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Cadena S, Cerqueda-García D, Uribe-Flores MM, Ramírez SI. Metagenomic profiling of halites from the Atacama Desert: an extreme environment with natural perchlorate does not promote high diversity of perchlorate reducing microorganisms. Extremophiles 2024; 28:25. [PMID: 38664270 DOI: 10.1007/s00792-024-01342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 04/12/2024] [Indexed: 07/17/2024]
Abstract
We surveyed the presence of perchlorate-reducing microorganisms in available metagenomic data of halite environments from the Atacama Desert, an extreme environment characterized by high perchlorate concentrations, intense ultraviolet radiation, saline and oxidizing soils, and severe desiccation. While the presence of perchlorate might suggest a broad community of perchlorate reducers or a high abundance of a dominant taxa, our search reveals a scarce presence. In fact, we identified only one halophilic species, Salinibacter sp003022435, carrying the pcrA and pcrC genes, represented in low abundance. Moreover, we also discovered some napA genes and organisms carrying the nitrate reductase nasB gene, which hints at the possibility of cryptic perchlorate reduction occurring in these ecosystems. Our findings contribute with the knowledge of perchlorate reduction metabolism potentially occurring in halites from Atacama Desert and point towards promising future research into the perchlorate-reducing mechanism in Salinibacter, a common halophilic bacterium found in hypersaline ecosystems, whose metabolic potential remains largely unknown.
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Affiliation(s)
- Santiago Cadena
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad #1001 Col. Chamilpa, C. P. 62209, Cuernavaca, Morelos, Mexico
| | - Daniel Cerqueda-García
- Red de Manejo Biorracional de Plagas y Vectores, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C., Carretera Antigua a Coatepec #351, Col. El Haya, C. P. 91073, Xalapa, Veracruz, Mexico
| | - María Magdalena Uribe-Flores
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad #1001 Col. Chamilpa, C. P. 62209, Cuernavaca, Morelos, Mexico
| | - Sandra I Ramírez
- Centro de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Av. Universidad #1001 Col. Chamilpa, C. P. 62209, Cuernavaca, Morelos, Mexico.
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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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Carr CE, Ramírez-Colón JL, Duzdevich D, Lee S, Taniguchi M, Ohshiro T, Komoto Y, Soderblom JM, Zuber MT. Solid-State Single-Molecule Sensing with the Electronic Life-Detection Instrument for Enceladus/Europa (ELIE). ASTROBIOLOGY 2023; 23:1056-1070. [PMID: 37782210 DOI: 10.1089/ast.2022.0119] [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: 10/03/2023]
Abstract
Growing evidence of the potential habitability of Ocean Worlds across our solar system is motivating the advancement of technologies capable of detecting life as we know it-sharing a common ancestry or physicochemical origin with life on Earth-or don't know it, representing a distinct emergence of life different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of-principle in a laboratory environment, we demonstrate the single-molecule detection of the amino acid L-proline at a 10 μM concentration in a compact system. Based on ELIE's solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO-LUMO gap (energy difference between a molecule's highest energy-occupied molecular orbital and lowest energy-unoccupied molecular orbital) as a novel metric to assess amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived α-amino acid abundance distributions to reduce the false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in a plume, surface, or subsurface of ice moons such as Enceladus or Europa. One-Sentence Summary: A solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we don't know it.
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Affiliation(s)
- Christopher E Carr
- Daniel Guggenheim School of Aerospace Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - José L Ramírez-Colón
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Daniel Duzdevich
- Massachusetts General Hospital, Department of Molecular Biology, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Boston, Massachusetts, USA
- Current address: Department of Chemistry, University of Chicago, Chicago, Illinois, USA
| | - Sam Lee
- MIT Department of Electrical Engineering and Computer Science, Cambridge, Massachusetts, USA
| | - Masateru Taniguchi
- Osaka University, Institute of Scientific and Industrial Research, Osaka, Japan
| | - Takahito Ohshiro
- Osaka University, Institute of Scientific and Industrial Research, Osaka, Japan
| | - Yuki Komoto
- Osaka University, Institute of Scientific and Industrial Research, Osaka, Japan
| | - Jason M Soderblom
- MIT Department of Earth, Atmospheric and Planetary Sciences, Cambridge, Massachusetts, USA
| | - M T Zuber
- MIT Department of Earth, Atmospheric and Planetary Sciences, Cambridge, Massachusetts, USA
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Remote Sensing Survey of Altiplano-Puna Volcanic Complex Rocks and Minerals for Planetary Analog Use. REMOTE SENSING 2022. [DOI: 10.3390/rs14092081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
The Altiplano-Puna Volcanic Complex (APVC) of the Central Andes is an arid region with extensive volcanism, possessing various geological features comparable to those of other solar system objects. The unique features of the APVC, e.g., hydrothermal fields and evaporite salars, have been used as planetary analogs before, but the complexity of the APVC presents a wealth of opportunities for more analog studies that have not been exploited previously. Motivated by the potential of using the APVC as an analog of the volcanic terrains of solar system objects, we mapped the mineralogy and silica content of the APVC up to ~100,000 km2 in northern Chile based on a combination of remote sensing data resembling those of the Moon and Mars. The band ratio indices of Landsat 8 Operational Land Imager multispectral images and mineral classifications based on spectral hourglass approach using Earth Observing-1 Hyperion hyperspectral images (both in the visible to shortwave infrared wavelengths) were used to map iron-bearing and alteration minerals. We also used Hyperion imagery to detect feldspar spectral signatures and demonstrated that feldspar minerals can be detected on non-anorthosites, which may influence interpretations of feldspar spectral signatures on Mars. From the Terra Advanced Spaceborne Thermal Emission and Reflection Radiometer Global Emissivity Dataset, we derived the silica percentage of non-evaporite rocks within errors of approximately 2–3 wt.% SiO2 for those in the 60–70 wt.% range (about 8 wt.% errors for the 50–60 wt.% range). Based on an integrated assessment of the three datasets, we highlighted three regions of particular interest worthy of further field investigation. We also evaluated the benefits and limitations of all three remote sensing methods for mapping key minerals and capturing rock diversity, based on available samples and existing geological maps.
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Raymond-Bouchard I, Maggiori C, Brennan L, Altshuler I, Manchado JM, Parro V, Whyte LG. Assessment of Automated Nucleic Acid Extraction Systems in Combination with MinION Sequencing As Potential Tools for the Detection of Microbial Biosignatures. ASTROBIOLOGY 2022; 22:87-103. [PMID: 34962136 DOI: 10.1089/ast.2020.2349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The utilization of nanopore technologies for the detection of organic biogenic compounds has garnered significant focus in recent years. Oxford Nanopore Technologies' (ONT) MinION instrument, which can detect and sequence nucleic acids (NAs), is one such example. These technologies have much promise for unambiguous life detection but require significant development in terms of methods for extraction and preparation of NAs for biosignature detection and their feasibility for use in astrobiology-focused field missions. In this study, we tested pre-existing, automated, or semiautomated NA extraction technologies, coupled with automated ONT VolTRAX NA sample preparation, and verification with Nanopore MinION sequencing. All of the extraction systems tested (SuperFastPrep2, ClaremontX1, and SOLID-Sample Preparation Unit) showed potential for extracting DNA from Canadian High Arctic environments analogous to Mars, Europa, and Enceladus, which could subsequently be detected and sequenced with the MinION. However, they differed with regard to efficacy, yield, purity, and sequencing and annotation quality. Overall, bead beating-based systems performed the best for these parameters. In addition, we showed that the MinION could sequence unpurified DNA contained in crude cell lysates. This is valuable from an astrobiology perspective because purification steps are time-consuming and complicate the requirements for an automated extraction and life detection system. Our results indicate that semiautomated NA extraction and preparation technologies hold much promise, and with increased optimization and automation could be coupled to a larger platform incorporating nanopore detection and sequencing of NAs for life detection applications.
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Affiliation(s)
| | - Catherine Maggiori
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | | | - Victor Parro
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
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Hallsworth JE, Mancinelli RL, Conley CA, Dallas TD, Rinaldi T, Davila AF, Benison KC, Rapoport A, Cavalazzi B, Selbmann L, Changela H, Westall F, Yakimov MM, Amils R, Madigan MT. Astrobiology of life on Earth. Environ Microbiol 2021; 23:3335-3344. [PMID: 33817931 DOI: 10.1111/1462-2920.15499] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/29/2022]
Abstract
Astrobiology is mistakenly regarded by some as a field confined to studies of life beyond Earth. Here, we consider life on Earth through an astrobiological lens. Whereas classical studies of microbiology historically focused on various anthropocentric sub-fields (such as fermented foods or commensals and pathogens of crop plants, livestock and humans), addressing key biological questions via astrobiological approaches can further our understanding of all life on Earth. We highlight potential implications of this approach through the articles in this Environmental Microbiology special issue 'Ecophysiology of Extremophiles'. They report on the microbiology of places/processes including low-temperature environments and chemically diverse saline- and hypersaline habitats; aspects of sulphur metabolism in hypersaline lakes, dysoxic marine waters, and thermal acidic springs; biology of extremophile viruses; the survival of terrestrial extremophiles on the surface of Mars; biological soils crusts and rock-associated microbes of deserts; subsurface and deep biosphere, including a salticle formed within Triassic halite; and interactions of microbes with igneous and sedimentary rocks. These studies, some of which we highlight here, contribute to our understanding of the spatiotemporal reach of Earth'sfunctional biosphere, and the tenacity of terrestrial life. Their findings will help set the stage for future work focused on the constraints for life, and how organisms adapt and evolve to circumvent these constraints.
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Affiliation(s)
- John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 7BL, UK
| | - Rocco L Mancinelli
- Bay Area Environmental Research Institute, NASA Ames Research Center, Mountain View, CA, 94035, USA
| | | | - Tiffany D Dallas
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, 19 Chlorine Gardens, Belfast, BT9 7BL, UK
| | - Teresa Rinaldi
- Department of Biology and Biotechnology, Sapienza University of Rome, Rome, 00185, Italy
| | | | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, WV, 26506-6300, USA
| | - Alexander Rapoport
- Laboratory of Cell Biology, Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas Str., 1-537, Riga, LV-1004, Latvia
| | - Barbara Cavalazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, 01100, Italy.,Italian Antarctic National Museum (MNA), Mycological Section, Genoa, 16128, Italy
| | - Hitesh Changela
- Key Laboratory of Earth and Planetary Physics, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, 100029, China.,Department of Earth and Planetary Science, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Frances Westall
- CNRS, Ctr Biophys Mol UPR 4301, Rue Charles Sadron, CS 80054, Orleans, F-45071, France
| | - Michail M Yakimov
- Institute of Marine Biological Resources and Biotechnology, IRBIM-CNR, Messina, 98122, Italy
| | - Ricardo Amils
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid (CBMSO, CSICUAM), Cantoblanco, Madrid, 28049, Spain.,Centro de Astrobiología (CAB, INTA-CSIC), Torrejón de Ardoz, 28055, Spain
| | - Michael T Madigan
- School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
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Riedo A, de Koning C, Stevens AH, Cockell CS, McDonald A, López AC, Grimaudo V, Tulej M, Wurz P, Ehrenfreund P. The Detection of Elemental Signatures of Microbes in Martian Mudstone Analogs Using High Spatial Resolution Laser Ablation Ionization Mass Spectrometry. ASTROBIOLOGY 2020; 20:1224-1235. [PMID: 33001758 DOI: 10.1089/ast.2019.2087] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The detection and identification of biosignatures on planetary bodies such as Mars in situ is extremely challenging. Current knowledge from space exploration missions suggests that a suite of complementary instruments is required in situ for a successful identification of past or present life. For future exploration missions, new and innovative instrumentation capable of high spatial resolution chemical (elemental and isotope) analysis of solids with improved measurement capabilities is of considerable interest because a multitude of potential signatures of extinct or extant life have dimensions on the micrometer scale. The aim of this study is to extend the current measurement capabilities of a miniature laser ablation ionization mass spectrometer (LIMS) designed for space exploration missions to detect signatures of microbial life. In total, 14 martian mudstone analogue samples were investigated regarding their elemental composition. Half the samples were artificially inoculated with a low number density of microbes, and half were used as abiotic controls. The samples were treated in a number of ways. Some were cultured anaerobically and some aerobically; some abiotic samples were incubated with water, and some remained dry. Some of the samples were exposed to a large dose of γ radiation, and some were left un-irradiated. While no significant elemental differences were observed between the applied sample treatments, the instrument showed the capability to detect biogenic element signatures of the inoculated microbes by monitoring biologically relevant elements, such as hydrogen, carbon, sulfur, iron, and so on. When an enrichment in carbon was measured in the samples but no simultaneous increase in other biologically relevant elements was detected, it suggests, for example, a carbon-containing inclusion; when the enrichment was in carbon and in bio-relevant elements, it suggests the presences of microbes. This study presents first results on the detection of biogenic element patterns of microbial life using a miniature LIMS system designed for space exploration missions.
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Affiliation(s)
- Andreas Riedo
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, Leiden, The Netherlands
- Space Research and Planetary Sciences, Physics Institute, University of Bern, Bern, Switzerland
| | - Coen de Koning
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, Leiden, The Netherlands
| | - Adam H Stevens
- School of Physics and Astronomy, UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Charles S Cockell
- School of Physics and Astronomy, UK Centre for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alison McDonald
- School of Engineering, Bioimaging Facility, University of Edinburgh, Edinburgh, United Kingdom
| | - Alena Cedeño López
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Valentine Grimaudo
- Space Research and Planetary Sciences, Physics Institute, University of Bern, Bern, Switzerland
| | - Marek Tulej
- Space Research and Planetary Sciences, Physics Institute, University of Bern, Bern, Switzerland
| | - Peter Wurz
- Space Research and Planetary Sciences, Physics Institute, University of Bern, Bern, Switzerland
| | - Pascale Ehrenfreund
- Laboratory for Astrophysics, Leiden Observatory, Leiden University, Leiden, The Netherlands
- Space Policy Institute, George Washington University, Washington, DC, USA
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Mora MF, Kehl F, Tavares da Costa E, Bramall N, Willis PA. Fully Automated Microchip Electrophoresis Analyzer for Potential Life Detection Missions. Anal Chem 2020; 92:12959-12966. [DOI: 10.1021/acs.analchem.0c01628] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Maria F. Mora
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, United States
| | - Florian Kehl
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, United States
| | - Eric Tavares da Costa
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, United States
| | - Nathan Bramall
- Leiden Measurement Technology LLC, 1230 Mountain View-Alviso Road Suite A, Sunnyvale, California 94089, United States
| | - Peter A. Willis
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, United States
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