1
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Mikucki JA, Schuler CG, Digel I, Kowalski J, Tuttle MJ, Chua M, Davis R, Purcell AM, Ghosh D, Francke G, Feldmann M, Espe C, Heinen D, Dachwald B, Clemens J, Lyons WB, Tulaczyk S. Field-Based Planetary Protection Operations for Melt Probes: Validation of Clean Access into the Blood Falls, Antarctica, Englacial Ecosystem. ASTROBIOLOGY 2023; 23:1165-1178. [PMID: 37962840 DOI: 10.1089/ast.2021.0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Subglacial environments on Earth offer important analogs to Ocean World targets in our solar system. These unique microbial ecosystems remain understudied due to the challenges of access through thick glacial ice (tens to hundreds of meters). Additionally, sub-ice collections must be conducted in a clean manner to ensure sample integrity for downstream microbiological and geochemical analyses. We describe the field-based cleaning of a melt probe that was used to collect brine samples from within a glacier conduit at Blood Falls, Antarctica, for geomicrobiological studies. We used a thermoelectric melting probe called the IceMole that was designed to be minimally invasive in that the logistical requirements in support of drilling operations were small and the probe could be cleaned, even in a remote field setting, so as to minimize potential contamination. In our study, the exterior bioburden on the IceMole was reduced to levels measured in most clean rooms, and below that of the ice surrounding our sampling target. Potential microbial contaminants were identified during the cleaning process; however, very few were detected in the final englacial sample collected with the IceMole and were present in extremely low abundances (∼0.063% of 16S rRNA gene amplicon sequences). This cleaning protocol can help minimize contamination when working in remote field locations, support microbiological sampling of terrestrial subglacial environments using melting probes, and help inform planetary protection challenges for Ocean World analog mission concepts.
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Affiliation(s)
- J A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - C G Schuler
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - I Digel
- FH Aachen - Campus Jülich, Institute of Bioengineering, Julich, Nordrhein-Westfalen, Germany
| | - J Kowalski
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - M J Tuttle
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - M Chua
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - R Davis
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - A M Purcell
- Northern Arizona University, Flagstaff, Arizona, USA
| | - D Ghosh
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - G Francke
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - M Feldmann
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - C Espe
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - D Heinen
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - B Dachwald
- RWTH Aachen University, Aachen, North Rhine-Westfalia, Germany
| | - J Clemens
- University of Bremen, Bremen, Germany
| | - W B Lyons
- The Ohio State University, Byrd Polar Research Center, Columbus, Ohio, USA
| | - S Tulaczyk
- University of California Santa Cruz, Santa Cruz, California, USA
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2
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Zoumplis A, Kolody B, Kaul D, Zheng H, Venepally P, McKnight DM, Takacs-Vesbach C, DeVries A, Allen AE. Impact of meltwater flow intensity on the spatiotemporal heterogeneity of microbial mats in the McMurdo Dry Valleys, Antarctica. ISME COMMUNICATIONS 2023; 3:3. [PMID: 36690784 PMCID: PMC9870883 DOI: 10.1038/s43705-022-00202-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 01/24/2023]
Abstract
The meltwater streams of the McMurdo Dry Valleys are hot spots of biological diversity in the climate-sensitive polar desert landscape. Microbial mats, largely comprised of cyanobacteria, dominate the streams which flow for a brief window of time (~10 weeks) over the austral summer. These communities, critical to nutrient and carbon cycling, display previously uncharacterized patterns of rapid destabilization and recovery upon exposure to variable and physiologically detrimental conditions. Here, we characterize changes in biodiversity, transcriptional responses and activity of microbial mats in response to hydrological disturbance over spatiotemporal gradients. While diverse metabolic strategies persist between marginal mats and main channel mats, data collected from 4 time points during the austral summer revealed a homogenization of the mat communities during the mid-season peak meltwater flow, directly influencing the biogeochemical roles of this stream ecosystem. Gene expression pattern analyses identified strong functional sensitivities of nitrogen-fixing marginal mats to changes in hydrological activities. Stress response markers detailed the environmental challenges of each microhabitat and the molecular mechanisms underpinning survival in a polar desert ecosystem at the forefront of climate change. At mid and end points in the flow cycle, mobile genetic elements were upregulated across all mat types indicating high degrees of genome evolvability and transcriptional synchronies. Additionally, we identified novel antifreeze activity in the stream microbial mats indicating the presence of ice-binding proteins (IBPs). Cumulatively, these data provide a new view of active intra-stream diversity, biotic interactions and alterations in ecosystem function over a high-flow hydrological regime.
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Affiliation(s)
- A Zoumplis
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - B Kolody
- Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA
| | - D Kaul
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - H Zheng
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - P Venepally
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA
| | - D M McKnight
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
| | - C Takacs-Vesbach
- Department of Biology, University of New Mexico, Albuquerque, NM, USA
| | - A DeVries
- Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - A E Allen
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA.
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA.
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3
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Guglielmin M, Azzaro M, Buzzini P, Battistel D, Roman M, Ponti S, Turchetti B, Sannino C, Borruso L, Papale M, Lo Giudice A. A possible unique ecosystem in the endoglacial hypersaline brines in Antarctica. Sci Rep 2023; 13:177. [PMID: 36604573 PMCID: PMC9814585 DOI: 10.1038/s41598-022-27219-2] [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: 09/01/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Here, we present the results related to a new unique terrestrial ecosystem found in an englacial hypersaline brine found in Northern Victoria Land (Antarctica). Both the geochemistry and microbial (prokaryotic and fungal) diversity revealed an unicity with respect to all the other known Antarctic brines and suggested a probable ancient origin mainly due a progressive cryoconcentration of seawater. The prokaryotic community presented some peculiarities, such as the occurrence of sequences of Patescibacteria (which can thrive in nutrient-limited water environments) or few Spirochaeta, and the presence of archaeal sequences of Methanomicrobia closely related to Methanoculleus, a methanogen commonly detected in marine and estuarine environments. The high percentage (35%) of unassigned fungal taxa suggested the presence of a high degree of undiscovered diversity within a structured fungal community (including both yeast and filamentous life forms) and reinforce the hypothesis of a high degree of biological uniqueness of the habitat under study.
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Affiliation(s)
- M. Guglielmin
- grid.18147.3b0000000121724807Department of Theoretical and Applied Sciences, Insubria University, Via Dunant, 3, 21100 Varese, Italy ,grid.18147.3b0000000121724807Climate Change Research Center, Insubria University, Via Regina Teodolinda, 37, 22100 Como, Italy
| | - M. Azzaro
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy
| | - P. Buzzini
- grid.9027.c0000 0004 1757 3630Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - D. Battistel
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy ,grid.7240.10000 0004 1763 0578Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino, 155, 30172 Mestre, VE Italy
| | - M. Roman
- grid.7240.10000 0004 1763 0578Department of Environmental Sciences, Informatics and Statistics, University Ca’ Foscari of Venice, Via Torino, 155, 30172 Mestre, VE Italy
| | - S. Ponti
- grid.18147.3b0000000121724807Department of Theoretical and Applied Sciences, Insubria University, Via Dunant, 3, 21100 Varese, Italy
| | - B. Turchetti
- grid.9027.c0000 0004 1757 3630Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - C. Sannino
- grid.9027.c0000 0004 1757 3630Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - L. Borruso
- grid.34988.3e0000 0001 1482 2038Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, 9100 Bozen-Bolzano, Italy
| | - M. Papale
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy
| | - A. Lo Giudice
- grid.5326.20000 0001 1940 4177Institute of Polar Sciences, National Research Council, Spianata S. Raineri. 86, 98122 Messina, Italy
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Zhong YW, Zhou P, Cheng H, Zhou YD, Pan J, Xu L, Li M, Tao CH, Wu YH, Xu XW. Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge. Microbiol Spectr 2022; 10:e0061422. [PMID: 36286994 PMCID: PMC9769843 DOI: 10.1128/spectrum.00614-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/25/2022] [Indexed: 01/05/2023] Open
Abstract
The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.
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Affiliation(s)
- Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Hong Cheng
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Ya-Dong Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Jie Pan
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Lin Xu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, PR China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, PR China
| | - Chun-Hui Tao
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Submarine Geosciences, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Yue-Hong Wu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou, PR China
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5
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Salwan R, Sharma V. Genomics of Prokaryotic Extremophiles to Unfold the Mystery of Survival in Extreme Environments. Microbiol Res 2022; 264:127156. [DOI: 10.1016/j.micres.2022.127156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 07/30/2022] [Accepted: 07/31/2022] [Indexed: 11/26/2022]
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6
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Cooper ZS, Rapp JZ, Shoemaker AMD, Anderson RE, Zhong ZP, Deming JW. Evolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics. Front Microbiol 2022; 13:879116. [PMID: 35733954 PMCID: PMC9207381 DOI: 10.3389/fmicb.2022.879116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner–Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited. Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.
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Affiliation(s)
- Zachary S. Cooper
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
- *Correspondence: Zachary S. Cooper, , orcid.org/0000-0001-6515-7971
| | - Josephine Z. Rapp
- Department of Biochemistry, Microbiology and Bioinformatics, Université Laval, Québec, QC, Canada
- Center for Northern Studies (CEN), Université Laval, Québec, QC, Canada
- Institute of Integrative Biology and Systems (IBIS), Université Laval, Québec, QC, Canada
| | - Anna M. D. Shoemaker
- Department of Earth Sciences, Montana State University, Bozeman, MT, United States
| | - Rika E. Anderson
- Department of Biology, Carleton College, Northfield, MN, United States
| | - Zhi-Ping Zhong
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States
- Department of Microbiology, Ohio State University, Columbus, OH, United States
- Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W. Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
- Astrobiology Program, University of Washington, Seattle, WA, United States
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7
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Mahmoudnia F. Isolation of a novel halothermophilic strain of the genus Gracilibacillus from Howz-e Sultan hypersaline lake in Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:399-406. [PMID: 34540179 PMCID: PMC8416581 DOI: 10.18502/ijm.v13i3.6403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background and Objectives: Halothermophilic bacteria are adapted to high osmolarity and can grow in high saline environments and high temperatures. This study was aimed at the isolation of halothermophilic bacteria from Howz-e Sultan hypersaline lake in the central desert zone in Iran. Materials and Methods: Samples were collected and after preparing dilutions, the samples were cultured on Molten haloid agar with different salt concentrations (5–35%), then the plates were incubated at 35–70ºC in both aerobic and anaerobic conditions. Biochemical characterizations, utilization of carbon sources, production of exoenzymes and antibiotic susceptibility were investigated. Taxonomic and phylogenetic analyses were performed using 16S rRNA gene sequences. Results: One of the isolated bacteria was found to be Gram-positive, hyperhalophilic, thermophilic, endospore-forming, and was named as 1–9 h isolate. The bacterial cells were bacilli-shaped, which produced endospores at a subterminal position. This isolate was an aerobe and facultative anaerobe and grew between pH 5.0 and 10.0 (optimal growth at pH 7.0–7.5), at temperature between 15°C and 65°C (optimal growth at 40–45°C) and at salinity of 9–32% (w/v) NaCl, growing optimally at 18% (w/v) NaCl. On the basis of 16S rRNA gene sequence analysis, isolate 1–9 h belongs to the genus Bacillus within the phylum Firmicutes and showed the closest phylogenetic similarity to Gracilibacillus sp. IBP-V003 (99.0%). Conclusion: Based on the results of its phenotypic and genotypic properties, strain 1–9 h represents a novel strain of the genus Gracilibacillus. It can be used in various fields of industry and biotechnology.
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Affiliation(s)
- Fahimeh Mahmoudnia
- Department of Biology, Faculty of Sciences, Farhangian University, Tehran, Iran
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8
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Fungal diversity in the coastal waters of King George Island (maritime Antarctica). World J Microbiol Biotechnol 2021; 37:142. [PMID: 34322842 DOI: 10.1007/s11274-021-03112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/14/2021] [Indexed: 12/19/2022]
Abstract
Fungi have been reported as common inhabitants of the maritime waters in Antarctica by studies based on culture-dependent methods. More recently, results obtained using DNA sequencing technologies, revealed that fungal diversity worldwide has been underestimated by culture methods. The present study provides the first characterization of fungal communities in the coastal waters of King George Island (maritime Antarctica) using both culture-dependent and high-throughput sequencing (HTS) methods. HTS demostrated a higher level of fungal diversity than the obtained by culture methods. A high prevalence of basidiomycetous yeasts and ascomycetous filamentous fungi was confirmed by both methods, however, Chythriomycota, Rozellomycota, lichenized fungi and Malassezia spp. were detected only by HTS. Correspondingly, members of some genera, such as Metschnikowia, were only found by culture-dependent methods. Our results confirm that culturing and HTS, should be seen as complementary approaches that enable one to obtain a more comprehensive picture of the composition of microbial communities.
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Rapp JZ, Sullivan MB, Deming JW. Divergent Genomic Adaptations in the Microbiomes of Arctic Subzero Sea-Ice and Cryopeg Brines. Front Microbiol 2021; 12:701186. [PMID: 34367102 PMCID: PMC8339730 DOI: 10.3389/fmicb.2021.701186] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Subzero hypersaline brines are liquid microbial habitats within otherwise frozen environments, where concentrated dissolved salts prevent freezing. Such extreme conditions presumably require unique microbial adaptations, and possibly altered ecologies, but specific strategies remain largely unknown. Here we examined prokaryotic taxonomic and functional diversity in two seawater-derived subzero hypersaline brines: first-year sea ice, subject to seasonally fluctuating conditions; and ancient cryopeg, under relatively stable conditions geophysically isolated in permafrost. Overall, both taxonomic composition and functional potential were starkly different. Taxonomically, sea-ice brine communities (∼105 cells mL–1) had greater richness, more diversity and were dominated by bacterial genera, including Polaribacter, Paraglaciecola, Colwellia, and Glaciecola, whereas the more densely inhabited cryopeg brines (∼108 cells mL–1) lacked these genera and instead were dominated by Marinobacter. Functionally, however, sea ice encoded fewer accessory traits and lower average genomic copy numbers for shared traits, though DNA replication and repair were elevated; in contrast, microbes in cryopeg brines had greater genetic versatility with elevated abundances of accessory traits involved in sensing, responding to environmental cues, transport, mobile elements (transposases and plasmids), toxin-antitoxin systems, and type VI secretion systems. Together these genomic features suggest adaptations and capabilities of sea-ice communities manifesting at the community level through seasonal ecological succession, whereas the denser cryopeg communities appear adapted to intense bacterial competition, leaving fewer genera to dominate with brine-specific adaptations and social interactions that sacrifice some members for the benefit of others. Such cryopeg genomic traits provide insight into how long-term environmental stability may enable life to survive extreme conditions.
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Affiliation(s)
- Josephine Z Rapp
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Matthew B Sullivan
- Byrd Polar and Climate Research Center, Ohio State University, Columbus, OH, United States.,Department of Microbiology, Ohio State University, Columbus, OH, United States.,Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, United States.,Center of Microbiome Science, Ohio State University, Columbus, OH, United States
| | - Jody W Deming
- School of Oceanography, University of Washington, Seattle, WA, United States
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Cooper ZS, Rapp JZ, Carpenter SD, Iwahana G, Eicken H, Deming JW. Distinctive microbial communities in subzero hypersaline brines from Arctic coastal sea ice and rarely sampled cryopegs. FEMS Microbiol Ecol 2020; 95:5593952. [PMID: 31626297 PMCID: PMC6859516 DOI: 10.1093/femsec/fiz166] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/15/2019] [Indexed: 11/29/2022] Open
Abstract
Hypersaline aqueous environments at subzero temperatures are known to be inhabited by microorganisms, yet information on community structure in subzero brines is very limited. Near Utqiaġvik, Alaska, we sampled subzero brines (–6°C, 115–140 ppt) from cryopegs, i.e. unfrozen sediments within permafrost that contain relic (late Pleistocene) seawater brine, as well as nearby sea-ice brines to examine microbial community composition and diversity using 16S rRNA gene amplicon sequencing. We also quantified the communities microscopically and assessed environmental parameters as possible determinants of community structure. The cryopeg brines harbored surprisingly dense bacterial communities (up to 108 cells mL–1) and millimolar levels of dissolved and particulate organic matter, extracellular polysaccharides and ammonia. Community composition and diversity differed between the two brine environments by alpha- and beta-diversity indices, with cryopeg brine communities appearing less diverse and dominated by one strain of the genus Marinobacter, also detected in other cold, hypersaline environments, including sea ice. The higher density and trend toward lower diversity in the cryopeg communities suggest that long-term stability and other features of a subzero brine are more important selective forces than in situ temperature or salinity, even when the latter are extreme.
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Affiliation(s)
- Zachary S Cooper
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
| | - Josephine Z Rapp
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
| | - Shelly D Carpenter
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
| | - Go Iwahana
- International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Hajo Eicken
- International Arctic Research Center, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
| | - Jody W Deming
- School of Oceanography, University of Washington, P.O. Box 357940 Seattle, WA 98195, USA
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11
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Zhang MX, Li AZ, Wu Q, Yao Q, Zhu HH. Marinobacter denitrificans sp. nov., isolated from marine sediment of southern Scott Coast, Antarctica. Int J Syst Evol Microbiol 2020; 70:2918-2924. [PMID: 32213256 DOI: 10.1099/ijsem.0.004120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A novel bacterium, designated JB02H27T, was isolated from marine sediment collected from the southern Scott Coast, Antarctica. Cells were Gram-stain-negative, facultatively anaerobic, polar-flagellated and motile rods. Growth occurred at 4-45 °C, at pH 7.0-9.0 and with 3-25 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain JB02H27T consistently fell within the genus Marinobacter and formed a clade together with Marinobacter algicola DG893T (98.8 % similarity), Marinobacter confluentis KCTC 42705T (98.4 %), Marinobacter salarius R9SW1T (98.4%) and Marinobacter halotolerans CP12T (97.9 %), which were subsequently used as reference strains for comparisons of phenotypic and chemotaxonomic characteristics. Average nucleotide identity values between strain JB02H27T and the four related type strains were 80.9, 76.6, 81.9 and 76.3 %, respectively. The major fatty acids were summed feature 3, C16 : 0, C18 : 1 ω9c and C16 : 0 N alcohol. The polar lipids included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unidentified phospholipid, aminolipid, aminophospholipid and glycolipids. The sole respiratory quinone was ubiquinone-9. The DNA G+C content was 56.9 mol%. Based on the genomic, phylogenetic, phenotypic and chemotaxonomic analysis, we propose that strain JB02H27T represents a novel species of the genus Marinobacter, for which the name Marinobacter denitrificans sp. nov. is proposed. The type strain is JB02H27T (=GDMCC 1.1528T=KCTC 62941T).
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Affiliation(s)
- Ming-Xia Zhang
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - An-Zhang Li
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qingping Wu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Guangzhou 510642, PR China
| | - Hong-Hui Zhu
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Microbial Culture Collection Center (GDMCC), Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, PR China
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12
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Ding W, Liu P, Xu Y, Fang J, Cao J. Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench. FEMS Microbiol Lett 2019; 366:5698325. [PMID: 31913437 DOI: 10.1093/femsle/fnaa004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/07/2020] [Indexed: 11/12/2022] Open
Abstract
A novel Rhodobacteraceae bacterium, strain W43T, was isolated from a deep-sea water sample from the New Britain Trench. Strain W43T exhibited the highest 16S rRNA gene sequence similarity of 96.5% to Sedimentitalea nanhaiensis DSM 24252T, Phaeobacter gallaeciensis DSM 26640T, Phaeobacter inhibens DSM 16374T, and Phaeobacter porticola P97T. Phylogenetic analysis of the 16S rRNA gene and phylogenomic analysis of the genome showed that strain W43T formed an independent monophyletic branch within the family Rhodobacteraceae. Strain W43T was Gram-stain-negative, rod-shaped, and grew optimally at 16-20°C, pH 6.5-7.0 and 2% (w/v) NaCl. The principal fatty acids were C18:1ω7c/C18:1ω6c, major respiratory quinone was ubiquinone-10 and predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The 5 080 916 bp long genome, comprising a circular chromosome and four plasmids, exhibits a G + C content of 55.9 mol%. The combined phenotypic, chemotaxonomic and molecular data show that strain W43T represents a novel species of a novel genus, for which the name Parasedimentitalea marina gen. nov. sp. nov. is proposed (type strain W43T = MCCC 1K03532T = KCTC 62635T).
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Affiliation(s)
- Wanzhen Ding
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Pudong, Shanghai 201306, PR China
| | - Ping Liu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Pudong, Shanghai 201306, PR China
| | - Yunping Xu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Pudong, Shanghai 201306, PR China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Pudong, Shanghai 201306, PR China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, PR China.,Department of Natural Sciences, Hawaii Pacific University, Waterfront Plaza 500 Ala Moana Blvd Ste 4-545, Honolulu, HI 96813, USA
| | - Junwei Cao
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Pudong, Shanghai 201306, PR China
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13
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Papale M, Lo Giudice A, Conte A, Rizzo C, Rappazzo AC, Maimone G, Caruso G, La Ferla R, Azzaro M, Gugliandolo C, Paranhos R, Cabral AS, Romano Spica V, Guglielmin M. Microbial Assemblages in Pressurized Antarctic Brine Pockets (Tarn Flat, Northern Victoria Land): A Hotspot of Biodiversity and Activity. Microorganisms 2019; 7:microorganisms7090333. [PMID: 31505750 PMCID: PMC6780602 DOI: 10.3390/microorganisms7090333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 12/03/2022] Open
Abstract
Two distinct pressurized hypersaline brine pockets (named TF4 and TF5), separated by a thin ice layer, were detected below an ice-sealed Antarctic lake. Prokaryotic (bacterial and archaeal) diversity, abundances (including virus-like particles) and metabolic profiles were investigated by an integrated approach, including traditional and new-generation methods. Although similar diversity indices were computed for both Bacteria and Archaea, distinct bacterial and archaeal assemblages were observed. Bacteroidetes and Gammaproteobacteria were more abundant in the shallowest brine pocket, TF4, and Deltaproteobacteria, mainly represented by versatile sulphate-reducing bacteria, dominated in the deepest, TF5. The detection of sulphate-reducing bacteria and methanogenic Archaea likely reflects the presence of a distinct synthrophic consortium in TF5. Surprisingly, members assigned to hyperthermophilic Crenarchaeota and Euryarchaeota were common to both brines, indicating that these cold habitats host the most thermally tolerant Archaea. The patterns of microbial communities were different, coherently with the observed microbiological diversity between TF4 and TF5 brines. Both the influence exerted by upward movement of saline brines from a sub-surface anoxic system and the possible occurrence of an ancient ice remnant from the Ross Ice Shelf were the likely main factors shaping the microbial communities.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Antonella Conte
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy.
| | - Carmen Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy.
| | - Alessandro C Rappazzo
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Giovanna Maimone
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Gabriella Caruso
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Rosabruna La Ferla
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Maurizio Azzaro
- Institute of Polar Sciences, National Research Council (ISP-CNR), 98122 Messina, Italy.
| | - Concetta Gugliandolo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, 98168 Messina, Italy.
| | - Rodolfo Paranhos
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro 21.941-590, Brazil.
| | - Anderson S Cabral
- Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro 21.941-590, Brazil.
| | - Vincenzo Romano Spica
- Department of Movement, Human and Health Sciences, Public Health Unit, University of Rome "Foro Italico", P.zza Lauro De Bosis 6, 00135 Rome, Italy.
| | - Mauro Guglielmin
- Dipartimento di Scienze Teoriche e Applicate, University of Insubria, 21100 Varese, Italy.
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14
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Campen R, Kowalski J, Lyons WB, Tulaczyk S, Dachwald B, Pettit E, Welch KA, Mikucki JA. Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert. Environ Microbiol 2019; 21:2290-2306. [PMID: 30927377 DOI: 10.1111/1462-2920.14607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 11/30/2022]
Abstract
Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.
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Affiliation(s)
- Richard Campen
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
| | | | | | - Slawek Tulaczyk
- University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Bernd Dachwald
- Faculty of Aerospace Engineering, FH Aachen University of Applied Sciences, Aachen, Germany
| | - Erin Pettit
- College of Earth, Ocean, and Atmospheric Science, Oregon State University, Corvallis, OR, 97331, USA
| | | | - Jill A Mikucki
- Department of Microbiology, University of Tennessee, Knoxville, TN, 37996, USA
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15
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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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