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Wang H, Pijl A, Liu B, Wamelink W, Korthals GW, Costa OYA, Kuramae EE. A Comparison of Different Protocols for the Extraction of Microbial DNA Inhabiting Synthetic Mars Simulant Soil. Microorganisms 2024; 12:760. [PMID: 38674704 PMCID: PMC11051824 DOI: 10.3390/microorganisms12040760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Compared with typical Earth soil, Martian soil and Mars simulant soils have distinct properties, including pH > 8.0 and high contents of silicates, iron-rich minerals, sulfates, and metal oxides. This unique soil matrix poses a major challenge for extracting microbial DNA. In particular, mineral adsorption and the generation of destructive hydroxyl radicals through cationic redox cycling may interfere with DNA extraction. This study evaluated different protocols for extracting microbial DNA from Mars Global Simulant (MGS-1), a Mars simulant soil. Two commercial kits were tested: the FastDNA SPIN Kit for soil ("MP kit") and the DNeasy PowerSoil Pro Kit ("PowerSoil kit"). MGS-1 was incubated with living soil for five weeks, and DNA was extracted from aliquots using the kits. After extraction, the DNA was quantified with a NanoDrop spectrophotometer and used as the template for 16S rRNA gene amplicon sequencing and qPCR. The MP kit was the most efficient, yielding approximately four times more DNA than the PowerSoil kit. DNA extracted using the MP kit with 0.5 g soil resulted in 28,642-37,805 16S rRNA gene sequence reads and 30,380-42,070 16S rRNA gene copies, whereas the 16S rRNA gene could not be amplified from DNA extracted using the PowerSoil kit. We suggest that the FastDNA SPIN Kit is the best option for studying microbial communities in Mars simulant soils.
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Affiliation(s)
- Han Wang
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Agata Pijl
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Binbin Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang 050021, China;
| | - Wieger Wamelink
- Biodiversity and Policy, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Gerard W. Korthals
- Bioindications and Plant Health, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB Wageningen, The Netherlands;
| | - Ohana Y. A. Costa
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6708 PB Wageningen, The Netherlands; (H.W.); (A.P.); (O.Y.A.C.)
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
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2
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Bomberg M, Miettinen H. Anionic nanocellulose as competing agent in microbial DNA extraction from mine process samples. J Microbiol Methods 2023; 215:106850. [PMID: 37907119 DOI: 10.1016/j.mimet.2023.106850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/04/2023] [Accepted: 10/25/2023] [Indexed: 11/02/2023]
Abstract
Microorganisms in flotation and minerals processing may significantly affect the grade and yield of metal concentrates. However, studying the phenomena requires working techniques to detach microorganisms and their DNA from mineral particles to which they strongly adhere. We developed a new method utilizing the competitive properties of anionic nanocellulose to block sorption of DNA to and detach microbial cells from mineral particles from ore processing. In general, up to one ng DNA mL-1 sample was obtained with the custom anionic nanocellulose method (CM) compared to DNA amounts below the Qubit assay's detection limit for extractions with a commercial kit (KIT). Similarly, 0.5-4 orders of magnitude more bacterial 16S and fungal 5.8S rRNA gene copies were detected by qPCR from CM treated samples compared to KIT extractions. A clear difference in the detected microbial community structure between CM and KIT extracted samples was also observed. Commercial kits optimized for mineral soils are easy to use and time efficient but may miss a considerable part of the microbial communities. A competing agent such as anionic nanocellulose may decrease the interaction between microorganisms or their DNA and minerals and provide a comprehensive view into the microbial communities in mineral processing environments.
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Affiliation(s)
- Malin Bomberg
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland.
| | - Hanna Miettinen
- VTT Technical Research Centre of Finland, P.O. Box 1000, 02044 VTT, Finland
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3
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Xia Z, Patchin M, McKay CP, Drndić M. Deoxyribonucleic Acid Extraction from Mars Analog Soils and Their Characterization with Solid-State Nanopores. ASTROBIOLOGY 2022; 22:992-1008. [PMID: 35731031 DOI: 10.1089/ast.2021.0051] [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: 06/15/2023]
Abstract
Life detection on Mars is an important topic that includes a direct search for biomarkers. This requires instruments for in situ biomarker detection that are compact, lightweight, and able to withstand operations in space. Solid-state nanopores are excellent candidates that allow fast single-molecule detection. They can withstand high temperatures and be sterilized to minimize planetary contamination. The instruments are portable with low-power requirements. We demonstrate a few key results in advancing the use of nanopores for in-space applications. First, we developed modified deoxyribonucleic acid (DNA) extraction protocols to extract DNA from Mars analog soils. Second, we used silicon nitride nanopores to demonstrate the detection of extracted DNA and corresponding current characteristics. The yields and properties of extracted DNA (e.g., estimated diameters) varied somewhat by soil types, extraction methods, and nanopores used. The yields varied from a minimum of 0.9 ng DNA/g soil for a magnesium carbonate sample from Lake Salda to a maximum of 210 ng DNA/g soil for a calcium carbonate sample from Trona Pinnacles. For a given soil type, yields from different methods varied by a factor of up to 50. These observations motivate future studies with a broader range of Mars-like soils and improved instruments to increase signal-to-noise-ratio at higher measurement bandwidths.
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Affiliation(s)
- Zehui Xia
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Margaret Patchin
- Goeppert LLC, Pennovation Works, Philadelphia, Pennsylvania, USA
| | - Christopher P McKay
- Space Science Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Marija Drndić
- David Rittenhouse Laboratory, Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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4
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MacKenzie SM, Neveu M, Davila AF, Lunine JI, Cable ML, Phillips-Lander CM, Eigenbrode JL, Waite JH, Craft KL, Hofgartner JD, McKay CP, Glein CR, Burton D, Kounaves SP, Mathies RA, Vance SD, Malaska MJ, Gold R, German CR, Soderlund KM, Willis P, Freissinet C, McEwen AS, Brucato JR, de Vera JPP, Hoehler TM, Heldmann J. Science Objectives for Flagship-Class Mission Concepts for the Search for Evidence of Life at Enceladus. ASTROBIOLOGY 2022; 22:685-712. [PMID: 35290745 PMCID: PMC9233532 DOI: 10.1089/ast.2020.2425] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/21/2022] [Indexed: 05/07/2023]
Abstract
Cassini revealed that Saturn's Moon Enceladus hosts a subsurface ocean that meets the accepted criteria for habitability with bio-essential elements and compounds, liquid water, and energy sources available in the environment. Whether these conditions are sufficiently abundant and collocated to support life remains unknown and cannot be determined from Cassini data. However, thanks to the plume of oceanic material emanating from Enceladus' south pole, a new mission to Enceladus could search for evidence of life without having to descend through kilometers of ice. In this article, we outline the science motivations for such a successor to Cassini, choosing the primary science goal to be determining whether Enceladus is inhabited and assuming a resource level equivalent to NASA's Flagship-class missions. We selected a set of potential biosignature measurements that are complementary and orthogonal to build a robust case for any life detection result. This result would be further informed by quantifications of the habitability of the environment through geochemical and geophysical investigations into the ocean and ice shell crust. This study demonstrates that Enceladus' plume offers an unparalleled opportunity for in situ exploration of an Ocean World and that the planetary science and astrobiology community is well equipped to take full advantage of it in the coming decades.
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Affiliation(s)
| | - Marc Neveu
- Department of Astronomy, University of Maryland, College Park, Maryland, USA
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - Alfonso F. Davila
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| | - Jonathan I. Lunine
- Department of Astronomy, Cornell University, Ithaca, New York, USA
- Carl Sagan Institute, Cornell University, Ithaca, New York, USA
| | - Morgan L. Cable
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Jennifer L. Eigenbrode
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
| | - J. Hunter Waite
- Space Science and Engineering Division, Southwest Research Institute, San Antonio, Texas, USA
| | - Kate L. Craft
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Jason D. Hofgartner
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Chris P. McKay
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| | - Christopher R. Glein
- Space Science and Engineering Division, Southwest Research Institute, San Antonio, Texas, USA
| | - Dana Burton
- Department of Anthropology, George Washington University, Washington, District of Columbia, USA
| | | | - Richard A. Mathies
- Chemistry Department and Space Sciences Laboratory, University of California, Berkeley, Berkeley, California, USA
| | - Steven D. Vance
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Michael J. Malaska
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Robert Gold
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Christopher R. German
- Department of Geology & Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Krista M. Soderlund
- Institute for Geophysics, Jackson School of Geosciences, The University of Texas at Austin, Austin, Texas, USA
| | - Peter Willis
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | - Alfred S. McEwen
- Lunar and Planetary Lab, University of Arizona, Tucson, Arizona, USA
| | | | - Jean-Pierre P. de Vera
- Space Operations and Astronaut Training, MUSC, German Aerospace Center (DLR), Cologne, Germany
| | - Tori M. Hoehler
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
| | - Jennifer Heldmann
- Division of Space Science and Astrobiology, NASA Ames Research Center, Moffett Field, California, USA
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5
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Cassaro A, Pacelli C, Baqué M, Cavalazzi B, Gasparotto G, Saladino R, Botta L, Böttger U, Rabbow E, de Vera JP, Onofri S. Investigation of fungal biomolecules after Low Earth Orbit exposure: a testbed for the next Moon missions. Environ Microbiol 2022; 24:2938-2950. [PMID: 35437941 PMCID: PMC9540993 DOI: 10.1111/1462-2920.15995] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 11/28/2022]
Abstract
The Moon is characterized by extremely harsh conditions due to ultraviolet irradiation, wide temperature extremes, vacuum resulting from the absence of an atmosphere and high ionizing radiation. Therefore, its surface may provide a unique platform to investigate the effects of such conditions. For lunar exploration with the Lunar Gateway platform, exposure experiments in Low Earth Orbit are useful testbeds to prepare for lunar space experiments and to understand how and if potential biomarkers are influenced by extra‐terrestrial conditions. During the BIOMEX (BIOlogy and Mars EXperiment) project, dried colonies of the fungus Cryomyces antarcticus grown on Lunar Regolith Analogue (LRA) were exposed to space conditions for 16 months aboard the EXPOSE‐R2 payload outside the International Space Station. In this study, we investigated the stability/degradation of fungal biomarkers in LRA after exposure to (i) simulated space and (ii) real space conditions, using Raman spectroscopy, gas chromatography–mass spectrometry and DNA amplification. The results demonstrated that fungal biomarkers were detectable after 16 months of real space exposure. This work will contribute to the interpretation of data from future biological experiments in the Cislunar orbit with the Lunar Gateway platform and/or on the lunar surface, in preparation for the next step of human exploration.
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Affiliation(s)
- Alessia Cassaro
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Claudia Pacelli
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy.,Human Spaceflight and Scientific Research Unit, Italian Space Agency, via del Politecnico, Rome, 00133, Italy
| | - Mickael Baqué
- German Aerospace Center (DLR), Institute of Planetary Research, Planetary Laboratories Department, Rutherfordstraße 2, Berlin, Germany
| | - Barbara Cavalazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Zamboni 67, Bologna, 40126, Italy.,Department of Geology, University of Johannesburg, Auckland Park, Johannesburg, 2006, South Africa.,Le Studium Loire Valley Institute for Advanced Studies, Rue Dupanloup 1, Orléans, France
| | - Giorgio Gasparotto
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Zamboni 67, Bologna, 40126, Italy
| | - Raffaele Saladino
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
| | - Ute Böttger
- German Aerospace Center (DLR), Institute of Optical Sensor Systems, Rutherfordstraße 2, Berlin, Germany
| | - Elke Rabbow
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology, Linder Höhe, Cologne, 51147, Germany
| | - Jean-Pierre de Vera
- Space Operations and Astronaut Training, MUSC, German Aerospace Center (DLR), Linder Höhe, Cologne, 51147, Germany
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'Università snc, Viterbo, 01100, Italy
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6
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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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7
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Seyler L, Kujawinski EB, Azua-Bustos A, Lee MD, Marlow J, Perl SM, Cleaves II HJ. Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. ASTROBIOLOGY 2020; 20:1251-1261. [PMID: 32551936 PMCID: PMC7116171 DOI: 10.1089/ast.2019.2135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It is now routinely possible to sequence and recover microbial genomes from environmental samples. To the degree it is feasible to assign transcriptional and translational functions to these genomes, it should be possible, in principle, to largely understand the complete molecular inputs and outputs of a microbial community. However, gene-based tools alone are presently insufficient to describe the full suite of chemical reactions and small molecules that compose a living cell. Metabolomic tools have developed quickly and now enable rapid detection and identification of small molecules within biological and environmental samples. The convergence of these technologies will soon facilitate the detection of novel enzymatic activities, novel organisms, and potentially extraterrestrial life-forms on solar system bodies. This review explores the methodological problems and scientific opportunities facing researchers who hope to apply metabolomic methods in astrobiology-related fields, and how present challenges might be overcome.
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Affiliation(s)
- Lauren Seyler
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Address correspondence to: Lauren Seyler, Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, 86 Water Street, Woods Hole, MA 02543, USA
| | - Elizabeth B. Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Armando Azua-Bustos
- Department of Planetology and Habitability, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Michael D. Lee
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Exobiology Branch, NASA Ames Research Center, Moffett Field, California, USA
| | - Jeffrey Marlow
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Scott M. Perl
- Geological and Planetary Sciences, California Institute of Technology/NASA Jet Propulsion Laboratory, Pasadena, California, USA
- Mineral Sciences, Los Angeles Natural History Museum, Los Angeles, California, USA
| | - Henderson James Cleaves II
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- School of Natural Sciences, Institute for Advanced Study, Princeton, New Jersey, USA
- Geographical Research Laboratory, Carnegie Institution of Washington
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8
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The search for organic compounds with TMAH thermochemolysis: From Earth analyses to space exploration experiments. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.115896] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Mojarro A, Hachey J, Bailey R, Brown M, Doebler R, Ruvkun G, Zuber MT, Carr CE. Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection. ASTROBIOLOGY 2019; 19:1139-1152. [PMID: 31204862 PMCID: PMC6708270 DOI: 10.1089/ast.2018.1929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recent studies regarding the origins of life and Mars-Earth meteorite transfer simulations suggest that biological informational polymers, such as nucleic acids (DNA and RNA), have the potential to provide unambiguous evidence of life on Mars. To this end, we are developing a metagenomics-based life-detection instrument which integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG). Our goal is to isolate and sequence nucleic acids from extant or preserved life on Mars in order to determine if a particular genetic sequence (1) is distantly related to life on Earth, indicating a shared ancestry due to lithological exchange, or (2) is unrelated to life on Earth, suggesting convergent origins of life on Mars. In this study, we validate prior work on nucleic acid extraction from cells deposited in Mars analog soils down to microbial concentrations (i.e., 104 cells in 50 mg of soil) observed in the driest and coldest regions on Earth. In addition, we report low-input nanopore sequencing results from 2 pg of purified Bacillus subtilis spore DNA simulating ideal extraction yields equivalent to 1 ppb life-detection sensitivity. We achieve this by employing carrier sequencing, a method of sequencing sub-nanogram DNA in the background of a genomic carrier. After filtering of carrier, low-quality, and low-complexity reads we detected 5 B. subtilis reads, 18 contamination reads (including Homo sapiens), and 6 high-quality noise reads believed to be sequencing artifacts.
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Address correspondence to: Angel Mojarro, Massachusetts Institute of Technology, 77 Massachusetts Ave, Room E25-647, Cambridge, MA 02139
| | | | - Ryan Bailey
- Claremont Biosolutions, LLC, Upland, California
| | - Mark Brown
- Claremont Biosolutions, LLC, Upland, California
| | | | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Maria T. Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Christopher E. Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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10
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Chan MA, Hinman NW, Potter-McIntyre SL, Schubert KE, Gillams RJ, Awramik SM, Boston PJ, Bower DM, Des Marais DJ, Farmer JD, Jia TZ, King PL, Hazen RM, Léveillé RJ, Papineau D, Rempfert KR, Sánchez-Román M, Spear JR, Southam G, Stern JC, Cleaves HJ. Deciphering Biosignatures in Planetary Contexts. ASTROBIOLOGY 2019; 19:1075-1102. [PMID: 31335163 PMCID: PMC6708275 DOI: 10.1089/ast.2018.1903] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 03/10/2019] [Indexed: 05/05/2023]
Abstract
Microbial life permeates Earth's critical zone and has likely inhabited nearly all our planet's surface and near subsurface since before the beginning of the sedimentary rock record. Given the vast time that Earth has been teeming with life, do astrobiologists truly understand what geological features untouched by biological processes would look like? In the search for extraterrestrial life in the Universe, it is critical to determine what constitutes a biosignature across multiple scales, and how this compares with "abiosignatures" formed by nonliving processes. Developing standards for abiotic and biotic characteristics would provide quantitative metrics for comparison across different data types and observational time frames. The evidence for life detection falls into three categories of biosignatures: (1) substances, such as elemental abundances, isotopes, molecules, allotropes, enantiomers, minerals, and their associated properties; (2) objects that are physical features such as mats, fossils including trace-fossils and microbialites (stromatolites), and concretions; and (3) patterns, such as physical three-dimensional or conceptual n-dimensional relationships of physical or chemical phenomena, including patterns of intermolecular abundances of organic homologues, and patterns of stable isotopic abundances between and within compounds. Five key challenges that warrant future exploration by the astrobiology community include the following: (1) examining phenomena at the "right" spatial scales because biosignatures may elude us if not examined with the appropriate instrumentation or modeling approach at that specific scale; (2) identifying the precise context across multiple spatial and temporal scales to understand how tangible biosignatures may or may not be preserved; (3) increasing capability to mine big data sets to reveal relationships, for example, how Earth's mineral diversity may have evolved in conjunction with life; (4) leveraging cyberinfrastructure for data management of biosignature types, characteristics, and classifications; and (5) using three-dimensional to n-D representations of biotic and abiotic models overlain on multiple overlapping spatial and temporal relationships to provide new insights.
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Affiliation(s)
- Marjorie A. Chan
- Department of Geology & Geophysics, University of Utah, Salt Lake City, Utah
| | - Nancy W. Hinman
- Department of Geosciences, University of Montana, Missoula, Montana
| | | | - Keith E. Schubert
- Department of Electrical and Computer Engineering, Baylor University, Waco, Texas
| | - Richard J. Gillams
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Electronics and Computer Science, Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Stanley M. Awramik
- Department of Earth Science, University of California, Santa Barbara, Santa Barbara, California
| | - Penelope J. Boston
- NASA Astrobiology Institute, NASA Ames Research Center, Moffett Field, California
| | - Dina M. Bower
- Department of Astronomy, University of Maryland College Park (CRESST), College Park, Maryland
- NASA Goddard Space Flight Center, Greenbelt, Maryland
| | | | - Jack D. Farmer
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona
| | - Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Penelope L. King
- Research School of Earth Sciences, The Australian National University, Canberra, Australia
| | - Robert M. Hazen
- Geophysical Laboratory, Carnegie Institution for Science, Washington, District of Columbia
| | - Richard J. Léveillé
- Department of Earth and Planetary Sciences, McGill University, Montreal, Canada
- Geosciences Department, John Abbott College, Sainte-Anne-de-Bellevue, Canada
| | - Dominic Papineau
- London Centre for Nanotechnology, University College London, London, United Kingdom
- Department of Earth Sciences, University College London, London, United Kingdom
- Centre for Planetary Sciences, University College London, London, United Kingdom
- BioGeology and Environmental Geology State Key Laboratory, School of Earth Sciences, China University of Geosciences, Wuhan, China
| | - Kaitlin R. Rempfert
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado
| | - Mónica Sánchez-Román
- Earth Sciences Department, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado
| | - Gordon Southam
- School of Earth and Environmental Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | | | - Henderson James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
- Program in Interdisciplinary Studies, Institute for Advanced Study, Princeton, New Jersey
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11
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Sutton MA, Burton AS, Zaikova E, Sutton RE, Brinckerhoff WB, Bevilacqua JG, Weng MM, Mumma MJ, Johnson SS. Radiation Tolerance of Nanopore Sequencing Technology for Life Detection on Mars and Europa. Sci Rep 2019; 9:5370. [PMID: 30926841 PMCID: PMC6441015 DOI: 10.1038/s41598-019-41488-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/28/2019] [Indexed: 12/02/2022] Open
Abstract
The search for life beyond Earth is a key motivator in space exploration. Informational polymers, like DNA and RNA, are key biosignatures for life as we know it. The MinION is a miniature DNA sequencer based on versatile nanopore technology that could be implemented on future planetary missions. A critical unanswered question is whether the MinION and its protein-based nanopores can withstand increased radiation exposure outside Earth's shielding magnetic field. We evaluated the effects of ionizing radiation on the MinION platform - including flow cells, reagents, and hardware - and discovered limited performance loss when exposed to ionizing doses comparable to a mission to Mars. Targets with harsher radiation environments, like Europa, would require improved radiation resistance via additional shielding or design refinements.
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Affiliation(s)
- Mark A Sutton
- Solar System Exploration Division and Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
- Wichita State University, Wichita, KS, 67260, USA
| | - Aaron S Burton
- Astromaterials Research and Exploration Science Division, NASA Johnson Space Center, Houston, TX, 77058, USA
| | - Elena Zaikova
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | | | - William B Brinckerhoff
- Solar System Exploration Division and Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Julie G Bevilacqua
- Department of Biology, Georgetown University, Washington, DC, 20057, USA
| | - Margaret M Weng
- Department of Earth and Planetary Science, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Michael J Mumma
- Solar System Exploration Division and Goddard Center for Astrobiology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, DC, 20057, USA.
- Science, Technology, and International Affairs Program, Georgetown University, Washington, DC, 20057, USA.
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12
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Experimental studies addressing the longevity of Bacillus subtilis spores - The first data from a 500-year experiment. PLoS One 2018; 13:e0208425. [PMID: 30513104 PMCID: PMC6279046 DOI: 10.1371/journal.pone.0208425] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/17/2018] [Indexed: 11/23/2022] Open
Abstract
The ability to form endospores allows certain Gram-positive bacteria (e.g. Bacillus subtilis) to challenge the limits of microbial resistance and survival. Thus, B. subtilis is able to tolerate many environmental extremes by transitioning into a dormant state as spores, allowing survival under otherwise unfavorable conditions. Despite thorough study of spore resistance to external stresses, precisely how long B. subtilis spores can lie dormant while remaining viable, a period that potentially far exceeds the human lifespan; is not known although convincing examples of long term spore survival have been recorded. In this study, we report the first data from a 500-year microbial experiment, which started in 2014 and will finish in 2514. A set of vials containing a defined concentration of desiccated B. subtilis spores is opened and tested for viability every two years for the first 24 years and then every 25 years until experiment completion. Desiccated baseline spore samples were also exposed to environmental stresses, including X-rays, 254 nm UV-C, 10% H2O2, dry heat (120°C) and wet heat (100°C) to investigate how desiccated spores respond to harsh environmental conditions after long periods of storage. Data from the first 2 years of storage show no significant decrease in spore viability. Additionally, spores of B. subtilis were subjected to various short-term storage experiments, revealing that space-like vacuum and high NaCl concentration negatively affected spore viability.
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13
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Mojarro A, Hachey J, Ruvkun G, Zuber MT, Carr CE. CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing. BMC Bioinformatics 2018; 19:108. [PMID: 29587645 PMCID: PMC5872496 DOI: 10.1186/s12859-018-2124-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 03/21/2018] [Indexed: 01/31/2023] Open
Abstract
Background Long-read nanopore sequencing technology is of particular significance for taxonomic identification at or below the species level. For many environmental samples, the total extractable DNA is far below the current input requirements of nanopore sequencing, preventing “sample to sequence” metagenomics from low-biomass or recalcitrant samples. Results Here we address this problem by employing carrier sequencing, a method to sequence low-input DNA by preparing the target DNA with a genomic carrier to achieve ideal library preparation and sequencing stoichiometry without amplification. We then use CarrierSeq, a sequence analysis workflow to identify the low-input target reads from the genomic carrier. We tested CarrierSeq experimentally by sequencing from a combination of 0.2 ng Bacillus subtilis ATCC 6633 DNA in a background of 1000 ng Enterobacteria phage λ DNA. After filtering of carrier, low quality, and low complexity reads, we detected target reads (B. subtilis), contamination reads, and “high quality noise reads” (HQNRs) not mapping to the carrier, target or known lab contaminants. These reads appear to be artifacts of the nanopore sequencing process as they are associated with specific channels (pores). Conclusion By treating sequencing as a Poisson arrival process, we implement a statistical test to reject data from channels dominated by HQNRs while retaining low-input target reads.
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Affiliation(s)
- Angel Mojarro
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave, E25-610, Cambridge, MA, 02139, USA.
| | | | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Maria T Zuber
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave, E25-610, Cambridge, MA, 02139, USA
| | - Christopher E Carr
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave, E25-610, Cambridge, MA, 02139, USA.,Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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14
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Fairén AG, Parro V, Schulze-Makuch D, Whyte L. Is Searching for Martian Life a Priority for the Mars Community? ASTROBIOLOGY 2018; 18:101-107. [PMID: 29359967 PMCID: PMC5820680 DOI: 10.1089/ast.2017.1772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/02/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Alberto G. Fairén
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
- Department of Astronomy, Cornell University, Ithaca, New York, USA
| | - Victor Parro
- Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Dirk Schulze-Makuch
- Center of Astronomy and Astrophysics, Technical University Berlin, Berlin, Germany
- School of the Environment, Washington State University, Pullman, Washington, USA
| | - Lyle Whyte
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, Canada
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15
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Goordial J, Altshuler I, Hindson K, Chan-Yam K, Marcolefas E, Whyte LG. In Situ Field Sequencing and Life Detection in Remote (79°26'N) Canadian High Arctic Permafrost Ice Wedge Microbial Communities. Front Microbiol 2017; 8:2594. [PMID: 29326684 PMCID: PMC5742409 DOI: 10.3389/fmicb.2017.02594] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 12/12/2017] [Indexed: 11/18/2022] Open
Abstract
Significant progress is being made in the development of the next generation of low cost life detection instrumentation with much smaller size, mass and energy requirements. Here, we describe in situ life detection and sequencing in the field in soils over laying ice wedges in polygonal permafrost terrain on Axel Heiberg Island, located in the Canadian high Arctic (79°26'N), an analog to the polygonal permafrost terrain observed on Mars. The life detection methods used here include (1) the cryo-iPlate for culturing microorganisms using diffusion of in situ nutrients into semi-solid media (2) a Microbial Activity Microassay (MAM) plate (BIOLOG Ecoplate) for detecting viable extant microorganisms through a colourimetric assay, and (3) the Oxford Nanopore MinION for nucleic acid detection and sequencing of environmental samples and the products of MAM plate and cryo-iPlate. We obtained 39 microbial isolates using the cryo-iPlate, which included several putatively novel strains based on the 16S rRNA gene, including a Pedobacter sp. (96% closest similarity in GenBank) which we partially genome sequenced using the MinION. The MAM plate successfully identified an active community capable of L-serine metabolism, which was used for metagenomic sequencing with the MinION to identify the active and enriched community. A metagenome on environmental ice wedge soil samples was completed, with base calling and uplink/downlink carried out via satellite internet. Validation of MinION sequencing using the Illumina MiSeq platform was consistent with the results obtained with the MinION. The instrumentation and technology utilized here is pre-existing, low cost, low mass, low volume, and offers the prospect of equipping micro-rovers and micro-penetrators with aggressive astrobiological capabilities. Since potentially habitable astrobiology targets have been identified (RSLs on Mars, near subsurface water ice on Mars, the plumes and oceans of Europa and Enceladus), future astrobiology missions will certainly target these areas and there is a need for direct life detection instrumentation.
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Affiliation(s)
- J Goordial
- Department of Natural Resource Sciences, McGill University, Ste. Anne-de-Bellevue, QC, Canada
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Ianina Altshuler
- Department of Natural Resource Sciences, McGill University, Ste. Anne-de-Bellevue, QC, Canada
| | - Katherine Hindson
- Department of Natural Resource Sciences, McGill University, Ste. Anne-de-Bellevue, QC, Canada
| | - Kelly Chan-Yam
- Department of Natural Resource Sciences, McGill University, Ste. Anne-de-Bellevue, QC, Canada
| | - Evangelos Marcolefas
- Department of Natural Resource Sciences, McGill University, Ste. Anne-de-Bellevue, QC, Canada
| | - Lyle G Whyte
- Department of Natural Resource Sciences, McGill University, Ste. Anne-de-Bellevue, QC, Canada
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16
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Selbmann L, Pacelli C, Zucconi L, Dadachova E, Moeller R, de Vera JP, Onofri S. Resistance of an Antarctic cryptoendolithic black fungus to radiation gives new insights of astrobiological relevance. Fungal Biol 2017; 122:546-554. [PMID: 29801799 DOI: 10.1016/j.funbio.2017.10.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 11/18/2022]
Abstract
The Antarctic black meristematic fungus Cryomyces antarcticus CCFEE 515 occurs endolithically in the McMurdo Dry Valleys of Antarctica, one of the best analogue for Mars environment on Earth. To date, this fungus is considered one of the best eukaryotic models for astrobiological studies and has been repeatedly selected for space experiments in the last decade. The obtained results are reviewed here, with special focus on responses to space relevant irradiation, UV radiation, and both sparsely and densely ionizing radiation, which represent the major injuries for a putative space-traveller. The remarkable resistance of this model organism to space stress, its radioresistance in particular, and mechanisms involved, significantly contributed to expanding our concept of limits for life and provided new insights on the origin and evolution of life in planetary systems, habitability, and biosignatures for life detection as well as on human protection during space missions.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
| | - Claudia Pacelli
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada.
| | - Ralf Moeller
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Cologne (Köln), Germany.
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Institute of Planetary Research, Management and Infrastructure, Astrobiological Laboratories, Rutherfordstr. 2, 12489 Berlin, Germany.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
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17
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Pacelli C, Selbmann L, Moeller R, Zucconi L, Fujimori A, Onofri S. Cryptoendolithic Antarctic Black Fungus Cryomyces antarcticus Irradiated with Accelerated Helium Ions: Survival and Metabolic Activity, DNA and Ultrastructural Damage. Front Microbiol 2017; 8:2002. [PMID: 29089932 PMCID: PMC5650992 DOI: 10.3389/fmicb.2017.02002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/28/2017] [Indexed: 11/22/2022] Open
Abstract
Space represents an extremely harmful environment for life and survival of terrestrial organisms. In the last decades, a considerable deal of attention was paid to characterize the effects of spaceflight relevant radiation on various model organisms. The aim of this study was to test the survival capacity of the cryptoendolithic black fungus Cryomyces antarcticus CCFEE 515 to space relevant radiation, to outline its endurance to space conditions. In the frame of an international radiation campaign, dried fungal colonies were irradiated with accelerated Helium ion (150 MeV/n, LET 2.2 keV/μm), up to a final dose of 1,000 Gy, as one of the space-relevant ionizing radiation. Results showed that the fungus maintained high survival and metabolic activity with no detectable DNA and ultrastructural damage, even after the highest dose irradiation. These data give clues on the resistance of life toward space ionizing radiation in general and on the resistance and responses of eukaryotic cells in particular.
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Affiliation(s)
- Claudia Pacelli
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Laura Selbmann
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Ralf Moeller
- German Aerospace Center, Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Cologne, Germany
| | - Laura Zucconi
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
| | - Akira Fujimori
- National Institute of Radiological Sciences, Research Center for Charged Particle Therapy, Chiba, Japan
| | - Silvano Onofri
- Department of Ecological and Biological Sciences, University of Tuscia, Viterbo, Italy
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