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Pozarycki C, Seaton KM, C Vincent E, Novak Sanders C, Nuñez N, Castillo M, Ingall E, Klempay B, Pontefract A, Fisher LA, Paris ER, Buessecker S, Alansson NB, Carr CE, Doran PT, Bowman JS, Schmidt BE, Stockton AM. Biosignature Molecules Accumulate and Persist in Evaporitic Brines: Implications for Planetary Exploration. ASTROBIOLOGY 2024; 24:795-812. [PMID: 39159437 DOI: 10.1089/ast.2023.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
The abundance of potentially habitable hypersaline environments in our solar system compels us to understand the impacts of high-salt matrices and brine dynamics on biosignature detection efforts. We identified and quantified organic compounds in brines from South Bay Salt Works (SBSW), where evapoconcentration of ocean water enables exploration of the impact of NaCl- and MgCl2-dominated brines on the detection of potential biosignature molecules. In SBSW, organic biosignature abundance and distribution are likely influenced by evapoconcentration, osmolyte accumulation, and preservation effects. Bioluminescence assays show that adenosine triphosphate (ATP) concentrations are higher in NaCl-rich, low water activity (aw) samples (<0.85) from SBSW. This is consistent with the accumulation and preservation of ATP at low aw as described in past laboratory studies. The water-soluble small organic molecule inventory was determined by using microchip capillary electrophoresis paired with high-resolution mass spectrometry (µCE-HRMS). We analyzed the relative distribution of proteinogenic amino acids with a recently developed quantitative method using CE-separation and laser-induced fluorescence (LIF) detection of amino acids in hypersaline brines. Salinity trends for dissolved free amino acids were consistent with amino acid residue abundance determined from the proteome of the microbial community predicted from metagenomic data. This highlights a tangible connection up and down the "-omics" ladder across changing geochemical conditions. The detection of water-soluble organic compounds, specifically proteinogenic amino acids at high abundance (>7 mM) in concentrated brines, demonstrates that potential organic biomarkers accumulate at hypersaline sites and suggests the possibility of long-term preservation. The detection of such molecules in high abundance when using diverse analytical tools appropriate for spacecraft suggests that life detection within hypersaline environments, such as evaporates on Mars and the surface or subsurface brines of ocean world Europa, is plausible and argues such environments should be a high priority for future exploration. Key Words: Salts-Analytical chemistry-Amino acids-Biosignatures-Capillary electrophoresis-Preservation. Astrobiology 24, 795-812.
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Affiliation(s)
- Chad Pozarycki
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Kenneth M Seaton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Emily C Vincent
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Carlie Novak Sanders
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nickie Nuñez
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mariah Castillo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Ellery Ingall
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Benjamin Klempay
- Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA
| | | | - Luke A Fisher
- Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA
| | - Emily R Paris
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Steffen Buessecker
- Department of Earth System Science, Stanford University, Stanford, California, USA
| | - Nikolas B Alansson
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Christopher E Carr
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter T Doran
- Geology and Geophysics, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Jeff S Bowman
- Scripps Institution of Oceanography, University of California San Diego, San Diego, California, USA
| | - Britney E Schmidt
- Departments of Astronomy and Earth & Atmospheric Sciences, Cornell University, Ithaca, New York, USA
| | - Amanda M Stockton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
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2
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Garvin ZK, Abades SR, Trefault N, Alfaro FD, Sipes K, Lloyd KG, Onstott TC. Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert. THE ISME JOURNAL 2024; 18:wrae062. [PMID: 38625060 PMCID: PMC11094475 DOI: 10.1093/ismejo/wrae062] [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: 09/26/2023] [Revised: 01/29/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing their impact on trace gas-oxidizers in the surrounding soils. We assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy/carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.
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Affiliation(s)
- Zachary K Garvin
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
| | - Sebastián R Abades
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Nicole Trefault
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Faculty of Interdisciplinary Studies, Universidad Mayor, 8580745, Santiago, Chile
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Tullis C Onstott
- Department of Geosciences, Princeton University, Princeton, NJ 08544, United States
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3
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Coffer MM, Schaeffer BA, Salls WB, Urquhart E, Loftin KA, Stumpf RP, Werdell PJ, Darling JA. Satellite remote sensing to assess cyanobacterial bloom frequency across the United States at multiple spatial scales. ECOLOGICAL INDICATORS 2021; 128:1-107822. [PMID: 35558093 PMCID: PMC9088058 DOI: 10.1016/j.ecolind.2021.107822] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Cyanobacterial blooms can have negative effects on human health and local ecosystems. Field monitoring of cyanobacterial blooms can be costly, but satellite remote sensing has shown utility for more efficient spatial and temporal monitoring across the United States. Here, satellite imagery was used to assess the annual frequency of surface cyanobacterial blooms, defined for each satellite pixel as the percentage of images for that pixel throughout the year exhibiting detectable cyanobacteria. Cyanobacterial frequency was assessed across 2,196 large lakes in 46 states across the continental United States (CONUS) using imagery from the European Space Agency's Ocean and Land Colour Instrument for the years 2017 through 2019. In 2019, across all satellite pixels considered, annual bloom frequency had a median value of 4% and a maximum value of 100%, the latter indicating that for those satellite pixels, a cyanobacterial bloom was detected by the satellite sensor for every satellite image considered. In addition to annual pixel-scale cyanobacterial frequency, results were summarized at the lake- and state-scales by averaging annual pixel-scale results across each lake and state. For 2019, average annual lake-scale frequencies also had a maximum value of 100%, and Oregon and Ohio had the highest average annual state-scale frequencies at 65% and 52%. Pixel-scale frequency results can assist in identifying portions of a lake that are more prone to cyanobacterial blooms, while lake- and state-scale frequency results can assist in the prioritization of sampling resources and mitigation efforts. Satellite imagery is limited by the presence of snow and ice, as imagery collected in these conditions are quality flagged and discarded. Thus, annual bloom frequencies within nine climate regions were investigated to determine whether missing data biased results in climate regions more prone to snow and ice, given that their annual summaries would be weighted toward the summer months when cyanobacterial blooms tend to occur. Results were unbiased by the time period selected in most climate regions, but a large bias was observed for the Northwest Rockies and Plains climate region. Moderate biases were observed for the Ohio Valley and the Southeast climate regions. Finally, a clustering analysis was used to identify areas of high and low cyanobacterial frequency across CONUS based on average annual lake-scale cyanobacterial frequencies for 2019. Several clusters were identified that transcended state, watershed, and eco-regional boundaries. Combined with additional data, results from the clustering analysis may offer insight regarding large-scale drivers of cyanobacterial blooms.
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Affiliation(s)
- Megan M Coffer
- ORISE Fellow, U.S. EPA, Office of Research and Development, Durham, NC, USA
- Center for Geospatial Analytics, North Carolina State University, Raleigh, NC, USA
| | | | - Wilson B Salls
- U.S. EPA, Office of Research and Development, Durham, NC, USA
| | - Erin Urquhart
- Science Systems and Applications, Inc., Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - Keith A Loftin
- U.S. Geological Survey, Kansas Water Science Center, Lawrence, KS, USA
| | - Richard P Stumpf
- National Oceanic and Atmospheric Administration, National Centers for Coastal Ocean Science, Silver Spring, MD, USA
| | - P Jeremy Werdell
- Ocean Ecology Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - John A Darling
- U.S. EPA, Office of Research and Development, Durham, NC, USA
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Schulze-Makuch D, Lipus D, Arens FL, Baqué M, Bornemann TLV, de Vera JP, Flury M, Frösler J, Heinz J, Hwang Y, Kounaves SP, Mangelsdorf K, Meckenstock RU, Pannekens M, Probst AJ, Sáenz JS, Schirmack J, Schloter M, Schmitt-Kopplin P, Schneider B, Uhl J, Vestergaard G, Valenzuela B, Zamorano P, Wagner D. Microbial Hotspots in Lithic Microhabitats Inferred from DNA Fractionation and Metagenomics in the Atacama Desert. Microorganisms 2021; 9:microorganisms9051038. [PMID: 34065975 PMCID: PMC8151210 DOI: 10.3390/microorganisms9051038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/29/2021] [Accepted: 05/05/2021] [Indexed: 01/04/2023] Open
Abstract
The existence of microbial activity hotspots in temperate regions of Earth is driven by soil heterogeneities, especially the temporal and spatial availability of nutrients. Here we investigate whether microbial activity hotspots also exist in lithic microhabitats in one of the most arid regions of the world, the Atacama Desert in Chile. While previous studies evaluated the total DNA fraction to elucidate the microbial communities, we here for the first time use a DNA separation approach on lithic microhabitats, together with metagenomics and other analysis methods (i.e., ATP, PLFA, and metabolite analysis) to specifically gain insights on the living and potentially active microbial community. Our results show that hypolith colonized rocks are microbial hotspots in the desert environment. In contrast, our data do not support such a conclusion for gypsum crust and salt rock environments, because only limited microbial activity could be observed. The hypolith community is dominated by phototrophs, mostly Cyanobacteria and Chloroflexi, at both study sites. The gypsum crusts are dominated by methylotrophs and heterotrophic phototrophs, mostly Chloroflexi, and the salt rocks (halite nodules) by phototrophic and halotolerant endoliths, mostly Cyanobacteria and Archaea. The major environmental constraints in the organic-poor arid and hyperarid Atacama Desert are water availability and UV irradiation, allowing phototrophs and other extremophiles to play a key role in desert ecology.
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Affiliation(s)
- Dirk Schulze-Makuch
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Experimental Limnology, 16775 Stechlin, Germany
- School of the Environment, Washington State University, Pullman, WA 99163, USA
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
| | - Felix L. Arens
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Mickael Baqué
- German Aerospace Center (DLR), Institute of Planetary Research, 12489 Berlin, Germany;
| | - Till L. V. Bornemann
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Microgravity User Support Center (MUSC), 51147 Cologne, Germany;
| | - Markus Flury
- Department of Crop and Soil Science, Washington State University, Pullman, WA 99164, USA;
- Department of Crop and Soil Science, Washington State University, Puyallup, WA 98371, USA
| | - Jan Frösler
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Jacob Heinz
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Yunha Hwang
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Samuel P. Kounaves
- Department of Chemistry, Tufts University, Boston, MA 02155, USA;
- Department of Earth Science & Engineering, Imperial College London, London SW7 2AZ, UK
| | - Kai Mangelsdorf
- GFZ German Research Centre for Geosciences, Section Organic Geochemistry, 14473 Potsdam, Germany;
| | - Rainer U. Meckenstock
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Mark Pannekens
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Alexander J. Probst
- Environmental Microbiology and Biotechnology, Department of Chemistry, University of Duisburg-Essen, 45141 Essen, Germany; (T.L.V.B.); (J.F.); (R.U.M.); (M.P.); (A.J.P.)
| | - Johan S. Sáenz
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Janosch Schirmack
- Center for Astronomy and Astrophysics, Technische Universität Berlin, 10623 Berlin, Germany; (F.L.A.); (J.H.); (Y.H.); (J.S.)
| | - Michael Schloter
- Research Unit for Comparative Microbiome Analysis, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (J.S.S.); (M.S.)
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Beate Schneider
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Federal Institute for Materials Research and Testing (BAM), 12205 Berlin, Germany
| | - Jenny Uhl
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany; (P.-S.K.); (J.U.)
| | - Gisle Vestergaard
- Department of Health Technology, Technical University of Denmark, 2800 Lyngby, Denmark;
| | - Bernardita Valenzuela
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, Instituto Antofagasta, Universidad de Antofagasta, Av. Angamos 601, Antofagasta 1240000, Chile; (B.V.); (P.Z.)
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, Telegrafenberg, 14473 Potsdam, Germany; (D.L.); (B.S.)
- Institute of Geosciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Correspondence: (D.S.-M.); (D.W.); Tel.: +49-(30)-314-23736 (D.S.-M.); +49-(331)-288-28800 (D.W.)
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Zárate A, Dorador C, Araya R, Guajardo M, Z Florez J, Icaza G, Cornejo D, Valdés J. Connectivity of bacterial assemblages along the Loa River in the Atacama Desert, Chile. PeerJ 2020; 8:e9927. [PMID: 33062423 PMCID: PMC7533063 DOI: 10.7717/peerj.9927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/21/2020] [Indexed: 01/04/2023] Open
Abstract
The Loa River is the only perennial artery that crosses the Atacama Desert in northern Chile. It plays an important role in the ecological and economic development of the most water-stressed region, revealing the impact of the mining industry, which exacerbate regional water shortages for many organisms and ecological processes. Despite this, the river system has remained understudied. To our knowledge, this study provides the first effort to attempt to compare the microbial communities at spatial scale along the Loa River, as well as investigate the physicochemical factors that could modulate this important biological component that still remains largely unexplored. The analysis of the spatial bacterial distribution and their interconnections in the water column and sediment samples from eight sites located in three sections along the river catchment (upper, middle and lower) was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. Among a total of 543 ASVs identified at the family level, over 40.5% were cosmopolitan in the river and distributed within a preference pattern by the sediment substrate with 162 unique ASVs, while only 87 were specific to the column water. Bacterial diversity gradually decreased from the headwaters, where the upper section had the largest number of unique families. Distinct groupings of bacterial communities often associated with anthropogenic disturbance, including Burkholderiaceae and Flavobacteriaceae families were predominant in the less-impacted upstream section. Members of the Arcobacteraceae and Marinomonadaceae were prominent in the agriculturally and mining-impacted middle sector while Rhodobacteraceae and Coxiellaceae were most abundant families in downstream sites. Such shifts in the community structure were also related to the influence of salinity, chlorophyll, dissolved oxygen and redox potential. Network analyses corroborated the strong connectivity and modular structure of bacterial communities across this desert river, shedding light on taxonomic relatedness of co-occurring species and highlighting the need for planning the integral conservation of this basin.
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Affiliation(s)
- Ana Zárate
- Doctorado en Ciencias Aplicadas mención Sistemas Marinos Costeros, Universidad de Antofagasta, Antofagasta, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile.,Humedales del Caribe colombiano, Universidad del Atlantico, Barranquilla, Colombia
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Ruben Araya
- Laboratorio de Microbiología de Sedimentos, Departamento de Acuicultura, Facultad de Recursos del Mar, Universidad de Antofagasta, Antofagasta, Chile
| | - Mariela Guajardo
- Doctorado en Genómica Integrativa y Centro GEMA, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - July Z Florez
- Humedales del Caribe colombiano, Universidad del Atlantico, Barranquilla, Colombia.,Centro i mar and CeBiB, Universidad de Los Lagos, Puerto Montt, Chile.,Departamento de Ciencias Farmacéuticas, Universidad Católica del Norte, Antofagasta, Chile
| | - Gonzalo Icaza
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
| | - Diego Cornejo
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centro de Bioingeniería y Biotecnología (CeBiB), Universidad de Antofagasta, Antofagasta, Chile.,Chair of Technical Biochemistry, Technische Universitāt, Dresden Dresden, Germany
| | - Jorge Valdés
- Laboratorio de Sedimentología y Paleoambientes, Instituto de Ciencias Naturales A. von Humboldt, Facultad de Ciencias del Mar y de Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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6
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Qu EB, Omelon CR, Oren A, Meslier V, Cowan DA, Maggs-Kölling G, DiRuggiero J. Trophic Selective Pressures Organize the Composition of Endolithic Microbial Communities From Global Deserts. Front Microbiol 2020; 10:2952. [PMID: 31969867 PMCID: PMC6960110 DOI: 10.3389/fmicb.2019.02952] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/09/2019] [Indexed: 11/29/2022] Open
Abstract
Studies of microbial biogeography are often convoluted by extremely high diversity and differences in microenvironmental factors such as pH and nutrient availability. Desert endolithic (inside rock) communities are relatively simple ecosystems that can serve as a tractable model for investigating long-range biogeographic effects on microbial communities. We conducted a comprehensive survey of endolithic sandstones using high-throughput marker gene sequencing to characterize global patterns of diversity in endolithic microbial communities. We also tested a range of abiotic variables in order to investigate the factors that drive community assembly at various trophic levels. Macroclimate was found to be the primary driver of endolithic community composition, with the most striking difference witnessed between hot and polar deserts. This difference was largely attributable to the specialization of prokaryotic and eukaryotic primary producers to different climate conditions. On a regional scale, microclimate and properties of the rock substrate were found to influence community assembly, although to a lesser degree than global hot versus polar conditions. We found new evidence that the factors driving endolithic community assembly differ between trophic levels. While phototrophic taxa, mostly oxygenic photosynthesizers, were rigorously selected for among different sites, heterotrophic taxa were more cosmopolitan, suggesting that stochasticity plays a larger role in heterotroph assembly. This study is the first to uncover the global drivers of desert endolithic diversity using high-throughput sequencing. We demonstrate that phototrophs and heterotrophs in the endolithic community assemble under different stochastic and deterministic influences, emphasizing the need for studies of microorganisms in context of their functional niche in the community.
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Affiliation(s)
- Evan B. Qu
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Chris R. Omelon
- Department of Geography and Planning, Queen’s University, Kingston, ON, Canada
| | - Aharon Oren
- Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Victoria Meslier
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Jocelyne DiRuggiero
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States
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7
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Evans SE, Dueker ME, Logan JR, Weathers KC. The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 647:1547-1556. [PMID: 30180359 DOI: 10.1016/j.scitotenv.2018.08.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 07/28/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources. Fog from both sites contained Actinobacteria and Firmicutes, commonly soil- and air-associated phyla, but also contained bacterial taxa associated with marine environments including Cyanobacteria, Oceanospirillales, Novosphingobium, Pseudoalteromonas, and Bradyrhizobiaceae. Marine influence on fog communities was greatest near the coast, but still evident in Namib fogs 50 km inland. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. Fog is likely to enhance viability of transported microbes and facilitate their deposition, making fog biology ecologically important in fog-dominated environments. Fog may introduce novel species to terrestrial ecosystems, including human and plant pathogens, warranting further work on the drivers of this important and underrecognized aerobiological transfer between marine and terrestrial systems.
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Affiliation(s)
- Sarah E Evans
- Kellogg Biological Station, Department of Integrative Biology, Department of Microbiology and Molecular Genetics, Michigan State University, Hickory Corners, MI, USA.
| | - M Elias Dueker
- Biology Program & Environmental and Urban Studies Program, Bard College, Campus Road, PO Box 5000, Annandale-on-Hudson, NY 12504, USA; Cary Institute of Ecosystem Studies, Box AB, Millbrook, NY 12545-0129, USA; Bard Center for the Study of Land, Air, and Water, Bard College, Campus Road, PO Box 5000, Annandale-on-Hudson, NY 12504, USA.
| | - J Robert Logan
- Kellogg Biological Station, Department of Integrative Biology, Department of Microbiology and Molecular Genetics, Michigan State University, Hickory Corners, MI, USA
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Gómez-Silva B. Lithobiontic life: "Atacama rocks are well and alive". Antonie Van Leeuwenhoek 2018; 111:1333-1343. [PMID: 29392527 DOI: 10.1007/s10482-018-1033-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/28/2018] [Indexed: 11/29/2022]
Abstract
Our knowledge on the Microbiology of the Atacama Desert has increased steadily and substantially during the last two decades. This information now supports a paradigmatic change on the Atacama Desert from a sterile, uninhabitable territory to a hyperarid region colonized by a rich microbiota that includes extremophiles and extreme-tolerant microorganisms. Also, extensive reports are available on the prevalent physical and chemical environmental conditions, ecological niches and, the abundance, diversity and organization of the microbial life in the Atacama Desert. This territory is a highly desiccated environment due to the absence of regular rain events. Liquid water scarcity is the most serious environmental factor affecting the Atacama Desert microorganisms. The intense solar irradiation in this region contributes, in a synergistic fashion with desiccation, to limit the survival and growth of the microbial life. In order to overcome these two extreme conditions, successful microorganisms, organized as microbial consortia, take advantage of (a) the physical characteristics of lithic habitats, which provide sites for colonization on, within or below the rock substrate, the attenuation and filtration of the intense solar irradiation and, the collection of liquid water from incoming fog formations and by water vapour condensation and deliquescence on or within their surfaces, and (b) the biological adaptations of members of the microbial communities that allow them to synthesize hydrophilic macromolecules, antioxidants and UV-light absorbents. Lithic habitats have been considered specialized shelters where life forms can reach protection at environments subjected to extremes of desiccation and solar irradiation, here on Earth or elsewhere. This review is an overview of part of the scientific information collected on lithobionts from the Atacama Desert, their rock substrates and their strategies to cope with extremes of desiccation and intense photosynthetic active radiation and UV irradiations.
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Affiliation(s)
- Benito Gómez-Silva
- Laboratory of Biochemistry, Biomedical Department, Faculty of Health Sciences, and Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, 601 Angamos Ave., Antofagasta, Chile.
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Bull AT, Asenjo JA, Goodfellow M, Gómez-Silva B. The Atacama Desert: Technical Resources and the Growing Importance of Novel Microbial Diversity. Annu Rev Microbiol 2017; 70:215-34. [PMID: 27607552 DOI: 10.1146/annurev-micro-102215-095236] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The Atacama Desert of northern Chile is the oldest and most arid nonpolar environment on Earth. It is a coastal desert covering approximately 180,000 km(2), and together with the greater Atacama region it comprises a dramatically wide range of ecological niches. Long known and exploited for its mineral resources, the Atacama Desert harbors a rich microbial diversity that has only recently been discovered; the great majority of it has not yet been recovered in culture or even taxonomically identified. This review traces the progress of microbiology research in the Atacama and dispels the popular view that this region is virtually devoid of life. We examine reasons for such research activity and demonstrate that microbial life is the latest recognized and least explored resource in this inspiring biome.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, United Kingdom;
| | - Juan A Asenjo
- Center for Biotechnology and Bioengineering, University of Chile, Santiago, Chile.,Department of Chemical Engineering and Biotechnology, University of Chile, Santiago, Chile;
| | - Michael Goodfellow
- School of Biology, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom;
| | - Benito Gómez-Silva
- Biochemistry Laboratory, Biomedical Department, Faculty of Health Sciences, University of Antofagasta, Chile;
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10
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Marques J, Vázquez-Nion D, Paz-Bermúdez G, Prieto B. The susceptibility of weathered versus unweathered schist to biological colonization in the Côa Valley Archaeological Park (north-east Portugal). Environ Microbiol 2014; 17:1805-16. [DOI: 10.1111/1462-2920.12642] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Joana Marques
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Porto Portugal
- Escola Universitaria de Enxeñeria Forestal; Universidade de Vigo; Pontevedra Spain
| | - Daniel Vázquez-Nion
- Departamento de Edafología y Química Agrícola; Facultad de Farmacia; Universidad de Santiago de Compostela; Santiago de Compostela Spain
| | | | - Beatriz Prieto
- Departamento de Edafología y Química Agrícola; Facultad de Farmacia; Universidad de Santiago de Compostela; Santiago de Compostela Spain
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11
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Tracy CR, Streten-Joyce C, Dalton R, Nussear KE, Gibb KS, Christian KA. Microclimate and limits to photosynthesis in a diverse community of hypolithic cyanobacteria in northern Australia. Environ Microbiol 2009; 12:592-607. [PMID: 19919538 DOI: 10.1111/j.1462-2920.2009.02098.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hypolithic microbes, primarily cyanobacteria, inhabit the highly specialized microhabitats under translucent rocks in extreme environments. Here we report findings from hypolithic cyanobacteria found under three types of translucent rocks (quartz, prehnite, agate) in a semiarid region of tropical Australia. We investigated the photosynthetic responses of the cyanobacterial communities to light, temperature and moisture in the laboratory, and we measured the microclimatic variables of temperature and soil moisture under rocks in the field over an annual cycle. We also used molecular techniques to explore the diversity of hypolithic cyanobacteria in this community and their phylogenetic relationships within the context of hypolithic cyanobacteria from other continents. Based on the laboratory experiments, photosynthetic activity required a minimum soil moisture of 15% (by mass). Peak photosynthetic activity occurred between approximately 8 degrees C and 42 degrees C, though some photosynthesis occurred between -1 degrees C and 51 degrees C. Maximum photosynthesis rates also occurred at light levels of approximately 150-550 micromol m(-2) s(-1). We used the field microclimatic data in conjunction with these measurements of photosynthetic efficiency to estimate the amount of time the hypolithic cyanobacteria could be photosynthetically active in the field. Based on these data, we estimated that conditions were appropriate for photosynthetic activity for approximately 942 h (approximately 75 days) during the year. The hypolithic cyanobacteria community under quartz, prehnite and agate rocks was quite diverse both within and between rock types. We identified 115 operational taxonomic units (OTUs), with each rock hosting 8-24 OTUs. A third of the cyanobacteria OTUs from northern Australia grouped with Chroococcidiopsis, a genus that has been identified from hypolithic and endolithic communities from the Gobi, Mojave, Atacama and Antarctic deserts. Several OTUs identified from northern Australia have not been reported to be associated with hypolithic communities previously.
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Affiliation(s)
- Christopher R Tracy
- School of Environmental and Life Sciences, Charles Darwin University, Darwin, NT 0909, Australia.
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12
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Gómez-Silva B, Rainey FA, Warren-Rhodes KA, McKay CP, Navarro-González R. Atacama Desert Soil Microbiology. SOIL BIOLOGY 2008. [DOI: 10.1007/978-3-540-74231-9_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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13
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Warren-Rhodes K, Weinstein S, Piatek JL, Dohm J, Hock A, Minkley E, Pane D, Ernst LA, Fisher G, Emani S, Waggoner AS, Cabrol NA, Wettergreen DS, Grin E, Coppin P, Diaz C, Moersch J, Oril GG, Smith T, Stubbs K, Thomas G, Wagner M, Wyatt M, Boyle LN. Robotic ecological mapping: Habitats and the search for life in the Atacama Desert. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2006jg000301] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - S. Weinstein
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - J. L. Piatek
- Department of Earth and Planetary Sciences; University of Tennessee; Knoxville Tennessee USA
| | - J. Dohm
- Department of Hydrology and Water Resources; University of Arizona; Tucson Arizona USA
| | - A. Hock
- Department of Earth and Space Sciences; University of California; Los Angeles California USA
| | - E. Minkley
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - D. Pane
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - L. A. Ernst
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - G. Fisher
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - S. Emani
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - A. S. Waggoner
- Molecular Biosensor and Imaging Center; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | | | - D. S. Wettergreen
- Robotics Institute; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - E. Grin
- SETI Institute; Mountain View California USA
| | - P. Coppin
- Eventscope; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - Chong Diaz
- Universidad Católica del Norte; Antofagasta Chile
| | - J. Moersch
- Department of Earth and Planetary Sciences; University of Tennessee; Knoxville Tennessee USA
| | - G. G. Oril
- Robotics Institute; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - T. Smith
- Robotics Institute; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - K. Stubbs
- Robotics Institute; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - G. Thomas
- Department of Mechanical and Industrial Engineering; University of Iowa; Iowa City Iowa USA
| | - M. Wagner
- Robotics Institute; Carnegie Mellon University; Pittsburgh Pennsylvania USA
| | - M. Wyatt
- Department of Hydrology and Water Resources; University of Arizona; Tucson Arizona USA
| | - L. Ng Boyle
- Department of Mechanical and Industrial Engineering; University of Iowa; Iowa City Iowa USA
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Cáceres L, Gómez-Silva B, Garró X, Rodríguez V, Monardes V, McKay CP. Relative humidity patterns and fog water precipitation in the Atacama Desert and biological implications. ACTA ACUST UNITED AC 2007. [DOI: 10.1029/2006jg000344] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luis Cáceres
- Chemical Engineering Department; Universidad de Antofagasta; Antofagasta Chile
| | | | - Ximena Garró
- Chemical Engineering Department; Universidad de Antofagasta; Antofagasta Chile
| | - Violeta Rodríguez
- Instituto del Desierto; Universidad de Antofagasta; Antofagasta Chile
| | - Vinka Monardes
- Instituto del Desierto; Universidad de Antofagasta; Antofagasta Chile
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