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Johnston N, Dubay MM, Serabyn E, Nadeau JL. Detectability of unresolved particles in off-axis digital holographic microscopy. APPLIED OPTICS 2024; 63:B114-B125. [PMID: 38437262 DOI: 10.1364/ao.507375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/09/2024] [Indexed: 03/06/2024]
Abstract
Off-axis digital holographic microscopy (DHM) provides both amplitude and phase images, and so it may be used for label-free 3D tracking of micro- and nano-sized particles of different compositions, including biological cells, strongly absorbing particles, and strongly scattering particles. Contrast is provided by differences in either the real or imaginary parts of the refractive index (phase contrast and absorption) and/or by scattering. While numerous studies have focused on phase contrast and improving resolution in DHM, particularly axial resolution, absent have been studies quantifying the limits of detection for unresolved particles. This limit has important implications for microbial detection, including in life-detection missions for space flight. Here we examine the limits of detection of nanosized particles as a function of particle optical properties, microscope optics (including camera well depth and substrate), and data processing techniques and find that DHM provides contrast in both amplitude and phase for unresolved spheres, in rough agreement with Mie theory scattering cross-sections. Amplitude reconstructions are more useful than phase for low-index spheres and should not be neglected in DHM analysis.
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2
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Vannier P, Farrant GK, Klonowski A, Gaidos E, Thorsteinsson T, Marteinsson VÞ. Metagenomic analyses of a microbial assemblage in a subglacial lake beneath the Vatnajökull ice cap, Iceland. Front Microbiol 2023; 14:1122184. [PMID: 37065146 PMCID: PMC10098204 DOI: 10.3389/fmicb.2023.1122184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/13/2023] [Indexed: 04/01/2023] Open
Abstract
Skaftárkatlar are two subglacial lakes located beneath the Vatnajökull ice cap in Iceland associated with geothermal and volcanic activity. Previous studies of these lakes with ribosomal gene (16S rDNA) tag sequencing revealed a limited diversity of bacteria adapted to cold, dark, and nutrient-poor waters. In this study, we present analyses of metagenomes from the lake which give new insights into its microbial ecology. Analyses of the 16S rDNA genes in the metagenomes confirmed the existence of a low-diversity core microbial assemblage in the lake and insights into the potential metabolisms of the dominant members. Seven taxonomic genera, Sulfuricurvum, Sulfurospirillum, Acetobacterium, Pelobacter/Geobacter, Saccharibacteria, Caldisericum, and an unclassified member of Prolixibacteraceae, comprised more than 98% of the rDNA reads in the library. Functional characterisation of the lake metagenomes revealed complete metabolic pathways for sulphur cycling, nitrogen metabolism, carbon fixation via the reverse Krebs cycle, and acetogenesis. These results show that chemolithoautotrophy constitutes the main metabolism in this subglacial ecosystem. This assemblage and its metabolisms are not reflected in enrichment cultures, demonstrating the importance of in situ investigations of this environment.
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Affiliation(s)
- Pauline Vannier
- MATIS, Department of Research and Innovation, Reykjavík, Iceland
- *Correspondence: Pauline Vannier,
| | | | | | - Eric Gaidos
- Department of Earth Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | | | - Viggó þór Marteinsson
- MATIS, Department of Research and Innovation, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
- Viggó þór Marteinsson,
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3
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Kellogg CTE, McClelland JW, Dunton KH, Crump BC. Strong Seasonality in Arctic Estuarine Microbial Food Webs. Front Microbiol 2019; 10:2628. [PMID: 31849850 PMCID: PMC6896822 DOI: 10.3389/fmicb.2019.02628] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/29/2019] [Indexed: 11/17/2022] Open
Abstract
Microbial communities in the coastal Arctic Ocean experience extreme variability in organic matter and inorganic nutrients driven by seasonal shifts in sea ice extent and freshwater inputs. Lagoons border more than half of the Beaufort Sea coast and provide important habitats for migratory fish and seabirds; yet, little is known about the planktonic food webs supporting these higher trophic levels. To investigate seasonal changes in bacterial and protistan planktonic communities, amplicon sequences of 16S and 18S rRNA genes were generated from samples collected during periods of ice-cover (April), ice break-up (June), and open water (August) from shallow lagoons along the eastern Alaska Beaufort Sea coast from 2011 through 2013. Protist communities shifted from heterotrophic to photosynthetic taxa (mainly diatoms) during the winter–spring transition, and then back to a heterotroph-dominated summer community that included dinoflagellates and mixotrophic picophytoplankton such as Micromonas and Bathycoccus. Planktonic parasites belonging to Syndiniales were abundant under ice in winter at a time when allochthonous carbon inputs were low. Bacterial communities shifted from coastal marine taxa (Oceanospirillaceae, Alteromonadales) to estuarine taxa (Polaromonas, Bacteroidetes) during the winter-spring transition, and then to oligotrophic marine taxa (SAR86, SAR92) in summer. Chemolithoautotrophic taxa were abundant under ice, including iron-oxidizing Zetaproteobacteria. These results suggest that wintertime Arctic bacterial communities capitalize on the unique biogeochemical gradients that develop below ice near shore, potentially using chemoautotrophic metabolisms at a time when carbon inputs to the system are low. Co-occurrence networks constructed for each season showed that under-ice networks were dominated by relationships between parasitic protists and other microbial taxa, while spring networks were by far the largest and dominated by bacteria-bacteria co-occurrences. Summer networks were the smallest and least connected, suggesting a more detritus-based food web less reliant on interactions among microbial taxa. Eukaryotic and bacterial community compositions were significantly related to trends in concentrations of stable isotopes of particulate organic carbon and nitrogen, among other physiochemical variables such as dissolved oxygen, salinity, and temperature. This suggests the importance of sea ice cover and terrestrial carbon subsidies in contributing to seasonal trends in microbial communities in the coastal Beaufort Sea.
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Affiliation(s)
| | - James W McClelland
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX, United States
| | - Kenneth H Dunton
- Marine Science Institute, University of Texas at Austin, Port Aransas, TX, United States
| | - Byron C Crump
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, United States
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Yang Z, Zhang Y, Lv Y, Yan W, Xiao X, Sun B, Ma H. H 2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica. J Microbiol 2019; 57:1095-1104. [PMID: 31758395 DOI: 10.1007/s12275-019-9366-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/14/2019] [Accepted: 11/06/2019] [Indexed: 01/17/2023]
Abstract
Subglacial ecosystems harbor diverse chemoautotrophic microbial communities in areas with limited organic carbon, and lithological H2 produced during glacial erosion has been considered an important energy source in these ecosystems. To verify the H2-utilizing potential there and to identify the related energy-converting metabolic mechanisms of these communities, we performed metagenomic analysis on subglacial sediment samples from East Antarctica with and without H2 supplementation. Genes coding for several [NiFe]-hydrogenases were identified in raw sediment and were enriched after H2 incubation. All genes in the dissimilatory nitrate reduction and denitrification pathways were detected in the subglacial community, and the genes coding for these pathways became enriched after H2 was supplied. Similarly, genes transcribing key enzymes in the Calvin cycle were detected in raw sediment and were also enriched. Moreover, key genes involved in H2 oxidization, nitrate reduction, oxidative phosphorylation, and the Calvin cycle were identified within one metagenome-assembled genome belonging to a Polaromonas sp. As suggested by our results, the microbial community in the subglacial environment we investigated consisted of chemoautotrophic populations supported by H2 oxidation. These results further confirm the importance of H2 in the cryosphere.
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Affiliation(s)
- Zhifeng Yang
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, P. R. China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yu Zhang
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Yongxin Lv
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Wenkai Yan
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Xiang Xiao
- State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, P. R. China.,School of Oceanography, Shanghai Jiao Tong University, Shanghai, P. R. China
| | - Bo Sun
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, P. R. China
| | - Hongmei Ma
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, P. R. China.
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Abstract
Few subglacial lakes have been identified beneath the Greenland Ice Sheet (GrIS) despite extensive documentation in Antarctica, where periodic release of water can impact ice flow. Here we present an ice-sheet-wide survey of Greenland subglacial lakes, identifying 54 candidates from airborne radio-echo sounding, and 2 lakes from ice-surface elevation changes. These range from 0.2–5.9 km in length, and are mostly distributed away from ice divides, beneath relatively slow-moving ice. Based on our results and previous observations, we suggest three zones of formation: stable lakes in northern and eastern regions above the Equilibrium Line Altitude (ELA) but away from the interior; hydrologically-active lakes near the ELA recharged by surface meltwater and; small, seasonally-active lakes below the ELA, which form over winter and drain during the melt season. These observations provide important constraints on the GrIS's basal thermal regime and help refine our understanding of the subglacial hydrological system. Subglacial lakes can influence basal hydrology and ice flow in Antarctica, but are poorly constrained in Greenland. Here the authors provide the first ice sheet-wide inventory of subglacial lakes beneath GrIS, including 54 uncharted lakes.
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Margesin R, Collins T. Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge. Appl Microbiol Biotechnol 2019; 103:2537-2549. [PMID: 30719551 PMCID: PMC6443599 DOI: 10.1007/s00253-019-09631-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 01/04/2019] [Accepted: 01/07/2019] [Indexed: 11/28/2022]
Abstract
Microorganisms in cold ecosystems play a key ecological role in their natural habitats. Since these ecosystems are especially sensitive to climate changes, as indicated by the worldwide retreat of glaciers and ice sheets as well as permafrost thawing, an understanding of the role and potential of microbial life in these habitats has become crucial. Emerging technologies have added significantly to our knowledge of abundance, functional activity, and lifestyles of microbial communities in cold environments. The current knowledge of microbial ecology in glacial habitats and permafrost, the most studied habitats of the cryosphere, is reported in this review.
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Affiliation(s)
- Rosa Margesin
- Institute of Microbiology, University of Innsbruck, 6020, Innsbruck, Austria.
| | - Tony Collins
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, 4710-057, Braga, Portugal
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Russell MJ, Murray AE, Hand KP. The Possible Emergence of Life and Differentiation of a Shallow Biosphere on Irradiated Icy Worlds: The Example of Europa. ASTROBIOLOGY 2017; 17:1265-1273. [PMID: 29016193 PMCID: PMC5729856 DOI: 10.1089/ast.2016.1600] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 04/28/2017] [Indexed: 05/17/2023]
Abstract
Irradiated ice-covered ocean worlds with rocky mafic mantles may provide the conditions needed to drive the emergence and maintenance of life. Alkaline hydrothermal springs-relieving the geophysical, thermal, and chemical disequilibria between oceans and tidally stressed crusts-could generate inorganic barriers to the otherwise uncontrolled and kinetically disfavored oxidation of hydrothermal hydrogen and methane. Ionic gradients imposed across these inorganic barriers, comprising iron oxyhydroxides and sulfides, could drive the hydrogenation of carbon dioxide and the oxidation of methane through thermodynamically favorable metabolic pathways leading to early life-forms. In such chemostatic environments, fuels may eventually outweigh oxidants. Ice-covered oceans are primarily heated from below, creating convection that could transport putative microbial cells and cellular cooperatives upward to congregate beneath an ice shell, potentially giving rise to a highly focused shallow biosphere. It is here where electron acceptors, ultimately derived from the irradiated surface, could be delivered to such life-forms through exchange with the icy surface. Such zones would act as "electron disposal units" for the biosphere, and occupants might be transferred toward the surface by buoyant diapirs and even entrained into plumes. Key Words: Biofilms-Europa-Extraterrestrial life-Hydrothermal systems. Astrobiology 17, 1265-1273.
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Affiliation(s)
- Michael J. Russell
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
| | - Alison E. Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada
| | - Kevin P. Hand
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California
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Madigan MT, Kempher ML, Bender KS, Sullivan P, Matthew Sattley W, Dohnalkova AC, Joye SB. Characterization of a cold-active bacterium isolated from the South Pole "Ice Tunnel". Extremophiles 2017; 21:891-901. [PMID: 28681112 DOI: 10.1007/s00792-017-0950-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 06/23/2017] [Indexed: 11/26/2022]
Abstract
Extremely cold microbial habitats on Earth (those below -30 °C) are rare and have not been surveyed for microbes as extensively as environments in the 0 to -20 °C range. Using cryoprotected growth media incubated at -5 °C, we enriched a cold-active Pseudomonas species from -50 °C ice collected from a utility tunnel for wastewater pipes under Amundsen-Scott South Pole Station, Antarctica. The isolate, strain UC-1, is related to other cold-active Pseudomonas species, most notably P. psychrophila, and grew at -5 °C to +34-37 °C; growth of UC-1 at +3 °C was significantly faster than at +34 °C. Strain UC-1 synthesized a surface exopolymer and high levels of unsaturated fatty acids under cold growth conditions. A 16S rRNA gene diversity screen of the ice sample that yielded strain UC-1 revealed over 1200 operational taxonomic units (OTUs) distributed across eight major classes of Bacteria. Many of the OTUs were Clostridia and Bacteriodia and some of these were probably of wastewater origin. However, a significant fraction of the OTUs were Proteobacteria and Actinobacteria of likely environmental origin. Our results shed light on the lower temperature limits to life and the possible existence of functional microbial communities in ultra-cold environments.
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Affiliation(s)
- Michael T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Megan L Kempher
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Kelly S Bender
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Paul Sullivan
- United States Antarctic Program, Amundsen-Scott Station, Antarctica
| | - W Matthew Sattley
- Division of Natural Sciences, Indiana Wesleyan University, Marion, IN, 46953, USA
| | | | - Samantha B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA
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