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Poletto B, Silva GG, Souza Ramos de Carvalho AC, Vincenzi RA, de Almeida EY, Galante D, Bendia AG, Rodrigues F. Ultraviolet Resistance of Microorganisms Isolated from Uranium-Rich Minerals from Perus, Brazil. ASTROBIOLOGY 2024; 24:783-794. [PMID: 38853686 DOI: 10.1089/ast.2022.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The district of Perus, located in the city of São Paulo, Brazil, is renowned for its weathered granitic-pegmatitic masses, which harbor a significant number of uraniferous minerals that contribute to ionizing radiation levels up to 20 times higher than the background levels. In this study, aseptically collected mineral samples from the area were utilized to isolate 15 microorganisms, which were subjected to pre-screening tests involving UV-C and UV-B radiation. The microorganisms that exhibited the highest resistance to ultraviolet (UV) radiation were selected for the construction of survival curves for UV-C, broad-band UV-B, and solar simulation resistance testing. Subsequently, the four strains that demonstrated superior survival capabilities under UV radiation exposure were chosen for 16S rRNA gene sequencing. Among these, Nocardioides sp. O4R and Nocardioides sp. MA2R demonstrated the most promising outcomes in the UV radiation resistance assessments, showcasing comparable performance to the well-established radioresistant model organism Deinococcus radiodurans. These findings underscore the potential of naturally occurring high-radiation environments as valuable resources for the investigation of UV-resistant microorganisms. Astrobiology 24, 783-794.
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Affiliation(s)
- Bárbara Poletto
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
- Interunities Postgraduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil
| | | | - Ana Carolina Souza Ramos de Carvalho
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
- Interunities Postgraduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil
| | | | - Eiji Yamassaki de Almeida
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
- Interunities Postgraduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil
| | - Douglas Galante
- Interunities Postgraduate Program in Biotechnology, Universidade de São Paulo, São Paulo, Brazil
- Brazilian Synchrotron Light Laboratory, Campinas, Brazil
| | | | - Fabio Rodrigues
- Chemistry Institute, Universidade de São Paulo, São Paulo, Brazil
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Petersen C, Buonanno M, Guan L, Hinzer A, Urbano J, Hashmi R, Shuryak I, Parker C, Welch D. Susceptibility of extremophiles to far-UVC light for bioburden reduction in spacecraft assembly facilities. LIFE SCIENCES IN SPACE RESEARCH 2024; 41:56-63. [PMID: 38670653 DOI: 10.1016/j.lssr.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/02/2024] [Accepted: 01/25/2024] [Indexed: 04/28/2024]
Abstract
The prevention and reduction of microbial species entering and leaving Earth's biosphere is a critical aspect of planetary protection research. While various decontamination methods exist and are currently utilized for planetary protection purposes, the use of far-UVC light (200-230 nm) as a means for microbial reduction remains underexplored. Unlike conventional germicidal ultraviolet at 254 nm, which can pose a health risk to humans even with small exposure doses, far-UVC light poses minimal health hazard making it a suitable candidate for implementation in occupied areas of spacecraft assembly facilities. This study investigates the efficacy of far-UVC 222-nm light to inactivate bacteria using microbial species which are relevant to planetary protection either in vegetative cell or spore form. All the tested vegetative cells demonstrated susceptibility to 222-nm exposure, although susceptibility varied among the tested species. Notably, Deinococcus radiodurans, a species highly tolerant to extreme environmental conditions, exhibited the most resistance to far-UVC exposure with a dose of 112 mJ/cm2 required for a 1-log reduction in survival. While spore susceptibility was similar across the species tested, Bacillus pumilus spores were the most resistant of the tested spores when analyzed with a bi-exponential cell killing model (D90 of 6.8 mJ/cm2). Overall, these results demonstrate the efficacy of far-UVC light for reducing microbial bioburden to help ensure the success and safety of future space exploration missions.
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Affiliation(s)
- Camryn Petersen
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States
| | - Manuela Buonanno
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States
| | - Lisa Guan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Akemi Hinzer
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Joshua Urbano
- California State Polytechnic University, Pomona, CA, United States
| | - Raabia Hashmi
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States
| | - Ceth Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - David Welch
- Center for Radiological Research, Columbia University Irving Medical Center, New York, NY, United States.
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McKaig J, Caro T, Burton D, Tavares F, Vidaurri M. Chapter 10: Planetary Protection-History, Science, and the Future. ASTROBIOLOGY 2024; 24:S202-S215. [PMID: 38498825 DOI: 10.1089/ast.2021.0112] [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: 03/20/2024]
Abstract
Planetary protection is a principle in the design of interplanetary missions that aims to prevent biological cross contamination between the target body and Earth. Planetary protection policies and procedures have worked to mitigate forward contamination (from Earth) and back contamination (to Earth) since the beginning of the space age. Today, planetary protection policy is guided by international agreements, nongovernmental advisory councils, and national space agencies. The landscape of planetary protection science and policy is changing rapidly, as new technologies, crewed missions to Mars and the Moon, and even orbital settlements are being developed. Space exploration, whether specifically targeted toward questions in astrobiology or not, must consider planetary protection concerns to minimize contamination that poses a risk to both astrobiological investigations as well as Earth's biosphere. In this chapter, we provide an introduction to and overview of the history, motivations, and implementation of planetary protection in the United States.
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Affiliation(s)
- Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Monica Vidaurri
- Department of Physics and Astronomy, Howard University, Washington DC, USA
- Center for Research and Exploration in Space Science and Technology, NASA/GSFC, Greenbelt, Maryland, USA
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
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Green SJ, Torok T, Allen JE, Eloe-Fadrosh E, Jackson SA, Jiang SC, Levine SS, Levy S, Schriml LM, Thomas WK, Wood JM, Tighe SW. Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report. ASTROBIOLOGY 2023; 23:897-907. [PMID: 37102710 PMCID: PMC10457625 DOI: 10.1089/ast.2022.0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 01/23/2023] [Indexed: 06/19/2023]
Abstract
Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.
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Affiliation(s)
- Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, USA
| | - Tamas Torok
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Emiley Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Scott A. Jackson
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Sunny C. Jiang
- Department of Civil and Environmental Engineering, University of California, Irvine, California, USA
| | - Stuart S. Levine
- MIT BioMicro Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - Lynn M. Schriml
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - W. Kelley Thomas
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, New Hampshire, USA
| | - Jason M. Wood
- Research Informatics Core, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Scott W. Tighe
- Vermont Integrative Genomics, University of Vermont, Burlington, Vermont, USA
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Highlander SK, Wood JM, Gillece JD, Folkerts M, Fofanov V, Furstenau T, Singh NK, Guan L, Seuylemezian A, Benardini JN, Engelthaler DM, Venkateswaran K, Keim PS. Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition. PLoS One 2023; 18:e0282428. [PMID: 36947490 PMCID: PMC10032485 DOI: 10.1371/journal.pone.0282428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/14/2023] [Indexed: 03/23/2023] Open
Abstract
The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.
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Affiliation(s)
- Sarah K Highlander
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Jason M Wood
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - John D Gillece
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Megan Folkerts
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Viacheslav Fofanov
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- School of Informatics, Computing and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Tara Furstenau
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Nitin K Singh
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Lisa Guan
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Arman Seuylemezian
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - James N Benardini
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - David M Engelthaler
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Biotechnology and Planetary Protection Group, Pasadena, California, United States of America
| | - Paul S Keim
- Pathogen and Microbiome Division, The Translational Genomics Research Institute, Flagstaff, Arizona, United States of America
- Pathogen & Microbiome Institute (PMI), Northern Arizona University, Flagstaff, Arizona, United States of America
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces-Recommendations for Two New Genera and One Species. J Fungi (Basel) 2022; 9:jof9010031. [PMID: 36675851 PMCID: PMC9864340 DOI: 10.3390/jof9010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/17/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022] Open
Abstract
National Aeronautics and Space Administration’s (NASA) spacecraft assembly facilities are monitored for the presence of any bacteria or fungi that might conceivably survive a transfer to an extraterrestrial environment. Fungi present a broad and diverse range of phenotypic and functional traits to adapt to extreme conditions, hence the detection of fungi and subsequent eradication of them are needed to prevent forward contamination for future NASA missions. During the construction and assembly for the Mars 2020 mission, three fungal strains with unique morphological and phylogenetic properties were isolated from spacecraft assembly facilities. The reconstruction of phylogenetic trees based on several gene loci (ITS, LSU, SSU, RPB, TUB, TEF1) using multi-locus sequence typing (MLST) and whole genome sequencing (WGS) analyses supported the hypothesis that these were novel species. Here we report the genus or species-level classification of these three novel strains via a polyphasic approach using phylogenetic analysis, colony and cell morphology, and comparative analysis of WGS. The strain FJI-L9-BK-P1 isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) exhibited a putative phylogenetic relationship with the strain Aaosphaeria arxii CBS175.79 but showed distinct morphology and microscopic features. Another JPL-SAF strain, FJII-L3-CM-DR1, was phylogenetically distinct from members of the family Trichomeriaceae and exhibited morphologically different features from the genera Lithohypha and Strelitziana. The strain FKI-L1-BK-DR1 isolated from the Kennedy Space Center facility was identified as a member of Dothideomycetes incertae sedis and is closely related to the family Kirschsteiniotheliaceae according to a phylogenetic analysis. The polyphasic taxonomic approach supported the recommendation for establishing two novel genera and one novel species. The names Aaosphaeria pasadenensis (FJI-L9-BK-P1 = NRRL 64424 = DSM 114621), Pasadenomyces melaninifex (FJII-L3-CM-DR1 = NRRL 64433 = DSM 114623), and Floridaphiala radiotolerans (FKI-L1-BK-DR1 = NRRL 64434 = DSM 114624) are proposed as type species. Furthermore, resistance to ultraviolet-C and presence of specific biosynthetic gene cluster(s) coding for metabolically active compounds are unique to these strains.
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Siems K, Runzheimer K, Rehm A, Schwengers O, Heidler von Heilborn D, Kaser L, Arndt F, Neidhöfer C, Mengel JP, Parcina M, Lipski A, Hain T, Moeller R. Phenotypic and genomic assessment of the potential threat of human spaceflight-relevant Staphylococcus capitis isolates under stress conditions. Front Microbiol 2022; 13:1007143. [PMID: 36406458 PMCID: PMC9669719 DOI: 10.3389/fmicb.2022.1007143] [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: 07/30/2022] [Accepted: 10/06/2022] [Indexed: 08/05/2023] Open
Abstract
Previous studies have reported that spaceflight specific conditions such as microgravity lead to changes in bacterial physiology and resistance behavior including increased expression of virulence factors, enhanced biofilm formation and decreased susceptibility to antibiotics. To assess if spaceflight induced physiological changes can manifest in human-associated bacteria, we compared three spaceflight relevant Staphylococcus capitis isolates (DSM 111179, ISS; DSM 31028, clean room; DSM 113836; artificial gravity bedrest study) with the type strain (DSM 20326T). We tested the three strains regarding growth, colony morphology, metabolism, fatty acid and polar lipid pattern, biofilm formation, susceptibility to antibiotics and survival in different stress conditions such as treatment with hydrogen peroxide, exposure to desiccation, and irradiation with X-rays and UV-C. Moreover, we sequenced, assembled, and analyzed the genomes of all four strains. Potential genetic determinants for phenotypic differences were investigated by comparative genomics. We found that all four strains show similar metabolic patterns and the same susceptibility to antibiotics. All four strains were considered resistant to fosfomycin. Physiological differences were mainly observed compared to the type strain and minor differences among the other three strains. The ISS isolate and the bedrest study isolate exhibit a strong delayed yellow pigmentation, which is absent in the other two strains. Pigments were extracted and analyzed by UV/Vis spectroscopy showing characteristic carotenoid spectra. The ISS isolate showed the highest growth rate as well as weighted average melting temperature (WAMT) of fatty acids (41.8°C) of all strains. The clean room isolate showed strongest biofilm formation and a high tolerance to desiccation. In general, all strains survived desiccation better in absence of oxygen. There were no differences among the strains regarding radiation tolerance. Phenotypic and genomic differences among the strains observed in this study are not inevitably indicating an increased virulence of the spaceflight isolate. However, the increased growth rate, higher WAMT and colony pigmentation of the spaceflight isolate are relevant phenotypes that require further research within the human spaceflight context. We conclude that combining genetic analysis with classical microbiological methods allows the detailed assessment of the potential threat of bacteria in highly regulated and extreme environments such as spaceflight environments.
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Affiliation(s)
- Katharina Siems
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Katharina Runzheimer
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Anna Rehm
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Oliver Schwengers
- Department of Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - David Heidler von Heilborn
- Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Liv Kaser
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Franca Arndt
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Claudio Neidhöfer
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - Jan Philipp Mengel
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
| | - Marijo Parcina
- Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Bonn, Germany
| | - André Lipski
- Institute of Nutritional and Food Sciences, Food Microbiology and Hygiene, University of Bonn, Bonn, Germany
| | - Torsten Hain
- Institute of Medical Microbiology, Justus Liebig University Giessen, Giessen, Germany
- German Center for Infection Research (DZIF), Justus Liebig University Giessen, Partner Site Giessen-Marburg-Langen, Giessen, Germany
| | - Ralf Moeller
- Department of Radiation Biology, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
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Microbial Burden Estimation of Food Items, Built Environments, and the International Space Station Using Film Media. Microorganisms 2022; 10:microorganisms10091714. [PMID: 36144316 PMCID: PMC9503880 DOI: 10.3390/microorganisms10091714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
The use of film media involves considerably less preparation, waste, and incubator space than conventional agar-media-based assays and has proven in past studies to provide counts of cultivable microbes similar to those of traditional agar media. Film media also have the advantage of allowing sample volumes similar to those used in pour plates and, therefore, are well-suited for cultivable microbial counts in extremely low-biomass environments such as clean rooms or space habitats, particularly where the subsequent isolation of colonies is necessary. As the preparation of film media plates relies on water cohesion/adhesion rather than manual spreading, they may have future applications in low- or microgravity settings. In this study, cultivable microbial count performance was compared between agar media and film media in three kinds of samples: food items, surfaces in built environments on Earth (homes), and on the environmental surfaces of the International Space Station (ISS). Easy Plates (Kikkoman Corporation) and Petrifilm (3M) were compared with traditional agar plating for food and home surfaces, while only Easy Plates were compared with agar for ISS samples. For both food items and built environments on Earth, both types of film media performed comparably to agar media for bacterial counts, with R2 values of 0.94–0.96. Fungal counts for built-environment samples had a lower correlation between film and agar counts, with R2 values of 0.72–0.73. Samples from the ISS, which ranged from below detection to 103 CFU per 100 cm2, had R2 values of 0.80 for bacterial counts and 0.73 for fungal counts, partially due to multiple samples recording below the detection limit for agar or too numerous to count, and the growth of fungal species on R2A medium. The species compositions of isolates picked from agar vs. film media plates were similar; however, further phylogenetic analysis is needed to confirm the differential microbial diversity composition. Overall, film media such as Easy Plates and Petrifilm are viable alternatives to agar plates for low-biomass built environments as well as for food samples, and the two brands tested in this study performed equally well.
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Liu Z, Wei Y, Li J, Ding GC. Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 144:357-365. [PMID: 35436715 DOI: 10.1016/j.wasman.2022.04.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 06/14/2023]
Abstract
Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared >99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.
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Affiliation(s)
- Zixiu Liu
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China
| | - Yuquan Wei
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Ji Li
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China
| | - Guo-Chun Ding
- College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Beijing, China; Organic Recycling Institute (Suzhou) of China Agricultural University, Wuzhong District, 215128, Jiangsu Province, China.
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10
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Stott KV, Morgan L, Shearer C, Steadham MB, Ballarotto M, Hendrickson R. Qualification of Membrane Filtration for Planetary Protection Flight Implementation. Front Microbiol 2022; 13:871110. [PMID: 35572631 PMCID: PMC9100389 DOI: 10.3389/fmicb.2022.871110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/12/2022] [Indexed: 11/25/2022] Open
Abstract
Planetary protection is the practice of preventing forward and backward contamination of solar system bodies. Spacecraft and associated surfaces are sampled to ensure compliance with bioburden requirements. Current planetary protection sampling and processing methodologies consist of extracting microbial cells from wipe or swab samples through a procedure (NASA Standard Assay) that includes sonication, heat shock, and pour-plate steps. The pour-plate steps are laborious and prolonged. Moreover, results can be imprecise because only a fraction of the sample fluid is plated for CFU enumeration (80% for swabs and 25% for wipes). Thus, analysis requires that a pour fraction extrapolation factor be applied to CFU counts to account for bioburden in the remaining sample volume that is not plated. This extrapolation results in large variances for data, decreasing the accuracy of spore bioburden estimation of spacecraft hardware. In this study, we investigated the use of membrane filtration as an alternative method to pour-plate processing. Membrane filtration is an appealing methodology for planetary protection because it can process greater sample volumes and reduces the data variance for bioburden enumeration. A pour fraction extrapolation factor is still applied for both swabs and wipes (92%), however, it is a greater pour fraction than the pour-plate method. Here we present data collected by the Jet Propulsion Laboratory and the Applied Physics Laboratory to experimentally determine the equivalency of membrane filtration to pour-plate methodology for implementation during the NASA Standard Assay. Additionally, we outline the planned procedures for two membrane filtration systems: Pall® Laboratory Manifold system and Milliflex® Plus Vacuum Pump System. Both systems demonstrated equivalence of the membrane filtration method to the pour-plate method.
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Affiliation(s)
| | - Lyssa Morgan
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Caitlin Shearer
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
| | | | - Mihaela Ballarotto
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, United States
| | - Ryan Hendrickson
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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11
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Lee YJ, You HS, Lee SH, Lee SL, Lee H, Sung HJ, Kang HG, Hyun SH. Comparison of Optimal Storage Temperature and Collection Reagents for Living Bacterial Cells in Swab Samples. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2021. [DOI: 10.15324/kjcls.2021.53.4.326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Yeong Ju Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu, Korea
| | - Hee Sang You
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Uijeongbu, Korea
| | - Song Hee Lee
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu, Korea
| | - So Lip Lee
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Uijeongbu, Korea
| | - Han Lee
- Department of Biomedical Laboratory Science, Eulji University, Uijeongbu, Korea
| | - Ho Joong Sung
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu, Korea
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Uijeongbu, Korea
- Department of Biomedical Laboratory Science, Eulji University, Uijeongbu, Korea
| | - Hee Gyoo Kang
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu, Korea
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Uijeongbu, Korea
- Department of Biomedical Laboratory Science, Eulji University, Uijeongbu, Korea
| | - Sung Hee Hyun
- Department of Biomedical Laboratory Science, Graduate School, Eulji University, Uijeongbu, Korea
- Department of Senior Healthcare, BK21 Plus Program, Graduate School, Eulji University, Uijeongbu, Korea
- Department of Biomedical Laboratory Science, Eulji University, Uijeongbu, Korea
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12
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Hendrickson R, Urbaniak C, Minich JJ, Aronson HS, Martino C, Stepanauskas R, Knight R, Venkateswaran K. Clean room microbiome complexity impacts planetary protection bioburden. MICROBIOME 2021; 9:238. [PMID: 34861887 PMCID: PMC8643001 DOI: 10.1186/s40168-021-01159-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 08/13/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND The Spacecraft Assembly Facility (SAF) at the NASA's Jet Propulsion Laboratory is the primary cleanroom facility used in the construction of some of the planetary protection (PP)-sensitive missions developed by NASA, including the Mars 2020 Perseverance Rover that launched in July 2020. SAF floor samples (n=98) were collected, over a 6-month period in 2016 prior to the construction of the Mars rover subsystems, to better understand the temporal and spatial distribution of bacterial populations (total, viable, cultivable, and spore) in this unique cleanroom. RESULTS Cleanroom samples were examined for total (living and dead) and viable (living only) microbial populations using molecular approaches and cultured isolates employing the traditional NASA standard spore assay (NSA), which predominantly isolated spores. The 130 NSA isolates were represented by 16 bacterial genera, of which 97% were identified as spore-formers via Sanger sequencing. The most spatially abundant isolate was Bacillus subtilis, and the most temporally abundant spore-former was Virgibacillus panthothenticus. The 16S rRNA gene-targeted amplicon sequencing detected 51 additional genera not found in the NSA method. The amplicon sequencing of the samples treated with propidium monoazide (PMA), which would differentiate between viable and dead organisms, revealed a total of 54 genera: 46 viable non-spore forming genera and 8 viable spore forming genera in these samples. The microbial diversity generated by the amplicon sequencing corresponded to ~86% non-spore-formers and ~14% spore-formers. The most common spatially distributed genera were Sphinigobium, Geobacillus, and Bacillus whereas temporally distributed common genera were Acinetobacter, Geobacilllus, and Bacillus. Single-cell genomics detected 6 genera in the sample analyzed, with the most prominent being Acinetobacter. CONCLUSION This study clearly established that detecting spores via NSA does not provide a complete assessment for the cleanliness of spacecraft-associated environments since it failed to detect several PP-relevant genera that were only recovered via molecular methods. This highlights the importance of a methodological paradigm shift to appropriately monitor bioburden in cleanrooms for not only the aeronautical industry but also for pharmaceutical, medical industries, etc., and the need to employ molecular sequencing to complement traditional culture-based assays. Video abstract.
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Affiliation(s)
- Ryan Hendrickson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Camilla Urbaniak
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Jeremiah J Minich
- Marine Biology Research Division, Scripps Institute of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Heidi S Aronson
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA
| | - Cameron Martino
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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13
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Wood JM, Singh NK, Guan L, Seuylemezian A, Benardini JN, Venkateswaran K. Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility. Front Microbiol 2021; 12:685254. [PMID: 34650522 PMCID: PMC8508200 DOI: 10.3389/fmicb.2021.685254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 08/27/2021] [Indexed: 11/24/2022] Open
Abstract
NASA planetary protection (PP) requires an assessment of the biological contamination of the potential microbial burden on spacecraft destined to explore planetary bodies that may harbor signs of life, like Mars and Europa. To help meet these goals, the performance of multiple metagenomic pipelines were compared and assessed for their ability to detect microbial diversity of a low-biomass clean room environment used to build spacecraft destined to these planetary bodies. Four vendors were chosen to implement their own metagenomic analysis pipeline on the shotgun sequences retrieved from environmental surfaces in the relevant environments at NASA's Jet Propulsion Laboratory. None of the vendors showed the same microbial profile patterns when analyzing same raw dataset since each vendor used different pipelines, which begs the question of the validity of a single pipeline to be recommended for future NASA missions. All four vendors detected species of interest, including spore-forming and extremotolerant bacteria, that have the potential to hitch-hike on spacecraft and contaminate the planetary bodies explored. Some vendors demonstrated through functional analysis of the metagenomes that the molecular mechanisms for spore-formation and extremotolerance were represented in the data. However, relative abundances of these microorganisms varied drastically between vendor analyses, questioning the ability of these pipelines to quantify the number of PP-relevant microorganisms on a spacecraft surface. Metagenomics offers tantalizing access to the genetic and functional potential of a microbial community that may offer NASA a viable method for microbial burden assays for planetary protection purposes. However, future development of technologies such as streamlining the processing of shotgun metagenome sequence data, long read sequencing, and all-inclusive larger curated and annotated microbial genome databases will be required to validate and translate relative abundances into an actionable assessment of PP-related microbes of interest. Additionally, the future development of machine learning and artificial intelligence techniques could help enhance the quality of these metagenomic analyses by providing more accurate identification of the genetic and functional potential of a microbial community.
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Affiliation(s)
| | | | | | | | | | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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14
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Schwendner P, Nguyen AN, Schuerger AC. Use of NanoSIMS to Identify the Lower Limits of Metabolic Activity and Growth by Serratia liquefaciens Exposed to Sub-Zero Temperatures. Life (Basel) 2021; 11:life11050459. [PMID: 34065549 PMCID: PMC8161314 DOI: 10.3390/life11050459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/12/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Serratia liquefaciens is a cold-adapted facultative anaerobic astrobiology model organism with the ability to grow at a Martian atmospheric pressure of 7 hPa. Currently there is a lack of data on its limits of growth and metabolic activity at sub-zero temperatures found in potential habitable regions on Mars. Growth curves and nano-scale secondary ion mass spectrometry (NanoSIMS) were used to characterize the growth and metabolic threshold for S. liquefaciens ATCC 27,592 grown at and below 0 °C. Cells were incubated in Spizizen medium containing three stable isotopes substituting their unlabeled counterparts; i.e., 13C-glucose, (15NH4)2SO4, and H218O; at 0, −1.5, −3, −5, −10, or −15 °C. The isotopic ratios of 13C/12C, 15N/14N, and 18O/16O and their corresponding fractions were determined for 240 cells. NanoSIMS results revealed that with decreasing temperature the cellular amounts of labeled ions decreased indicating slower metabolic rates for isotope uptake and incorporation. Metabolism was significantly reduced at −1.5 and −3 °C, almost halted at −5 °C, and shut-down completely at or below −10 °C. While growth was observed at 0 °C after 5 days, samples incubated at −1.5 and −3 °C exhibited significantly slower growth rates until growth was detected at 70 days. In contrast, cell densities decreased by at least half an order of magnitude over 70 days in cultures incubated at ≤ −5 °C. Results suggest that S. liquefaciens, if transported to Mars, might be able to metabolize and grow in shallow sub-surface niches at temperatures above −5 °C and might survive—but not grow—at temperatures below −5 °C.
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Affiliation(s)
- Petra Schwendner
- Space Life Sciences Lab, Department of Plant Pathology, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL 32953, USA;
- Correspondence:
| | - Ann N. Nguyen
- Jacobs, NASA Johnson Space Center, Houston, TX 77058, USA;
| | - Andrew C. Schuerger
- Space Life Sciences Lab, Department of Plant Pathology, University of Florida, 505 Odyssey Way, Exploration Park, Merritt Island, FL 32953, USA;
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15
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Lebeuf M, Turgeon N, Faubert C, Robillard J, Paradis É, Duchaine C. Managing the bacterial contamination risk in an axenic mice animal facility. Can J Microbiol 2021; 67:657-666. [PMID: 33844954 DOI: 10.1139/cjm-2020-0519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A gap exists between good laboratory practices with axenic animals and the procedures applied. This work examined the efficacy of sodium dichloroisocyanurate (MB-10) and potassium peroxymonosulfate (Virkon™) disinfectants, as well as the appropriate soaking time for materials used with the ISOcage Biosafety Station™. We also compared the microbial load in cage systems hosting mice over 2 weeks in axenic rooms (ARs) and in typical specific-pathogen-free (SPF) non-axenic rooms (NARs) to identify resistant microorganisms, targeted for longer soaking disinfection, and evaluated the necessary procedures for reducing the microbial load in AR. Staphylococcus was the most frequently isolated genus (in both ARs and NARs). An average of three spore-forming microorganisms per cage were counted from AR. The disinfection time to reach 1 log reduction for Bacillus atrophaeus spores varied from 138 s (100 ppm MB-10) to 290 (Virkon™) to <20 s for S. epidermidis (100 ppm MB-10). AR management protocols lead to a microbial load that is 1000 times lower than that found in NARs. Data comparing the microbial load in SPF and axenic facilities can be used to improve the effectiveness of their microbial control procedures.
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Affiliation(s)
- Maria Lebeuf
- Département de biochimie, microbiologie et bioinformatique, Université Laval, Quebec city, Quebec, Canada
| | - Nathalie Turgeon
- Research center, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Cynthia Faubert
- Research animal facility, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Justin Robillard
- Research animal facility, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Éric Paradis
- Research center, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Caroline Duchaine
- Département de biochimie, microbiologie et bioinformatique, Université Laval, Quebec city, Quebec, Canada; Tier-1, Canada Research Chair on Bioaerosols, Institutuniversitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
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16
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Obulisamy PK, Mehariya S. Polyhydroxyalkanoates from extremophiles: A review. BIORESOURCE TECHNOLOGY 2021; 325:124653. [PMID: 33465644 DOI: 10.1016/j.biortech.2020.124653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Polyhydroxyalkanoates (PHAs) are group monomers/heteropolymers that are biodegradable and widely used in biomedical applications. They are considered as alternatives to fossil derived polymers and accumulated by microbes including extremophilic archaea as energy storage inclusions under nutrient limitations. The use of extremophilic archaea for PHA production is an economically viable option for conventional aerobic processes, but less is known about their pathways and PHA accumulation capacities. This review summarized: (a) specific adaptive mechanisms towards extreme environments by extremophiles and specific role of PHAs; (b) understanding of PHA synthesis/metabolism in archaea and specific functional genes; (c) genetic engineering and process engineering approaches required for high-rate PHA production using extremophilic archaea. To conclude, the future studies are suggested to understand the membrane lipids and PHAs accumulation to explain the adaptation mechanism of extremophiles and exploiting it for commercial production of PHAs.
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Affiliation(s)
| | - Sanjeet Mehariya
- Department of Engineering, University of Campania "Luigi Vanvitelli", Real Casa dell'Annunziata, Italy
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17
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Danko DC, Sierra MA, Benardini JN, Guan L, Wood JM, Singh N, Seuylemezian A, Butler DJ, Ryon K, Kuchin K, Meleshko D, Bhattacharya C, Venkateswaran KJ, Mason CE. A comprehensive metagenomics framework to characterize organisms relevant for planetary protection. MICROBIOME 2021; 9:82. [PMID: 33795001 PMCID: PMC8016160 DOI: 10.1186/s40168-021-01020-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Clean rooms of the Space Assembly Facility (SAF) at the Jet Propulsion Laboratory (JPL) at NASA are the final step of spacecraft cleaning and assembly before launching into space. Clean rooms have stringent methods of air-filtration and cleaning to minimize microbial contamination for exoplanetary research and minimize the risk of human pathogens, but they are not sterile. Clean rooms make a selective environment for microorganisms that tolerate such cleaning methods. Previous studies have attempted to characterize the microbial cargo through sequencing and culture-dependent protocols. However, there is not a standardized metagenomic workflow nor analysis pipeline for spaceflight hardware cleanroom samples to identify microbial contamination. Additionally, current identification methods fail to characterize and profile the risk of low-abundance microorganisms. RESULTS A comprehensive metagenomic framework to characterize microorganisms relevant for planetary protection in multiple cleanroom classifications (from ISO-5 to ISO-8.5) and sample types (surface, filters, and debris collected via vacuum devices) was developed. Fifty-one metagenomic samples from SAF clean rooms were sequenced and analyzed to identify microbes that could potentially survive spaceflight based on their microbial features and whether the microbes expressed any metabolic activity or growth. Additionally, an auxiliary testing was performed to determine the repeatability of our techniques and validate our analyses. We find evidence that JPL clean rooms carry microbes with attributes that may be problematic in space missions for their documented ability to withstand extreme conditions, such as psychrophilia and ability to form biofilms, spore-forming capacity, radiation resistance, and desiccation resistance. Samples from ISO-5 standard had lower microbial diversity than those conforming to ISO-6 or higher filters but still carried a measurable microbial load. CONCLUSIONS Although the extensive cleaning processes limit the number of microbes capable of withstanding clean room condition, it is important to quantify thresholds and detect organisms that can inform ongoing Planetary Protection goals, provide a biological baseline for assembly facilities, and guide future mission planning. Video Abstract.
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Affiliation(s)
- David C Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Maria A Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - James N Benardini
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Lisa Guan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Jason M Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Nitin Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Arman Seuylemezian
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA
| | - Daniel J Butler
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Katerina Kuchin
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Dmitry Meleshko
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Chandrima Bhattacharya
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kasthuri J Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, CA, 91109, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10065, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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18
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Pasqua S, Vitale G, Pasquariello A, Douradinha B, Tuzzolino F, Cardinale F, Cusimano C, Di Bartolo C, Conaldi PG, D'Apolito D. Use of 27G needles improves sensitivity and performance of ATCC anaerobe reference microorganism detection in BacT/Alert system. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2021; 20:542-550. [PMID: 33665224 PMCID: PMC7890369 DOI: 10.1016/j.omtm.2021.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/18/2021] [Indexed: 11/26/2022]
Abstract
Effective detection of microbiological contaminations present in medicinal cellular products is a crucial step to ensure patients' safety. In recent decades, several rapid microbiological methods have been developed and validated, but variabilities linked to the use of different resources have led to discordant validation of methods and performance results. Considering this, while developing an in-house BacT/Alert-based method, we evaluated all of the materials used in its validation. Of particular importance, we noticed that the syringe gauge used to inject the samples into the bottles was crucial to obtain robust results. We chose to conduct a comparative test between the BacT/Alert system and the compendial method described in the European Pharmacopoeia, using five dilutions of nine reference microorganism strains and 21G or 27G needles. Our results confirmed that the BacT/Alert system is a valid and faster alternative method to assess sterility of clinical cell therapy products, and that the use of 27G needles increases its sensitivity to detect reference anaerobe microorganisms.
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Affiliation(s)
- Salvatore Pasqua
- Unità Prodotti Cellulari (GMP), Fondazione Ri.MED c/o IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Via E. Tricomi 5, 90127 Palermo, Italy
| | - Giampiero Vitale
- Unità Prodotti Cellulari (GMP), Fondazione Ri.MED c/o IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Via E. Tricomi 5, 90127 Palermo, Italy
| | - Anna Pasquariello
- Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Bruno Douradinha
- Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy.,Unità Medicina Rigenerativa ed Immunologia, Fondazione Ri.MED c/o IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Fabio Tuzzolino
- Ufficio Ricerca, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Francesca Cardinale
- Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Chiara Cusimano
- Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Chiara Di Bartolo
- Unità Prodotti Cellulari (GMP), Fondazione Ri.MED c/o IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Via E. Tricomi 5, 90127 Palermo, Italy.,Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Pier Giulio Conaldi
- Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
| | - Danilo D'Apolito
- Unità Prodotti Cellulari (GMP), Fondazione Ri.MED c/o IRCCS-ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione), Via E. Tricomi 5, 90127 Palermo, Italy.,Unità di Medicina di Laboratorio e Biotecnologie Avanzate, IRCCS-ISMETT, Via E. Tricomi 5, 90127 Palermo, Italy
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Osborne P, Hall LJ, Kronfeld-Schor N, Thybert D, Haerty W. A rather dry subject; investigating the study of arid-associated microbial communities. ENVIRONMENTAL MICROBIOME 2020; 15:20. [PMID: 33902728 PMCID: PMC8067391 DOI: 10.1186/s40793-020-00367-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 11/12/2020] [Indexed: 05/08/2023]
Abstract
Almost one third of Earth's land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.
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Affiliation(s)
- Peter Osborne
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK.
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Chair of Intestinal Microbiome, School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, 85354, Freising, Germany
| | | | - David Thybert
- EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park Innovation Centre, Colney Lane, Norwich, NR4 7UZ, UK
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20
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Stone W, Tolmay J, Tucker K, Wolfaardt GM. Disinfectant, Soap or Probiotic Cleaning? Surface Microbiome Diversity and Biofilm Competitive Exclusion. Microorganisms 2020; 8:microorganisms8111726. [PMID: 33158159 PMCID: PMC7694204 DOI: 10.3390/microorganisms8111726] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 10/15/2020] [Accepted: 10/28/2020] [Indexed: 11/16/2022] Open
Abstract
This study extends probiotic cleaning research to a built environment. Through an eight-month cleaning trial, we compared the effect of three cleaning products (disinfectant, plain soap, and a probiotic cleaner containing a patented Bacillus spore consortium), and tap water as the control, on the resident microbiome of three common hospital surfaces (linoleum, ceramic, and stainless steel). Pathogens, Escherichia coli and Staphylococcus aureus, were deposited and desiccated, and competitive exclusion was assessed for each microbiome. Cell survival was shown to be an incomplete tool for measuring microbial competitive exclusion. Biofilm competition offered a fuller understanding of competitive dynamics. A test for culturable cell survival showed that both plain soap and probiotic cleaner regimes established a surface microbiome that outcompeted the two pathogens. A different picture emerged when observing biofilms with a deposited and desiccated GFP-labeled pathogen, Pseudomonas aeruginosa. Competitive exclusion was again demonstrated. On surfaces cleaned with disinfectant the pathogen outcompeted the microbiomes. On surfaces cleaned with plain soap, the microbiomes outcompeted the pathogen. However, on surfaces cleaned with probiotic cleaner, despite the exponentially higher surface microbial loads, the microbiome did not completely outcompete the pathogen. Thus, the standard culturable cell test for survival on a surface confirmed the competitive advantage that is typically reported for probiotic cleaners. However, observation of competition in biofilms showed that the more diverse microbiome (according to alpha and beta indices) established on a surface cleaned with plain soap had a better competitive advantage than the monoculture established by the probiotic cleaner. Therefore, microbial diversity appears to be as critical to the competitive exclusion principle as cell numbers. The study showed that both plain soap and probiotic cleaner fostered competitive exclusion far more effectively than disinfectant. Probiotic cleaners with microbial diversity could be worth considering for hospital cleaning.
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Affiliation(s)
- Wendy Stone
- Environmental Microbiology Laboratory, Water Institute, Department of Microbiology, Stellenbosch University, 7602 Stellenbosch, South Africa; (J.T.); (K.T.); (G.M.W.)
- Correspondence:
| | - Janke Tolmay
- Environmental Microbiology Laboratory, Water Institute, Department of Microbiology, Stellenbosch University, 7602 Stellenbosch, South Africa; (J.T.); (K.T.); (G.M.W.)
| | - Keira Tucker
- Environmental Microbiology Laboratory, Water Institute, Department of Microbiology, Stellenbosch University, 7602 Stellenbosch, South Africa; (J.T.); (K.T.); (G.M.W.)
| | - Gideon M. Wolfaardt
- Environmental Microbiology Laboratory, Water Institute, Department of Microbiology, Stellenbosch University, 7602 Stellenbosch, South Africa; (J.T.); (K.T.); (G.M.W.)
- Environmental Microbiology Laboratory, Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
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Hendrickson R, Kazarians G, Benardini Iii JN. Planetary Protection Implementation on the Interior Exploration Using Seismic Investigations, Geodesy and Heat Transport Mission. ASTROBIOLOGY 2020; 20:1151-1157. [PMID: 32551882 DOI: 10.1089/ast.2019.2098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The InSight (Interior Exploration using Seismic Investigations, Geodesy and Heat Transport) Mars flight system is made up of a cruise stage, an aeroshell, and a Phoenix heritage-based lander that successfully landed in the Elysium Planitia on November 26, 2018. InSight has primary science objectives that are aimed at understanding more about the interior of Mars and the formation and evolution of terrestrial planets. As with previous Mars missions, InSight was obligated to satisfy bioburden requirements and verify compliance with international treaty obligations and National Aeronautics and Space Administration requirements before launch. InSight implemented a series of policies and procedures to minimize biological risk and comply with all applicable requirements for a Planetary Protection Category IVa mission. At launch, InSight had an estimated total bacterial spore burden of 1.50 × 105 spores on the entire spacecraft, including the cruise stage, satisfying the requirement of 5 × 105 spores. The landed hardware components required <3 × 105 spores and a bioburden density of <300 spores/m2. At launch, the landed hardware of InSight contained an estimated total spore bioburden of 1.35 × 105 spores and an estimated bioburden density of 129 spores/m2.
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Affiliation(s)
- Ryan Hendrickson
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Gayane Kazarians
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - James N Benardini Iii
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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22
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Hendrickson R, Kazarians G, Yearicks S, Guan L, Seuylemezian A, Matthias LL, Schrepel T, Benardini Iii JN. Planetary Protection Implementation of the InSight Mission Launch Vehicle and Associated Ground Support Hardware. ASTROBIOLOGY 2020; 20:1158-1167. [PMID: 32907354 DOI: 10.1089/ast.2019.2099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The InSight (Interior Exploration using Seismic Investigations, Geodesy and Heat Transport) Mars mission launched from Vandenberg Air Force Base on an Atlas V 401 rocket on May 5, 2018. Prior to launch, the InSight spacecraft, associated launch vehicle hardware, and ground support equipment were required to satisfy Planetary Protection requirements to comply with international treaty obligations and demonstrate compliance with National Aeronautics and Space Administration (NASA) levied bioburden requirements. InSight was the first bioburden-controlled mission to launch from Vandenberg Air Force Base and required mission-unique policies and procedures to ensure Planetary Protection requirements were satisfied. All the launch vehicle hardware and associated ground support equipment with direct contact or line of sight to flight hardware were required to demonstrate a bioburden density of less than 1,000 spores/m2. Additionally, the environmental control system air ducts were required to demonstrate more stringent bioburden limits on internal duct surfaces (<100 spore/m2) and on air passing through the ducts (88 colony-forming units/m3). Although conservative approaches were used with the data analysis and launch recontamination analysis, InSight, the launch vehicle hardware, and ground support equipment were able to demonstrate compliance with the Planetary Protection requirements needed for launch approval. Here we detail the biological practices implemented on the launch vehicle hardware and ground support equipment that resulted in biologically clean hardware and the satisfaction of Planetary Protection.
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Affiliation(s)
- Ryan Hendrickson
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Gayane Kazarians
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Sarah Yearicks
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Lisa Guan
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Arman Seuylemezian
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - James N Benardini Iii
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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23
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Horve PF, Lloyd S, Mhuireach GA, Dietz L, Fretz M, MacCrone G, Van Den Wymelenberg K, Ishaq SL. Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2020; 30:219-235. [PMID: 31308484 PMCID: PMC7100162 DOI: 10.1038/s41370-019-0157-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/23/2019] [Accepted: 06/30/2019] [Indexed: 05/06/2023]
Abstract
In the constructed habitat in which we spend up to 90% of our time, architectural design influences occupants' behavioral patterns, interactions with objects, surfaces, rituals, the outside environment, and each other. Within this built environment, human behavior and building design contribute to the accrual and dispersal of microorganisms; it is a collection of fomites that transfer microorganisms; reservoirs that collect biomass; structures that induce human or air movement patterns; and space types that encourage proximity or isolation between humans whose personal microbial clouds disperse cells into buildings. There have been recent calls to incorporate building microbiology into occupant health and exposure research and standards, yet the built environment is largely viewed as a repository for microorganisms which are to be eliminated, instead of a habitat which is inexorably linked to the microbial influences of building inhabitants. Health sectors have re-evaluated the role of microorganisms in health, incorporating microorganisms into prevention and treatment protocols, yet no paradigm shift has occurred with respect to microbiology of the built environment, despite calls to do so. Technological and logistical constraints often preclude our ability to link health outcomes to indoor microbiology, yet sufficient study exists to inform the theory and implementation of the next era of research and intervention in the built environment. This review presents built environment characteristics in relation to human health and disease, explores some of the current experimental strategies and interventions which explore health in the built environment, and discusses an emerging model for fostering indoor microbiology rather than fearing it.
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Affiliation(s)
- Patrick F Horve
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Savanna Lloyd
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Gwynne A Mhuireach
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Leslie Dietz
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Mark Fretz
- Institute for Health and the Built Environment, University of Oregon, Portland, OR, 97209, USA
| | - Georgia MacCrone
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
| | - Kevin Van Den Wymelenberg
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA
- Institute for Health and the Built Environment, University of Oregon, Portland, OR, 97209, USA
| | - Suzanne L Ishaq
- Biology and the Built Environment Center, University of Oregon, Eugene, OR, 97403, USA.
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24
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Bajerski F, Bürger A, Glasmacher B, Keller ERJ, Müller K, Mühldorfer K, Nagel M, Rüdel H, Müller T, Schenkel J, Overmann J. Factors determining microbial colonization of liquid nitrogen storage tanks used for archiving biological samples. Appl Microbiol Biotechnol 2019; 104:131-144. [PMID: 31781817 PMCID: PMC6942587 DOI: 10.1007/s00253-019-10242-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/25/2019] [Accepted: 11/04/2019] [Indexed: 01/19/2023]
Abstract
The availability of bioresources is a precondition for life science research, medical applications, and diagnostics, but requires a dedicated quality management to guarantee reliable and safe storage. Anecdotal reports of bacterial isolates and sample contamination indicate that organisms may persist in liquid nitrogen (LN) storage tanks. To evaluate the safety status of cryocollections, we systematically screened organisms in the LN phase and in ice layers covering inner surfaces of storage tanks maintained in different biobanking facilities. We applied a culture-independent approach combining cell detection by epifluorescence microscopy with the amplification of group-specific marker genes and high-throughput sequencing of bacterial ribosomal genes. In the LN phase, neither cells nor bacterial 16S rRNA gene copy numbers were detectable (detection limit, 102 cells per ml, 103 gene copies per ml). In several cases, small numbers of bacteria of up to 104 cells per ml and up to 106 gene copies per ml, as well as Mycoplasma, or fungi were detected in the ice phase formed underneath the lids or accumulated at the bottom. The bacteria most likely originated from the stored materials themselves (Elizabethingia, Janthibacterium), the technical environment (Pseudomonas, Acinetobacter, Methylobacterium), or the human microbiome (Bacteroides, Streptococcus, Staphylococcus). In single cases, bacteria, Mycoplasma, fungi, and human cells were detected in the debris at the bottom of the storage tanks. In conclusion, the limited microbial load of the ice phase and in the debris of storage tanks can be effectively avoided by minimizing ice formation and by employing hermetically sealed sample containers.
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Affiliation(s)
- F Bajerski
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany.
| | - A Bürger
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Developmental Genetics, München, Germany
| | - B Glasmacher
- Institute for Multiphase Processes, Leibniz University Hannover, Hannover, Germany
| | - E R J Keller
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - K Müller
- Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany
| | - K Mühldorfer
- Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW), Berlin, Germany
| | - M Nagel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - H Rüdel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schmallenberg, Germany
| | | | - J Schenkel
- German Cancer Research Centre, Heidelberg, Germany
- Institute of Physiology and Pathophysiology, University of Heidelberg, Heidelberg, Germany
| | - J Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, Braunschweig, Germany
- Microbiology, Braunschweig University of Technology, Braunschweig, Germany
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25
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Velazquez S, Griffiths W, Dietz L, Horve P, Nunez S, Hu J, Shen J, Fretz M, Bi C, Xu Y, Van Den Wymelenberg KG, Hartmann EM, Ishaq SL. From one species to another: A review on the interaction between chemistry and microbiology in relation to cleaning in the built environment. INDOOR AIR 2019; 29:880-894. [PMID: 31429989 PMCID: PMC6852270 DOI: 10.1111/ina.12596] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 05/12/2023]
Abstract
Since the advent of soap, personal hygiene practices have revolved around removal, sterilization, and disinfection-both of visible soil and microscopic organisms-for a myriad of cultural, aesthetic, or health-related reasons. Cleaning methods and products vary widely in their recommended use, effectiveness, risk to users or building occupants, environmental sustainability, and ecological impact. Advancements in science and technology have facilitated in-depth analyses of the indoor microbiome, and studies in this field suggest that the traditional "scorched-earth cleaning" mentality-that surfaces must be completely sterilized and prevent microbial establishment-may contribute to long-term human health consequences. Moreover, the materials, products, activities, and microbial communities indoors all contribute to, or remove, chemical species to the indoor environment. This review examines the effects of cleaning with respect to the interaction of chemistry, indoor microbiology, and human health.
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Affiliation(s)
| | - Willem Griffiths
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Leslie Dietz
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Patrick Horve
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Susie Nunez
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Jinglin Hu
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIL
| | - Jiaxian Shen
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIL
| | - Mark Fretz
- Institute for Health and the Built EnvironmentUniversity of OregonPortlandOR
| | - Chenyang Bi
- Department of Civil Environmental EngineeringVirginia Polytechnic Institute and State UniversityBlacksburgVA
| | - Ying Xu
- Department of Building ScienceTsinghua UniversityBeijingChina
| | - Kevin G. Van Den Wymelenberg
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
- Institute for Health and the Built EnvironmentUniversity of OregonPortlandOR
| | - Erica M. Hartmann
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIL
| | - Suzanne L. Ishaq
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
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Microscopic Characterization of Biological and Inert Particles Associated with Spacecraft Assembly Cleanroom. Sci Rep 2019; 9:14251. [PMID: 31582832 PMCID: PMC6776515 DOI: 10.1038/s41598-019-50782-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
NASA cleanrooms are certified by particle counts and are humidity-controlled, temperature-regulated, and oligotrophic in nature for assembling spacecraft subsystems. Microorganisms, which are not part of the cleanroom certification metrics, should not be overlooked when assessing the cleanliness of the facility since they can enter through soil or air, shed from humans, adapt to the oligotrophic conditions, and subsequently could contaminate spacecraft. These biogenic particles need to be identified to extend our knowledge of biological contamination for future NASA mission use. This study collected particles from the cleanroom and estimated the distribution of fallout microbial cell and inert dust particles using microscopy and molecular techniques. Aluminum coupon-based polycarbonate filter assemblies were deployed in the spacecraft assembly cleanroom facility to collect fallout particles. Epifluorescence and electron microscopy showed that particles varied in size and structure, and displayed live/dead biological and inert particle signatures from sources that include spores and fungal hyphae. Additionally, correlative epifluorescence and field emission scanning electron microscopy, combined with energy-dispersive X-ray analysis (for elemental compositions) methods, differentiated whether microbes adhering to particles were live/dead cells or inert particles. This visualization approach allowed for the classification of microorganisms as being standalone (free-living) or associated with a particle, as well as its characteristic size. Furthermore, time-course microscopy was used to determine the microbial cell growth and confirm the biological/molecular identification. Routine investigation of cleanroom biological and inert fallout particles will help to determine the biological load of spacecraft components and will also have direct relevance to the pharmaceutical and medical industries. One of the main objectives for NASA’s current and future missions is to prevent forward and back contamination of exploring planets. The goal of this study is to determine the association of microorganisms with the inert, natural cleanroom fallout particles and to ascertain whether microorganisms prefer to adhere to a particle size. A novel microscopy technique was developed, and by utilizing various molecular techniques, particles and associated microbial phylogeny were characterized. An accurate assessment of the microbes associated with cleanroom particles is necessary to protect the health of the people who occupy the room for long duration for aeronautical, medical, and pharmaceutical industries.
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Habitability of Mars: How Welcoming Are the Surface and Subsurface to Life on the Red Planet? GEOSCIENCES 2019. [DOI: 10.3390/geosciences9090361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mars is a planet of great interest in the search for signatures of past or present life beyond Earth. The years of research, and more advanced instrumentation, have yielded a lot of evidence which may be considered by the scientific community as proof of past or present habitability of Mars. Recent discoveries including seasonal methane releases and a subglacial lake are exciting, yet challenging findings. Concurrently, laboratory and environmental studies on the limits of microbial life in extreme environments on Earth broaden our knowledge of the possibility of Mars habitability. In this review, we aim to: (1) Discuss the characteristics of the Martian surface and subsurface that may be conducive to habitability either in the past or at present; (2) discuss laboratory-based studies on Earth that provide us with discoveries on the limits of life; and (3) summarize the current state of knowledge in terms of direction for future research.
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Schuerger AC, Moores JE, Smith DJ, Reitz G. A Lunar Microbial Survival Model for Predicting the Forward Contamination of the Moon. ASTROBIOLOGY 2019; 19:730-756. [PMID: 30810338 DOI: 10.1089/ast.2018.1952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The surface conditions on the Moon are extremely harsh with high doses of ultraviolet (UV) irradiation (26.8 W · m-2 UVC/UVB), wide temperature extremes (-171°C to 140°C), low pressure (10-10 Pa), and high levels of ionizing radiation. External spacecraft surfaces on the Moon are generally >100°C during daylight hours and can reach as high as 140°C at local noon. A Lunar Microbial Survival (LMS) model was developed that estimated (1) the total viable bioburden of all spacecraft landed on the Moon as ∼4.57 × 1010 microbial cells/spores at contact, (2) the inactivation kinetics of Bacillus subtilis spores to vacuum as approaching -2 logs per 2107 days, (3) the inactivation of spores on external surfaces due to concomitant low-pressure and high-temperature conditions as -6 logs per 8 h for local noon conditions, and (4) the ionizing radiation by solar wind particles as approaching -3 logs per lunation on external surfaces only. When the biocidal factors of solar UV, vacuum, high-temperature, and ionizing radiation were combined into an integrated LMS model, a -231 log reduction in viable bioburden was predicted for external spacecraft surfaces per lunation at the equator. Results indicate that external surfaces of landed or crashed spacecraft are unlikely to harbor viable spores after only one lunation, that shallow internal surfaces will be sterilized due to the interactive effects of vacuum and thermal cycling from solar irradiation, and that deep internal surfaces would be affected only by vacuum with a degradation rate of -0.02 logs per lunation.
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Affiliation(s)
- Andrew C Schuerger
- 1 Department of Plant Pathology, University of Florida, Gainesville, Florida
| | - John E Moores
- 2 Centre for Research in Earth and Space Science (CRESS), York University, Toronto, ON Canada
| | - David J Smith
- 3 Space Biosciences Division, NASA, Ames Research Center, Moffett Field, California
| | - Günther Reitz
- 4 Department of Radiation Dosimetry, Nuclear Physics Institute of the CAS, Praha, Czech Republic
- 5 Radiation Biology Division, Institute of Aerospace Medicine, German Aerospace Center, Cologne, Germany
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29
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Johnson RC, Deming C, Conlan S, Zellmer CJ, Michelin AV, Lee-Lin S, Thomas PJ, Park M, Weingarten RA, Less J, Dekker JP, Frank KM, Musser KA, McQuiston JR, Henderson DK, Lau AF, Palmore TN, Segre JA. Investigation of a Cluster of Sphingomonas koreensis Infections. N Engl J Med 2018; 379:2529-2539. [PMID: 30586509 PMCID: PMC6322212 DOI: 10.1056/nejmoa1803238] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Plumbing systems are an infrequent but known reservoir for opportunistic microbial pathogens that can infect hospitalized patients. In 2016, a cluster of clinical sphingomonas infections prompted an investigation. METHODS We performed whole-genome DNA sequencing on clinical isolates of multidrug-resistant Sphingomonas koreensis identified from 2006 through 2016 at the National Institutes of Health (NIH) Clinical Center. We cultured S. koreensis from the sinks in patient rooms and performed both whole-genome and shotgun metagenomic sequencing to identify a reservoir within the infrastructure of the hospital. These isolates were compared with clinical and environmental S. koreensis isolates obtained from other institutions. RESULTS The investigation showed that two isolates of S. koreensis obtained from the six patients identified in the 2016 cluster were unrelated, but four isolates shared more than 99.92% genetic similarity and were resistant to multiple antibiotic agents. Retrospective analysis of banked clinical isolates of sphingomonas from the NIH Clinical Center revealed the intermittent recovery of a clonal strain over the past decade. Unique single-nucleotide variants identified in strains of S. koreensis elucidated the existence of a reservoir in the hospital plumbing. Clinical S. koreensis isolates from other facilities were genetically distinct from the NIH isolates. Hospital remediation strategies were guided by results of microbiologic culturing and fine-scale genomic analyses. CONCLUSIONS This genomic and epidemiologic investigation suggests that S. koreensis is an opportunistic human pathogen that both persisted in the NIH Clinical Center infrastructure across time and space and caused health care-associated infections. (Funded by the NIH Intramural Research Programs.).
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Affiliation(s)
- Ryan C Johnson
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Clay Deming
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Sean Conlan
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Caroline J Zellmer
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Angela V Michelin
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - ShihQueen Lee-Lin
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Pamela J Thomas
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Morgan Park
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Rebecca A Weingarten
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John Less
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John P Dekker
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Karen M Frank
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Kimberlee A Musser
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - John R McQuiston
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - David K Henderson
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Anna F Lau
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Tara N Palmore
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
| | - Julia A Segre
- From the National Human Genome Research Institute (R.C.J., C.D., S.C., S.L.-L., J.A.S.), National Institutes of Health (NIH) Clinical Center (C.J.Z., A.V.M., R.A.W., J.P.D., K.M.F., D.K.H., A.F.L., T.N.P.), and the Division of Facilities, Operations, and Maintenance (J.L.), NIH, Bethesda, and the NIH Intramural Sequencing Center, NIH, Rockville (P.J.T., M.P.) - all in Maryland; Wadsworth Center, New York State Department of Health, Albany (K.A.M.); and the Special Bacteriology Reference Laboratory, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (J.R.M.). Dr. Park serves as an author on behalf of the NIH Intramural Sequencing Center Comparative Sequencing Program
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Mogul R, Barding GA, Lalla S, Lee S, Madrid S, Baki R, Ahmed M, Brasali H, Cepeda I, Gornick T, Gunadi S, Hearn N, Jain C, Kim EJ, Nguyen T, Nguyen VB, Oei A, Perkins N, Rodriguez J, Rodriguez V, Savla G, Schmitz M, Tedjakesuma N, Walker J. Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter. ASTROBIOLOGY 2018; 18:1517-1527. [PMID: 29672134 PMCID: PMC6276816 DOI: 10.1089/ast.2017.1814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/23/2018] [Indexed: 05/17/2023]
Abstract
Spacecraft assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2 × M9 minimal medium containing 26 μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2 × M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (∼1.5-log loss, ∼108 colony forming units (cfu)/mL, 10 mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gregory A. Barding
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sidharth Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Sooji Lee
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Steve Madrid
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ryan Baki
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Mahjabeen Ahmed
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Hania Brasali
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Ivonne Cepeda
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Trevor Gornick
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Shawn Gunadi
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Hearn
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Chirag Jain
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Eun Jin Kim
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Thi Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Vinh Bao Nguyen
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicole Perkins
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Gautam Savla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Megan Schmitz
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Nicholas Tedjakesuma
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
| | - Jillian Walker
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona (Cal Poly Pomona), Pomona, California
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Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species. Appl Microbiol Biotechnol 2018; 102:10425-10437. [PMID: 30310966 DOI: 10.1007/s00253-018-9422-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.
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Tirumalai MR, Stepanov VG, Wünsche A, Montazari S, Gonzalez RO, Venkateswaran K, Fox GE. Bacillus safensis FO-36b and Bacillus pumilus SAFR-032: a whole genome comparison of two spacecraft assembly facility isolates. BMC Microbiol 2018; 18:57. [PMID: 29884123 PMCID: PMC5994023 DOI: 10.1186/s12866-018-1191-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 05/18/2018] [Indexed: 11/16/2022] Open
Abstract
Background Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. pumilus or B. safensis. Results The FO-36b gene order is essentially the same as that in SAFR-032 and other B. pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. Conclusions It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. pumilus likely belong to the B. safensis group. Electronic supplementary material The online version of this article (10.1186/s12866-018-1191-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Madhan R Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Andrea Wünsche
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Saied Montazari
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Racquel O Gonzalez
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA
| | - Kasturi Venkateswaran
- Biotechnology & Planetary Protection Group, NASA Jet Propulsion Laboratories, California Institute of Technology, Pasadena, CA, 91109, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, 77204-5001, USA.
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Nicholson WL, Schuerger AC, Douki T. The Photochemistry of Unprotected DNA and DNA inside Bacillus subtilis Spores Exposed to Simulated Martian Surface Conditions of Atmospheric Composition, Temperature, Pressure, and Solar Radiation. ASTROBIOLOGY 2018; 18:393-402. [PMID: 29589975 DOI: 10.1089/ast.2017.1721] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
DNA is considered a potential biomarker for life-detection experiments destined for Mars. Experiments were conducted to examine the photochemistry of bacterial DNA, either unprotected or within Bacillus subtilis spores, in response to exposure to simulated martian surface conditions consisting of the following: temperature (-10°C), pressure (0.7 kPa), atmospheric composition [CO2 (95.54%), N2 (2.7%), Ar (1.6%), O2 (0.13%), and H2O (0.03%)], and UV-visible-near IR solar radiation spectrum (200-1100 nm) calibrated to 4 W/m2 of UVC (200-280 nm). While the majority (99.9%) of viable spores deposited in multiple layers on spacecraft-qualified aluminum coupons were inactivated within 5 min, a detectable fraction survived for up to the equivalent of ∼115 martian sols. Spore photoproduct (SP) was the major lesion detected in spore DNA, with minor amounts of cyclobutane pyrimidine dimers (CPD), in the order TT CPD > TC CPD >> CT CPD. In addition, the (6-4)TC, but not the (6-4)TT, photoproduct was detected in spore DNA. When unprotected DNA was exposed to simulated martian conditions, all photoproducts were detected. Surprisingly, the (6-4)TC photoproduct was the major photoproduct, followed by SP ∼ TT CPD > TC CPD > (6-4)TT > CT CPD > CC CPD. Differences in the photochemistry of unprotected DNA and spore DNA in response to simulated martian surface conditions versus laboratory conditions are reviewed and discussed. The results have implications for the planning of future life-detection experiments that use DNA as the target, and for the long-term persistence on Mars of forward contaminants or their DNA. Key Words: Bacillus subtilis-DNA-Mars-Photochemistry-Spore-Ultraviolet. Astrobiology 18, 393-402.
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Affiliation(s)
- Wayne L Nicholson
- 1 Department of Microbiology and Cell Science, University of Florida , Merritt Island, Florida, USA
| | - Andrew C Schuerger
- 2 Department of Plant Pathology, University of Florida , Merritt Island, Florida, USA
| | - Thierry Douki
- 3 Univ. Grenoble Alpes , CEA, CNRS, INAC, SyMMES/CIBEST, Grenoble, France
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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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Zaikova E, Benison KC, Mormile MR, Johnson SS. Microbial communities and their predicted metabolic functions in a desiccating acid salt lake. Extremophiles 2018; 22:367-379. [PMID: 29350297 DOI: 10.1007/s00792-018-1000-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/02/2018] [Indexed: 11/30/2022]
Abstract
The waters of Lake Magic in Western Australia are among the most geochemically extreme on Earth. This ephemeral saline lake is characterized by pH as low as 1.6 salinity as high as 32% total dissolved solids, and unusually complex geochemistry, including extremely high concentrations of aluminum, silica, and iron. We examined the microbial composition and putative function in this extreme acid brine environment by analyzing lake water, groundwater, and sediment samples collected during the austral summer near peak evapoconcentration. Our results reveal that the lake water metagenome, surprisingly, was comprised of mostly eukaryote sequences, particularly fungi and to a lesser extent, green algae. Groundwater and sediment samples were dominated by acidophilic Firmicutes, with eukaryotic community members only detected at low abundances. The lake water bacterial community was less diverse than that in groundwater and sediment, and was overwhelmingly represented by a single OTU affiliated with Salinisphaera. Pathways associated with halotolerance were found in the metagenomes, as were genes associated with biosynthesis of protective carotenoids. During periods of complete desiccation of the lake, we hypothesize that dormancy and entrapment in fluid inclusions in halite crystals may increase long-term survival, leading to the resilience of complex eukaryotes in this extreme environment.
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Affiliation(s)
- Elena Zaikova
- Department of Biology, Georgetown University, Washington, USA
| | - Kathleen C Benison
- Department of Geology and Geography, West Virginia University, Morgantown, USA
| | - Melanie R Mormile
- Department of Biology, Missouri University of Science and Technology, Rolla, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, USA. .,Program on Science, Technology, and International Affairs, Georgetown University, Washington, USA.
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Pervasiveness of UVC254-resistant Geobacillus strains in extreme environments. Appl Microbiol Biotechnol 2018; 102:1869-1887. [DOI: 10.1007/s00253-017-8712-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/09/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
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38
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39
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Beblo-Vranesevic K, Bohmeier M, Perras AK, Schwendner P, Rabbow E, Moissl-Eichinger C, Cockell CS, Pukall R, Vannier P, Marteinsson VT, Monaghan EP, Ehrenfreund P, Garcia-Descalzo L, Gómez F, Malki M, Amils R, Gaboyer F, Westall F, Cabezas P, Walter N, Rettberg P. The responses of an anaerobic microorganism, Yersinia intermedia MASE-LG-1 to individual and combined simulated Martian stresses. PLoS One 2017; 12:e0185178. [PMID: 29069099 PMCID: PMC5656303 DOI: 10.1371/journal.pone.0185178] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 09/07/2017] [Indexed: 11/18/2022] Open
Abstract
The limits of life of aerobic microorganisms are well understood, but the responses of anaerobic microorganisms to individual and combined extreme stressors are less well known. Motivated by an interest in understanding the survivability of anaerobic microorganisms under Martian conditions, we investigated the responses of a new isolate, Yersinia intermedia MASE-LG-1 to individual and combined stresses associated with the Martian surface. This organism belongs to an adaptable and persistent genus of anaerobic microorganisms found in many environments worldwide. The effects of desiccation, low pressure, ionizing radiation, varying temperature, osmotic pressure, and oxidizing chemical compounds were investigated. The strain showed a high tolerance to desiccation, with a decline of survivability by four orders of magnitude during a storage time of 85 days. Exposure to X-rays resulted in dose-dependent inactivation for exposure up to 600 Gy while applied doses above 750 Gy led to complete inactivation. The effects of the combination of desiccation and irradiation were additive and the survivability was influenced by the order in which they were imposed. Ionizing irradiation and subsequent desiccation was more deleterious than vice versa. By contrast, the presence of perchlorates was not found to significantly affect the survival of the Yersinia strain after ionizing radiation. These data show that the organism has the capacity to survive and grow in physical and chemical stresses, imposed individually or in combination that are associated with Martian environment. Eventually it lost its viability showing that many of the most adaptable anaerobic organisms on Earth would be killed on Mars today.
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Affiliation(s)
- Kristina Beblo-Vranesevic
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- * E-mail:
| | - Maria Bohmeier
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Alexandra K. Perras
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Department of Microbiology and Archaea, University of Regensburg, Regensburg, Germany
| | - Petra Schwendner
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Elke Rabbow
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Charles S. Cockell
- School of Physics and Astronomy, UK Center for Astrobiology, University of Edinburgh, Edinburgh, United Kingdom
| | - Rüdiger Pukall
- German Collection of Microorganisms and Cell Cultures, Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Viggo T. Marteinsson
- MATIS—Prokaria, Reykjavík, Iceland
- Faculty of Food Science and Nutrition, University of Iceland, Reykjavík, Iceland
| | | | - Pascale Ehrenfreund
- Leiden Observatory, Universiteit Leiden, Leiden, Netherland
- Space Policy Institute, George Washington University, Washington DC, United States of America
| | - Laura Garcia-Descalzo
- Instituto Nacional de Técnica Aeroespacial—Centro de Astrobiología (INTA-CAB), Madrid, Spain
| | - Felipe Gómez
- Instituto Nacional de Técnica Aeroespacial—Centro de Astrobiología (INTA-CAB), Madrid, Spain
| | | | | | - Frédéric Gaboyer
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Orléans, France
| | - Frances Westall
- Centre de Biophysique Moléculaire, Centre National de la Recherche Scientifique (CNRS), Orléans, France
| | | | | | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
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40
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Mogul R, Vaishampayan P, Bashir M, McKay CP, Schubert K, Bornaccorsi R, Gomez E, Tharayil S, Payton G, Capra J, Andaya J, Bacon L, Bargoma E, Black D, Boos K, Brant M, Chabot M, Chau D, Cisneros J, Chu G, Curnutt J, DiMizio J, Engelbrecht C, Gott C, Harnoto R, Hovanesian R, Johnson S, Lavergne B, Martinez G, Mans P, Morales E, Oei A, Peplow G, Piaget R, Ponce N, Renteria E, Rodriguez V, Rodriguez J, Santander M, Sarmiento K, Scheppelmann A, Schroter G, Sexton D, Stephenson J, Symer K, Russo-Tait T, Weigel B, Wilhelm MB. Microbial Community and Biochemical Dynamics of Biological Soil Crusts across a Gradient of Surface Coverage in the Central Mojave Desert. Front Microbiol 2017; 8:1974. [PMID: 29109701 PMCID: PMC5660283 DOI: 10.3389/fmicb.2017.01974] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/25/2017] [Indexed: 02/01/2023] Open
Abstract
In this study, we expand upon the biogeography of biological soil crusts (BSCs) and provide molecular insights into the microbial community and biochemical dynamics along the vertical BSC column structure, and across a transect of increasing BSC surface coverage in the central Mojave Desert, CA, United States. Next generation sequencing reveals a bacterial community profile that is distinct among BSCs in the southwestern United States. Distribution of major phyla in the BSC topsoils included Cyanobacteria (33 ± 8%), Proteobacteria (26 ± 6%), and Chloroflexi (12 ± 4%), with Phormidium being the numerically dominant genus. Furthermore, BSC subsurfaces contained Proteobacteria (23 ± 5%), Actinobacteria (20 ± 5%), and Chloroflexi (18 ± 3%), with an unidentified genus from Chloroflexi (AKIW781, order) being numerically dominant. Across the transect, changes in distribution at the phylum (p < 0.0439) and genus (p < 0.006) levels, including multiple biochemical and geochemical trends (p < 0.05), positively correlated with increasing BSC surface coverage. This included increases in (a) Chloroflexi abundance, (b) abundance and diversity of Cyanobacteria, (b) OTU-level diversity in the topsoil, (c) OTU-level differentiation between the topsoil and subsurface, (d) intracellular ATP abundances and catalase activities, and (e) enrichments in clay, silt, and varying elements, including S, Mn, Co, As, and Pb, in the BSC topsoils. In sum, these studies suggest that BSCs from regions of differing surface coverage represent early successional stages, which exhibit increasing bacterial diversity, metabolic activities, and capacity to restructure the soil. Further, these trends suggest that BSC successional maturation and colonization across the transect are inhibited by metals/metalloids such as B, Ca, Ti, Mn, Co, Ni, Mo, and Pb.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Parag Vaishampayan
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Blue Marble Space Institute of Science, Seattle, WA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Mina Bashir
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Chris P McKay
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States
| | - Keith Schubert
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, Baylor University, Waco, TX, United States
| | - Rosalba Bornaccorsi
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,SETI Institute, Mountain View, CA, United States
| | - Ernesto Gomez
- Science Team, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Department of Computer Science, California State University, San Bernardino, San Bernardino, CA, United States
| | - Sneha Tharayil
- College of Education, University of Texas at Austin, Austin, TX, United States.,Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoffrey Payton
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Orchard Academies 2B: Arts and Media, Bell, CA, United States
| | - Juliana Capra
- Teacher Core, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Foothills Middle School, Arcadia, CA, United States
| | - Jessica Andaya
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Leonard Bacon
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Maple Hill High School, Castleton-on-Hudson, NY, United States
| | - Emily Bargoma
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - David Black
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,American Academy of Innovation, Jordan, UT, United States
| | - Katie Boos
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michaela Brant
- College of Education, University of Texas at Austin, Austin, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Michael Chabot
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Danny Chau
- Orchard Academies 2B: Arts and Media, Bell, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica Cisneros
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Geoff Chu
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jane Curnutt
- Department of Computer Science, Baylor University, Waco, TX, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jessica DiMizio
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Christian Engelbrecht
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Caroline Gott
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Raechel Harnoto
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Ruben Hovanesian
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Shane Johnson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Britne Lavergne
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Gabriel Martinez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Paul Mans
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Ernesto Morales
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Alex Oei
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Gary Peplow
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Smiley Elementary School, Redlands, CA, United States
| | - Ryan Piaget
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Nicole Ponce
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Eduardo Renteria
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Veronica Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Joseph Rodriguez
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Monica Santander
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Khamille Sarmiento
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Allison Scheppelmann
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Gavin Schroter
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Devan Sexton
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Jenin Stephenson
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Kristin Symer
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Excellence in STEM Education, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Tatiane Russo-Tait
- Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States.,Center for Math and Science Education, San Francisco State University, San Francisco, CA, United States
| | - Bill Weigel
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, Pomona, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
| | - Mary B Wilhelm
- Ames Research Center, National Aeronautics and Space Administration, Mountain View, CA, United States.,Research Cohorts, NASA/CSU Spaceward Bound, Pomona, CA, United States
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41
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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42
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Perchlorates on Mars enhance the bacteriocidal effects of UV light. Sci Rep 2017; 7:4662. [PMID: 28684729 PMCID: PMC5500590 DOI: 10.1038/s41598-017-04910-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/11/2022] Open
Abstract
Perchlorates have been identified on the surface of Mars. This has prompted speculation of what their influence would be on habitability. We show that when irradiated with a simulated Martian UV flux, perchlorates become bacteriocidal. At concentrations associated with Martian surface regolith, vegetative cells of Bacillus subtilis in Martian analogue environments lost viability within minutes. Two other components of the Martian surface, iron oxides and hydrogen peroxide, act in synergy with irradiated perchlorates to cause a 10.8-fold increase in cell death when compared to cells exposed to UV radiation after 60 seconds of exposure. These data show that the combined effects of at least three components of the Martian surface, activated by surface photochemistry, render the present-day surface more uninhabitable than previously thought, and demonstrate the low probability of survival of biological contaminants released from robotic and human exploration missions.
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43
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Mickol RL, Page JL, Schuerger AC. Magnesium Sulfate Salt Solutions and Ices Fail to Protect Serratia liquefaciens from the Biocidal Effects of UV Irradiation under Martian Conditions. ASTROBIOLOGY 2017; 17:401-412. [PMID: 28459604 DOI: 10.1089/ast.2015.1448] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The growth of Serratia liquefaciens has been demonstrated under martian conditions of 0.7 kPa (7 mbar), 0°C, and CO2-enriched anoxic atmospheres (Schuerger et al., 2013, Astrobiology 13:115-131), but studies into the survivability of cells under hypersaline conditions that are likely to be encountered on Mars are lacking. Serratia liquefaciens cells were suspended in aqueous MgSO4 solutions, or frozen brines, and exposed to terrestrial (i.e., 101.3 kPa, 24°C, O2/N2-normal atmosphere) or martian (i.e., 0.7 kPa, -25°C, CO2-anoxic atmosphere) conditions to assess the roles of MgSO4 and UV irradiation on the survival of S. liquefaciens. Four solutions were tested for their capability to attenuate martian UV irradiation in both liquid and frozen forms: sterile deionized water (SDIW), 10 mM PO4 buffer, 5% MgSO4, and 10% MgSO4. None of the solutions in either liquid or frozen forms provided enhanced protection against martian UV irradiation. Sixty minutes of UV irradiation reduced cell densities from 2.0 × 106 cells/mL to less than 10 cells/mL for both liquid and frozen solutions. In contrast, 3-4 mm of a Mars analog soil were sufficient to attenuate 100% of UV irradiation. Results suggest that terrestrial microorganisms may not survive on Sun-exposed surfaces on Mars, even if the cells are embedded in frozen martian brines composed of MgSO4. However, if dispersed microorganisms can be covered by only a few millimeters of dust or regolith, long-term survival is probable. Key Words: Hypobaria-Mars-Planetary protection-Brines. Astrobiology 17, 401-412.
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Affiliation(s)
- Rebecca L Mickol
- 1 Center for Space and Planetary Sciences, University of Arkansas , Fayetteville, Arkansas
| | - Jessica L Page
- 2 Department of Physics and Space Science, Florida Institute of Technology , Melbourne, Florida
| | - Andrew C Schuerger
- 3 Department of Plant Pathology, University of Florida , Gainesville, Florida
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44
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Wadsworth J, Cockell CS. The Janus face of iron on anoxic worlds: iron oxides are both protective and destructive to life on the early Earth and present-day Mars. FEMS Microbiol Ecol 2017; 93:3778240. [PMID: 28460085 DOI: 10.1093/femsec/fix056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/26/2017] [Indexed: 11/15/2022] Open
Abstract
The surface of the early Earth was probably subjected to a higher flux of ultraviolet (UV) radiation than today. UV radiation is known to severely damage DNA and other key molecules of life. Using a liquid culture and a rock analogue system, we investigated the interplay of protective and deleterious effects of iron oxides under UV radiation on the viability of the model organism, Bacillus subtilis. In the presence of hydrogen peroxide, there exists a fine balance between iron oxide's protective effects against this radiation and its deleterious effects caused by Photo-Fenton reactions. The maximum damage was caused by a concentration of hematite of ∼1 mg/mL. Concentrations above this confer increasing protection by physical blockage of the UV radiation, concentrations below this cause less effective UV radiation blockage, but also a correspondingly less effective Photo-Fenton reaction, providing an overall advantage. These results show that on anoxic worlds, surface habitability under a high UV flux leaves life precariously poised between the beneficial and deleterious effects of iron oxides. These results have relevance to the Archean Earth, but also the habitability of the Martian surface, where high levels of UV radiation in combination with iron oxides and hydrogen peroxide can be found.
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Affiliation(s)
- Jennifer Wadsworth
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH10 4EP, UK
| | - Charles S Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH10 4EP, UK
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45
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Smith SA, Benardini JN, Anderl D, Ford M, Wear E, Schrader M, Schubert W, DeVeaux L, Paszczynski A, Childers SE. Identification and Characterization of Early Mission Phase Microorganisms Residing on the Mars Science Laboratory and Assessment of Their Potential to Survive Mars-like Conditions. ASTROBIOLOGY 2017; 17:253-265. [PMID: 28282220 PMCID: PMC5373329 DOI: 10.1089/ast.2015.1417] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 10/04/2016] [Indexed: 05/23/2023]
Abstract
Planetary protection is governed by the Outer Space Treaty and includes the practice of protecting planetary bodies from contamination by Earth life. Although studies are constantly expanding our knowledge about life in extreme environments, it is still unclear what the probability is for terrestrial organisms to survive and grow on Mars. Having this knowledge is paramount to addressing whether microorganisms transported from Earth could negatively impact future space exploration. The objectives of this study were to identify cultivable microorganisms collected from the surface of the Mars Science Laboratory, to distinguish which of the cultivable microorganisms can utilize energy sources potentially available on Mars, and to determine the survival of the cultivable microorganisms upon exposure to physiological stresses present on the martian surface. Approximately 66% (237) of the 358 microorganisms identified are related to members of the Bacillus genus, although surprisingly, 22% of all isolates belong to non-spore-forming genera. A small number could grow by reduction of potential growth substrates found on Mars, such as perchlorate and sulfate, and many were resistant to desiccation and ultraviolet radiation (UVC). While most isolates either grew in media containing ≥10% NaCl or at 4°C, many grew when multiple physiological stresses were applied. The study yields details about the microorganisms that inhabit the surfaces of spacecraft after microbial reduction measures, information that will help gauge whether microorganisms from Earth pose a forward contamination risk that could impact future planetary protection policy. Key Words: Planetary protection-Spore-Bioburden-MSL-Curiosity-Contamination-Mars. Astrobiology 17, 253-265.
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Affiliation(s)
| | - James N Benardini
- 2 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - David Anderl
- 1 School of Food Science, University of Idaho , Moscow, Idaho
| | - Matt Ford
- 3 Department of Biological Sciences, Idaho State University , Pocatello, Idaho
| | - Emmaleen Wear
- 1 School of Food Science, University of Idaho , Moscow, Idaho
| | | | - Wayne Schubert
- 2 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Linda DeVeaux
- 4 Department of Chemistry and Applied Biological Sciences, South Dakota School of Mines and Technology , Rapid City, South Dakota
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Mora M, Perras A, Alekhova TA, Wink L, Krause R, Aleksandrova A, Novozhilova T, Moissl-Eichinger C. Resilient microorganisms in dust samples of the International Space Station-survival of the adaptation specialists. MICROBIOME 2016; 4:65. [PMID: 27998314 PMCID: PMC5175303 DOI: 10.1186/s40168-016-0217-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/03/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND The International Space Station (ISS) represents a unique biotope for the human crew but also for introduced microorganisms. Microbes experience selective pressures such as microgravity, desiccation, poor nutrient-availability due to cleaning, and an increased radiation level. We hypothesized that the microbial community inside the ISS is modified by adapting to these stresses. For this reason, we analyzed 8-12 years old dust samples from Russian ISS modules with major focus on the long-time surviving portion of the microbial community. We consequently assessed the cultivable microbiota of these samples in order to analyze their extremotolerant potential against desiccation, heat-shock, and clinically relevant antibiotics. In addition, we studied the bacterial and archaeal communities from the stored Russian dust samples via molecular methods (next-generation sequencing, NGS) and compared our new data with previously derived information from the US American ISS dust microbiome. RESULTS We cultivated and identified in total 85 bacterial, non-pathogenic isolates (17 different species) and 1 fungal isolate from the 8-12 year old dust samples collected in the Russian segment of the ISS. Most of these isolates exhibited robust resistance against heat-shock and clinically relevant antibiotics. Microbial 16S rRNA gene and archaeal 16S rRNA gene targeting Next Generation Sequencing showed signatures of human-associated microorganisms (Corynebacterium, Staphylococcus, Coprococcus etc.), but also specifically adapted extremotolerant microorganisms. Besides bacteria, the detection of archaeal signatures in higher abundance was striking. CONCLUSIONS Our findings reveal (i) the occurrence of living, hardy microorganisms in archived Russian ISS dust samples, (ii) a profound resistance capacity of ISS microorganisms against environmental stresses, and (iii) the presence of archaeal signatures on board. In addition, we found indications that the microbial community in the Russian segment dust samples was different to recently reported US American ISS microbiota.
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Affiliation(s)
- Maximilian Mora
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Alexandra Perras
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
- Department for Microbiology, University of Regensburg, Universitätsstr. 31, 93053 Regensburg, Germany
| | | | - Lisa Wink
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Robert Krause
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Alina Aleksandrova
- Lomonosov Moscow State University, Leninskie Gory, 119991 Moscow, Russia
| | | | - Christine Moissl-Eichinger
- Department for Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed Graz, Krenngasse 37, 8010 Graz, Austria
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Benardini JN, Venkateswaran K. Application of the ATP assay to rapidly assess cleanliness of spacecraft surfaces: a path to set a standard for future missions. AMB Express 2016; 6:113. [PMID: 27844457 PMCID: PMC5108744 DOI: 10.1186/s13568-016-0286-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/07/2016] [Indexed: 11/10/2022] Open
Abstract
The National Aeronautics and Space Administration (NASA) measures and validates the biological cleanliness of spacecraft surfaces by counting endospores using the NASA standard assay (NSA). NASA has also approved an adenosine-5'-triphosphate (ATP)-based detection methodology as a means to prescreen surfaces for the presence of microbial contamination, prior to the spore assay. During Mars Science Laboratory (MSL) spacecraft assembly, test, and launch operations, 4853 surface samples were collected to verify compliance with the bioburden requirement at launch. A subset of these samples was measured for microbial cleanliness using both the NSA (n = 272) and ATP assay (n = 249). NSA results revealed that ~8% (22/272) of the samples showed the presence of at least one spore, whereas ATP assay measurements indicated that ~15% (35/249) of samples exceeded the "threshold cleanliness limit" of 2.3 × 10-11 mmol ATP per 25 cm2 used by MSL. Of the 22 NSA samples with a spore, 18% (4/22) were considered above the level of acceptance by both techniques. Based on post launch data analysis presented here, it was determined that this threshold cleanliness limit of 2.3 × 10-11 mmol ATP per 25 cm2 could be adopted as a benchmark for assessing spacecraft surface cleanliness. This study clearly demonstrates the value of using alternative methods to rapidly assess spacecraft cleanliness, and provides useful information regarding the process.
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Filippidou S, Wunderlin T, Junier T, Jeanneret N, Dorador C, Molina V, Johnson DR, Junier P. A Combination of Extreme Environmental Conditions Favor the Prevalence of Endospore-Forming Firmicutes. Front Microbiol 2016; 7:1707. [PMID: 27857706 PMCID: PMC5094177 DOI: 10.3389/fmicb.2016.01707] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/12/2016] [Indexed: 12/21/2022] Open
Abstract
Environmental conditions unsuitable for microbial growth are the rule rather than the exception in most habitats. In response to this, microorganisms have developed various strategies to withstand environmental conditions that limit active growth. Endospore-forming Firmicutes (EFF) deploy a myriad of survival strategies in order to resist adverse conditions. Like many bacterial groups, they can form biofilms and detect nutrient scarcity through chemotaxis. Moreover, within this paraphyletic group of Firmicutes, ecophysiological optima are diverse. Nonetheless, a response to adversity that delimits this group is the formation of wet-heat resistant spores. These strategies are energetically demanding and therefore might affect the biological success of EFF. Therefore, we hypothesize that abundance and diversity of EFF should be maximized in those environments in which the benefits of these survival strategies offsets the energetic cost. In order to address this hypothesis, geothermal and mineral springs and drillings were selected because in these environments of steep physicochemical gradients, diversified survival strategies may become a successful strategy.We collected 71 samples from geothermal and mineral environments characterized by none (null), single or multiple limiting environmental factors (temperature, pH, UV radiation, and specific mineral composition). To measure success, we quantified EFF gene copy numbers (GCN; spo0A gene) in relation to total bacterial GCN (16S rRNA gene), as well as the contribution of EFF to community composition. The quantification showed that relative GCN for EFF reached up to 20% at sites characterized by multiple limiting environmental factors, whereas it corresponded to less than 1% at sites with one or no limiting environmental factor. Pyrosequencing of the 16S rRNA gene supports a higher contribution of EFF at sites with multiple limiting factors. Community composition suggested a combination of phylotypes for which active growth could be expected, and phylotypes that are most likely in the state of endospores, in all the sites. In summary, our results suggest that diversified survival strategies, including sporulation and metabolic adaptations, explain the biological success of EFF in geothermal and natural springs, and that multiple extreme environmental factors favor the prevalence of EFF.
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Affiliation(s)
- Sevasti Filippidou
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Tina Wunderlin
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Thomas Junier
- Laboratory of Microbiology, University of NeuchâtelNeuchâtel, Switzerland; Vital-IT group, Swiss Institute of BioinformaticsLausanne, Switzerland
| | - Nicole Jeanneret
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional and Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de AntofagastaAntofagasta, Chile; Centre for Biotechnology and Bioengineering, CeBiB, University of ChileSantiago, Chile
| | - Veronica Molina
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas. Universidad de Playa Ancha Valparaíso, Chile
| | - David R Johnson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf, Switzerland
| | - Pilar Junier
- Laboratory of Microbiology, University of Neuchâtel Neuchâtel, Switzerland
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Mora M, Mahnert A, Koskinen K, Pausan MR, Oberauner-Wappis L, Krause R, Perras AK, Gorkiewicz G, Berg G, Moissl-Eichinger C. Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station. Front Microbiol 2016; 7:1573. [PMID: 27790191 PMCID: PMC5061736 DOI: 10.3389/fmicb.2016.01573] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 09/20/2016] [Indexed: 01/15/2023] Open
Abstract
Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 – and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards.
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Affiliation(s)
- Maximilian Mora
- Department for Internal Medicine, Medical University of Graz, Graz Austria
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz Austria
| | - Kaisa Koskinen
- Department for Internal Medicine, Medical University of Graz, GrazAustria; BioTechMed-Graz, GrazAustria
| | - Manuela R Pausan
- Department for Internal Medicine, Medical University of Graz, Graz Austria
| | | | - Robert Krause
- Department for Internal Medicine, Medical University of Graz, Graz Austria
| | - Alexandra K Perras
- Department for Internal Medicine, Medical University of Graz, GrazAustria; Department for Microbiology, University of Regensburg, RegensburgGermany
| | - Gregor Gorkiewicz
- BioTechMed-Graz, GrazAustria; Department of Pathology, Medical University of Graz, GrazAustria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz Austria
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Bashir M, Ahmed M, Weinmaier T, Ciobanu D, Ivanova N, Pieber TR, Vaishampayan PA. Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. Front Microbiol 2016; 7:1321. [PMID: 27667984 PMCID: PMC5017214 DOI: 10.3389/fmicb.2016.01321] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 08/10/2016] [Indexed: 01/09/2023] Open
Abstract
Strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. Therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. We wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. Three geographically distinct cleanrooms were sampled during the assembly of three NASA spacecraft: The Lockheed Martin Aeronautics' Multiple Testing Facility during DAWN, the Kennedy Space Center's Payload Hazardous Servicing Facility (KSC-PHSF) during Phoenix, and the Jet Propulsion Laboratory's Spacecraft Assembly Facility during Mars Science Laboratory. Sample sets were collected from the KSC-PHSF cleanroom at three time points: before arrival of the Phoenix spacecraft, during the assembly and testing of the Phoenix spacecraft, and after removal of the spacecraft from the KSC-PHSF facility. All samples were subjected to metagenomic shotgun sequencing on an Illumina HiSeq 2500 platform. Strict decontamination procedures had a greater impact on microbial communities than sampling location Samples collected during spacecraft assembly were dominated by Acinetobacter spp. We found pathogens and potential virulence factors, which determine pathogenicity in all the samples tested during this study. Though the relative abundance of pathogens was lowest during the Phoenix assembly, potential virulence factors were higher during assembly compared to before and after assembly, indicating a survival advantage. Decreased phylogenetic and pathogenic diversity indicates that decontamination and preventative measures were effective against the majority of microorganisms and well implemented, however, pathogen abundance still increased over time. Four potential pathogens, Acinetobacter baumannii, Acinetobacter lwoffii, Escherichia coli and Legionella pneumophila, and their corresponding virulence factors were present in all cleanroom samples. This is the first functional metagenomics study describing presence of pathogens and their corresponding virulence factors in cleanroom environments. The results of this study should be considered for microbial monitoring of enclosed environments such as schools, homes, hospitals and more isolated habitation such the International Space Station and future manned missions to Mars.
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Affiliation(s)
- Mina Bashir
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Division of Endocrinology and Diabetology, Medical University of GrazGraz, Austria
| | - Mahjabeen Ahmed
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of TechnologyPasadena, CA, USA; Department of Biological Sciences, California State Polytechnic UniversityPomona, CA, USA
| | - Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna Vienna, Austria
| | - Doina Ciobanu
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Natalia Ivanova
- Department of Energy, Joint Genome Institute Walnut Creek, CA, USA
| | - Thomas R Pieber
- Division of Endocrinology and Diabetology, Medical University of Graz Graz, Austria
| | - Parag A Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology Pasadena, CA, USA
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