh conditions like those in other celestial bodies, Antarctica offers good terrestrial analogues for celestial body (Mars or icy moons; Léveillé, CR Palevol 8:637-648, https://doi.org/10.1016/j.crpv.2009.03.005 , 2009). The continent could be distinguished into several habitats, each with characteristics similar to those existing on other bodies. Here, we reported a description of each simulated parameter within the habitats, in relation to each of the simulated extraterrestrial environments.
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Fernández-Martínez MÁ, García-Villadangos M, Moreno-Paz M, Gangloff V, Carrizo D, Blanco Y, González S, Sánchez-García L, Prieto-Ballesteros O, Altshuler I, Whyte LG, Parro V, Fairén AG. Geomicrobiological Heterogeneity of Lithic Habitats in the Extreme Environment of Antarctic Nunataks: A Potential Early Mars Analog. Front Microbiol 2021; 12:670982. [PMID: 34276605 PMCID: PMC8284421 DOI: 10.3389/fmicb.2021.670982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/21/2021] [Indexed: 11/13/2022] Open
Abstract
Nunataks are permanent ice-free rocky peaks that project above ice caps in polar regions, thus being exposed to extreme climatic conditions throughout the year. They undergo extremely low temperatures and scarcity of liquid water in winter, while receiving high incident and reflected (albedo) UVA-B radiation in summer. Here, we investigate the geomicrobiology of the permanently exposed lithic substrates of nunataks from Livingston Island (South Shetlands, Antarctic Peninsula), with focus on prokaryotic community structure and their main metabolic traits. Contrarily to first hypothesis, an extensive sampling based on different gradients and multianalytical approaches demonstrated significant differences for most geomicrobiological parameters between the bedrock, soil, and loose rock substrates, which overlapped any other regional variation. Brevibacillus genus dominated on bedrock and soil substrates, while loose rocks contained a diverse microbial community, including Actinobacteria, Alphaproteobacteria and abundant Cyanobacteria inhabiting the milder and diverse microhabitats within. Archaea, a domain never described before in similar Antarctic environments, were also consistently found in the three substrates, but being more abundant and potentially more active in soils. Stable isotopic ratios of total carbon (δ 13C) and nitrogen (δ 15N), soluble anions concentrations, and the detection of proteins involved in key metabolisms via the Life Detector Chip (LDChip), suggest that microbial primary production has a pivotal role in nutrient cycling at these exposed areas with limited deposition of nutrients. Detection of stress-resistance proteins, such as molecular chaperons, suggests microbial molecular adaptation mechanisms to cope with these harsh conditions. Since early Mars may have encompassed analogous environmental conditions as the ones found in these Antarctic nunataks, our study also contributes to the understanding of the metabolic features and biomarker profiles of a potential Martian microbiota, as well as the use of LDChip in future life detection missions.
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Affiliation(s)
- Miguel Ángel Fernández-Martínez
- Centro de Astrobiología, CSIC-INTA, Madrid, Spain.,Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | | | | | | | | | | | - Sergi González
- Antarctic Group, Agencia Estatal de Meteorología, Barcelona, Spain
| | | | | | - Ianina Altshuler
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Victor Parro
- Centro de Astrobiología, CSIC-INTA, Madrid, Spain
| | - Alberto G Fairén
- Centro de Astrobiología, CSIC-INTA, Madrid, Spain.,Department of Astronomy, Cornell University, Ithaca, NY, United States
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8
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Cultivation and characterization of snowbound microorganisms from the South Pole. Extremophiles 2021; 25:159-172. [PMID: 33590336 DOI: 10.1007/s00792-021-01218-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/28/2021] [Indexed: 02/03/2023]
Abstract
Little is known about microbial ecosystems of interior Antarctica, if indeed such ecosystems exist. Although considerable research has assessed microorganisms indigenous to coastal regions of Antarctica, particularly their lakes, ponds, and soils, to our knowledge only one characterized bacterium, a strain of Pseudomonas, has been isolated from South Pole ice or snow. Metagenomic community analyses described in this work and elsewhere reveal that a diversity of bacteria exists in inland polar snows, yet attempts to culture and characterize these microbes from this extreme environment have been few to date. In this molecular and culture-dependent investigation of the microbiology of inland Antarctica, we enriched and isolated two new strains of bacteria and one strain of yeast (Fungi) from South Pole snow samples. The bacteria were of the genera Methylobacterium and Sphingomonas, and the yeast grouped with species of Naganishia (class Tremellocytes). In addition to phylogenetic analyses, characterization of these isolates included determinations of cell morphology, growth as a function of temperature, salinity tolerance, and carbon and energy source versatility. All organisms were found to be cold-adapted, and the yeast strain additionally showed considerable halotolerance. These descriptions expand our understanding of the diversity and metabolic activities of snowbound microorganisms of interior Antarctica.
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9
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Ortiz M, Bosch J, Coclet C, Johnson J, Lebre P, Salawu-Rotimi A, Vikram S, Makhalanyane T, Cowan D. Microbial Nitrogen Cycling in Antarctic Soils. Microorganisms 2020; 8:E1442. [PMID: 32967081 PMCID: PMC7564152 DOI: 10.3390/microorganisms8091442] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Antarctic continent is widely considered to be one of the most hostile biological habitats on Earth. Despite extreme environmental conditions, the ice-free areas of the continent, which constitute some 0.44% of the total continental land area, harbour substantial and diverse communities of macro-organisms and especially microorganisms, particularly in the more "hospitable" maritime regions. In the more extreme non-maritime regions, exemplified by the McMurdo Dry Valleys of South Victoria Land, nutrient cycling and ecosystem servicing processes in soils are largely driven by microbial communities. Nitrogen turnover is a cornerstone of ecosystem servicing. In Antarctic continental soils, specifically those lacking macrophytes, cold-active free-living diazotrophic microorganisms, particularly Cyanobacteria, are keystone taxa. The diazotrophs are complemented by heterotrophic bacterial and archaeal taxa which show the genetic capacity to perform elements of the entire N cycle, including nitrification processes such as the anammox reaction. Here, we review the current literature on nitrogen cycling genes, taxa, processes and rates from studies of Antarctic soils. In particular, we highlight the current gaps in our knowledge of the scale and contribution of these processes in south polar soils as critical data to underpin viable predictions of how such processes may alter under the impacts of future climate change.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Don Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (M.O.); (J.B.); (C.C.); (J.J.); (P.L.); (A.S.-R.); (S.V.); (T.M.)
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10
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Zhang E, Thibaut LM, Terauds A, Raven M, Tanaka MM, van Dorst J, Wong SY, Crane S, Ferrari BC. Lifting the veil on arid-to-hyperarid Antarctic soil microbiomes: a tale of two oases. MICROBIOME 2020; 8:37. [PMID: 32178729 PMCID: PMC7076931 DOI: 10.1186/s40168-020-00809-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/20/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Resident soil microbiota play key roles in sustaining the core ecosystem processes of terrestrial Antarctica, often involving unique taxa with novel functional traits. However, the full scope of biodiversity and the niche-neutral processes underlying these communities remain unclear. In this study, we combine multivariate analyses, co-occurrence networks and fitted species abundance distributions on an extensive set of bacterial, micro-eukaryote and archaeal amplicon sequencing data to unravel soil microbiome patterns of nine sites across two east Antarctic regions, the Vestfold Hills and Windmill Islands. To our knowledge, this is the first microbial biodiversity report on the hyperarid Vestfold Hills soil environment. RESULTS Our findings reveal distinct regional differences in phylogenetic composition, abundance and richness amongst microbial taxa. Actinobacteria dominated soils in both regions, yet Bacteroidetes were more abundant in the Vestfold Hills compared to the Windmill Islands, which contained a high abundance of novel phyla. However, intra-region comparisons demonstrate greater homogeneity of soil microbial communities and measured environmental parameters between sites at the Vestfold Hills. Community richness is largely driven by a variable suite of parameters but robust associations between co-existing members highlight potential interactions and sharing of niche space by diverse taxa from all three microbial domains of life examined. Overall, non-neutral processes appear to structure the polar soil microbiomes studied here, with niche partitioning being particularly strong for bacterial communities at the Windmill Islands. Eukaryotic and archaeal communities reveal weaker niche-driven signatures accompanied by multimodality, suggesting the emergence of neutrality. CONCLUSION We provide new information on assemblage patterns, environmental drivers and non-random occurrences for Antarctic soil microbiomes, particularly the Vestfold Hills, where basic diversity, ecology and life history strategies of resident microbiota are largely unknown. Greater understanding of these basic ecological concepts is a pivotal step towards effective conservation management.
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Affiliation(s)
- Eden Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Loïc M Thibaut
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Aleks Terauds
- Australian Antarctic Division, Department of Environment, Antarctic Conservation and Management, 203 Channel Highway, Kingston, TAS, 7050, Australia
| | - Mark Raven
- Commonwealth Scientific and Industrial Research Organisation, Mineralogical Services, Urrbrae, SA, 5064, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Josie van Dorst
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Sin Yin Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Sally Crane
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Belinda C Ferrari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
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11
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Li W, Feng D, Yang G, Deng Z, Rui J, Chen H. Soil water content and pH drive archaeal distribution patterns in sediment and soils of water-level-fluctuating zones in the East Dongting Lake wetland, China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:29127-29137. [PMID: 31392608 DOI: 10.1007/s11356-019-06109-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 07/29/2019] [Indexed: 06/10/2023]
Abstract
Archaea play a vital role in Earth's geochemical cycles, but the factors that drive their distribution between sediments and water-level-fluctuating zones in the East Dongting Lake (EDL) wetland are poorly understood. Here, we used Illumina MiSeq to investigate the variation in the soil archaeal community structure and diversity among sediments and four water-level-fluctuating zones (mudflat, sedge, sedge-Phragmites, and Phragmites) in the EDL wetland. Diverse archaeal assemblages were found in our study, Crenarchaeota, Euryarchaeota, and ammonia-oxidizing and methanogenic subset were the dominant groups, and all their abundances shifted from sediment to water-level-fluctuating zones. The principal coordinates analysis and cluster analysis showed that the overall archaeal community structure was separated into two clusters: cluster I contained nine samples from sediment, mudflat, and sedge zones, whereas cluster II contained six samples from sedge-Phragmites and Phragmites zones. Archaeal diversity was significantly highest in sediment and lowest in Phragmites zone soils. The Mantel test showed that the variation in archaeal community structure was significantly positively correlated with soil water content and pH. The relative abundances of Crenarchaeota and Nitrososphaerales decreased with soil water content, while Euryarchaeota and Methanomicrobiales increased with soil water content. The relative abundance of Methanomicrobiales significantly decreased with pH (R2 = 0.34-0.48). Chao 1, observed operational taxonomic units, Shannon index, and Simpson index all correlated significantly positively with water content (R2 = 0.40-0.60), while Shannon and Simpson indexes both correlated significantly negatively with pH (R2 = 0.20-0.37). Our results demonstrated that the variations in the archaeal community structure were markedly driven by soil water content and pH in the EDL wetland. Our findings suggested that archaeal communities shifted among sediment and four water-level-fluctuating zones, highlighting that the spatiotemporal heterogeneity of greenhouse gas flux in small scale should be taken into account for accurate prediction of greenhouse gas emissions in the Dongting Lake area, especially on the background of climate change and human activities.
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Affiliation(s)
- Wei Li
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- School of Ecology and Environmental Sciences & Yunnan Key Laboratory for Plateau Mountain Ecology and Restoration of Degraded Environments, Yunnan University, Kunming, 650091, China
| | - Defeng Feng
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming, 650224, China
| | - Gang Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Zhengmiao Deng
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Hunan, 410125, China
| | - Junpeng Rui
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huai Chen
- Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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12
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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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13
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Lambrechts S, Willems A, Tahon G. Uncovering the Uncultivated Majority in Antarctic Soils: Toward a Synergistic Approach. Front Microbiol 2019; 10:242. [PMID: 30828325 PMCID: PMC6385771 DOI: 10.3389/fmicb.2019.00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 01/29/2019] [Indexed: 01/22/2023] Open
Abstract
Although Antarctica was once believed to be a sterile environment, it is now clear that the microbial communities inhabiting the Antarctic continent are surprisingly diverse. Until the beginning of the new millennium, little was known about the most abundant inhabitants of the continent: prokaryotes. From then on, however, the rising use of deep sequencing techniques has led to a better understanding of the Antarctic prokaryote diversity and provided insights in the composition of prokaryotic communities in different Antarctic environments. Although these cultivation-independent approaches can produce millions of sequences, linking these data to organisms is hindered by several problems. The largest difficulty is the lack of biological information on large parts of the microbial tree of life, arising from the fact that most microbial diversity on Earth has never been characterized in laboratory cultures. These unknown prokaryotes, also known as microbial dark matter, have been dominantly detected in all major environments on our planet. Laboratory cultures provide access to the complete genome and the means to experimentally verify genomic predictions and metabolic functions and to provide evidence of horizontal gene transfer. Without such well-documented reference data, microbial dark matter will remain a major blind spot in deep sequencing studies. Here, we review our current understanding of prokaryotic communities in Antarctic ice-free soils based on cultivation-dependent and cultivation-independent approaches. We discuss advantages and disadvantages of both approaches and how these strategies may be combined synergistically to strengthen each other and allow a more profound understanding of prokaryotic life on the frozen continent.
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Affiliation(s)
- Sam Lambrechts
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | | | - Guillaume Tahon
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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14
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Lee CK, Laughlin DC, Bottos EM, Caruso T, Joy K, Barrett JE, Brabyn L, Nielsen UN, Adams BJ, Wall DH, Hopkins DW, Pointing SB, McDonald IR, Cowan DA, Banks JC, Stichbury GA, Jones I, Zawar-Reza P, Katurji M, Hogg ID, Sparrow AD, Storey BC, Allan Green TG, Cary SC. Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem. Commun Biol 2019; 2:62. [PMID: 30793041 PMCID: PMC6377621 DOI: 10.1038/s42003-018-0274-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 12/03/2018] [Indexed: 12/01/2022] Open
Abstract
Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplinary investigation to capture ecologically relevant biotic and abiotic attributes of more than 500 sites in the Dry Valleys, encompassing observed landscape heterogeneities across more than 200 km2. Using richness of autotrophic and heterotrophic taxa as a proxy for functional complexity, we linked measured variables in a parsimonious yet comprehensive structural equation model that explained significant variations in biological complexity and identified landscape-scale and fine-scale abiotic factors as the primary drivers of diversity. However, the inclusion of linkages among functional groups was essential for constructing the best-fitting model. Our findings support the notion that biotic interactions make crucial contributions even in an extremely simple ecosystem. Charles Lee, Daniel Laughlin et al. use structural equation modeling to analyze ecological data from more than 500 sites in the Antarctic Dry Valleys. They find that although abiotic factors are the primary drivers of biodiversity variation, biotic interactions are needed to explain the data fully and may play previously underestimated roles.
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Affiliation(s)
- Charles K Lee
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand
| | - Daniel C Laughlin
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Eric M Bottos
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Department of Biology, Thompson Rivers University, Kamloops, BC, V2C 0C8, Canada
| | - Tancredi Caruso
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,School of Biological Sciences and Institute for Global Food Security, Queen's University Belfast, Belfast, BT7 1NN, UK
| | - Kurt Joy
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand
| | - John E Barrett
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Lars Brabyn
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,School of Social Sciences, University of Waikato, Hamilton, 3240, New Zealand
| | - Uffe N Nielsen
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Byron J Adams
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Department of Biology, Evolutionary Ecology Laboratories, and Monte L. Bean Museum, Brigham Young University, Provo, UT, 84602, USA
| | - Diana H Wall
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Department of Biology & School of Global Environmental Sustainability, Colorado State University, Fort Collins, CO, 80523, USA
| | - David W Hopkins
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,SRUC - Scotland's Rural College, Edinburgh, EH9 3JG, UK
| | - Stephen B Pointing
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Yale-NUS College and Department of Biological Sciences, National University of Singapore, Singapore, 138527, Singapore
| | - Ian R McDonald
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand
| | - Don A Cowan
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0002, South Africa
| | - Jonathan C Banks
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Cawthron Institute, Nelson, 7010, New Zealand
| | - Glen A Stichbury
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Environmental Research Institute, University of Waikato, Hamilton, 3240, New Zealand
| | - Irfon Jones
- Gateway Antarctica, University of Canterbury, Christchurch, 8041, New Zealand
| | - Peyman Zawar-Reza
- Centre for Atmospheric Research, Department of Geography, University of Canterbury, Christchurch, 8041, New Zealand
| | - Marwan Katurji
- Centre for Atmospheric Research, Department of Geography, University of Canterbury, Christchurch, 8041, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Polar Knowledge Canada, Canadian High Arctic Research Station, Cambridge, Bay, X0B 0C0, Nunavut, Canada
| | | | - Bryan C Storey
- International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Gateway Antarctica, University of Canterbury, Christchurch, 8041, New Zealand
| | - T G Allan Green
- School of Science, University of Waikato, Hamilton, 3240, New Zealand.,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand.,Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, 28040, Spain
| | - S Craig Cary
- School of Science, University of Waikato, Hamilton, 3240, New Zealand. .,International Centre for Terrestrial Antarctic Research, University of Waikato, Hamilton, 3240, New Zealand. .,College of Earth and Ocean Sciences, University of Delaware, Newark, DE, 19958, USA.
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15
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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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16
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Abele D, Vazquez S, Buma AGJ, Hernandez E, Quiroga C, Held C, Frickenhaus S, Harms L, Lopez JL, Helmke E, Mac Cormack WP. Pelagic and benthic communities of the Antarctic ecosystem of Potter Cove: Genomics and ecological implications. Mar Genomics 2017; 33:1-11. [PMID: 28479280 DOI: 10.1016/j.margen.2017.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/12/2022]
Abstract
Molecular technologies are more frequently applied in Antarctic ecosystem research and the growing amount of sequence-based information available in databases adds a new dimension to understanding the response of Antarctic organisms and communities to environmental change. We apply molecular techniques, including fingerprinting, and amplicon and metagenome sequencing, to understand biodiversity and phylogeography to resolve adaptive processes in an Antarctic coastal ecosystem from microbial to macrobenthic organisms and communities. Interpretation of the molecular data is not only achieved by their combination with classical methods (pigment analyses or microscopy), but furthermore by combining molecular with environmental data (e.g., sediment characteristics, biogeochemistry or oceanography) in space and over time. The studies form part of a long-term ecosystem investigation in Potter Cove on King-George Island, Antarctica, in which we follow the effects of rapid retreat of the local glacier on the cove ecosystem. We formulate and encourage new approaches to integrate molecular tools into Antarctic ecosystem research, environmental conservation actions, and polar ocean observatories.
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Affiliation(s)
- D Abele
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany.
| | - S Vazquez
- Universidad de Buenos Aires, CONICET, Instituto de Nanobiotecnología (NANOBIOTEC), Junín 954, 1113 Buenos Aires, Argentina
| | - A G J Buma
- Dept. Ocean Ecosystems, Energy and Sustainability Research Groningen, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - E Hernandez
- Instituto Antártico Argentino (IAA), 25 de Mayo 1143, 1650 San Martin, Buenos Aires, Argentina
| | - C Quiroga
- Universidad de Buenos Aires, CONICET, Instituto de Medicina y Parasitologia Medica (IMPaM), Paraguay 2155 P.12, 1121 Buenos Aires, Argentina
| | - C Held
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - S Frickenhaus
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - L Harms
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - J L Lopez
- Universidad de Buenos Aires, Catedra de Virologia, Junín 954, 1113 Buenos Aires, Argentina
| | - E Helmke
- Dept. Biosciences, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27470 Bremerhaven, Germany
| | - W P Mac Cormack
- Instituto Antártico Argentino (IAA), 25 de Mayo 1143, 1650 San Martin, Buenos Aires, Argentina
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17
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Shi Y, Adams JM, Ni Y, Yang T, Jing X, Chen L, He JS, Chu H. The biogeography of soil archaeal communities on the eastern Tibetan Plateau. Sci Rep 2016; 6:38893. [PMID: 27958324 PMCID: PMC5153633 DOI: 10.1038/srep38893] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/14/2016] [Indexed: 12/13/2022] Open
Abstract
The biogeographical distribution of soil bacterial communities has been widely investigated. However, there has been little study of the biogeography of soil archaeal communities on a regional scale. Here, using high-throughput sequencing, we characterized the archaeal communities of 94 soil samples across the eastern Tibetan Plateau. Thaumarchaeota was the predominant archael phylum in all the soils, and Halobacteria was dominant only in dry soils. Archaeal community composition was significantly correlated with soil moisture content and C:N ratio, and archaeal phylotype richness was negatively correlated with soil moisture content (r = −0.47, P < 0.01). Spatial distance, a potential measure of the legacy effect of evolutionary and dispersal factors, was less important than measured environmental factors in determining the broad scale archaeal community pattern. These results indicate that soil moisture and C:N ratio are the key factors structuring soil archaeal communities on the eastern Tibetan Plateau. Our findings suggest that archaeal communities have adjusted their distributions rapidly enough to reach range equilibrium in relation to past environmental changes e.g. in water availability and soil nutrient status. This responsiveness may allow better prediction of future responses of soil archaea to environmental change in these sensitive ecosystems.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Jonathan M Adams
- Department of Biological Sciences, Seoul National University, Gwanak, Seoul 151, Republic of Korea
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
| | - Xin Jing
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 5 Yiheyuan Road, Beijing 100871, China
| | - Litong Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining 810008, China
| | - Jin-Sheng He
- Department of Ecology, College of Urban and Environmental Sciences and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, 5 Yiheyuan Road, Beijing 100871, China.,Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, 23 Xinning Road, Xining 810008, China
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, East Beijing Road 71, Nanjing 210008, China
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18
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Learman DR, Henson MW, Thrash JC, Temperton B, Brannock PM, Santos SR, Mahon AR, Halanych KM. Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure. Front Microbiol 2016; 7:284. [PMID: 27047451 PMCID: PMC4803750 DOI: 10.3389/fmicb.2016.00284] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/22/2016] [Indexed: 02/01/2023] Open
Abstract
Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ13C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4+) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability.
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Affiliation(s)
- Deric R Learman
- Department of Biology, Institute for Great Lakes Research, Central Michigan University Mt. Pleasant, MI, USA
| | - Michael W Henson
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
| | - J Cameron Thrash
- Department of Biological Sciences, Louisiana State University Baton Rouge, LA, USA
| | - Ben Temperton
- Department of Biosciences, University of Exeter Exeter, UK
| | - Pamela M Brannock
- Department of Biological Sciences, Auburn University Auburn, AL, USA
| | - Scott R Santos
- Department of Biological Sciences, Auburn University Auburn, AL, USA
| | - Andrew R Mahon
- Department of Biology, Institute for Great Lakes Research, Central Michigan University Mt. Pleasant, MI, USA
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19
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Makhalanyane TP, Van Goethem MW, Cowan DA. Microbial diversity and functional capacity in polar soils. Curr Opin Biotechnol 2016; 38:159-66. [PMID: 26921734 DOI: 10.1016/j.copbio.2016.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/25/2016] [Accepted: 01/28/2016] [Indexed: 11/18/2022]
Abstract
Global change is disproportionately affecting cold environments (polar and high elevation regions), with potentially negative impacts on microbial diversity and functional processes. In most cold environments the combination of low temperatures, and physical stressors, such as katabatic wind episodes and limited water availability result in biotic systems, which are in trophic terms very simple and primarily driven by microbial communities. Metagenomic approaches have provided key insights on microbial communities in these systems and how they may adapt to stressors and contribute towards mediating crucial biogeochemical cycles. Here we review, the current knowledge regarding edaphic-based microbial diversity and functional processes in Antarctica, and the Artic. Such insights are crucial and help to establish a baseline for understanding the impact of climate change on Polar Regions.
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Affiliation(s)
- Thulani Peter Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa
| | - Marc Warwick Van Goethem
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa
| | - Don Arthur Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria 0028, South Africa.
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20
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de Gannes V, Eudoxie G, Bekele I, Hickey WJ. Relations of microbiome characteristics to edaphic properties of tropical soils from Trinidad. Front Microbiol 2015; 6:1045. [PMID: 26483772 PMCID: PMC4588118 DOI: 10.3389/fmicb.2015.01045] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/14/2015] [Indexed: 11/15/2022] Open
Abstract
Understanding how community structure of Bacteria, Archaea, and Fungi varies as a function of edaphic characteristics is key to elucidating associations between soil ecosystem function and the microbiome that sustains it. In this study, non-managed tropical soils were examined that represented a range of edaphic characteristics, and a comprehensive soil microbiome analysis was done by Illumina sequencing of amplicon libraries that targeted Bacteria (universal prokaryotic 16S rRNA gene primers), Archaea (primers selective for archaeal 16S rRNA genes), or Fungi (internal transcribed spacer region). Microbiome diversity decreased in the order: Bacteria > Archaea > Fungi. Bacterial community composition had a strong relationship to edaphic factors while that of Archaea and Fungi was comparatively weak. Bacterial communities were 70–80% alike, while communities of Fungi and Archaea had 40–50% similarity. While each of the three component communities differed in species turnover patterns, soils having relatively similar bacterial communities also housed similar archaeal communities. In contrast, the composition of fungal communities had no correlation to bacterial or archaeal communities. Bacterial and archaeal diversity had significant (negative) correlations to pH, whereas fungal diversity was not correlated to pH. Edaphic characteristics that best explained variation between soils in bacterial community structure were: total carbon, sodium, magnesium, and zinc. For fungi, the best variables were: sodium, magnesium, phosphorus, boron, and C/N. Archaeal communities had two sets of edaphic factors of equal strength, one contained sulfur, sodium, and ammonium-N and the other was composed of clay, potassium, ammonium-N, and nitrate-N. Collectively, the data indicate that Bacteria, Archaea, and Fungi did not closely parallel one another in community structure development, and thus microbiomes in each soil acquired unique identities. This divergence could in part reflect the finding that unknown factor(s) were stronger than edaphic characteristics in shaping fungal and archaeal communities.
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Affiliation(s)
- Vidya de Gannes
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - Gaius Eudoxie
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - Isaac Bekele
- Department Food Production, University of the West Indies St. Augustine, Trinidad and Tobago
| | - William J Hickey
- O.N. Allen Laboratory for Soil Microbiology, Department Soil Science, University of Wisconsin-Madison Madison, WI, USA
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21
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Oton EV, Quince C, Nicol GW, Prosser JI, Gubry-Rangin C. Phylogenetic congruence and ecological coherence in terrestrial Thaumarchaeota. ISME JOURNAL 2015; 10:85-96. [PMID: 26140533 PMCID: PMC4604658 DOI: 10.1038/ismej.2015.101] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/13/2015] [Accepted: 05/08/2015] [Indexed: 11/09/2022]
Abstract
Thaumarchaeota form a ubiquitously distributed archaeal phylum, comprising both the ammonia-oxidising archaea (AOA) and other archaeal groups in which ammonia oxidation has not been demonstrated (including Group 1.1c and Group 1.3). The ecology of AOA in terrestrial environments has been extensively studied using either a functional gene, encoding ammonia monooxygenase subunit A (amoA) or 16S ribosomal RNA (rRNA) genes, which show phylogenetic coherence with respect to soil pH. To test phylogenetic congruence between these two markers and to determine ecological coherence in all Thaumarchaeota, we performed high-throughput sequencing of 16S rRNA and amoA genes in 46 UK soils presenting 29 available contextual soil characteristics. Adaptation to pH and organic matter content reflected strong ecological coherence at various levels of taxonomic resolution for Thaumarchaeota (AOA and non-AOA), whereas nitrogen, total mineralisable nitrogen and zinc concentration were also important factors associated with AOA thaumarchaeotal community distribution. Other significant associations with environmental factors were also detected for amoA and 16S rRNA genes, reflecting different diversity characteristics between these two markers. Nonetheless, there was significant statistical congruence between the markers at fine phylogenetic resolution, supporting the hypothesis of low horizontal gene transfer between Thaumarchaeota. Group 1.1c Thaumarchaeota were also widely distributed, with two clusters predominating, particularly in environments with higher moisture content and organic matter, whereas a similar ecological pattern was observed for Group 1.3 Thaumarchaeota. The ecological and phylogenetic congruence identified is fundamental to understand better the life strategies, evolutionary history and ecosystem function of the Thaumarchaeota.
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Affiliation(s)
- Eduard Vico Oton
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK.,School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | | | - Graeme W Nicol
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK.,Laboratoire Ampère UMR CNRS 5005, École Centrale de Lyon, Université de Lyon, Ecully CEDEX, France
| | - James I Prosser
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
| | - Cécile Gubry-Rangin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, UK
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22
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Wei STS, Higgins CM, Adriaenssens EM, Cowan DA, Pointing SB. Genetic signatures indicate widespread antibiotic resistance and phage infection in microbial communities of the McMurdo Dry Valleys, East Antarctica. Polar Biol 2015. [DOI: 10.1007/s00300-015-1649-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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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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