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Fair H, Hamilton TL, Smiley PC, Liu Q. Determinants of microbial community structure in supraglacial pool sediments of monsoonal Tibetan Plateau. Microbiol Spectr 2024:e0075424. [PMID: 39078165 DOI: 10.1128/spectrum.00754-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/24/2024] [Indexed: 07/31/2024] Open
Abstract
Supraglacial pools are prevalent on debris-covered mountain glaciers, yet only limited information is available on the microbial communities within these habitats. Our research questions for this preliminary study were: (1) What microbes occur in supraglacial pool sediments of monsoonal Tibet?; (2) Which abiotic and biotic habitat variables have the most influence on the microbial community structure?; and (3) Does microbial composition of supraglacial pool sediments differ from that of glacial-melt stream pool sediments? We collected microbial samples for 16S rRNA sequencing and invertebrates for enumeration and identification and measured 14 abiotic variables from 46 supraglacial pools and nine glacial-melt stream pools in 2018 and 2019. Generalized linear model analyses, small sample Akaike information criterion, and variable importance scores were used to identify the best predictor variables of microbial community structure. Multi-response permutation procedure (MRPP) was used to compare taxa composition between supraglacial pools and stream pools. The most abundant phyla in supraglacial pool sediments were Proteobacteria, Actinobacteria, Bacteroidota, Chloroflexi, and Cyanobacteria. Genera richness, indicator genera richness, and Polaromonas relative abundance were best predicted by Chironomidae larvae abundance. Angustibacter and Oryzihumus relative abundance were best predicted by pH, Acidiphilium relative abundance was best predicted by turbidity, and Sphingomonas relative abundance was best predicted by glacier zone. Taxa composition was similar between supraglacial and stream pools at the class, genus, and ASV taxonomic levels. Our results indicate that Chironomidae larvae may play a keystone species role in shaping bacterial communities of supraglacial pools on debris-covered glaciers.IMPORTANCEGlacier meltwater habitats (cryoconite holes, supraglacial pools, supraglacial ponds and lakes, glacial streams) and their biota have not been well-studied, especially on debris-covered glaciers in temperate monsoonal regions. Our study is the first to document the microbial community-habitat relationships in supraglacial pools on a debris-covered glacier in Tibet. Microbial genera richness, indicator genera richness, and Polaromonas relative abundance declined with increasing larval Chironomidae abundance, which is a novel finding that highlights the importance of larval insects in structuring microbial communities in supraglacial pools.
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Affiliation(s)
- Heather Fair
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
- Soil Drainage Research Unit, Agricultural Research Service, USDA, Columbus, Ohio, USA
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
- the Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
| | - Peter C Smiley
- Soil Drainage Research Unit, Agricultural Research Service, USDA, Columbus, Ohio, USA
| | - Qiao Liu
- Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu, China
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2
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Gladkov GV, Kimeklis AK, Tembotov RK, Ivanov MN, Andronov EE, Abakumov EV. Linking the composition of cryoconite prokaryotic communities in the Arctic, Antarctic, and Central Caucasus with their chemical characteristics. Sci Rep 2024; 14:15838. [PMID: 38982048 PMCID: PMC11233692 DOI: 10.1038/s41598-024-64452-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Cryoconites are the deposits on the surface of glaciers that create specific ecological niches for the development of microorganism communities. The sediment material can vary in origin, structure, and nutrient content, creating local variations in the growth conditions. An additional factor of variability is the location of the glaciers, as they are found in different climatic zones in the high mountain regions and closer to the poles. Here, using the analysis of amplicon sequencing of the 16S rRNA gene, we studied the taxonomic composition of the prokaryotic communities from glaciers from remote regions, including the Arctic (Mushketova on the Severnaya Zemlya, IGAN in Polar Ural), Antarctic (Pimpirev on the Livingstone Island) and Central Caucasus (Skhelda and Garabashi) and connected it with the variation of the physicochemical characteristics of the substrate: pH, carbon, nitrogen, macro- and microelements. The cryoconite microbiomes were comprised of specific for this environment phyla (mostly Pseudomonadota, Cyanobacteria, Bacteroidota, Acidobacteriota, and Actinobacteriota), but each glacier had a unique taxonomic imprint. The core microbiome between regions was composed of only a few ASVs, among which the most likely globally distributed ones attributed to Polaromonas sp., Rhodoferax sp., Cryobacterium sp., and Hymenobacter frigidus. The WGSNA defined clusters of co-occurring ASVs between microbiomes, that significantly change their abundance corresponding with the variation of chemical parameters of cryoconites, but do not fully coincide with their regional separation. Thus, our work demonstrates that the chemical characteristics of the sediment material can explain the variation in the cryoconite prokaryotic community which is not always linked to geographic isolation.
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Affiliation(s)
- Grigory V Gladkov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
| | - Anastasiia K Kimeklis
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
| | - Rustam Kh Tembotov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034
- Tembotov Institute of Ecology of Mountain Territories, Russian Academy of Sciences, Nalchik, Russia, 360051
| | - Mikhail N Ivanov
- Department of Cryolithology and Glaciology, Lomonosov Moscow State University, GSP-1, Leninskie Gory, Moscow, Russia, 119991
| | - Evgeny E Andronov
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608
- V.V. Dokuchaev Soil Science Institute, Moscow, Russia, 119017
| | - Evgeny V Abakumov
- Department of Applied Ecology, St. Petersburg State University, Saint-Petersburg, Russia, 199034.
- Laboratory of Microbiological Monitoring and Bioremediation of Soils, All-Russian Research Institute for Agricultural Microbiology, Pushkin, Russia, 196608.
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3
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Hassan S, Mushtaq M, Ganiee SA, Zaman M, Yaseen A, Shah AJ, Ganai BA. Microbial oases in the ice: A state-of-the-art review on cryoconite holes as diversity hotspots and their scientific connotations. ENVIRONMENTAL RESEARCH 2024; 252:118963. [PMID: 38640991 DOI: 10.1016/j.envres.2024.118963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 04/13/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Cryoconite holes, small meltwater pools on the surface of glaciers and ice sheets, represent extremely cold ecosystems teeming with diverse microbial life. Cryoconite holes exhibit greater susceptibility to the impacts of climate change, underlining the imperative nature of investigating microbial communities as an essential module of polar and alpine ecosystem monitoring efforts. Microbes in cryoconite holes play a critical role in nutrient cycling and can produce bioactive compounds, holding promise for industrial and pharmaceutical innovation. Understanding microbial diversity in these delicate ecosystems is essential for effective conservation strategies. Therefore, this review discusses the microbial diversity in these extreme environments, aiming to unveil the complexity of their microbial communities. The current study envisages that cryoconite holes as distinctive ecosystems encompass a multitude of taxonomically diverse and functionally adaptable microorganisms that exhibit a rich microbial diversity and possess intricate ecological functions. By investigating microbial diversity and ecological functions of cryoconite holes, this study aims to contribute valuable insights into the broader field of environmental microbiology and enhance further understanding of these ecosystems. This review seeks to provide a holistic overview regarding the formation, evolution, characterization, and molecular adaptations of cryoconite holes. Furthermore, future research directions and challenges underlining the need for long-term monitoring, and ethical considerations in preserving these pristine environments are also provided. Addressing these challenges and resolutely pursuing future research directions promises to enrich our comprehension of microbial diversity within cryoconite holes, revealing the broader ecological and biogeochemical implications. The inferences derived from the present study will provide researchers, ecologists, and policymakers with a profound understanding of the significance and utility of cryoconite holes in unveiling the microbial diversity and its potential applications.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Misba Mushtaq
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India
| | - Shahid Ahmad Ganiee
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Muzafar Zaman
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Aarif Yaseen
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Abdul Jalil Shah
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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4
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Sanyal A, Antony R, Samui G, Thamban M. Autotrophy to Heterotrophy: Shift in Bacterial Functions During the Melt Season in Antarctic Cryoconite Holes. J Microbiol 2024:10.1007/s12275-024-00140-1. [PMID: 38814540 DOI: 10.1007/s12275-024-00140-1] [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: 11/03/2023] [Revised: 03/27/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024]
Abstract
Microbes residing in cryoconite holes (debris, water, and nutrient-rich ecosystems) on the glacier surface actively participate in carbon and nutrient cycling. Not much is known about how these communities and their functions change during the summer melt-season when intense ablation and runoff alter the influx and outflux of nutrients and microbes. Here, we use high-throughput-amplicon sequencing, predictive metabolic tools and Phenotype MicroArray techniques to track changes in bacterial communities and functions in cryoconite holes in a coastal Antarctic site and the surrounding fjord, during the summer season. The bacterial diversity in cryoconite hole meltwater was predominantly composed of heterotrophs (Proteobacteria) throughout the season. The associated functional potentials were related to heterotrophic-assimilatory and -dissimilatory pathways. Autotrophic Cyanobacterial lineages dominated the debris community at the beginning and end of summer, while heterotrophic Bacteroidota- and Proteobacteria-related phyla increased during the peak melt period. Predictive functional analyses based on taxonomy show a shift from predominantly phototrophy-related functions to heterotrophic assimilatory pathways as the melt-season progressed. This shift from autotrophic to heterotrophic communities within cryoconite holes can affect carbon drawdown and nutrient liberation from the glacier surface during the summer. In addition, the flushing out and export of cryoconite hole communities to the fjord could influence the biogeochemical dynamics of the fjord ecosystem.
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Affiliation(s)
- Aritri Sanyal
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India.
- School of Earth, Ocean and Atmospheric Sciences, Goa University, Goa, 403206, India.
| | - Runa Antony
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
- GFZ German Research Centre for Geosciences, 14473, Potsdam, Germany
| | - Gautami Samui
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Meloth Thamban
- National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Goa, 403804, India
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Zhao M, Jiang M, Qin L, Hu N, Meng J, Wang M, Wang G. The recovery of soil eukaryotic alpha and beta diversity after wetland restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 925:171814. [PMID: 38508279 DOI: 10.1016/j.scitotenv.2024.171814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Soil eukaryotes play an important role in regulating the ecological processes and ecosystem functioning. However, the recovery potential of soil eukaryotic diversity during wetland restoration is largely unknown. We compared the alpha and beta diversity of soil eukaryotes of farmlands and natural and restored wetlands to explore the underlying abiotic and biotic driving forces in the Sanjiang Plain, China. We found that there was no significant difference of the alpha diversity of soil eukaryotes, while the beta diversity of soil eukaryotes differed significantly between the three land use types, with the mean values in the restored wetlands in between those in the natural wetlands and farmlands. The composition of soil eukaryotic communities were less diverse in farmlands compared to restored and natural wetlands. Network property of soil eukaryotes community (positive: negative edges) increased from farmlands to restored wetlands to natural wetlands, indicating enhanced species positive: negative interactions during restoration. The structural equation modeling indicated that species positive: negative interactions and soil nutrients directly affected soil eukaryotic beta diversity. Soil pH and soil water content indirectly affected soil eukaryotic beta diversity by directly affecting species interactions. Our findings suggest that wetland restoration could change soil environment, strengthen microbial cooperation, and increase eukaryotic beta diversity. However, it may take a very long time to reach the original level of soil eukaryotic structure and diversity.
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Affiliation(s)
- Meiling Zhao
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Jiang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Lei Qin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Nanlin Hu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingci Meng
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Ming Wang
- State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun 130024, China
| | - Guodong Wang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
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6
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Singh P, Singh SM, Segawa T, Singh PK. Bacterial diversity and biopotentials of Hamtah glacier cryoconites, Himalaya. Front Microbiol 2024; 15:1362678. [PMID: 38751720 PMCID: PMC11094618 DOI: 10.3389/fmicb.2024.1362678] [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: 12/28/2023] [Accepted: 04/01/2024] [Indexed: 05/18/2024] Open
Abstract
Cryoconite is a granular structure present on the glaciers and ice sheets found in polar regions including the Himalayas. It is composed of organic and inorganic matter which absorb solar radiations and reduce ice surface albedo, therefore impacting the melting and retreat of glaciers. Though climate warming has a serious impact on Himalayan glaciers, the biodiversity of sub-glacier ecosystems is poorly understood. Moreover, cryoconite holes are unique habitats for psychrophile biodiversity hotspots in the NW Himalayas, but unfortunately, studies on the microbial diversity of such habitats remain elusive. Therefore, the current study was designed to explore the bacterial diversity of the Hamtah Glacier Himalaya using both culturable and non-culturable approaches. The culturable bacterial count ranged from 2.0 × 103 to 8.8 × 105 colony-forming units (CFUs)/g at the different locations of the glacier. A total of 88 bacterial isolates were isolated using the culturable approach. Based on the 16S ribosomal RNA gene (16S rRNA), the identified species belong to seven genera, namely, Cryobacterium, Duganella, Janthinobacterium, Pseudomonas, Peribacillus, Psychrobacter, and Sphingomonas. In the non-culturable approach, high-throughput sequencing of 16S rRNA genes (using MiSeq) showed unique bacterial community profiles and represented 440 genera belonging to 20 phyla, namely, Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Acidobacteria, Planctomycetes, Cyanobacteria, Verrucomicrobia, Spirochaetes, Elusimicrobia, Armatimonadetes, Gemmatimonadetes, Deinococcus-Thermus, Nitrospirae, Chlamydiae, Chlorobi, Deferribacteres, Fusobacteria, Lentisphaerae, and others. High relative abundances of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes were observed in the samples. Phototrophic (Cyanobacteria and Chloroflexi) and nitrifier (Nitrospirae) in bacterial populations indicated sustenance of the micro-ecosystem in the oligotrophic glacier environment. The isolates varied in their phenotypic characteristics, enzyme activities, and antibiotic sensitivity. Furthermore, the fatty acid profiles of bacterial isolates indicate the predominance of branched fatty acids. Iso-, anteiso-, unsaturated and saturated fatty acids together constituted a major proportion of the total fatty acid composition. High cold-adapted enzyme activities such as lipase and cellulase expressed by Cryobacterium arcticum (KY783365) and protease and cellulase activities by Pseudomonas sp. strains (KY783373, KY783377-79, KY783382) provide evidence of the possible applications of these organisms. Additionally, antibiotic tests indicated that most isolates were sensitive to antibiotics. In conclusion, the present study contributed for the first time to bacterial diversity and biopotentials of cryoconites of Hamtah Glacier, Himalayas. Furthermore, the cold-adapted enzymes and polyunsaturated fatty acids (PUFAs) may provide an opportunity for biotechnology in the Himalayas. Inductively coupled plasma mass spectrometry (ICPMS) analyses showed the presence of several elements in cryoconites, providing a clue for the accelerating melting and retreating of the Hamtah glacier.
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Affiliation(s)
- Purnima Singh
- Indian Institute of Technology, Banaras Hindu University (IIT-BHU), Varanasi, India
| | | | - Takahiro Segawa
- National Institute of Polar Research, Tachikawa-shi, Tokyo, Japan
| | - Prashant Kumar Singh
- Department of Biotechnology, Pachhunga University College, Mizoram University (A Central University), Aizawl, India
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Wei J, Fontaine L, Valiente N, Dörsch P, Hessen DO, Eiler A. Trajectories of freshwater microbial genomics and greenhouse gas saturation upon glacial retreat. Nat Commun 2023; 14:3234. [PMID: 37270637 DOI: 10.1038/s41467-023-38806-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 05/15/2023] [Indexed: 06/05/2023] Open
Abstract
Due to climate warming, ice sheets around the world are losing mass, contributing to changes across terrestrial landscapes on decadal time spans. However, landscape repercussions on climate are poorly constrained mostly due to limited knowledge on microbial responses to deglaciation. Here, we reveal the genomic succession from chemolithotrophy to photo- and heterotrophy and increases in methane supersaturation in freshwater lakes upon glacial retreat. Arctic lakes at Svalbard also revealed strong microbial signatures form nutrient fertilization by birds. Although methanotrophs were present and increased along lake chronosequences, methane consumption rates were low even in supersaturated systems. Nitrous oxide oversaturation and genomic information suggest active nitrogen cycling across the entire deglaciated landscape, and in the high Arctic, increasing bird populations serve as major modulators at many sites. Our findings show diverse microbial succession patterns, and trajectories in carbon and nitrogen cycle processes representing a positive feedback loop of deglaciation on climate warming.
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Affiliation(s)
- Jing Wei
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Laurent Fontaine
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Nicolas Valiente
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
- Division of Terrestrial Ecosystem Research, Center of Microbiology and Environmental Systems Science, University of Vienna, 1030, Vienna, Austria
| | - Peter Dörsch
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dag O Hessen
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway
| | - Alexander Eiler
- Department of Biosciences and Centre for Biogeochemistry in the Anthropocene, University of Oslo, 0316, Oslo, Norway.
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Pittino F, Ambrosini R, Seeger M, Azzoni RS, Diolaiuti G, Alviz Gazitua P, Franzetti A. Geographical variability of bacterial communities of cryoconite holes of Andean glaciers. Sci Rep 2023; 13:2633. [PMID: 36788266 PMCID: PMC9929092 DOI: 10.1038/s41598-022-24373-5] [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: 04/20/2022] [Accepted: 11/14/2022] [Indexed: 02/16/2023] Open
Abstract
Cryoconite holes, ponds full of melting water with sediment on the bottom, are hotspots of biodiversity on glacier surfaces and host dynamic micro-ecosystems. They have been extensively investigated in different areas of the world (e.g., the Arctic, Antarctic, Alps, and Himalaya), but so far no study has described the bacterial communities of the glaciers in the Andes, the world's longest mountain range. In this study, we describe the bacterial communities of three small (< 2 km2) high-elevation (< 4200 m a.s.l.) glaciers of the Central Andes (Iver, East Iver and Morado glaciers) and two large (> 85 km2) glaciers of the Patagonian Andes (Exploradores and Perito Moreno glaciers) whose ablation tongues reach low altitude (< 300 m a.s.l.). Results show that the bacterial communities were generally similar to those observed in the cryoconite holes of other continents, but with few cyanobacteria (0.5% of sequences). The most abundant orders were Betaproteobacteriales, Cytophagales, Chitinophagales, Acetobacterales, Frankiales, Armatimonadales, Sphingobacteriales, Rhizobiales, Bacteroidales, Sphingomonadales, and Micrococcales. The bacterial communities differed between glaciers and both water pH and O2 concentration appeared to influence the bacterial community composition. This work thus provides the first description of the bacterial communities in cryoconite holes of South American glaciers.
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Affiliation(s)
- F. Pittino
- grid.7563.70000 0001 2174 1754Department of Earth and Environmental Sciences (DISAT), Università degli Studi di Milano-Bicocca, Milan, Italy ,grid.419754.a0000 0001 2259 5533WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - R. Ambrosini
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - M. Seeger
- grid.12148.3e0000 0001 1958 645XMolecular Microbiology and Environmental Biotechnology Laboratory, Department of Chemistry, Universidad Técnica Federico Santa María, Valparaiso, Chile
| | - R. S. Azzoni
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Earth Science “Ardito Desio”, Università degli Studi di Milano, Milan, Italy
| | - G. Diolaiuti
- grid.4708.b0000 0004 1757 2822Laboratory of Glacier Ecology, Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
| | - P. Alviz Gazitua
- grid.442234.70000 0001 2295 9069Departamento de Ciencias Biológicas, Universidad de los Lagos, Osorno, Chile
| | - A. Franzetti
- grid.7563.70000 0001 2174 1754Department of Earth and Environmental Sciences (DISAT), Università degli Studi di Milano-Bicocca, Milan, Italy
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Two new tardigrade genera from New Zealand's Southern Alp glaciers display morphological stasis and parallel evolution. Mol Phylogenet Evol 2023; 178:107634. [PMID: 36208696 DOI: 10.1016/j.ympev.2022.107634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Tardigrada is an invertebrate phylum that often constitutes a dominant micrometazoan group on glaciers worldwide. We investigated tardigrades residing in surface ice above the equilibrium line altitude (ELA) on three temperate glaciers of New Zealand's Southern Alps. Morphological, morphometric and multilocus DNA analyses (CO1, 18S rRNA, 28S rRNA, ITS-2) revealed two new genera comprising four species, of which two are formally described here: Kopakaius gen. nov. nicolae sp. nov. and Kararehius gen. nov. gregorii sp. nov. The former is represented by three genetically distinct phyletic lineages akin to species. According to CO1, Kopakaius gen. nov. nicolae sp. nov. inhabits Whataroa Glacier only while the remaining two Kopakaius species occur on Fox and Franz Joseph Glaciers, suggesting low dispersal capabilities. Although morphological characteristics of the new genera could indicate affinity with the subfamily Itaquasconinae, phylogenetic analysis placed them confidently in the subfamily Diphasconinae. Kopakaius gen. nov. lack placoids in the pharynx similar with some Itaquasconinae, whereas dark pigmentation and claw shape aligns them with the glacier-obligate genus, Cryobiotus (subfamily Hypsibiinae), which is an example of parallel evolution. The second genus, Kararehius gen nov. could be classified as Adropion-like (subfamily Itaquasconinae), but differs greatly by genetics (placed in the subfamily Diphasconinae) as well as morphology (e.g., lack of septulum), exemplify deep stasis in Hypsibiidae. Our results suggest that glacier fragmentation during the Pleistocene triggered tardigrade speciation, making it a suitable model for studies on allopatric divergence in glacier meiofauna.
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Microinvertebrate Colonization of New Zealand’s Thermally Extreme Environments. Evol Biol 2022. [DOI: 10.1007/s11692-022-09578-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Murakami T, Takeuchi N, Mori H, Hirose Y, Edwards A, Irvine-Fynn T, Li Z, Ishii S, Segawa T. Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite. MICROBIOME 2022; 10:50. [PMID: 35317857 PMCID: PMC8941735 DOI: 10.1186/s40168-022-01238-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cryoconite granules are mineral-microbial aggregates found on glacier surfaces worldwide and are hotspots of biogeochemical reactions in glacier ecosystems. However, despite their importance within glacier ecosystems, the geographical diversity of taxonomic assemblages and metabolic potential of cryoconite communities around the globe remain unclear. In particular, the genomic content of cryoconite communities on Asia's high mountain glaciers, which represent a substantial portion of Earth's ice masses, has rarely been reported. Therefore, in this study, to elucidate the taxonomic and ecological diversities of cryoconite bacterial consortia on a global scale, we conducted shotgun metagenomic sequencing of cryoconite acquired from a range of geographical areas comprising Polar (Arctic and Antarctic) and Asian alpine regions. RESULTS Our metagenomic data indicate that compositions of both bacterial taxa and functional genes are particularly distinctive for Asian cryoconite. Read abundance of the genes responsible for denitrification was significantly more abundant in Asian cryoconite than the Polar cryoconite, implying that denitrification is more enhanced in Asian glaciers. The taxonomic composition of Cyanobacteria, the key primary producers in cryoconite communities, also differs between the Polar and Asian samples. Analyses on the metagenome-assembled genomes and fluorescence emission spectra reveal that Asian cryoconite is dominated by multiple cyanobacterial lineages possessing phycoerythrin, a green light-harvesting component for photosynthesis. In contrast, Polar cryoconite is dominated by a single cyanobacterial species Phormidesmis priestleyi that does not possess phycoerythrin. These findings suggest that the assemblage of cryoconite bacterial communities respond to regional- or glacier-specific physicochemical conditions, such as the availability of nutrients (e.g., nitrate and dissolved organic carbon) and light (i.e., incident shortwave radiation). CONCLUSIONS Our genome-resolved metagenomics provides the first characterization of the taxonomic and metabolic diversities of cryoconite from contrasting geographical areas, highlighted by the distinct light-harvesting approaches of Cyanobacteria and nitrogen utilization between Polar and Asian cryoconite, and implies the existence of environmental controls on the assemblage of cryoconite communities. These findings deepen our understanding of the biodiversity and biogeochemical cycles of glacier ecosystems, which are susceptible to ongoing climate change and glacier decline, on a global scale. Video abstract.
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Affiliation(s)
- Takumi Murakami
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Hiroshi Mori
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Aichi, Japan
| | - Arwyn Edwards
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, UK
- Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, Aberystwyth, UK
| | - Tristram Irvine-Fynn
- Interdisciplinary Centre for Environmental Microbiology, Aberystwyth University, Aberystwyth, UK
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, UK
| | - Zhongqin Li
- State Key Laboratory of Cryospheric Sciences/Tien Shan Glaciological Station, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Satoshi Ishii
- Department of Soil, Water and Climate, University of Minnesota, St. Paul, MN USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN USA
| | - Takahiro Segawa
- Center for Life Science Research, University of Yamanashi, Yamanashi, Japan
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12
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Rozwalak P, Podkowa P, Buda J, Niedzielski P, Kawecki S, Ambrosini R, Azzoni RS, Baccolo G, Ceballos JL, Cook J, Di Mauro B, Ficetola GF, Franzetti A, Ignatiuk D, Klimaszyk P, Łokas E, Ono M, Parnikoza I, Pietryka M, Pittino F, Poniecka E, Porazinska DL, Richter D, Schmidt SK, Sommers P, Souza-Kasprzyk J, Stibal M, Szczuciński W, Uetake J, Wejnerowski Ł, Yde JC, Takeuchi N, Zawierucha K. Cryoconite - From minerals and organic matter to bioengineered sediments on glacier's surfaces. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 807:150874. [PMID: 34627905 DOI: 10.1016/j.scitotenv.2021.150874] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/03/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Cryoconite is a mixture of mineral and organic material covering glacial ice, playing important roles in biogeochemical cycles and lowering the albedo of a glacier surface. Understanding the differences in structure of cryoconite across the globe can be important in recognizing past and future changes in supraglacial environments and ice-organisms-minerals interactions. Despite the worldwide distribution and over a century of studies, the basic characteristics of cryoconite, including its forms and geochemistry, remain poorly studied. The major purpose of our study is the presentation and description of morphological diversity, chemical and photoautotrophs composition, and organic matter content of cryoconite sampled from 33 polar and mountain glaciers around the globe. Observations revealed that cryoconite is represented by various morphologies including loose and granular forms. Granular cryoconite includes smooth, rounded, or irregularly shaped forms; with some having their surfaces covered by cyanobacteria filaments. The occurrence of granules increased with the organic matter content in cryoconite. Moreover, a major driver of cryoconite colouring was the concentration of organic matter and its interplay with minerals. The structure of cyanobacteria and algae communities in cryoconite differs between glaciers, but representatives of cyanobacteria families Pseudanabaenaceae and Phormidiaceae, and algae families Mesotaeniaceae and Ulotrichaceae were the most common. The most of detected cyanobacterial taxa are known to produce polymeric substances (EPS) that may cement granules. Organic matter content in cryoconite varied between glaciers, ranging from 1% to 38%. The geochemistry of all the investigated samples reflected local sediment sources, except of highly concentrated Pb and Hg in cryoconite collected from European glaciers near industrialized regions, corroborating cryoconite as element-specific collector and potential environmental indicator of anthropogenic activity. Our work supports a notion that cryoconite may be more than just simple sediment and instead exhibits complex structure with relevance for biodiversity and the functioning of glacial ecosystems.
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Affiliation(s)
- Piotr Rozwalak
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland; Geohazards Research Unit, Institute of Geology, Adam Mickiewicz University, Poznan, Poland
| | - Paweł Podkowa
- Department of Avian Biology and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jakub Buda
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Przemysław Niedzielski
- Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | | | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Roberto S Azzoni
- Department of Earth Sciences, "Ardito Desio", University of Milan, Milan, Italy
| | - Giovanni Baccolo
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Jorge L Ceballos
- Institute of Hydrology, Meteorology and Environmental Studies, IDEAM, Bogota, Colombia
| | - Joseph Cook
- Department of Environmental Sciences, Aarhus University, Aarhus, Denmark
| | - Biagio Di Mauro
- Institute of Polar Sciences, National Research Council, Venice, Italy
| | - Gentile Francesco Ficetola
- Department of Environmental Science and Policy, University of Milan, Milan, Italy; Laboratoire d'Ecologie Alpine, University Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Dariusz Ignatiuk
- University of Silesia in Katowice, Institute of Earth Sciences, Bedzinska 60, 41-200 Sosnowiec, Poland
| | - Piotr Klimaszyk
- Department of Water Protection, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznań, Poland
| | - Edyta Łokas
- Department of Mass Spectrometry, Institute of Nuclear Physics, Polish Academy of Sciences, Kraków, Poland
| | - Masato Ono
- Graduate School of Science and Engineering, Chiba University, Chiba, Japan
| | - Ivan Parnikoza
- State Institution National Antarctic Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine; Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Mirosława Pietryka
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Science, pl. Grunwaldzki 24a, 50-363 Wrocław, Poland
| | - Francesca Pittino
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Ewa Poniecka
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Dorota Richter
- Department of Botany and Plant Ecology, Wrocław University of Environmental and Life Science, pl. Grunwaldzki 24a, 50-363 Wrocław, Poland
| | - Steven K Schmidt
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
| | - Pacifica Sommers
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
| | - Juliana Souza-Kasprzyk
- Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Marek Stibal
- Department of Ecology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Witold Szczuciński
- Geohazards Research Unit, Institute of Geology, Adam Mickiewicz University, Poznan, Poland
| | - Jun Uetake
- Field Research Center for Northern Biosphere, Hokkaido University, Sapporo, Japan
| | - Łukasz Wejnerowski
- Department of Hydrobiology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Jacob C Yde
- Department of Environmental Sciences, Western Norway University of Applied Sciences, Sogndal, Norway
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Krzysztof Zawierucha
- Department of Animal Taxonomy and Ecology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
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13
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Chen Y, Liu Y, Liu K, Ji M, Li Y. Snowstorm Enhanced the Deterministic Processes of the Microbial Community in Cryoconite at Laohugou Glacier, Tibetan Plateau. Front Microbiol 2022; 12:784273. [PMID: 35154026 PMCID: PMC8829297 DOI: 10.3389/fmicb.2021.784273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/27/2021] [Indexed: 12/05/2022] Open
Abstract
Cryoconites harbor diverse microbial communities and are the metabolic hotspot in the glacial ecosystem. Glacial ecosystems are subjected to frequent climate disturbances such as precipitation (snowing), but little is known about whether microbial communities in cryoconite can maintain stability under such disturbance. Here, we investigated the bacterial community in supraglacial cryoconite before and after a snowfall event on the Laohugou Glacier (Tibetan Plateau), based on Illumina MiSeq sequencing of the 16S rRNA gene. Our results showed that the diversity of the microbial community significantly decreased, and the structure of the microbial community changed significantly after the disturbance of snowfall. This was partly due to the relative abundance increased of cold-tolerant bacterial taxa, which turned from rare into abundant sub-communities. After snowfall disturbance, the contribution of the deterministic process increased from 38 to 67%, which is likely due to the enhancement of environmental filtering caused by nitrogen limitation. These findings enhanced our understanding of the distribution patterns and assembly mechanisms of cryoconite bacterial communities on mountain glaciers.
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Affiliation(s)
- Yuying Chen
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Keshao Liu
- State Key Laboratory of Tibetan Plateau Earth System, Resources and Environment (TPESRE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, China
| | - Yang Li
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, China
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14
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Millar JL, Bagshaw EA, Edwards A, Poniecka EA, Jungblut AD. Polar Cryoconite Associated Microbiota Is Dominated by Hemispheric Specialist Genera. Front Microbiol 2021; 12:738451. [PMID: 34899626 PMCID: PMC8660574 DOI: 10.3389/fmicb.2021.738451] [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: 07/08/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Cryoconite holes, supraglacial depressions containing water and microbe-mineral aggregates, are known to be hotspots of microbial diversity on glacial surfaces. Cryoconite holes form in a variety of locations and conditions, which impacts both their structure and the community that inhabits them. Using high-throughput 16S and 18S rRNA gene sequencing, we have investigated the communities of a wide range of cryoconite holes from 15 locations across the Arctic and Antarctic. Around 24 bacterial and 11 eukaryotic first-rank phyla were observed in total. The various biotic niches (grazer, predator, photoautotroph, and chemotroph), are filled in every location. Significantly, there is a clear divide between the bacterial and microalgal communities of the Arctic and that of the Antarctic. We were able to determine the groups contributing to this difference and the family and genus level. Both polar regions contain a "core group" of bacteria that are present in the majority of cryoconite holes and each contribute >1% of total amplicon sequence variant (ASV) abundance. Whilst both groups contain Microbacteriaceae, the remaining members are specific to the core group of each polar region. Additionally, the microalgal communities of Arctic cryoconite holes are dominated by Chlamydomonas whereas the Antarctic cryoconite holes are dominated by Pleurastrum. Therefore cryoconite holes may be a global feature of glacier landscapes, but they are inhabited by regionally distinct microbial communities. Our results are consistent with the notion that cryoconite microbiomes are adapted to differing conditions within the cryosphere.
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Affiliation(s)
- Jasmin L Millar
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom.,Department of Life Sciences, The Natural History Museum, London, United Kingdom
| | - Elizabeth A Bagshaw
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, United Kingdom
| | - Ewa A Poniecka
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, United Kingdom
| | - Anne D Jungblut
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
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15
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Hu W, Schmidt SK, Sommers P, Darcy JL, Porazinska DL. Multiple‐trophic patterns of primary succession following retreat of a high‐elevation glacier. Ecosphere 2021. [DOI: 10.1002/ecs2.3400] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- Weiming Hu
- Department of Entomology and Nematology University of Florida Gainesville Florida32611USA
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| | - Pacifica Sommers
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
| | - John L. Darcy
- Anschutz Medical Campus University of Colorado, Denver Denver Colorado80204USA
| | - Dorota L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville Florida32611USA
- Department of Ecology and Evolutionary Biology University of Colorado, Boulder Boulder Colorado80309USA
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16
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Howell L, LaRue M, Flanagan SP. Environmental DNA as a tool for monitoring Antarctic vertebrates. NEW ZEALAND JOURNAL OF ZOOLOGY 2021. [DOI: 10.1080/03014223.2021.1900299] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lucy Howell
- Gateway Antarctica, School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | - Michelle LaRue
- Gateway Antarctica, School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
- School of Earth and Environment, University of Canterbury, Christchurch, New Zealand
| | - Sarah P. Flanagan
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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17
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16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02843-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.
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18
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Greco C, Andersen DT, Hawes I, Bowles AMC, Yallop ML, Barker G, Jungblut AD. Microbial Diversity of Pinnacle and Conical Microbial Mats in the Perennially Ice-Covered Lake Untersee, East Antarctica. Front Microbiol 2020; 11:607251. [PMID: 33362751 PMCID: PMC7759091 DOI: 10.3389/fmicb.2020.607251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 11/20/2020] [Indexed: 01/04/2023] Open
Abstract
Antarctic perennially ice-covered lakes provide a stable low-disturbance environment where complex microbially mediated structures can grow. Lake Untersee, an ultra-oligotrophic lake in East Antarctica, has the lake floor covered in benthic microbial mat communities, where laminated organo-sedimentary structures form with three distinct, sympatric morphologies: small, elongated cuspate pinnacles, large complex cones and flat mats. We examined the diversity of prokaryotes and eukaryotes in pinnacles, cones and flat microbial mats using high-throughput sequencing of 16S and 18S rRNA genes and assessed how microbial composition may underpin the formation of these distinct macroscopic mat morphologies under the same environmental conditions. Our analysis identified distinct clustering of microbial communities according to mat morphology. The prokaryotic communities were dominated by Cyanobacteria, Proteobacteria, Verrucomicrobia, Planctomycetes, and Actinobacteria. While filamentous Tychonema cyanobacteria were common in all mat types, Leptolyngbya showed an increased relative abundance in the pinnacle structures only. Our study provides the first report of the eukaryotic community structure of Lake Untersee benthic mats, which was dominated by Ciliophora, Chlorophyta, Fungi, Cercozoa, and Discicristata. The eukaryote richness was lower than for prokaryote assemblages and no distinct clustering was observed between mat morphologies. These findings suggest that cyanobacterial assemblages and potentially other bacteria and eukaryotes may influence structure morphogenesis, allowing distinct structures to form across a small spatial scale.
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Affiliation(s)
- Carla Greco
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, CA, United States
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | | | - Marian L Yallop
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Anne D Jungblut
- Department of Life Sciences, Natural History Museum, London, United Kingdom
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19
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Sommers P, Porazinska DL, Darcy JL, Gendron EMS, Vimercati L, Solon AJ, Schmidt SK. Microbial Species-Area Relationships in Antarctic Cryoconite Holes Depend on Productivity. Microorganisms 2020; 8:E1747. [PMID: 33171740 PMCID: PMC7694949 DOI: 10.3390/microorganisms8111747] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 01/04/2023] Open
Abstract
The island species-area relationship (ISAR) is a positive association between the number of species and the area of an isolated, island-like habitat. ISARs are ubiquitous across domains of life, yet the processes generating ISARs remain poorly understood, particularly for microbes. Larger and more productive islands are hypothesized to have more species because they support larger populations of each species and thus reduce the probability of stochastic extinctions in small population sizes. Here, we disentangled the effects of "island" size and productivity on the ISAR of Antarctic cryoconite holes. We compared the species richness of bacteria and microbial eukaryotes on two glaciers that differ in their productivity across varying hole sizes. We found that cryoconite holes on the more productive Canada Glacier gained more species with increasing hole area than holes on the less productive Taylor Glacier. Within each glacier, neither productivity nor community evenness explained additional variation in the ISAR. Our results are, therefore, consistent with productivity shaping microbial ISARs at broad scales. More comparisons of microbial ISARs across environments with limited confounding factors, such as cryoconite holes, and experimental manipulations within these systems will further contribute to our understanding of the processes shaping microbial biogeography.
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Affiliation(s)
- Pacifica Sommers
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Dorota L. Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA; (D.L.P.); (E.M.S.G.)
| | - John L. Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA;
| | - Eli M. S. Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL 32611, USA; (D.L.P.); (E.M.S.G.)
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Adam J. Solon
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
| | - Steven K. Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA; (L.V.); (A.J.S.); (S.K.S.)
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20
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Zawierucha K, Porazinska DL, Ficetola GF, Ambrosini R, Baccolo G, Buda J, Ceballos JL, Devetter M, Dial R, Franzetti A, Fuglewicz U, Gielly L, Łokas E, Janko K, Novotna Jaromerska T, Kościński A, Kozłowska A, Ono M, Parnikoza I, Pittino F, Poniecka E, Sommers P, Schmidt SK, Shain D, Sikorska S, Uetake J, Takeuchi N. A hole in the nematosphere: tardigrades and rotifers dominate the cryoconite hole environment, whereas nematodes are missing. J Zool (1987) 2020. [DOI: 10.1111/jzo.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- K. Zawierucha
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - D. L. Porazinska
- Department of Entomology and Nematology University of Florida Gainesville FL USA
| | - G. F. Ficetola
- Department of Environmental Science and Policy University of Milan Milan Italy
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - R. Ambrosini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - G. Baccolo
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - J. Buda
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. L. Ceballos
- Institute of Hydrology, Meteorology and Environmental Studies IDEAM Bogota' Colombia
| | - M. Devetter
- Institute of soil Biology Biology Centre CAS České Budějovice Czech Republic
- Centre for Polar Ecology Faculty of Science University of South Bohemia České Budějovice Czech Republic
| | - R. Dial
- Institute of Culture and the Environment Alaska Pacific University Anchorage AK USA
| | - A. Franzetti
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | | | - L. Gielly
- Laboratoire d'Ecologie Alpine University Grenoble Alpes Univ. Savoie Mont Blanc CNRS LECA Grenoble France
| | - E. Łokas
- Department of Mass Spectroscopy Institute of Nuclear Physics Polish Academy of Sciences Kraków Poland
| | - K. Janko
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Libechov Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | | | - A. Kozłowska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - M. Ono
- Graduate School of Science and Engineering Chiba University Chiba Japan
| | - I. Parnikoza
- State Institution National Antarctic Center of Ministry of Education and Science of Ukraine Kyiv Ukraine
- Institute of Molecular Biology and Genetics National Academy of Sciences of Ukraine Kyiv Ukraine
| | - F. Pittino
- Earth and Environmental Sciences Department University of Milano‐Bicocca Milan Italy
| | - E. Poniecka
- School of Earth and Ocean Sciences Cardiff University Cardiff UK
| | - P. Sommers
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - S. K. Schmidt
- Ecology and Evolutionary Biology Department University of Colorado Boulder CO USA
| | - D. Shain
- Biology Department Rutgers, The State University of New Jersey Camden NJ USA
| | - S. Sikorska
- Department of Animal Taxonomy and Ecology Adam Mickiewicz University Poznań Poland
| | - J. Uetake
- The Arctic Environment Research Center National Institute of Polar Research Tachikawa Japan
| | - N. Takeuchi
- Department of Earth Sciences Graduate School of Science Chiba University Chiba Japan
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21
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Bellas CM, Schroeder DC, Edwards A, Barker G, Anesio AM. Flexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems. Nat Commun 2020; 11:4403. [PMID: 32879312 PMCID: PMC7468147 DOI: 10.1038/s41467-020-18236-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/10/2020] [Indexed: 12/20/2022] Open
Abstract
Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage. Bacteriophages and their hosts are involved in a constant evolutionary arms race that should lead to divergence between phage genes over time. Here, the authors recruit metagenomic reads to virus reference genomes and genome fragments in samples from cryoconite holes and show that phages with near-identical core genomes maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants.
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Affiliation(s)
- Christopher M Bellas
- Department of Ecology, Lake and Glacier Ecology, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, 1333 Gortner Avenue, St. Paul, MN, 55108, USA.,School of Biological Sciences, University of Reading, Reading, UK
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EE, UK
| | - Gary Barker
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| | - Alexandre M Anesio
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
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22
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Trout-Haney JV, Heindel RC, Virginia RA. Picocyanobacterial cells in near-surface air above terrestrial and freshwater substrates in Greenland and Antarctica. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:296-305. [PMID: 32134187 DOI: 10.1111/1758-2229.12832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/26/2020] [Accepted: 03/01/2020] [Indexed: 06/10/2023]
Abstract
Bioaerosols are an important component of the total atmospheric aerosol load, with implications for human health, climate feedbacks and the distribution and dispersal of microbial taxa. Bioaerosols are sourced from marine, freshwater and terrestrial surfaces, with different mechanisms potentially responsible for releasing biological particles from these substrates. Little is known about the production of freshwater and terrestrial bioaerosols in polar regions. We used portable collection devices to test for the presence of picocyanobacterial aerosols above freshwater and soil substrates in the southwestern Greenland tundra and the McMurdo Dry Valleys of Antarctica. We show that picocyanobacterial cells are present in the near-surface air at concentrations ranging from 2,431 to 28,355 cells m-3 of air, with no significant differences among substrates or between polar regions. Our concentrations are lower than those measured using the same methods in temperate ecosystems. We suggest that aerosolization is an important process linking terrestrial and aquatic ecosystems in these polar environments, and that future work is needed to explore aerosolization mechanisms and taxon-specific aerosolization rates. Our study is a first step toward understanding the production of bioaerosols in extreme environments dominated by microbial life.
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Affiliation(s)
- Jessica V Trout-Haney
- Department of Biological Sciences, Life Sciences Center, Dartmouth College, Hanover, NH, 03755
| | - Ruth C Heindel
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO
| | - Ross A Virginia
- Environmental Studies Program and Institute of Arctic Studies, Dartmouth College, Hanover, NH, 03755
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23
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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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24
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Sommers P, Fontenele RS, Kringen T, Kraberger S, Porazinska DL, Darcy JL, Schmidt SK, Varsani A. Single-Stranded DNA Viruses in Antarctic Cryoconite Holes. Viruses 2019; 11:E1022. [PMID: 31689942 PMCID: PMC6893807 DOI: 10.3390/v11111022] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/28/2022] Open
Abstract
Antarctic cryoconite holes, or small melt-holes in the surfaces of glaciers, create habitable oases for isolated microbial communities with tightly linked microbial population structures. Viruses may influence the dynamics of polar microbial communities, but the viromes of the Antarctic cryoconite holes have yet to be characterized. We characterize single-stranded DNA (ssDNA) viruses from three cryoconite holes in the Taylor Valley, Antarctica, using metagenomics. Half of the assembled metagenomes cluster with those in the viral family Microviridae (n = 7), and the rest with unclassified circular replication associated protein (Rep)-encoding single-stranded (CRESS) DNA viruses (n = 7). An additional 18 virus-like circular molecules encoding either a Rep, a capsid protein gene, or other unidentified but viral-like open reading frames were identified. The samples from which the genomes were identified show a strong gradient in microbial diversity and abundances, and the number of viral genomes detected in each sample mirror that gradient. Additionally, one of the CRESS genomes assembled here shares ~90% genome-wide pairwise identity with a virus identified from a freshwater pond on the McMurdo Ice Shelf (Antarctica). Otherwise, the similarity of these viruses to those previously identified is relatively low. Together, these patterns are consistent with the presence of a unique regional virome present in fresh water host populations of the McMurdo Dry Valley region.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Tayele Kringen
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
| | - Dorota L Porazinska
- Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, USA.
| | - John L Darcy
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, USA.
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85287-5001, USA.
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Observatory, Cape Town 7701, South Africa.
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25
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Sommers P, Porazinska DL, Darcy JL, Zamora F, Fountain AG, Schmidt SK. Experimental cryoconite holes as mesocosms for studying community ecology. Polar Biol 2019. [DOI: 10.1007/s00300-019-02572-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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26
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Lutz S, Ziolkowski LA, Benning LG. The Biodiversity and Geochemistry of Cryoconite Holes in Queen Maud Land, East Antarctica. Microorganisms 2019; 7:microorganisms7060160. [PMID: 31159414 PMCID: PMC6616603 DOI: 10.3390/microorganisms7060160] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 01/27/2023] Open
Abstract
Cryoconite holes are oases of microbial diversity on ice surfaces. In contrast to the Arctic, where during the summer most cryoconite holes are ‘open’, in Continental Antarctica they are most often ‘lidded’ or completely frozen year-round. Thus, they represent ideal systems for the study of microbial community assemblies as well as carbon accumulation, since individual cryoconite holes can be isolated from external inputs for years. Here, we use high-throughput sequencing of the 16S and 18S rRNA genes to describe the bacterial and eukaryotic community compositions in cryoconite holes and surrounding lake, snow, soil and rock samples in Queen Maud Land. We cross correlate our findings with a broad range of geochemical data including for the first time 13C and 14C analyses of Antarctic cryoconites. We show that the geographic location has a larger effect on the distribution of the bacterial community compared to the eukaryotic community. Cryoconite holes are distinct from the local soils in both 13C and 14C and their isotopic composition is different from similar samples from the Arctic. Carbon contents were generally low (≤0.2%) and older (6–10 ky) than the surrounding soils, suggesting that the cryoconite holes are much more isolated from the atmosphere than the soils.
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Affiliation(s)
- Stefanie Lutz
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany.
| | - Lori A Ziolkowski
- University of South Carolina, School of the Earth, Ocean and Environment, 701 Sumter St., EWS 617, Columbia, SC 29208, USA.
| | - Liane G Benning
- GFZ German Research Centre for Geosciences, Telegrafenberg, 14473 Potsdam, Germany.
- Department of Earth Sciences, Free University of Berlin, 12249 Berlin, Germany.
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27
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Sommers P, Darcy JL, Porazinska DL, Gendron EMS, Fountain AG, Zamora F, Vincent K, Cawley KM, Solon AJ, Vimercati L, Ryder J, Schmidt SK. Comparison of Microbial Communities in the Sediments and Water Columns of Frozen Cryoconite Holes in the McMurdo Dry Valleys, Antarctica. Front Microbiol 2019; 10:65. [PMID: 30778338 PMCID: PMC6369369 DOI: 10.3389/fmicb.2019.00065] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/15/2019] [Indexed: 11/13/2022] Open
Abstract
Although cryoconite holes, sediment-filled melt holes on glacier surfaces, appear small and homogenous, their microbial inhabitants may be spatially partitioned. This partitioning could be particularly important for maintaining biodiversity in holes that remain isolated for many years, such as in Antarctica. We hypothesized that cryoconite holes with greater species richness and biomass should exhibit greater partitioning between the sediments and water, promoting greater biodiversity through spatial niche partitioning. We tested this hypothesis by sampling frozen cryoconite holes along a gradient of biomass and biodiversity in the Taylor Valley, Antarctica, where ice-lidded cryoconite holes are a ubiquitous feature of glaciers. We extracted DNA and chlorophyll a from the sediments and water of these samples to describe biodiversity and quantify proxies for biomass. Contrary to our expectation, we found that cryoconite holes with greater richness and biomass showed less partitioning of phylotypes by the sediments versus the water, perhaps indicating that the probability of sediment microbes being mixed into the water is higher from richer sediments. Another explanation may be that organisms from the water were compressed by freezing down to the sediment layer, leaving primarily relic DNA of dead cells to be detected higher in the frozen water. Further evidence of this explanation is that the dominant sequences unique to water closely matched organisms that do not live in cryoconite holes or the Dry Valleys (e.g., vertebrates); so this cryptic biodiversity could represent unknown microbial animals or DNA from atmospheric deposition of dead biomass in the otherwise low-biomass water. Although we cannot rule out spatial niche partitioning occurring at finer scales or in melted cryoconite holes, we found no evidence of partitioning between the sediments and water in frozen holes. Future work should include more sampling of cryoconite holes at a finer spatial scale, and characterizing the communities of the sediments and water when cryoconite holes are melted and active.
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Affiliation(s)
- Pacifica Sommers
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - John L Darcy
- Department of Botany, University of Hawai'i Mānoa, Honolulu, HI, United States
| | - Dorota L Porazinska
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States.,Department of Entomology and Nematology, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Eli M S Gendron
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Andrew G Fountain
- Geology Department, Portland State University, Portland, OR, United States
| | - Felix Zamora
- Geology Department, Portland State University, Portland, OR, United States
| | - Kim Vincent
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Kaelin M Cawley
- National Ecological Observatory Network Operated by Battelle, Boulder, CO, United States.,Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, CO, United States
| | - Adam J Solon
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Lara Vimercati
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Jenna Ryder
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
| | - Steven K Schmidt
- Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO, United States
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28
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Bowman JS. Identification of Microbial Dark Matter in Antarctic Environments. Front Microbiol 2018; 9:3165. [PMID: 30619224 PMCID: PMC6305705 DOI: 10.3389/fmicb.2018.03165] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022] Open
Abstract
Numerous studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI's Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumina platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6%. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2%, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0% for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.
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Affiliation(s)
- Jeff S. Bowman
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, United States
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29
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Darcy JL, Gendron EMS, Sommers P, Porazinska DL, Schmidt SK. Island Biogeography of Cryoconite Hole Bacteria in Antarctica's Taylor Valley and Around the World. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00180] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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30
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Stibal M, Jacobsen CS, Häggblom MM. Editorial: Polar and Alpine Microbiology. FEMS Microbiol Ecol 2018; 94:5054038. [DOI: 10.1093/femsec/fiy136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/13/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Marek Stibal
- Department of Ecology, Faculty of Science, Charles University, 128 44 Prague, Czechia
| | | | - Max M Häggblom
- Department of Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901-8525, USA
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31
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Koo H, Hakim JA, Morrow CD, Crowley MR, Andersen DT, Bej AK. Metagenomic Analysis of Microbial Community Compositions and Cold-Responsive Stress Genes in Selected Antarctic Lacustrine and Soil Ecosystems. Life (Basel) 2018; 8:life8030029. [PMID: 29997353 PMCID: PMC6161096 DOI: 10.3390/life8030029] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 11/16/2022] Open
Abstract
This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus, Anaeromyxobacter, Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes. Among CIPs, genes necessary for DNA replication, translation initiation, and transcription termination were highly abundant in all metagenomes. However, genes for fatty acid desaturase (FAD) and trehalose synthase (TS) were common in the soil and lake sediment metagenomes. Interestingly, the Lake Untersee water and sediment metagenome samples contained histone-like nucleoid structuring protein (H-NS) and all genes for CIPs. As for the CASPs, high abundances of a wide range of genes for cryo- and osmo-protectants (glutamate, glycine, choline, and betaine) were identified in all metagenomes. However, genes for exopolysaccharide biosynthesis were dominant in Lake Untersee water, sediment, and other soil metagenomes. The results from this study indicate that although diverse microbial communities are present in various metagenomes, they share common cold-responsive stress genes necessary for their survival and sustenance in the extreme Antarctic conditions.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Casey D Morrow
- Department of Cell, Developmental and Integrative Biology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Michael R Crowley
- Department of Genetics, Heflin Center Genomics Core, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, California, CA 94043, USA.
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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