1
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Greco C, Andersen DT, Yallop ML, Barker G, Jungblut AD. Genome-resolved metagenomics reveals diverse taxa and metabolic complexity in Antarctic lake microbial structures. Environ Microbiol 2024; 26:e16663. [PMID: 38881221 DOI: 10.1111/1462-2920.16663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024]
Abstract
Lake Untersee, a lake in Antarctica that is perennially covered with ice, is home to unique microbial structures that are not lithified. We have evaluated the structure of the community and its metabolic potential across the pigmented upper layers and the sediment-enriched deeper layers in these pinnacle and cone-shaped microbial structures using metagenomics. These microbial structures are inhabited by distinct communities. The upper layers of the cone-shaped structures have a higher abundance of the cyanobacterial MAG Microcoleus, while the pinnacle-shaped structures have a higher abundance of Elainellacea MAG. This suggests that cyanobacteria influence the morphologies of the mats. We identified stark contrasts in the composition of the community and its metabolic potential between the upper and lower layers of the mat. The upper layers of the mat, which receive light, have an increased abundance of photosynthetic pathways. In contrast, the lower layer has an increased abundance of heterotrophic pathways. Our results also showed that Lake Untersee is the first Antarctic lake with a substantial presence of ammonia-oxidizing Nitrospiracea and amoA genes. The genomic capacity for recycling biological molecules was prevalent across metagenome-assembled genomes (MAGs) that cover 19 phyla. This highlights the importance of nutrient scavenging in ultra-oligotrophic environments. Overall, our study provides new insights into the formation of microbial structures and the potential metabolic complexity of Antarctic laminated microbial mats. These mats are important environments for biodiversity that drives biogeochemical cycling in polar deserts.
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Affiliation(s)
- Carla Greco
- School of Biological Sciences, University of Bristol, Bristol, UK
- Department of Sciences, Natural History Museum, London, UK
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain View, California, USA
| | - Marian L Yallop
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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2
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Roncero-Ramos B, Savaglia V, Durieu B, Van de Vreken I, Richel A, Wilmotte A. Ecophysiological and genomic approaches to cyanobacterial hardening for restoration. JOURNAL OF PHYCOLOGY 2024; 60:465-482. [PMID: 38373045 DOI: 10.1111/jpy.13436] [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: 09/07/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 02/20/2024]
Abstract
Cyanobacteria inhabit extreme environments, including drylands, providing multiple benefits to the ecosystem. Soil degradation in warm drylands is increasing due to land use intensification. Restoration methods adapted to the extreme stress in drylands are being developed, such as cyanobacteria inoculation to recover biocrusts. For this type of restoration method to be a success, it is crucial to optimize the survival of inoculated cyanobacteria in the field. One strategy is to harden them to be acclimated to stressful conditions after laboratory culturing. Here, we analyzed the genome and ecophysiological response to osmotic desiccation and UVR stresses of an Antarctic cyanobacterium, Stenomitos frigidus ULC029, which is closely related to other cyanobacteria from warm and cold dryland soils. Chlorophyll a concentrations showed that preculturing ULC029 under moderate osmotic stress improved its survival during an assay of desiccation plus rehydration under UVR. Additionally, its sequential exposure to these stress factors increased the production of exopolysaccharides, carotenoids, and scytonemin. Desiccation, but not osmotic stress, increased the concentrations of the osmoprotectants trehalose and sucrose. However, osmotic stress might induce the production of other osmoprotectants, for which the complete pathways were observed in the ULC029 genome. In total, 140 genes known to be involved in stress resistance were annotated. Here, we confirm that the sequential application of moderate osmotic stress and dehydration could improve cyanobacterial hardening for soil restoration by inducing several resistance mechanisms. We provide a high-quality genome of ULC029 and a description of the main resistance mechanisms (i.e., production of exopolysaccharides, osmoprotectants, chlorophyll, and carotenoids; DNA repair; and oxidative stress protection).
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Affiliation(s)
- Beatriz Roncero-Ramos
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - Valentina Savaglia
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
- Laboratory of Protistology & Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Benoit Durieu
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
| | | | - Aurore Richel
- TERRA-Biomass and Green Technologies, University of Liège, Gembloux, Belgium
| | - Annick Wilmotte
- InBios-Molecular Diversity and Ecology of Cyanobacteria, University of Liège, Liege, Belgium
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3
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Lumian J, Sumner DY, Grettenberger CL, Jungblut AD, Irber L, Pierce-Ward NT, Brown CT. Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater. Front Microbiol 2024; 15:1328083. [PMID: 38440141 PMCID: PMC10909832 DOI: 10.3389/fmicb.2024.1328083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones.
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Affiliation(s)
- Jessica Lumian
- Department of Earth and Planetary Sciences, Microbiology Graduate Group, University of California Davis, Davis, CA, United States
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
| | - Christen L. Grettenberger
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
- Department of Environmental Toxicology, University of California Davis, Davis, CA, United States
| | - Anne D. Jungblut
- Department of Science, The Natural History Museum, London, United Kingdom
| | - Luiz Irber
- Population Health and Reproduction, University of California Davis, Davis, CA, United States
| | - N. Tessa Pierce-Ward
- Population Health and Reproduction, University of California Davis, Davis, CA, United States
| | - C. Titus Brown
- Population Health and Reproduction, University of California Davis, Davis, CA, United States
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4
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Lumian J, Grettenberger C, Jungblut AD, Mackey TJ, Hawes I, Alatorre-Acevedo E, Sumner DY. Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock. Front Microbiol 2024; 14:1330602. [PMID: 38282730 PMCID: PMC10812107 DOI: 10.3389/fmicb.2023.1330602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/29/2023] [Indexed: 01/30/2024] Open
Abstract
Cyanobacteria in polar environments face environmental challenges, including cold temperatures and extreme light seasonality with small diurnal variation, which has implications for polar circadian clocks. However, polar cyanobacteria remain underrepresented in available genomic data, and there are limited opportunities to study their genetic adaptations to these challenges. This paper presents four new Antarctic cyanobacteria metagenome-assembled genomes (MAGs) from microbial mats in Lake Vanda in the McMurdo Dry Valleys in Antarctica. The four MAGs were classified as Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, Microcoleus sp. MP8IB2.171, and Leptolyngbyaceae cyanobacterium MP9P1.79. The MAGs contain 2.76 Mbp - 6.07 Mbp, and the bin completion ranges from 74.2-92.57%. Furthermore, the four cyanobacteria MAGs have average nucleotide identities (ANIs) under 90% with each other and under 77% with six existing polar cyanobacteria MAGs and genomes. This suggests that they are novel cyanobacteria and demonstrates that polar cyanobacteria genomes are underrepresented in reference databases and there is continued need for genome sequencing of polar cyanobacteria. Analyses of the four novel and six existing polar cyanobacteria MAGs and genomes demonstrate they have genes coding for various cold tolerance mechanisms and most standard circadian rhythm genes with the Leptolyngbya sp. BulkMat.35 and Leptolyngbyaceae cyanobacterium MP9P1.79 contained kaiB3, a divergent homolog of kaiB.
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Affiliation(s)
- Jessica Lumian
- Department of Earth and Planetary Sciences, Microbiology Graduate Group, University of California Davis, Davis, CA, United States
| | - Christen Grettenberger
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
- Department of Environmental Toxicology, University of California Davis, Davis, CA, United States
| | - Anne D. Jungblut
- Department of Sciences, The Natural History Museum, London, United Kingdom
| | - Tyler J. Mackey
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM, United States
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga, New Zealand
| | - Eduardo Alatorre-Acevedo
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California Davis, Davis, CA, United States
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5
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Kollár J, Kopalová K, Kavan J, Vrbická K, Nývlt D, Nedbalová L, Stibal M, Kohler TJ. Recently formed Antarctic lakes host less diverse benthic bacterial and diatom communities than their older counterparts. FEMS Microbiol Ecol 2023; 99:fiad087. [PMID: 37516444 PMCID: PMC10446143 DOI: 10.1093/femsec/fiad087] [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: 02/03/2023] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 07/31/2023] Open
Abstract
Glacier recession is creating new water bodies in proglacial forelands worldwide, including Antarctica. Yet, it is unknown how microbial communities of recently formed "young" waterbodies (originating decades to a few centuries ago) compare with established "old" counterparts (millennia ago). Here, we compared benthic microbial communities of different lake types on James Ross Island, Antarctic Peninsula, using 16S rDNA metabarcoding and light microscopy to explore bacterial and diatom communities, respectively. We found that the older lakes host significantly more diverse bacterial and diatom communities compared to the young ones. To identify potential mechanisms for these differences, linear models and dbRDA analyses suggested combinations of water temperature, pH, and conductivity to be the most important factors for diversity and community structuring, while differences in geomorphological and hydrological stability, though more difficult to quantify, are likely also influential. These results, along with an indicator species analysis, suggest that physical and chemical constraints associated with individual lakes histories are likely more influential to the assembly of the benthic microbial communities than lake age alone. Collectively, these results improve our understanding of microbial community drivers in Antarctic freshwaters, and help predict how the microbial landscape may shift with future habitat creation within a changing environment.
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Affiliation(s)
- Jan Kollár
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Kateřina Kopalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Jan Kavan
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
- Alfred Jahn Cold Regions Research Centre, University of Wroclaw, pl. Uniwersytecki 1, Wroclaw 50-137, Poland
| | - Kristýna Vrbická
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Daniel Nývlt
- Polar-Geo-Lab, Faculty of Science, Department of Geography, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | - Linda Nedbalová
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Marek Stibal
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University, Viničná 7, Prague 2, CZ-12844, Czech Republic
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Wada T, Kudoh S, Koyama H, Iakovenko N, Elster J, Kvíderová J, Otani M, Shimada S, Imura S. Abundance and biomass of Bdelloid rotifers in the microbial mats from East Antarctica: The ecological relations between microscopic phototrophs and invertebrates. Ecol Res 2022. [DOI: 10.1111/1440-1703.12368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Tomotake Wada
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
| | - Sakae Kudoh
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
- National Institute of Polar Research Research Organization of Information and Systems Tokyo Japan
| | - Hiroshi Koyama
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
| | - Nataliia Iakovenko
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences Czech University of Life Sciences Prague Prague Czechia
- Department of Biology and Ecology, Faculty of Science University of Ostrava Ostrava Czechia
- Department of Invertebrate Fauna and Systematics Schmalhausen Institute of Zoology NAS of Ukraine Kiev Ukraine
- Laboratory of Fish Genetics Institute of Animal Physiology and Genetics AS ČR Liběchov Czech Republic
| | - Josef Elster
- Institute of Botany Academy of Sciences of the Czech Republic Třeboň Czechia
- Centre for Polar Ecology University of South Bohemia České Budějovice Czechia
| | - Jana Kvíderová
- Institute of Botany Academy of Sciences of the Czech Republic Třeboň Czechia
- Centre for Polar Ecology University of South Bohemia České Budějovice Czechia
| | | | - Sho Shimada
- Department of Microbiology and Infectious Diseases Toho University School of Medicine Tokyo Japan
- Department of Respiratory Medicine Tokyo Medical and Dental University Tokyo Japan
| | - Satoshi Imura
- Department of Polar Science SOKENDAI (The Graduate University for Advanced Studies) Tokyo Japan
- National Institute of Polar Research Research Organization of Information and Systems Tokyo Japan
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7
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LIZIERI CLAUDINEIA, SCHAEFER CARLOSERNESTOG, HAWES IAN. Morphological diversity of benthic cyanobacterial assemblages in meltwater ponds along environmental gradients in the McMurdo Sound region, Antarctica. AN ACAD BRAS CIENC 2022; 94:e20210814. [DOI: 10.1590/0001-3765202220210814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/17/2021] [Indexed: 11/22/2022] Open
Affiliation(s)
- CLAUDINEIA LIZIERI
- Universidade Federal de Viçosa, Brazil; Universidade Federal de Viçosa, Brazil
| | | | - IAN HAWES
- University of Canterbury, New Zealand; University of Waikato, New Zealand
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8
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Park C, Takeuchi N. Unmasking photogranulation in decreasing glacial albedo and net autotrophic wastewater treatment. Environ Microbiol 2021; 23:6391-6404. [PMID: 34545673 PMCID: PMC9292683 DOI: 10.1111/1462-2920.15780] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 11/29/2022]
Abstract
In both natural and built environments, microbes on occasions manifest in spherical aggregates instead of substratum‐affixed biofilms. These microbial aggregates are conventionally referred to as granules. Cryoconites are mineral rich granules that appear on glacier surfaces and are linked with expanding surface darkening, thus decreasing albedo, and enhanced melt. The oxygenic photogranules (OPGs) are organic rich granules that grow in wastewater, which enables wastewater treatment with photosynthetically produced oxygen and which presents potential for net autotrophic wastewater treatment in a compact system. Despite obvious differences inherent in the two, cryoconite and OPG pose striking resemblance. In both, the order Oscillatoriales in Cyanobacteria envelope inner materials and develop dense spheroidal aggregates. We explore the mechanism of photogranulation on account of high similarity between cryoconites and OPGs. We contend that there is no universal external cause for photogranulation. However, cryoconites and OPGs, as well as their intravariations, which are all under different stress fields, are the outcome of universal physiological processes of the Oscillatoriales interfacing with goldilocks interactions of stresses. Finding the rules of photogranulation may enhance engineering of glacier and wastewater systems to manipulate their ecosystem impacts.
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Affiliation(s)
- Chul Park
- Department of Civil and Environmental Engineering, University of Massachusetts Amherst, Amherst, Massachusetts, 01003, USA
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, 263-8522, Japan
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9
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Babich O, Shevchenko M, Ivanova S, Pavsky V, Zimina M, Noskova S, Anohova V, Chupakhin E, Sukhikh S. Antimicrobial Potential of Microorganisms Isolated from the Bottom Sediments of Lake Baikal. Antibiotics (Basel) 2021; 10:927. [PMID: 34438977 PMCID: PMC8388859 DOI: 10.3390/antibiotics10080927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 01/18/2023] Open
Abstract
Extremophilic microorganisms attract researchers by their unique characteristics, primarily antagonistic ones, acquired in the process of survival in extreme natural conditions. The antimicrobial potential of the metabolites of these microorganisms is quite broad, from the food industry to therapeutic drugs. Microbial mats of Lake Baikal are a source of unique and diverse microorganisms. The study aimed to evaluate the antimicrobial activity of bacterial strains isolated from the bottom sediments of the lake. Using heterotrophic growth conditions, seven bacterial strains were isolated from samples collected in several coastal zones of Lake Baikal. Thisstudy identified both widespread strains of the genera Pseudomonas and Bacillus and rare genera Micrococcus and Acinetobacterrepresentatives. Metabolites of five strains were found to have a broad spectrum of antimicrobial activity. Four large fractions of metabolites of the isolated strains wereidentified. Two peptides of the isolated fractions of metabolites (one is produced by microorganisms of all five isolated strains, another-only by Pseudomonas putida) are low molecular weight oligopeptides. These peptides were proved to be bacteriocins.
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Affiliation(s)
- Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
| | - Margarita Shevchenko
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
| | - Svetlana Ivanova
- Natural Nutraceutical Biotesting Laboratory, Kemerovo State University, Krasnaya Street 6, 650043 Kemerovo, Russia
- Department of General Mathematics and Informatics, Kemerovo State University, Krasnaya Street, 6, 650043 Kemerovo, Russia;
| | - Valery Pavsky
- Department of General Mathematics and Informatics, Kemerovo State University, Krasnaya Street, 6, 650043 Kemerovo, Russia;
| | - Maria Zimina
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
| | - Svetlana Noskova
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
| | - Veronika Anohova
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
| | - Evgeny Chupakhin
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, 236016 Kaliningrad, Russia; (O.B.); (M.S.); (M.Z.); (S.N.); (V.A.); (E.C.); (S.S.)
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10
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Ramoneda J, Hawes I, Pascual-García A, J Mackey T, Y Sumner D, D Jungblut A. Importance of environmental factors over habitat connectivity in shaping bacterial communities in microbial mats and bacterioplankton in an Antarctic freshwater system. FEMS Microbiol Ecol 2021; 97:6174672. [PMID: 33729491 DOI: 10.1093/femsec/fiab044] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/14/2021] [Indexed: 11/14/2022] Open
Abstract
Freshwater ecosystems are considered hotspots of biodiversity in Antarctic polar deserts. Anticipated warming is expected to change the hydrology of these systems due to increased meltwater and reduction of ice cover, with implications for environmental conditions and physical connectivity between habitats. Using 16S rRNA gene sequencing, we evaluated microbial mat and planktonic communities within a connected freshwater system in the McMurdo Wright Valley, Antarctica, to determine the roles of connectivity and habitat conditions in controlling microbial assemblage composition. We examined communities from glacial Lake Brownworth, the perennially ice-covered Lake Vanda and the Onyx River, which connects the two. In Lake Vanda, we found distinct microbial assemblages occupying sub-habitats at different lake depths, while the communities from Lake Brownworth and Onyx River were structurally similar. Despite the higher physical connectivity and dispersal opportunities between bacterial communities in the shallow parts of the system, environmental abiotic conditions dominated over dispersal in driving community structure. Functional metabolic pathway predictions suggested differences in the functional gene potential between the microbial mat communities located in shallower and deeper water depths. The findings suggest that increasing temperatures and meltwater due to future climate change will affect bacterial diversity and functioning in Antarctic freshwater ecosystems.
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Affiliation(s)
- Josep Ramoneda
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Tauranga 3110, New Zealand
| | - Alberto Pascual-García
- Theoretical Biology, Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich 8006, Switzerland
| | - Tyler J Mackey
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95618, USA
| | - Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
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11
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Hawes I, Howard-Williams C, Gilbert N, Joy K. Towards an Environmental Classification of Lentic Aquatic Ecosystems in the McMurdo Dry Valleys, Antarctica. ENVIRONMENTAL MANAGEMENT 2021; 67:600-622. [PMID: 33559688 DOI: 10.1007/s00267-021-01438-1] [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: 12/03/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
The McMurdo Dry Valleys are the largest single ice-free area in Antarctica, and of considerable scientific and conservation value as an extreme polar desert. This is recognised through the McMurdo Dry Valleys Antarctic Specially Managed Area (ASMA), where management's goals focus on protection of its unique features, while facilitating science access. Using a mix of remote sensing and existing cartography, we have identified over 6000 lakes and ponds in the ASMA. This study develops a classification of those aquatic ecosystems to provide a framework for management. It uses a limited top-down, hierarchical classification to define 13 class separations based on physical attributes that could largely be ascribed from existing databases or remotely sensed information. The first hierarchical level was based on landscape position, separating coastal kettle holes (reflecting recent glacial history), from other "topographic" water bodies. The second level was based on endorheic vs exorheic drainage, the third on mid-summer ice condition (no-ice cap; ice capped; frozen to base) and the fourth on source of inflow (glacial or non-glacial). Kettles were sub-classed by mid-summer ice only. Classes were tested against a set of field observations and an expert workshop validation process considered management implications for the ASMA. This study shows how the classification assists our understanding of Dry Valley landscapes and addresses management issues faced by researchers, environmental managers and policy makers. The approach to classification, rather than the detailed classes that may be specific to the Dry Valleys, has potential for wider use in other polar landscapes.
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Affiliation(s)
- Ian Hawes
- Coastal Marine Field Station, University of Waikato, 58 Cross Road, Sulphur Point, Tauranga, 3110, New Zealand.
| | - Clive Howard-Williams
- National Institute of Water and Atmospheric Research, Lt Box 8602, Christchurch, New Zealand
| | - Neil Gilbert
- Constantia Consulting Ltd, 310 Papanui Road, Christchurch, 8052, New Zealand
| | - Kurt Joy
- Department of Biological Science, University of Waikato, Hamilton, New Zealand
- Orbica Ltd, 128 Litchfield St., Christchurch, 8011, New Zealand
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12
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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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13
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A phylogenetically novel cyanobacterium most closely related to Gloeobacter. ISME JOURNAL 2020; 14:2142-2152. [PMID: 32424249 PMCID: PMC7368068 DOI: 10.1038/s41396-020-0668-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/09/2020] [Accepted: 04/24/2020] [Indexed: 01/01/2023]
Abstract
Clues to the evolutionary steps producing innovations in oxygenic photosynthesis may be preserved in the genomes of organisms phylogenetically placed between non-photosynthetic Vampirovibrionia (formerly Melainabacteria) and the thylakoid-containing Cyanobacteria. However, only two species with published genomes are known to occupy this phylogenetic space, both within the genus Gloeobacter. Here, we describe nearly complete, metagenome-assembled genomes (MAGs) of an uncultured organism phylogenetically placed near Gloeobacter, for which we propose the name Candidatus Aurora vandensis {Au’ro.ra. L. fem. n. aurora, the goddess of the dawn in Roman mythology; van.de’nsis. N.L. fem. adj. vandensis of Lake Vanda, Antarctica}. The MAG of A. vandensis contains homologs of most genes necessary for oxygenic photosynthesis including key reaction center proteins. Many accessory subunits associated with the photosystems in other species either are missing from the MAG or are poorly conserved. The MAG also lacks homologs of genes associated with the pigments phycocyanoerethrin, phycoeretherin and several structural parts of the phycobilisome. Additional characterization of this organism is expected to inform models of the evolution of oxygenic photosynthesis.
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14
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Dillon ML, Hawes I, Jungblut AD, Mackey TJ, Eisen JA, Doran PT, Sumner DY. Environmental control on the distribution of metabolic strategies of benthic microbial mats in Lake Fryxell, Antarctica. PLoS One 2020; 15:e0231053. [PMID: 32282803 PMCID: PMC7153904 DOI: 10.1371/journal.pone.0231053] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/15/2020] [Indexed: 11/19/2022] Open
Abstract
Ecological theories posit that heterogeneity in environmental conditions greatly affects community structure and function. However, the degree to which ecological theory developed using plant- and animal-dominated systems applies to microbiomes is unclear. Investigating the metabolic strategies found in microbiomes are particularly informative for testing the universality of ecological theories because microorganisms have far wider metabolic capacity than plants and animals. We used metagenomic analyses to explore the relationships between the energy and physicochemical gradients in Lake Fryxell and the metabolic capacity of its benthic microbiome. Statistical analysis of the relative abundance of metabolic marker genes and gene family diversity shows that oxygenic photosynthesis, carbon fixation, and flavin-based electron bifurcation differentiate mats growing in different environmental conditions. The pattern of gene family diversity points to the likely importance of temporal environmental heterogeneity in addition to resource gradients. Overall, we found that the environmental heterogeneity of photosynthetically active radiation (PAR) and oxygen concentration ([O2]) in Lake Fryxell provide the framework by which metabolic diversity and composition of the community is structured, in accordance with its phylogenetic structure. The organization of the resulting microbial ecosystems are consistent with the maximum power principle and the species sorting model.
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Affiliation(s)
- Megan L. Dillon
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States of America
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Hamilton, Waikato, New Zealand
| | - Anne D. Jungblut
- Life Sciences Department, Natural History Museum, London, England, United Kingdom
| | - Tyler J. Mackey
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Jonathan A. Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, California, United States of America
| | - Peter T. Doran
- Geology and Geophysics Department, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California, United States of America
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15
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Chrismas NAM, Williamson CJ, Yallop ML, Anesio AM, Sánchez-Baracaldo P. Photoecology of the Antarctic cyanobacterium Leptolyngbya sp. BC1307 brought to light through community analysis, comparative genomics and in vitro photophysiology. Mol Ecol 2019; 27:5279-5293. [PMID: 30565777 DOI: 10.1111/mec.14953] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are important photoautotrophs in extreme environments such as the McMurdo Dry Valleys, Antarctica. Terrestrial Antarctic cyanobacteria experience constant darkness during the winter and constant light during the summer which influences the ability of these organisms to fix carbon over the course of an annual cycle. Here, we present a unique approach combining community structure, genomic and photophysiological analyses to understand adaptation to Antarctic light regimes in the cyanobacterium Leptolyngbya sp. BC1307. We show that Leptolyngbya sp. BC1307 belongs to a clade of cyanobacteria that inhabits near-surface environments in the McMurdo Dry Valleys. Genomic analyses reveal that, unlike close relatives, Leptolyngbya sp. BC1307 lacks the genes necessary for production of the pigment phycoerythrin and is incapable of complimentary chromatic acclimation, while containing several genes responsible for known photoprotective pigments. Photophysiology experiments confirmed Leptolyngbya sp. BC1307 to be tolerant of short-term exposure to high levels of photosynthetically active radiation, while sustained exposure reduced its capacity for photoprotection. As such, Leptolyngbya sp. BC1307 likely exploits low-light microenvironments within cyanobacterial mats in the McMurdo Dry Valleys.
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Affiliation(s)
- Nathan A M Chrismas
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, UK.,School of Geographical Sciences, University of Bristol, Bristol, UK
| | - Christopher J Williamson
- School of Geographical Sciences, University of Bristol, Bristol, UK.,School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Marian L Yallop
- School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, UK
| | - Alexandre M Anesio
- School of Geographical Sciences, University of Bristol, Bristol, UK.,Department of Environmental Sciences, Aarhus University, Roskilde, Denmark
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16
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Mania I, Gorra R, Colombo N, Freppaz M, Martin M, Anesio AM. Prokaryotic Diversity and Distribution in Different Habitats of an Alpine Rock Glacier-Pond System. MICROBIAL ECOLOGY 2019; 78:70-84. [PMID: 30317429 DOI: 10.1007/s00248-018-1272-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 10/04/2018] [Indexed: 06/08/2023]
Abstract
Rock glaciers (RG) are assumed to influence the biogeochemistry of downstream ecosystems because of the high ratio of rock:water in those systems, but no studies have considered the effects of a RG inflow on the microbial ecology of sediments in a downstream pond. An alpine RG-pond system, located in the NW Italian Alps has been chosen as a model, and Bacteria and Archaea 16S rRNA genes abundance, distribution and diversity have been assessed by qPCR and Illumina sequencing, coupled with geochemical analyses on sediments collected along a distance gradient from the RG inflow. RG surface material and neighbouring soil have been included in the analysis to better elucidate relationships among different habitats.Our results showed that different habitats harboured different, well-separated microbial assemblages. Across the pond, the main variations in community composition (e.g. Thaumarchaeota and Cyanobacteria relative abundance) and porewater geochemistry (pH, DOC, TDN and NH4+) were not directly linked to RG proximity, but to differences in water depth. Some microbial markers potentially linked to the presence of meltwater inputs from the RG have been recognised, although the RG seems to have a greater influence on the pond microbial communities due to its contribution in terms of sedimentary material.
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Affiliation(s)
- I Mania
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy.
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK.
| | - R Gorra
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - N Colombo
- Department of Earth Sciences, University of Turin, Via Valperga Caluso 35, 10125, Torino, Italy
- Department of Geography and Environmental Studies, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - M Freppaz
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - M Martin
- Department of Agriculture, Forest and Food Sciences (DISAFA), University of Turin, Largo Braccini 2, 10095, Grugliasco, TO, Italy
| | - A M Anesio
- Bristol Glaciology Centre, School of Geographical Sciences, University of Bristol, University Road, Bristol, BS8 1SS, UK
- Department of Environmental Sciences, Aarhus University, 4000, Roskilde, Denmark
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17
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Matys ED, Mackey T, Grettenberger C, Mueller E, Sumner DY, Hawes I, Summons RE. Bacteriohopanepolyols across environmental gradients in Lake Vanda, Antarctica. GEOBIOLOGY 2019; 17:308-319. [PMID: 30707499 DOI: 10.1111/gbi.12335] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/24/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Abstract
Bacteriohopanepolyols (BHPs) are bacterial membrane lipids that may be used as biological or environmental biomarkers. Previous studies have described the diversity, distribution, and abundance of BHPs in a variety of modern environments. However, the regulation of BHP production in polar settings is not well understood. Benthic microbial mats from ice-covered lakes of the McMurdo Dry Valleys, Antarctica provide an opportunity to investigate the sources, physiological roles, and preservation of BHPs in high-latitude environments. Lake Vanda is one of the most stable lakes on Earth, with microbial communities occupying specific niches along environmental gradients. We describe the influence of mat morphology and local environmental conditions on the diversity and distribution of BHPs and their biological sources in benthic microbial mats from Lake Vanda. The abundance and diversity of C-2 methylated hopanoids (2-MeBHP) are of particular interest, given that their stable degradation products, 2-methylhopanes, are among the oldest and most prevalent taxonomically informative biomarkers preserved in sedimentary rocks. Furthermore, the interpretation of sedimentary 2-methylhopanes is of great interest to the geobiology community. We identify cyanobacteria as the sole source of 2-MeBHP in benthic microbial mats from Lake Vanda and assess the hypothesis that 2-MeBHP are regulated in response to a particular environmental variable, namely solar irradiance.
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Affiliation(s)
- Emily D Matys
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Tyler Mackey
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christen Grettenberger
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California
| | - Elliott Mueller
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Dawn Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, California
| | - Ian Hawes
- University of Waikato, Tauranga, New Zealand
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
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18
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Zaikova E, Goerlitz DS, Tighe SW, Wagner NY, Bai Y, Hall BL, Bevilacqua JG, Weng MM, Samuels-Fair MD, Johnson SS. Antarctic Relic Microbial Mat Community Revealed by Metagenomics and Metatranscriptomics. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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19
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Callejas C, Azziz G, Souza EM, Gill PR, Batista S. Prokaryotic diversity in four microbial mats on the Fildes Peninsula, King George Island, maritime Antarctica. Polar Biol 2018. [DOI: 10.1007/s00300-018-2256-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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20
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Jungblut AD, Hawes I. Using Captain Scott's Discovery specimens to unlock the past: has Antarctic cyanobacterial diversity changed over the last 100 years? Proc Biol Sci 2018. [PMID: 28637848 DOI: 10.1098/rspb.2017.0833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Evidence of climate-driven environmental change is increasing in Antarctica, and with it comes concern that this will propagate to impacts on biological communities. Recognition and prediction of change needs to incorporate the extent and timescales over which communities vary under extant conditions. However, few observations of Antarctic microbial communities, which dominate inland habitats, allow this. We therefore carried out the first molecular comparison of Cyanobacteria in historic herbarium microbial mats from freshwater ecosystems on Ross Island and the McMurdo Ice Shelf, collected by Captain R.F. Scott's 'Discovery' Expedition (1902-1903), with modern samples from those areas. Using 16S rRNA gene surveys, we found that modern and historic cyanobacteria assemblages showed some variation in community structure but were dominated by the same genotypes. Modern communities had a higher richness, including genotypes not found in historic samples, but they had the highest similarity to other cyanobacteria sequences from Antarctica. The results imply slow cyanobacterial 16S rRNA gene genotype turnover and considerable community stability within Antarctic microbial mats. We suggest that this relates to Antarctic freshwater 'organisms requiring a capacity to withstand diverse stresses, and that this could also provide a degree of resistance and resilience to future climatic-driven environmental change in Antarctica.
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Affiliation(s)
- Anne D Jungblut
- Life Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Ian Hawes
- University of Waikato, 58 Cross Road, Tauranga 3110, New Zealand
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21
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Kleinteich J, Hildebrand F, Bahram M, Voigt AY, Wood SA, Jungblut AD, Küpper FC, Quesada A, Camacho A, Pearce DA, Convey P, Vincent WF, Zarfl C, Bork P, Dietrich DR. Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00137] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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22
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Koo H, Mojib N, Hakim JA, Hawes I, Tanabe Y, Andersen DT, Bej AK. Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica. Front Microbiol 2017; 8:1347. [PMID: 28824553 PMCID: PMC5543034 DOI: 10.3389/fmicb.2017.01347] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/03/2017] [Indexed: 01/15/2023] Open
Abstract
In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1), middle (U2), and inner (U3) decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI) values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.
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Affiliation(s)
- Hyunmin Koo
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Nazia Mojib
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Joseph A Hakim
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
| | - Ian Hawes
- Gateway Antarctica, University of CanterburyChristchurch, New Zealand
| | - Yukiko Tanabe
- National Institute of Polar ResearchTachikawa, Japan
| | - Dale T Andersen
- Carl Sagan Center, SETI Institute, Mountain ViewCA, United States
| | - Asim K Bej
- Department of Biology, University of Alabama at Birmingham, BirminghamAL, United States
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23
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Characterisation of a deep-water moss from the perennially ice-covered Lake Vanda, Antarctica. Polar Biol 2017. [DOI: 10.1007/s00300-017-2127-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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24
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Palinska KA, Schneider T, Surosz W. Phenotypic and phylogenetic studies of benthic mat-forming cyanobacteria on the NW Svalbard. Polar Biol 2017. [DOI: 10.1007/s00300-017-2083-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Sumner DY, Jungblut AD, Hawes I, Andersen DT, Mackey TJ, Wall K. Growth of elaborate microbial pinnacles in Lake Vanda, Antarctica. GEOBIOLOGY 2016; 14:556-574. [PMID: 27474373 DOI: 10.1111/gbi.12188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 04/22/2016] [Indexed: 06/06/2023]
Abstract
Microbial pinnacles in ice-covered Lake Vanda, McMurdo Dry Valleys, Antarctica, extend from the base of the ice to more than 50 m water depth. The distribution of microbial communities, their photosynthetic potential, and pinnacle morphology affects the local accumulation of biomass, which in turn shapes pinnacle morphology. This feedback, plus environmental stability, promotes the growth of elaborate microbial structures. In Lake Vanda, all mats sampled from greater than 10 m water depth contained pinnacles with a gradation in size from <1-mm-tall tufts to pinnacles that were centimeters tall. Small pinnacles were cuspate, whereas larger ones had variable morphology. The largest pinnacles were up to ~30 cm tall and had cylindrical bases and cuspate tops. Pinnacle biomass was dominated by cyanobacteria from the morphological and genomic groups Leptolyngbya, Phormidium, and Tychonema. The photosynthetic potential of these cyanobacterial communities was high to depths of several millimeters into the mat based on PAM fluorometry, and sufficient light for photosynthesis penetrated ~5 mm into pinnacles. The distribution of photosynthetic potential and its correlation to pinnacle morphology suggests a working model for pinnacle growth. First, small tufts initiate from random irregularities in prostrate mat. Some tufts grow into pinnacles over the course of ~3 years. As pinnacles increase in size and age, their interiors become colonized by a more diverse community of cyanobacteria with high photosynthetic potential. Biomass accumulation within this subsurface community causes pinnacles to swell, expanding laminae thickness and creating distinctive cylindrical bases and cuspate tops. This change in shape suggests that pinnacle morphology emerges from a specific distribution of biomass accumulation that depends on multiple microbial communities fixing carbon in different parts of pinnacles. Similarly, complex patterns of biomass accumulation may be reflected in the morphology of elaborate ancient stromatolites.
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Affiliation(s)
- D Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA.
| | - A D Jungblut
- Life Sciences Department, The Natural History Museum, London, UK
| | - I Hawes
- Gateway Antarctica, University of Canterbury, Christchurch, New Zealand
| | - D T Andersen
- Carl Sagan Center for the Study of Life in the Universe, SETI Institute, Mountain View, CA, USA
| | - T J Mackey
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
| | - K Wall
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
- Microbiology Graduate Group, University of California, Davis, CA, USA
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26
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Van Horn DJ, Wolf CR, Colman DR, Jiang X, Kohler TJ, McKnight DM, Stanish LF, Yazzie T, Takacs-Vesbach CD. Patterns of bacterial biodiversity in the glacial meltwater streams of the McMurdo Dry Valleys, Antarctica. FEMS Microbiol Ecol 2016; 92:fiw148. [PMID: 27495241 DOI: 10.1093/femsec/fiw148] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2016] [Indexed: 12/26/2022] Open
Abstract
Microbial consortia dominate glacial meltwater streams from polar regions, including the McMurdo Dry Valleys (MDV), where they thrive under physiologically stressful conditions. In this study, we examined microbial mat types and sediments found in 12 hydrologically diverse streams to describe the community diversity and composition within and across sites. Sequencing of the 16S rRNA gene from 129 samples revealed ∼24 000 operational taxonomic units (<97% DNA similarity), making streams the most biodiverse habitat in the MDV. Principal coordinate analyses revealed significant but weak clustering by mat type across all streams (ANOSIM R-statistic = 0.28) but stronger clustering within streams (ANOSIM R-statistic from 0.28 to 0.94). Significant relationships (P < 0.05) were found between bacterial diversity and mat ash-free dry mass, suggesting that diversity is related to the hydrologic regimes of the various streams, which are predictive of mat biomass. However, correlations between stream chemistry and community members were weak, possibly reflecting the importance of internal processes and hydrologic conditions. Collectively, these results suggest that localized conditions dictate bacterial community composition of the same mat types and sediments from different streams, and while MDV streams are hotspots of biodiversity in an otherwise depauperate landscape, controls on community structure are complex and site specific.
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Affiliation(s)
- David J Van Horn
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Caitlin R Wolf
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Daniel R Colman
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Xiaoben Jiang
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
| | - Tyler J Kohler
- Faculty of Science, Department of Ecology, Charles University in Prague, Viničná 7, 12844 Prague 2, Prague, Czech Republic
| | - Diane M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, 1560 30th Street, Boulder, CO 80303, USA
| | - Lee F Stanish
- National Ecological Observatory Network, 1685 38th Street, Boulder, CO, 80301
| | - Terrill Yazzie
- Department of Biology, University of New Mexico MSCO3 2020, 1 UNM, Albuquerque, NM 87131, USA
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27
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Microbial Mat Communities along an Oxygen Gradient in a Perennially Ice-Covered Antarctic Lake. Appl Environ Microbiol 2015; 82:620-30. [PMID: 26567300 DOI: 10.1128/aem.02699-15] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 11/02/2015] [Indexed: 11/20/2022] Open
Abstract
Lake Fryxell is a perennially ice-covered lake in the McMurdo Dry Valleys, Antarctica, with a sharp oxycline in a water column that is density stabilized by a gradient in salt concentration. Dissolved oxygen falls from 20 mg liter(-1) to undetectable over one vertical meter from 8.9- to 9.9-m depth. We provide the first description of the benthic mat community that falls within this oxygen gradient on the sloping floor of the lake, using a combination of micro- and macroscopic morphological descriptions, pigment analysis, and 16S rRNA gene bacterial community analysis. Our work focused on three macroscopic mat morphologies that were associated with different parts of the oxygen gradient: (i) "cuspate pinnacles" in the upper hyperoxic zone, which displayed complex topography and were dominated by phycoerythrin-rich cyanobacteria attributable to the genus Leptolyngbya and a diverse but sparse assemblage of pennate diatoms; (ii) a less topographically complex "ridge-pit" mat located immediately above the oxic-anoxic transition containing Leptolyngbya and an increasing abundance of diatoms; and (iii) flat prostrate mats in the upper anoxic zone, dominated by a green cyanobacterium phylogenetically identified as Phormidium pseudopriestleyi and a single diatom, Diadesmis contenta. Zonation of bacteria was by lake depth and by depth into individual mats. Deeper mats had higher abundances of bacteriochlorophylls and anoxygenic phototrophs, including Chlorobi and Chloroflexi. This suggests that microbial communities form assemblages specific to niche-like locations. Mat morphologies, underpinned by cyanobacterial and diatom composition, are the result of local habitat conditions likely defined by irradiance and oxygen and sulfide concentrations.
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Mackey TJ, Sumner DY, Hawes I, Jungblut AD, Andersen DT. Growth of modern branched columnar stromatolites in Lake Joyce, Antarctica. GEOBIOLOGY 2015; 13:373-390. [PMID: 25867791 DOI: 10.1111/gbi.12138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/14/2015] [Indexed: 06/04/2023]
Abstract
Modern decimeter-scale columnar stromatolites from Lake Joyce, Antarctica, show a change in branching pattern during a period of lake level rise. Branching patterns correspond to a change in cyanobacterial community composition as preserved in authigenic calcite crystals. The transition in stromatolite morphology is preserved by mineralized layers that contain microfossils and cylindrical molds of cyanobacterial filaments. The molds are composed of two populations with different diameters. Large diameter molds (>2.8 μm) are abundant in calcite forming the oldest stromatolite layers, but are absent from younger layers. In contrast, <2.3 μm diameter molds are common in all stromatolites layers. Loss of large diameter molds corresponds to the transition from smooth-sided stromatolitic columns to branched and irregular columns. Mold diameters are similar to trichome diameters of the four most abundant living cyanobacteria morphotypes in Lake Joyce: Phormidium autumnale morphotypes have trichome diameters >3.5 μm, whereas Leptolyngbya antarctica, L. fragilis, and Pseudanabaena frigida morphotypes have diameters <2.3 μm. P. autumnale morphotypes were only common in mats at <12 m depth. Mats containing abundant P. autumnale morphotypes were smooth, whereas mats with few P. autumnale morphotypes contained small peaks and protruding bundles of filaments, suggesting that the absence of P. autumnale morphotypes allowed small-scale topography to develop on mats. Comparisons of living filaments and mold diameters suggest that P. autumnale morphotypes were present early in stromatolite growth, but disappeared from the community through time. We hypothesize that the mat-smoothing behavior of P. autumnale morphotypes inhibited nucleation of stromatolite branches. When P. autumnale morphotypes were excluded from the community, potentially reflecting a rise in lake level, short-wavelength roughness provided nuclei for stromatolite branches. This growth history provides a conceptual model for initiation of branched stromatolite growth resulting from a change in microbial community composition.
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Affiliation(s)
- T J Mackey
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
| | - D Y Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, CA, USA
| | - I Hawes
- Gateway Antarctica, University of Canterbury, Christchurch, NZ
| | - A D Jungblut
- Department of Life Sciences, The Natural History Museum, London, UK
| | - D T Andersen
- Carl Sagan Center for the Study of Life in the Universe, SETI Institute, Mountain View, CA, USA
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