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Leo P, de Melo Texeira M, Chander AM, Singh NK, Simpson AC, Yurkov A, Karouia F, Stajich JE, Mason CE, Venkateswaran K. Genomic characterization and radiation tolerance of Naganishia kalamii sp. nov. and Cystobasidium onofrii sp. nov. from Mars 2020 mission assembly facilities. IMA Fungus 2023; 14:15. [PMID: 37568226 PMCID: PMC10422843 DOI: 10.1186/s43008-023-00119-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/20/2023] [Indexed: 08/13/2023] Open
Abstract
During the construction and assembly of the Mars 2020 mission components at two different NASA cleanrooms, several fungal strains were isolated. Based on their colony morphology, two strains that showed yeast-like appearance were further characterized for their phylogenetic position. The species-level classification of these two novel strains, using traditional colony and cell morphology methods combined with the phylogenetic reconstructions using multi-locus sequence analysis (MLSA) based on several gene loci (ITS, LSU, SSU, RPB1, RPB2, CYTB and TEF1), and whole genome sequencing (WGS) was carried out. This polyphasic taxonomic approach supported the conclusion that the two basidiomycetous yeasts belong to hitherto undescribed species. The strain FJI-L2-BK-P3T, isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility, was placed in the Naganishia albida clade (Filobasidiales, Tremellomycetes), but is genetically and physiologically different from other members of the clade. Another yeast strain FKI-L6-BK-PAB1T, isolated from the Kennedy Space Center Payload Hazardous and Servicing Facility, was placed in the genus Cystobasidium (Cystobasidiales, Cystobasidiomycetes) and is distantly related to C. benthicum. Here we propose two novel species with the type strains, Naganishia kalamii sp. nov. (FJI-L2-BK-P3T = NRRL 64466 = DSM 115730) and Cystobasidium onofrii sp. nov. (FKI-L6-BK-PAB1T = NRRL 64426 = DSM 114625). The phylogenetic analyses revealed that single gene phylogenies (ITS or LSU) were not conclusive, and MLSA and WGS-based phylogenies were more advantageous for species discrimination in the two genera. The genomic analysis predicted proteins associated with dehydration and desiccation stress-response and the presence of genes that are directly related to osmotolerance and psychrotolerance in both novel yeasts described. Cells of these two newly-described yeasts were exposed to UV-C radiation and compared with N. onofrii, an extremophilic UV-C resistant cold-adapted Alpine yeast. Both novel species were UV resistant, emphasizing the need for collecting and characterizing extremotolerant microbes, including yeasts, to improve microbial reduction techniques used in NASA planetary protection programs.
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Affiliation(s)
- Patrick Leo
- Department of Environmental Sciences, Informatics and Statistics, University Ca' Foscari of Venice, Via Torino 155, 30172, Mestre, Italy
- Department of Ecological and Biological Sciences, University of Tuscia, Largo dell'università snc, 01100, Viterbo, Italy
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Marcus de Melo Texeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Núcleo de Medicina Tropical, Faculdade de Medicina, Universidade de Brasília, Brasília, 70910-900, Brazil
| | - Atul M Chander
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Nitin K Singh
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Anna C Simpson
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-103, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Andrey Yurkov
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Brunswick, Germany
| | - Fathi Karouia
- Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, PO BOX 1 MS 239/4, Moffett Field, CA, 94035, USA
- Space Research Within Reach, San Francisco, CA, 941110, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of CA-Riverside, Riverside, CA, 92521, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics and the WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Kasthuri Venkateswaran
- NASA-Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 245-104, 4800 Oak Grove Dr., Pasadena, CA, 91109, 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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Mogul R, Miller DR, Ramos B, Lalla SJ. Metabolomic and cultivation insights into the tolerance of the spacecraft-associated Acinetobacter toward Kleenol 30, a cleanroom floor detergent. Front Microbiol 2023; 14:1090740. [PMID: 36950167 PMCID: PMC10025500 DOI: 10.3389/fmicb.2023.1090740] [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: 11/05/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023] Open
Abstract
Introduction Stringent cleaning procedures during spacecraft assembly are critical to maintaining the integrity of life-detection missions. To ensure cleanliness, NASA spacecraft are assembled in cleanroom facilities, where floors are routinely cleansed with Kleenol 30 (K30), an alkaline detergent. Methods Through metabolomic and cultivation approaches, we show that cultures of spacecraft-associated Acinetobacter tolerate up to 1% v/v K30 and are fully inhibited at ≥2%; in comparison, NASA cleanrooms are cleansed with ~0.8-1.6% K30. Results For A. johnsonii 2P08AA (isolated from a cleanroom floor), cultivations with 0.1% v/v K30 yield (1) no changes in cell density at late-log phase, (2) modest decreases in growth rate (~17%), (3) negligible lag phase times, (4) limited changes in the intracellular metabolome, and (5) increases in extracellular sugar acids, monosaccharides, organic acids, and fatty acids. For A. radioresistens 50v1 (isolated from a spacecraft surface), cultivations yield (1) ~50% survivals, (2) no changes in growth rate, (3) ~70% decreases in the lag phase time, (4) differential changes in intracellular amino acids, compatible solutes, nucleotide-related metabolites, dicarboxylic acids, and saturated fatty acids, and (5) substantial yet differential impacts to extracellular sugar acids, monosaccharides, and organic acids. Discussion These combined results suggest that (1) K30 manifests strain-dependent impacts on the intracellular metabolomes, cultivation kinetics, and survivals, (2) K30 influences extracellular trace element acquisition in both strains, and (3) K30 is better tolerated by the floor-associated strain. Hence, this work lends support towards the hypothesis that repeated cleansing during spacecraft assembly serve as selective pressures that promote tolerances towards the cleaning conditions.
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Affiliation(s)
- Rakesh Mogul
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
- Blue Marble Institute of Science, Seattle, WA, United States
| | - Daniel R. Miller
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Brian Ramos
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
| | - Sidharth J. Lalla
- Chemistry and Biochemistry Department, California State Polytechnic University, Pomona, CA, United States
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Yang J, Hao Z, Zhang L, Fu Y, Liu H. Surface fungal diversity and several mycotoxin-related genes' expression profiles during the Lunar Palace 365 experiment. MICROBIOME 2022; 10:169. [PMID: 36224642 PMCID: PMC9555122 DOI: 10.1186/s40168-022-01350-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/19/2022] [Indexed: 05/07/2023]
Abstract
BACKGROUND Chinese Lunar Palace 1 (LP1) is a ground-based bio-regenerative life support system (BLSS) test bed integrating highly efficient plant cultivation, animal protein production, urine nitrogen recycling, and bioconversion of solid waste. To date, there has been no molecular method-based detailed investigation of the fungal community and mycotoxin potential in BLSS habitats. To ensure safe BLSS design for actual space missions, we analyzed the LP1 surface mycobiome and mycotoxin potential during the Lunar Palace 365 project through internal transcribed spacer region 1 (ITS1) amplicon sequencing and quantitative polymerase chain reaction (qPCR) with primers specific for idh, ver1, nor1, tri5, and ITS1. RESULTS The LP1 system exhibited significant differences in fungal community diversity compared to other confined habitats, with higher fungal alpha diversity and different community structures. Significant differences existed in the surface fungal communities of the LP1 habitat due to the presence of different occupant groups. However, there was no significant difference between fungal communities in the plant cabin with various occupants. Source tracker analysis shows that most of the surface fungi in LP1 originated from plants. Regardless of differences in occupants or location, there were no significant differences in mycotoxin gene copy number. CONCLUSIONS Our study reveals that plants are the most crucial source of the surface fungal microbiome; however, occupant turnover can induce significant perturbations in the surface fungal community in a BLSS. Growing plants reduced fungal fluctuations, maintaining a healthy balance in the surface fungal microbiome and mycotoxin potential. Moreover, our study provides data important to (i) future risk considerations in crewed space missions with long-term residency, (ii) an optimized design and planning of a space mission that incorporates crew shifts and plant growth, and (iii) the expansion of our knowledge of indoor fungal communities with plant growth, which is essential to maintain safe working and living environments. Video Abstract.
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Affiliation(s)
- Jianlou Yang
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191 China
| | - Zikai Hao
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191 China
| | - Lantao Zhang
- China Academy of Space Technology, Beijing, 100094 China
| | - Yuming Fu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191 China
- International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100191 China
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083 China
| | - Hong Liu
- Key Laboratory for Biomechanics and Mechanobiology of the Ministry of Education, Beijing Advanced Innovation Centre for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191 China
- International Joint Research Center of Aerospace Biotechnology & Medical Engineering, Beihang University, Beijing, 100191 China
- State Key Laboratory of Virtual Reality Technology and Systems, School of Computer Science and Engineering, Beihang University, Beijing, 100083 China
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Blachowicz A, Mhatre S, Singh NK, Wood JM, Parker CW, Ly C, Butler D, Mason CE, Venkateswaran K. The Isolation and Characterization of Rare Mycobiome Associated With Spacecraft Assembly Cleanrooms. Front Microbiol 2022; 13:777133. [PMID: 35558115 PMCID: PMC9087587 DOI: 10.3389/fmicb.2022.777133] [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: 09/14/2021] [Accepted: 03/04/2022] [Indexed: 11/15/2022] Open
Abstract
Ensuring biological cleanliness while assembling and launching spacecraft is critical for robotic exploration of the solar system. To date, when preventing forward contamination of other celestial bodies, NASA Planetary Protection policies have focused on endospore-forming bacteria while fungi were neglected. In this study, for the first time the mycobiome of two spacecraft assembly facilities at Jet Propulsion Laboratory (JPL) and Kennedy Space Center (KSC) was assessed using both cultivation and sequencing techniques. To facilitate enumeration of viable fungal populations and downstream molecular analyses, collected samples were first treated with chloramphenicol for 24 h and then with propidium monoazide (PMA). Among cultivable fungi, 28 distinct species were observed, 16 at JPL and 16 at KSC facilities, while 13 isolates were potentially novel species. Only four isolated species Aureobasidium melanogenum, Penicillium fuscoglaucum, Penicillium decumbens, and Zalaria obscura were present in both cleanroom facilities, which suggests that mycobiomes differ significantly between distant locations. To better visualize the biogeography of all isolated strains the network analysis was undertaken and confirmed higher abundance of Malassezia globosa and Cyberlindnera jadinii. When amplicon sequencing was performed, JPL-SAF and KSC-PHSF showed differing mycobiomes. Metagenomic fungal reads were dominated by Ascomycota (91%) and Basidiomycota (7.15%). Similar to amplicon sequencing, the number of fungal reads changed following antibiotic treatment in both cleanrooms; however, the opposite trends were observed. Alas, treatment with the antibiotic did not allow for definitive ascribing changes observed in fungal populations between treated and untreated samples in both cleanrooms. Rather, these substantial differences in fungal abundance might be attributed to several factors, including the geographical location, climate and the in-house cleaning procedures used to maintain the cleanrooms. This study is a first step in characterizing cultivable and viable fungal populations in cleanrooms to assess fungal potential as biocontaminants during interplanetary explorations. The outcomes of this and future studies could be implemented in other cleanrooms that require to reduce microbial burden, like intensive care units, operating rooms, or cleanrooms in the semiconducting and pharmaceutical industries.
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Affiliation(s)
- Adriana Blachowicz
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Snehit Mhatre
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Cynthia Ly
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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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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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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Assembly of Bacterial Genome Sequences from Metagenomes of Spacecraft Assembly Cleanrooms. Microbiol Resour Announc 2021; 10:10/7/e01439-20. [PMID: 33602737 PMCID: PMC7892670 DOI: 10.1128/mra.01439-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Characterizing the microbiome of spacecraft assembly cleanrooms is important for planetary protection. We report two bacterial metagenome-assembled genome sequences (MAGs) reconstructed from metagenomes produced from cleanroom samples from the Kennedy Space Center’s Payload Hazardous Servicing Facility (KSC-PHSF) during the handling of the Phoenix spacecraft. Characterization of these MAGs will enable identification of the strategies underpinning their survival. Characterizing the microbiome of spacecraft assembly cleanrooms is important for planetary protection. We report two bacterial metagenome-assembled genomes (MAGs) reconstructed from metagenomes produced from cleanroom samples from the Kennedy Space Center’s Payload Hazardous Servicing Facility (KSC-PHSF) during the handling of the Phoenix spacecraft. Characterization of these MAGs will enable identification of the strategies underpinning their survival.
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Regberg AB, Castro CL, Connolly HC, Davis RE, Dworkin JP, Lauretta DS, Messenger SR, Mclain HL, McCubbin FM, Moore JL, Righter K, Stahl-Rommel S, Castro-Wallace SL. Prokaryotic and Fungal Characterization of the Facilities Used to Assemble, Test, and Launch the OSIRIS-REx Spacecraft. Front Microbiol 2020; 11:530661. [PMID: 33250861 PMCID: PMC7676328 DOI: 10.3389/fmicb.2020.530661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 09/30/2020] [Indexed: 01/04/2023] Open
Abstract
To characterize the ATLO (Assembly, Test, and Launch Operations) environment of the OSIRIS-REx spacecraft, we analyzed 17 aluminum witness foils and two blanks for bacterial, archaeal, fungal, and arthropod DNA. Under NASA’s Planetary Protection guidelines, OSIRIS-REx is a Category II outbound, Category V unrestricted sample return mission. As a result, it has no bioburden restrictions. However, the mission does have strict organic contamination requirements to achieve its primary objective of returning pristine carbonaceous asteroid regolith to Earth. Its target, near-Earth asteroid (101955) Bennu, is likely to contain organic compounds that are biologically available. Therefore, it is useful to understand what organisms were present during ATLO as part of the larger contamination knowledge effort—even though it is unlikely that any of the organisms will survive the multi-year deep space journey. Even though these samples of opportunity were not collected or preserved for DNA analysis, we successfully amplified bacterial and archaeal DNA (16S rRNA gene) from 16 of the 17 witness foils containing as few as 7 ± 3 cells per sample. Fungal DNA (ITS1) was detected in 12 of the 17 witness foils. Despite observing arthropods in some of the ATLO facilities, arthropod DNA (COI gene) was not detected. We observed 1,009 bacterial and archaeal sOTUs (sub-operational taxonomic units, 100% unique) and 167 fungal sOTUs across all of our samples (25–84 sOTUs per sample). The most abundant bacterial sOTU belonged to the genus Bacillus. This sOTU was present in blanks and may represent contamination during sample handling or storage. The sample collected from inside the fairing just prior to launch contained several unique bacterial and fungal sOTUs that describe previously uncharacterized potential for contamination during the final phase of ATLO. Additionally, fungal richness (number of sOTUs) negatively correlates with the number of carbon-bearing particles detected on samples. The total number of fungal sequences positively correlates with total amino acid concentration. These results demonstrate that it is possible to use samples of opportunity to characterize the microbiology of low-biomass environments while also revealing the limitations imposed by sample collection and preservation methods not specifically designed with biology in mind.
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Affiliation(s)
- Aaron B Regberg
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | | | - Harold C Connolly
- Department of Geology, Rowan University, Glassboro, NJ, United States.,Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, United States
| | - Richard E Davis
- Jacobs@NASA/Johnson Space Center, Houston, TX, United States
| | - Jason P Dworkin
- Astrochemistry Laboratory, Goddard Space Flight Center, Greenbelt, MD, United States
| | - Dante S Lauretta
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, United States
| | - Scott R Messenger
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | - Hannah L Mclain
- Astrochemistry Laboratory, Goddard Space Flight Center, Greenbelt, MD, United States
| | - Francis M McCubbin
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | - Jamie L Moore
- Lockheed Martin Space Systems, Littleton, CO, United States
| | - Kevin Righter
- Astromaterials Research and Exploration Science Division, National Aeronautics and Space Administration (NASA) Johnson Space Center, Houston TX, United States
| | | | - Sarah L Castro-Wallace
- Biomedical Research and Environmental Sciences Division, Johnson Space Center, Houston, TX, United States
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Mhatre S, Singh NK, Wood JM, Parker CW, Pukall R, Verbarg S, Tindall BJ, Neumann-Schaal M, Venkateswaran K. Description of Chloramphenicol Resistant Kineococcus rubinsiae sp. nov. Isolated From a Spacecraft Assembly Facility. Front Microbiol 2020; 11:1957. [PMID: 32973710 PMCID: PMC7472656 DOI: 10.3389/fmicb.2020.01957] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 07/24/2020] [Indexed: 11/13/2022] Open
Abstract
A Gram-positive, coccoid, motile, aerobic bacterium, designated strain B12T was isolated from a Jet Propulsion Laboratory spacecraft assembly cleanroom, Pasadena, CA, United States. Strain B12T was resistant to chloramphenicol (100 μg/mL), and is a relatively slow grower (3-5 days optimal). Strain B12T was found to grow optimally at 28 to 32°C, pH 7 to 8, and 0.5% NaCl. Fatty acid methyl ester analysis showed that the major fatty acid of the strain B12T was anteiso C15 : 0 (66.3%), which is also produced by other Kineococcus species. However, arachidonic acid (C20 : 4 ω6,9,12,16c) was present in strain B12T and Kineococcus glutinatus YIM 75677T but absent in all other Kineococcus species. 16S rRNA analysis revealed that strain B12T was 97.9% similar to Kineococcus radiotolerans and falls within the Kineococcus clade. Low 16S rRNA gene sequence similarities (<94%) with other genera in the family Kineosporiaceae, including Angustibacter (93%), Kineosporia (94% to 95%), Pseudokineococcus (93%), Quadrisphaera (93%), and Thalassiella (94%) demonstrated that the strain B12T does not belong to these genera. Phylogenetic analysis of the gyrB gene show that all known Kineococcus species exhibited <86% sequence similarity with B12T. Multi-locus sequence and whole genome sequence analyses confirmed that B12T clades with other Kineococcus species. Average nucleotide identity of strain B12T were 75-78% with other Kineococcus species, while values ranged from 72-75% with species from other genera within family Kineosporiaceae. Average amino-acid identities were 66-72% with other Kineococcus species, while they ranged from 50-58% with species from other genera. The dDDH comparison of strain B12T genome with members of genera Kineococcus showed 20-22% similarity, again demonstrating that B12T is distantly related to other members of the genus. Furthermore, analysis of whole proteome deduced from WGS places strain B12T in order Kineosporiales, confirming that strain B12T is a novel member of family Kineosporiaceae. Based on these analyses and other genome characteristics, strain B12T is assigned to a novel species within the genus Kineococcus, and the name Kineococcus rubinsiae sp. nov., is proposed. The type strain is B12T (=FJII-L1-CM-PAB2T; NRRL B-65556T, DSM 110506T).
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Affiliation(s)
- Snehit Mhatre
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Nitin K. Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Jason M. Wood
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Ceth W. Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Rüdiger Pukall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Susanne Verbarg
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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Li P, Zhang Y, Meng Q, Liu Y, Tuyiringire D, Chen Z, Liang S. Trichloroethylene inhibits nitrogen transformation and microbial community structure in Mollisol. ECOTOXICOLOGY (LONDON, ENGLAND) 2020; 29:801-813. [PMID: 32445014 DOI: 10.1007/s10646-020-02230-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/05/2020] [Indexed: 06/11/2023]
Abstract
Trichloroethylene (TCE) is the most ubiquitous halogenated organic pollutant in the environment, it is one of the 129 priority control pollutants. In order to clarify the influence of TCE on microorganisms and nitrogen transformation in Mollisol is the core purpose of this study. Results showed that 10 mg kg-1 TCE is the concentration limit of ammonification in Mollisol. When the concentration of TCE reached 10 mg kg-1 and the effect lasted for over 7 days, the process of ammonia oxidation to nitric acid in Mollisol will be affected. TCE affected the process of nitrate (NO3-) transformation into nitrite (NO2-) by affecting the activity of nitrate reductase, thereby affected the denitrification process in soil. When the concentration of TCE is more than 10 mg kg-1 it reduced the ability of soil microorganisms to obtain nitrogen, thereby affecting soil nitrogen transformation. RDA (Redundancy analysis) showed that the activity of nitrate reductase and the number of nitrifying bacteria and denitrifying bacteria in soil was negatively correlated with the incubation of TCE. In addition, soil nitrate reductase, nitrite reductase, peroxidase activity, ammonifying bacteria, nitrifying bacteria and denitrifying bacteria were negatively correlated with TCE concentration. Beyond that PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) of functional gene structure depend on KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that 20 mg kg-1 TCE significantly inhibited the metabolism of energy and other substances in Mollisol. Based on the above, it is found that TCE significantly affected nitrification and denitrification in Mollisol, thus the nitrogen transformation in Mollisol was affected by TCE contamination.
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Affiliation(s)
- Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
- College of Geographical Science, Harbin Normal University, 150025, Harbin, China
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China.
| | - Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
| | - Diogene Tuyiringire
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, 116600, Dalian, China
| | - Shichao Liang
- College of Resources and Environment, Northeast Agricultural University, 150030, Harbin, China
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12
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Abstract
This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats. Microbial contamination during long-term confinements of space exploration presents potential risks for both crew members and spacecraft life support systems. A novel swab kit was used to sample various surfaces from a submerged, closed, analog habitat to characterize the microbial populations. Samples were collected from various locations across the habitat which were constructed from various surface materials (linoleum, dry wall, particle board, glass, and metal), and microbial populations were examined by culture, quantitative PCR (qPCR), microbiome 16S rRNA gene sequencing, and shotgun metagenomics. Propidium monoazide (PMA)-treated samples identified the viable/intact microbial population of the habitat. The cultivable microbial population ranged from below the detection limit to 106 CFU/sample, and their identity was characterized using Sanger sequencing. Both 16S rRNA amplicon and shotgun sequencing were used to characterize the microbial dynamics, community profiles, and functional attributes (metabolism, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable (after PMA treatment) Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia, and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus, and Oceanobacillus), and Proteobacteria (especially Acinetobacter) on linoleum, dry wall, and particle board (LDP) surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Nonmetric multidimensional scaling determined from both 16S rRNA and metagenomic analyses revealed differential microbial species on LDP surfaces and glass/metal surfaces. The shotgun metagenomic sequencing of samples after PMA treatment showed bacterial predominance of viable Brevibacterium (53.6%), Brachybacterium (7.8%), Pseudonocardia (9.9%), Mycobacterium (3.7%), and Staphylococcus (2.1%), while fungal analyses revealed Aspergillus and Penicillium dominance. IMPORTANCE This study provides the first assessment of monitoring cultivable and viable microorganisms on surfaces within a submerged, closed, analog habitat. The results of the analyses presented herein suggest that the surface material plays a role in microbial community structure, as the microbial populations differed between LDP and metal/glass surfaces. The metal/glass surfaces had less-complex community, lower bioburden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Finally, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft, the majority of the microbial ecology of the submerged analog habitat differs greatly from that of previously studied analog habitats.
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Understanding the Biosynthetic Changes that Give Origin to the Distinctive Flavor of Sotol: Microbial Identification and Analysis of the Volatile Metabolites Profiles During Sotol ( Dasylirion sp.) Must Fermentation. Biomolecules 2020; 10:biom10071063. [PMID: 32708695 PMCID: PMC7408159 DOI: 10.3390/biom10071063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/02/2022] Open
Abstract
In northern Mexico, the distilled spirit sotol with a denomination of origin is made from species of Dasylirion. The configuration of the volatile metabolites produced during the spontaneous fermentation of Dasylirion sp. must is insufficiently understood. In this study, the aim was to investigate the composition of the microbial consortia, describe the variation of volatile metabolites, and relate such profiles with their particular flavor attributes during the fermentation of sotol (Dasylirion sp.) must. Ascomycota was the phylum of most strains identified with 75% of total abundance. The genus of fermenting yeasts constituted of 101 Pichia strains and 13 Saccharomyces strains. A total of 57 volatile metabolites were identified and grouped into ten classes. The first stage of fermentation was composed of diesel, green, fruity, and cheesy attributes due to butyl 2-methylpropanoate, octan-1-ol, ethyl octanoate, and butanal, respectively, followed by a variation to pungent and sweet descriptors due to 3-methylbutan-1-ol and butyl 2-methylpropanoate. The final stage was described by floral, ethereal-winey, and vinegar attributes related to ethyl ethanimidate, 2-methylpropan-1-ol, and 2-hydroxyacetic acid. Our results improve the knowledge of the variations of volatile metabolites during the fermentation of sotol must and their contribution to its distinctive flavor.
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Floc’h JB, Hamel C, Lupwayi N, Harker KN, Hijri M, St-Arnaud M. Bacterial Communities of the Canola Rhizosphere: Network Analysis Reveals a Core Bacterium Shaping Microbial Interactions. Front Microbiol 2020; 11:1587. [PMID: 32849330 PMCID: PMC7418181 DOI: 10.3389/fmicb.2020.01587] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 06/17/2020] [Indexed: 11/24/2022] Open
Abstract
The rhizosphere hosts a complex web of prokaryotes interacting with one another that may modulate crucial functions related to plant growth and health. Identifying the key factors structuring the prokaryotic community of the plant rhizosphere is a necessary step toward the enhancement of plant production and crop yield with beneficial associative microorganisms. We used a long-term field experiment conducted at three locations in the Canadian prairies to verify that: (1) the level of cropping system diversity influences the α- and β-diversity of the prokaryotic community of canola (Brassica napus) rhizosphere; (2) the canola rhizosphere community has a stable prokaryotic core; and (3) some highly connected taxa of this community fit the description of hub-taxa. We sampled the rhizosphere of canola grown in monoculture, in a 2-phase rotation (canola-wheat), in a 3-phase rotation (pea-barley-canola), and in a highly diversified 6-phase rotation, five and eight years after cropping system establishment. We detected only one core bacterial Amplicon Sequence Variant (ASV) in the prokaryotic component of the microbiota of canola rhizosphere, a hub taxon identified as cf. Pseudarthrobacter sp. This ASV was also the only hub taxon found in the networks of interactions present in both years and at all three sites. We highlight a cohort of bacteria and archaea that were always connected with the core taxon in the network analyses.
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Affiliation(s)
- Jean-Baptiste Floc’h
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Chantal Hamel
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
- Quebec Research and Development Centre, Agriculture and Agri-Food Canada, Quebec City, QC, Canada
| | - Newton Lupwayi
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - K. Neil Harker
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Mohamed Hijri
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
- AgroBiosciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Marc St-Arnaud
- Institut de Recherche en Biologie Végétale, Université de Montréal and Jardin Botanique de Montréal, Montreal, QC, Canada
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15
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Antifungal and Antibacterial Activity of Terpenes for Improvement of Indoor Air Quality. CURRENT FUNGAL INFECTION REPORTS 2020. [DOI: 10.1007/s12281-020-00397-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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16
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Li P, Zhang Y, Meng Q, Liu Y, Tuyiringire D, Chen Z, Liang S. Effects of trichloroethylene stress on the microbiological characteristics of Mollisol. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 184:109595. [PMID: 31470249 DOI: 10.1016/j.ecoenv.2019.109595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 06/10/2023]
Abstract
Trichloroethylene (TCE), one of 129 kinds of priority pollutants, is the most common halogenated organic pollutant in the environment. To explore the changes in soil physicochemical properties and biological activities then clarify the effects of these factors on bacterial, fungal and actinomycetes communities in Mollisol under TCE stress is the significance of our research. The results indicated that when TCE concentration was greater than 10 mg kg-1, soil quality declined and soil decomposition of organic matter and cycling of mineral nutrients were inhibited through an effect on soil microbial biomass. Operational taxonomic units (OTUs) richness of the bacteria in Mollisol was altered by TCE contamination. The SChao1 and HShannon indices of bacterial communities in Mollisol decreased when 40 mg kg-1 TCE was applied. Meanwhile, the OTU richness of fungi in Mollisol was altered by TCE contamination. The HShannon indices of the fungal communities in Mollisol were inhibited by higher TCE concentrations (20 and 40 mg kg-1 TCE). TCE altered the content of some bacteria, fungi and actinomycetes involved in soil carbon and nitrogen cycling and metabolism, such as Acidobacteria, Proteobacteria, Planctomycetes, Chytridiomycota, Streptomycetales, Pseudonocardiales, Propionibacteriales and Rhizobiales, and thus influenced nutrient cycling and the process of energy metabolism in Mollisol. In addition, redundancy analysis (RDA) results indicated that physicochemical properties and biological activities under TCE contamination significantly affected soil microbial community composition thus confirming that TCE interfered with the carbon and nitrogen cycling and metabolism of soil microorganisms. The results of this study are of great importance for revealing the effects of TCE stress on the microbiological characteristics of Mollisol, and also provide more useful information for determining the potential ecological risk of organic pollutants in Mollisol.
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Affiliation(s)
- Pengfei Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Ying Zhang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China.
| | - Qingjuan Meng
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Diogene Tuyiringire
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
| | - Zhaobo Chen
- College of Environment and Resources, Dalian Minzu University, 18 Liaohe West Road, Dalian, 116600, China
| | - Shichao Liang
- College of Resources and Environment, Northeast Agricultural University, Harbin, 150030, China
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17
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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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18
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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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19
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Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC. Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know? ASTROBIOLOGY 2019; 19:951-974. [PMID: 30762429 PMCID: PMC6767865 DOI: 10.1089/ast.2018.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.
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Affiliation(s)
- Petra Rettberg
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
- Address correspondence to: Petra Rettberg, German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Research Group Astrobiology, Linder Höhe, 51147 Köln, Germany
| | - André Antunes
- GEMM—Group for Extreme and Marine Microbiology, Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - John Brucato
- Department of Physics and Astronomy, Astrophysical Observatory of Arcetri, National Institute for Astrophysics (INAF), Florence, Italy
| | - Patricia Cabezas
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Geoffrey Collins
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Alissa Haddaji
- Committee on Space Research (COSPAR), Montpellier, France
| | - Gerhard Kminek
- Committee on Space Research (COSPAR), Montpellier, France
| | - Stefan Leuko
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | | | | | - Jean-Louis Fellous
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering & Mathematics, School of Environment, Earth & Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - David Pearce
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
| | - Elke Rabbow
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Samuel Royle
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Mark Saunders
- Independent Consultant for the US National Academies of Sciences (NAS), Washington, District of Columbia
| | - Mark Sephton
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Andy Spry
- Carl Sagan Center, SETI, Mountain View, California
| | - Nicolas Walter
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Robert Wimmer Schweingruber
- Institut für Experimentelle und Angewandte Physik, Abteilung Extraterrestrische Physik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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20
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De Middeleer G, Leys N, Sas B, De Saeger S. Fungi and Mycotoxins in Space-A Review. ASTROBIOLOGY 2019; 19:915-926. [PMID: 30973270 DOI: 10.1089/ast.2018.1854] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Fungi are not only present on Earth but colonize spacecraft and space stations as well. This review provides an extensive overview of the large and diverse group of fungal species that have been found in space, as well as those corresponding detection methods used and the existing and potential future prevention and control strategies. Many of the identified fungal species in space, such as Aspergillus flavus and Alternaria sp., are mycotoxigenic; thus, they are potential mycotoxin producers. This indicates that, although the fungal load in space stations tends to be non-alarming, the effects should not be underestimated, since the effect of the space environment on mycotoxin production should be sufficiently studied as well. However, research focused on mycotoxin production under conditions found on space stations is essentially nonexistent, since these kinds of spaceflight experiments are rare. Consequently, it is recommended that detection and monitoring systems for fungi and mycotoxins in space are at some point prioritized such that investigations into the impact of the space environment on mycotoxin production is addressed.
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Affiliation(s)
- Gilke De Middeleer
- 1Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Natalie Leys
- 2Microbiology Unit, Interdisciplinary BioSciences Expert Group, Belgian Nuclear Research Centre SCK•CEN, Mol, Belgium
| | - Benedikt Sas
- 3Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sarah De Saeger
- 1Laboratory of Food Analysis, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
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21
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Blachowicz A, Chiang AJ, Elsaesser A, Kalkum M, Ehrenfreund P, Stajich JE, Torok T, Wang CCC, Venkateswaran K. Proteomic and Metabolomic Characteristics of Extremophilic Fungi Under Simulated Mars Conditions. Front Microbiol 2019; 10:1013. [PMID: 31156574 PMCID: PMC6529585 DOI: 10.3389/fmicb.2019.01013] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/24/2019] [Indexed: 12/13/2022] Open
Abstract
Filamentous fungi have been associated with extreme habitats, including nuclear power plant accident sites and the International Space Station (ISS). Due to their immense adaptation and phenotypic plasticity capacities, fungi may thrive in what seems like uninhabitable niches. This study is the first report of fungal survival after exposure of monolayers of conidia to simulated Mars conditions (SMC). Conidia of several Chernobyl nuclear accident-associated and ISS-isolated strains were tested for UV-C and SMC sensitivity, which resulted in strain-dependent survival. Strains surviving exposure to SMC for 30 min, ISSFT-021-30 and IMV 00236-30, were further characterized for proteomic, and metabolomic changes. Differential expression of proteins involved in ribosome biogenesis, translation, and carbohydrate metabolic processes was observed. No significant metabolome alterations were revealed. Lastly, ISSFT-021-30 conidia re-exposed to UV-C exhibited enhanced UV-C resistance when compared to the conidia of unexposed ISSFT-021.
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Affiliation(s)
- Adriana Blachowicz
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States.,Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
| | - Abby J Chiang
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | | | - Markus Kalkum
- Department of Molecular Imaging and Therapy, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | | | - Jason E Stajich
- Department of Microbiology and Plant Pathology, Institute of Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Tamas Torok
- Department of Ecology, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, United States.,Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, United States
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, United States
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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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Liang B, Ma C, Fan L, Wang Y, Yuan Y. Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard. Microbiol Res 2018; 216:1-11. [PMID: 30269849 DOI: 10.1016/j.micres.2018.07.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 05/14/2018] [Accepted: 07/19/2018] [Indexed: 11/30/2022]
Abstract
Compost amendment reportedly improved apple tree growth in replant soils. However, its effects should be evaluated at different soil depths and locations. This study investigated the impact of soil improvement with compost on soil physicochemical properties and bacterial community structure of a replanted apple orchard in comparison with the original orchard without compost improvement. The V1-V3 region of the bacterial 16S rRNA gene was subjected to high-throughput 454 pyrosequencing, and data were analyzed using the Mothur pipeline. The results showed that the soil improvement benefited tree growth and fruit quality during the study period. The compost amendment markedly increased tree height and stem diameter by a range of 6.1%-21.0% and 4.0%-14.0%, respectively. Fruit yield (9.5%), average weight (9.6%), and soluble solid content (5.6%) were also increased by compost amendment compared to those of the unimproved treatment. The pH, organic matter, and available N, P, and K contents were significantly increased by 5.7%-21.9%, 0.2%-62.9%, 9.3%-29.3%, 36.7%-64.5%, and 17.2%-100.3% in the compost improved soil. The pyrosequencing data showed that the soil improvement changed the bacterial community structure at all soil depths (0-20 cm and 20-40 cm) and locations (in-row and inter-row) considered; e.g., the relative abundance of Proteobacteria (20.2%), Bacteroidetes (2.5%), and Cyanobacteria (1.0%) was increased while that of Chloroflexi (5.5%), Acidobacteria (5.2%), Nitrospirae (4.5%), Gemmatimonadetes (3.8%), and Actinobacteria (1.8%) was decreased. The relative abundance of some dominant genera Burkholderia (2.3%), Pseudomonas (1.0%), and Paenibacillus (0.5%) were enhanced in the compost improved soil. Moreover, other dominant genera such as Nitrospira (6.4%), Gemmatimonas (2.2%), and Phenylobacterium (0.3%) were reduced by the application of compost. Our results indicate that soil improvement benefits the growth of tree and fruit quality, and is likely mediated by increased soil pH, organic matter, and available nutrient contents and beneficial bacterial community composition.
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Affiliation(s)
- Bowen Liang
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Changqing Ma
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Lianmei Fan
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yongzhang Wang
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Yongbing Yuan
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, Qingdao Agricultural University, Qingdao, China; College of Horticulture, Qingdao Agricultural University, Qingdao, China.
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Dworkin JP, Adelman LA, Ajluni T, Andronikov AV, Aponte JC, Bartels AE, Beshore E, Bierhaus EB, Brucato JR, Bryan BH, Burton AS, Callahan MP, Castro-Wallace SL, Clark BC, Clemett SJ, Connolly HC, Cutlip WE, Daly SM, Elliott VE, Elsila JE, Enos HL, Everett DF, Franchi IA, Glavin DP, Graham HV, Hendershot JE, Harris JW, Hill SL, Hildebrand AR, Jayne GO, Jenkens RW, Johnson KS, Kirsch JS, Lauretta DS, Lewis AS, Loiacono JJ, Lorentson CC, Marshall JR, Martin MG, Matthias LL, McLain HL, Messenger SR, Mink RG, Moore JL, Nakamura-Messenger K, Nuth JA, Owens CV, Parish CL, Perkins BD, Pryzby MS, Reigle CA, Righter K, Rizk B, Russell JF, Sandford SA, Schepis JP, Songer J, Sovinski MF, Stahl SE, Thomas-Keprta K, Vellinga JM, Walker MS. OSIRIS-REx Contamination Control Strategy and Implementation. SPACE SCIENCE REVIEWS 2018; 214:19. [PMID: 30713357 PMCID: PMC6350808 DOI: 10.1007/s11214-017-0439-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 10/27/2017] [Indexed: 05/10/2023]
Abstract
OSIRIS-REx will return pristine samples of carbonaceous asteroid Bennu. This article describes how pristine was defined based on expectations of Bennu and on a realistic understanding of what is achievable with a constrained schedule and budget, and how that definition flowed to requirements and implementation. To return a pristine sample, the OSIRIS-REx spacecraft sampling hardware was maintained at level 100 A/2 and <180 ng/cm2 of amino acids and hydrazine on the sampler head through precision cleaning, control of materials, and vigilance. Contamination is further characterized via witness material exposed to the spacecraft assembly and testing environment as well as in space. This characterization provided knowledge of the expected background and will be used in conjunction with archived spacecraft components for comparison with the samples when they are delivered to Earth for analysis. Most of all, the cleanliness of the OSIRIS-REx spacecraft was achieved through communication among scientists, engineers, managers, and technicians.
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Affiliation(s)
- J P Dworkin
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - L A Adelman
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Arctic Slope Research Corporation, Beltsville, MD USA
| | - T Ajluni
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Arctic Slope Research Corporation, Beltsville, MD USA
| | | | - J C Aponte
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | - A E Bartels
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - E Beshore
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - E B Bierhaus
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - J R Brucato
- INAF Astrophysical Observatory of Arcetri, Florence, Italy
| | - B H Bryan
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - A S Burton
- NASA Johnson Space Center, Houston, TX, USA
| | | | | | - B C Clark
- Space Science Institute, Boulder, CO, USA
| | - S J Clemett
- NASA Johnson Space Center, Houston, TX, USA
- Jacobs Technology, Tullahoma, TN, USA
| | | | - W E Cutlip
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - S M Daly
- NASA Kennedy Space Center, Titusville, FL, USA
| | - V E Elliott
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J E Elsila
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - H L Enos
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - D F Everett
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - D P Glavin
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - H V Graham
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- University of Maryland, College Park, MD, USA
| | - J E Hendershot
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Ball Aerospace, Boulder, CO, USA
| | - J W Harris
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - S L Hill
- Jacobs Technology, Tullahoma, TN, USA
- NASA Kennedy Space Center, Titusville, FL, USA
| | | | - G O Jayne
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Arctic Slope Research Corporation, Beltsville, MD USA
| | - R W Jenkens
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - K S Johnson
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - J S Kirsch
- Jacobs Technology, Tullahoma, TN, USA
- NASA Kennedy Space Center, Titusville, FL, USA
| | - D S Lauretta
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - A S Lewis
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J J Loiacono
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - C C Lorentson
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | | | - M G Martin
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | - L L Matthias
- NASA Kennedy Space Center, Titusville, FL, USA
- Analex, Titusville, FL, USA
| | - H L McLain
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- Catholic University of America, Washington, DC, USA
| | | | - R G Mink
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J L Moore
- Lockheed Martin Space Systems, Littleton, CO, USA
| | | | - J A Nuth
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - C V Owens
- NASA Kennedy Space Center, Titusville, FL, USA
| | - C L Parish
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - B D Perkins
- NASA Kennedy Space Center, Titusville, FL, USA
| | - M S Pryzby
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
- ATA Aerospace, Albuquerque, NM, USA
| | - C A Reigle
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - K Righter
- NASA Johnson Space Center, Houston, TX, USA
| | - B Rizk
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA
| | - J F Russell
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - S A Sandford
- NASA Ames Research Center, Moffett Field, CA, USA
| | - J P Schepis
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - J Songer
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - M F Sovinski
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
| | - S E Stahl
- NASA Johnson Space Center, Houston, TX, USA
- JES Tech., Houston, TX, USA
| | - K Thomas-Keprta
- NASA Johnson Space Center, Houston, TX, USA
- Jacobs Technology, Tullahoma, TN, USA
| | - J M Vellinga
- Lockheed Martin Space Systems, Littleton, CO, USA
| | - M S Walker
- NASA Goddard Space Flight Center, Greenbelt, MD, USA
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26
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Maske H, Cajal-Medrano R, Villegas-Mendoza J. Substrate-Limited and -Unlimited Coastal Microbial Communities Show Different Metabolic Responses with Regard to Temperature. Front Microbiol 2017; 8:2270. [PMID: 29218033 PMCID: PMC5703737 DOI: 10.3389/fmicb.2017.02270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 11/03/2017] [Indexed: 11/29/2022] Open
Abstract
Bacteria are the principal consumers of dissolved organic carbon (DOC) in the ocean and predation of bacteria makes organic carbon available to higher trophic levels. The efficiency with which bacteria convert the consumed carbon (C) into biomass (i.e., carbon growth efficiency, Y) determines their ecological as well as biogeochemical role in marine ecosystems. Yet, it is still unclear how changes in temperature will affect Y and, hence, the transfer of consumed C to higher trophic levels. Here, we experimentally investigated the effect of temperature on metabolic functions of coastal microbial communities inoculated in both nutrient-limited chemostats and nutrient–unlimited turbidostats. We inoculated chemostats and turbidostats with coastal microbial communities into seawater culture medium augmented with 20 and 100 μmol L−1 of glucose respectively and measured CO2 production, carbon biomass and cell abundance. Chemostats were cultured between 14 and 26°C and specific growth rates (μ) between 0.05 and 6.0 day−1, turbidostats were cultured between 10 and 26°C with specific growth rates ranging from 28 to 62 day−1. In chemostats under substrate limitation, which is common in the ocean, the specific respiration rate (r, day−1) showed no trend with temperature and was roughly proportional to μ, implying that carbon growth efficiency (Y) displayed no tendency with temperature. The response was very different in turbidostats under temperature-limited, nutrient-repleted growth, here μ increased with temperature but r decreased resulting in an increase of Y with temperature (Q10: 2.6). Comparison of our results with data from the literature on the respiration rate and cell weight of monospecific bacteria indicates that in general the literature data behaved similar to chemostat data, showing no trend in specific respiration with temperature. We conclude that respiration rates of nutrient-limited bacteria measured at a certain temperature cannot be adjusted to different temperatures with a temperature response function similar to Q10 or Arrhenius. However, the cellular respiration rate and carbon demand rate (both: mol C cell−1 day−1) show statistically significant relations with cellular carbon content (mol C cell−1) in chemostats, turbidostats, and the literature data.
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Affiliation(s)
- Helmut Maske
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico
| | - Ramón Cajal-Medrano
- Departamento de Oceanografía Biológica, Centro de Investigación Científica y de Educación Superior de Ensenada (CICESE), Ensenada, Mexico.,Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Mexico
| | - Josué Villegas-Mendoza
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California (UABC), Ensenada, Mexico
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27
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Schwendner P, Mahnert A, Koskinen K, Moissl-Eichinger C, Barczyk S, Wirth R, Berg G, Rettberg P. Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing. MICROBIOME 2017; 5:129. [PMID: 28974259 PMCID: PMC5627443 DOI: 10.1186/s40168-017-0345-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 09/18/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herein described "MIcrobial ecology of Confined Habitats and humAn health" (MICHA) experiment was implemented to acquire comprehensive microbiota data from this unique, confined manned habitat, to retrieve important information on the occurring microbiota dynamics, the microbial load and diversity in the air and on various surfaces. In total, 360 samples from 20 (9 air, 11 surface) locations were taken at 18 time-points and processed by extensive cultivation, PhyloChip and next generation sequencing (NGS) of 16S rRNA gene amplicons. RESULTS Cultivation assays revealed a Staphylococcus and Bacillus-dominated microbial community on various surfaces, with an average microbial load that did not exceed the allowed limits for ISS in-flight requirements indicating adequate maintenance of the facility. Areas with high human activity were identified as hotspots for microbial accumulation. Despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal. Opportunistic pathogens, stress-tolerant or potentially mobile element-bearing microorganisms were predicted to be prevalent throughout the confinement, while the overall microbial diversity dropped significantly over time. CONCLUSIONS Our findings clearly indicate that under confined conditions, the community structure remains a highly dynamic system which adapts to the prevailing habitat and micro-conditions. Since a sterile environment is not achievable, these dynamics need to be monitored to avoid spreading of highly resistant or potentially pathogenic microorganisms and a potentially harmful decrease of microbial diversity. If necessary, countermeasures are required, to maintain a healthy, diverse balance of beneficial, neutral and opportunistic pathogenic microorganisms. Our results serve as an important data collection for (i) future risk estimations of crewed space flight, (ii) an optimized design and planning of a spacecraft mission and (iii) for the selection of appropriate microbial monitoring approaches and potential countermeasures, to ensure a microbiologically safe space-flight environment.
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Affiliation(s)
- Petra Schwendner
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
- Institute for Microbiology, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
- Present address: UK Center for Astrobiology, University of Edinburgh, School of Physics and Astronomy, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Kaisa Koskinen
- Medical University of Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Christine Moissl-Eichinger
- Medical University of Graz, Department of Internal Medicine, Auenbruggerplatz 15, 8036 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Simon Barczyk
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
| | - Reinhard Wirth
- Institute for Microbiology, University of Regensburg, Universitaetsstrasse 31, 93053 Regensburg, Germany
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010 Graz, Austria
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center e.V. (DLR), Linder Höhe, 51147 Cologne, Germany
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Blachowicz A, Mayer T, Bashir M, Pieber TR, De León P, Venkateswaran K. Human presence impacts fungal diversity of inflated lunar/Mars analog habitat. MICROBIOME 2017; 5:62. [PMID: 28693587 PMCID: PMC5504618 DOI: 10.1186/s40168-017-0280-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 06/02/2017] [Indexed: 05/21/2023]
Abstract
BACKGROUND An inflatable lunar/Mars analog habitat (ILMAH), simulated closed system isolated by HEPA filtration, mimics International Space Station (ISS) conditions and future human habitation on other planets except for the exchange of air between outdoor and indoor environments. The ILMAH was primarily commissioned to measure physiological, psychological, and immunological characteristics of human inhabiting in isolation, but it was also available for other studies such as examining its microbiological aspects. Characterizing and understanding possible changes and succession of fungal species is of high importance since fungi are not only hazardous to inhabitants but also deteriorate the habitats. Observing the mycobiome changes in the presence of human will enable developing appropriate countermeasures with reference to crew health in a future closed habitat. RESULTS Succession of fungi was characterized utilizing both traditional and state-of-the-art molecular techniques during the 30-day human occupation of the ILMAH. Surface samples were collected at various time points and locations to observe both the total and viable fungal populations of common environmental and opportunistic pathogenic species. To estimate the cultivable fungal population, potato dextrose agar plate counts method was utilized. The internal transcribed spacer region-based iTag Illumina sequencing was employed to measure the community structure and fluctuation of the mycobiome over time in various locations. Treatment of samples with propidium monoazide (PMA; a DNA intercalating dye for selective detection of viable microbial populations) had a significant effect on the microbial diversity compared to non-PMA-treated samples. Statistical analysis confirmed that viable fungal community structure changed (increase in diversity and decrease in fungal burden) over the occupation time. Samples collected at day 20 showed distinct fungal profiles from samples collected at any other time point (before or after). Viable fungal families like Davidiellaceae, Teratosphaeriaceae, Pleosporales, and Pleosporaceae were shown to increase during the occupation time. CONCLUSIONS The results of this study revealed that the overall fungal diversity in the closed habitat changed during human presence; therefore, it is crucial to properly maintain a closed habitat to preserve it from deteriorating and keep it safe for its inhabitants. Differences in community profiles were observed when statistically treated, especially of the mycobiome of samples collected at day 20. On a genus level Epiccocum, Alternaria, Pleosporales, Davidiella, and Cryptococcus showed increased abundance over the occupation time.
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Affiliation(s)
- A Blachowicz
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., M/S 89-2, Pasadena, CA, 91109, USA
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA, 90089, USA
| | - T Mayer
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., M/S 89-2, Pasadena, CA, 91109, USA
| | - M Bashir
- Division of Endocrinology and Metabolism, Medical University Graz, Graz, Austria
| | - T R Pieber
- Division of Endocrinology and Metabolism, Medical University Graz, Graz, Austria
| | - P De León
- Department of Space Studies, University of North Dakota, Grand Forks, ND, 58202, USA
| | - K Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Dr., M/S 89-2, Pasadena, CA, 91109, USA.
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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Khodadad CL, Wong GM, James LM, Thakrar PJ, Lane MA, Catechis JA, Smith DJ. Stratosphere Conditions Inactivate Bacterial Endospores from a Mars Spacecraft Assembly Facility. ASTROBIOLOGY 2017; 17:337-350. [PMID: 28323456 PMCID: PMC5399745 DOI: 10.1089/ast.2016.1549] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 11/04/2016] [Indexed: 06/06/2023]
Abstract
Every spacecraft sent to Mars is allowed to land viable microbial bioburden, including hardy endospore-forming bacteria resistant to environmental extremes. Earth's stratosphere is severely cold, dry, irradiated, and oligotrophic; it can be used as a stand-in location for predicting how stowaway microbes might respond to the martian surface. We launched E-MIST, a high-altitude NASA balloon payload on 10 October 2015 carrying known quantities of viable Bacillus pumilus SAFR-032 (4.07 × 107 spores per sample), a radiation-tolerant strain collected from a spacecraft assembly facility. The payload spent 8 h at ∼31 km above sea level, exposing bacterial spores to the stratosphere. We found that within 120 and 240 min, spore viability was significantly reduced by 2 and 4 orders of magnitude, respectively. By 480 min, <0.001% of spores carried to the stratosphere remained viable. Our balloon flight results predict that most terrestrial bacteria would be inactivated within the first sol on Mars if contaminated spacecraft surfaces receive direct sunlight. Unfortunately, an instrument malfunction prevented the acquisition of UV light measurements during our balloon mission. To make up for the absence of radiometer data, we calculated a stratosphere UV model and conducted ground tests with a 271.1 nm UVC light source (0.5 W/m2), observing a similarly rapid inactivation rate when using a lower number of contaminants (640 spores per sample). The starting concentration of spores and microconfiguration on hardware surfaces appeared to influence survivability outcomes in both experiments. With the relatively few spores that survived the stratosphere, we performed a resequencing analysis and identified three single nucleotide polymorphisms compared to unexposed controls. It is therefore plausible that bacteria enduring radiation-rich environments (e.g., Earth's upper atmosphere, interplanetary space, or the surface of Mars) may be pushed in evolutionarily consequential directions. Key Words: Planetary protection-Stratosphere-Balloon-Mars analog environment-E-MIST payload-Bacillus pumilus SAFR-032. Astrobiology 17, 337-350.
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Affiliation(s)
| | - Gregory M. Wong
- Department of Geosciences, Pennsylvania State University, University Park, Pennsylvania
| | | | | | - Michael A. Lane
- NASA, Engineering Directorate, Kennedy Space Center, Florida
| | | | - David J. Smith
- NASA, Space Biosciences Division, Ames Research Center, Moffett Field, California
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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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Abarenkov K, Adams RI, Laszlo I, Agan A, Ambrosio E, Antonelli A, Bahram M, Bengtsson-Palme J, Bok G, Cangren P, Coimbra V, Coleine C, Gustafsson C, He J, Hofmann T, Kristiansson E, Larsson E, Larsson T, Liu Y, Martinsson S, Meyer W, Panova M, Pombubpa N, Ritter C, Ryberg M, Svantesson S, Scharn R, Svensson O, Töpel M, Unterseher M, Visagie C, Wurzbacher C, Taylor AF, Kõljalg U, Schriml L, Nilsson RH. Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard – a report from a May 23-24, 2016 workshop (Gothenburg, Sweden). MycoKeys 2016. [DOI: 10.3897/mycokeys.16.10000] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city. Sci Rep 2016; 6:29235. [PMID: 27378552 PMCID: PMC4932501 DOI: 10.1038/srep29235] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 06/13/2016] [Indexed: 12/03/2022] Open
Abstract
Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.
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Rime T, Hartmann M, Frey B. Potential sources of microbial colonizers in an initial soil ecosystem after retreat of an alpine glacier. THE ISME JOURNAL 2016; 10:1625-41. [PMID: 26771926 PMCID: PMC4918445 DOI: 10.1038/ismej.2015.238] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 10/09/2015] [Accepted: 11/08/2015] [Indexed: 11/09/2022]
Abstract
Rapid disintegration of alpine glaciers has led to the formation of new terrain consisting of mineral debris colonized by microorganisms. Despite the importance of microbial pioneers in triggering the formation of terrestrial ecosystems, their sources (endogenous versus exogenous) and identities remain elusive. We used 454-pyrosequencing to characterize the bacterial and fungal communities in endogenous glacier habitats (ice, sub-, supraglacial sediments and glacier stream leaving the glacier forefront) and in atmospheric deposition (snow, rain and aeolian dust). We compared these microbial communities with those occurring in recently deglaciated barren soils before and after snow melt (snow-covered soil and barren soil). Atmospheric bacteria and fungi were dominated by plant-epiphytic organisms and differed from endogenous glacier habitats and soils indicating that atmospheric input of microorganisms is not a major source of microbial pioneers in newly formed soils. We found, however, that bacterial communities in newly exposed soils resembled those of endogenous habitats, which suggests that bacterial pioneers originating from sub- and supraglacial sediments contributed to the colonization of newly exposed soils. Conversely, fungal communities differed between habitats suggesting a lower dispersal capability than bacteria. Yeasts putatively adapted to cold habitats characteristic of snow and supraglacial sediments were similar, despite the fact that these habitats were not spatially connected. These findings suggest that environmental filtering selects particular fungi in cold habitats. Atmospheric deposition provided important sources of dissolved organic C, nitrate and ammonium. Overall, microbial colonizers triggering soil development in alpine environments mainly originate from endogenous glacier habitats, whereas atmospheric deposition contributes to the establishment of microbial communities by providing sources of C and N.
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Affiliation(s)
- Thomas Rime
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Martin Hartmann
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
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Mayer T, Blachowicz A, Probst AJ, Vaishampayan P, Checinska A, Swarmer T, de Leon P, Venkateswaran K. Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation. MICROBIOME 2016; 4:22. [PMID: 27250991 PMCID: PMC4890489 DOI: 10.1186/s40168-016-0167-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/18/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. RESULTS Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a significant effect on the microbial diversity compared to non-PMA-treated samples. CONCLUSIONS Statistical analyses revealed a significant difference in community structure of samples over time, particularly of the bacteriomes existing before human occupation of the habitat (Day 0 sampling) and after occupation (Day 13, Day 20, and Day 30 samplings). Actinobacteria (mainly Corynebacteriaceae) and Firmicutes (mainly Clostridiales Incertae Sedis XI and Staphylococcaceae) were shown to increase over the occupation time period. The results of this study revealed a strong relationship between human presence and succession of microbial diversity in a closed habitat. Consequently, it is necessary to develop methods and tools for effective maintenance of a closed system to enable safe human habitation in enclosed environments on Earth and beyond.
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Affiliation(s)
- Teresa Mayer
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Adriana Blachowicz
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA, USA
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Aleksandra Checinska
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA
| | - Tiffany Swarmer
- Department of Space Studies, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Pablo de Leon
- Department of Space Studies, University of North Dakota, Grand Forks, ND, 58202, USA
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
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Fox-Powell MG, Hallsworth JE, Cousins CR, Cockell CS. Ionic Strength Is a Barrier to the Habitability of Mars. ASTROBIOLOGY 2016; 16:427-42. [PMID: 27213516 DOI: 10.1089/ast.2015.1432] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
UNLABELLED The thermodynamic availability of water (water activity) strictly limits microbial propagation on Earth, particularly in hypersaline environments. A considerable body of evidence indicates the existence of hypersaline surface waters throughout the history of Mars; therefore it is assumed that, as on Earth, water activity is a major limiting factor for martian habitability. However, the differing geological histories of Earth and Mars have driven variations in their respective aqueous geochemistry, with as-yet-unknown implications for habitability. Using a microbial community enrichment approach, we investigated microbial habitability for a suite of simulated martian brines. While the habitability of some martian brines was consistent with predictions made from water activity, others were uninhabitable even when the water activity was biologically permissive. We demonstrate experimentally that high ionic strength, driven to extremes on Mars by the ubiquitous occurrence of multivalent ions, renders these environments uninhabitable despite the presence of biologically available water. These findings show how the respective geological histories of Earth and Mars, which have produced differences in the planets' dominant water chemistries, have resulted in different physicochemical extremes which define the boundary space for microbial habitability. KEY WORDS Habitability-Mars-Salts-Water activity-Life in extreme environments. Astrobiology 16, 427-442.
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Affiliation(s)
- Mark G Fox-Powell
- 1 UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh , UK
| | - John E Hallsworth
- 2 Institute for Global Food Security, Queen's University Belfast , UK
| | - Claire R Cousins
- 3 Department of Earth and Environmental Sciences, University of St. Andrews , UK
| | - Charles S Cockell
- 1 UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh , UK
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Biological Low-pH Mn(II) Oxidation in a Manganese Deposit Influenced by Metal-Rich Groundwater. Appl Environ Microbiol 2016; 82:3009-3021. [PMID: 26969702 DOI: 10.1128/aem.03844-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/04/2016] [Indexed: 01/11/2023] Open
Abstract
UNLABELLED The mechanisms, key organisms, and geochemical significance of biological low-pH Mn(II) oxidation are largely unexplored. Here, we investigated the structure of indigenous Mn(II)-oxidizing microbial communities in a secondary subsurface Mn oxide deposit influenced by acidic (pH 4.8) metal-rich groundwater in a former uranium mining area. Microbial diversity was highest in the Mn deposit compared to the adjacent soil layers and included the majority of known Mn(II)-oxidizing bacteria (MOB) and two genera of known Mn(II)-oxidizing fungi (MOF). Electron X-ray microanalysis showed that romanechite [(Ba,H2O)2(Mn(4+),Mn(3+))5O10] was conspicuously enriched in the deposit. Canonical correspondence analysis revealed that certain fungal, bacterial, and archaeal groups were firmly associated with the autochthonous Mn oxides. Eight MOB within the Proteobacteria, Actinobacteria, and Bacteroidetes and one MOF strain belonging to Ascomycota were isolated at pH 5.5 or 7.2 from the acidic Mn deposit. Soil-groundwater microcosms demonstrated 2.5-fold-faster Mn(II) depletion in the Mn deposit than adjacent soil layers. No depletion was observed in the abiotic controls, suggesting that biological contribution is the main driver for Mn(II) oxidation at low pH. The composition and species specificity of the native low-pH Mn(II) oxidizers were highly adapted to in situ conditions, and these organisms may play a central role in the fundamental biogeochemical processes (e.g., metal natural attenuation) occurring in the acidic, oligotrophic, and metalliferous subsoil ecosystems. IMPORTANCE This study provides multiple lines of evidence to show that microbes are the main drivers of Mn(II) oxidation even at acidic pH, offering new insights into Mn biogeochemical cycling. A distinct, highly adapted microbial community inhabits acidic, oligotrophic Mn deposits and mediates biological Mn oxidation. These data highlight the importance of biological processes for Mn biogeochemical cycling and show the potential for new bioremediation strategies aimed at enhancing biological Mn oxidation in low-pH environments for contaminant mitigation.
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Weinmaier T, Probst AJ, La Duc MT, Ciobanu D, Cheng JF, Ivanova N, Rattei T, Vaishampayan P. A viability-linked metagenomic analysis of cleanroom environments: eukarya, prokaryotes, and viruses. MICROBIOME 2015; 3:62. [PMID: 26642878 PMCID: PMC4672508 DOI: 10.1186/s40168-015-0129-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/29/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND Recent studies posit a reciprocal dependency between the microbiomes associated with humans and indoor environments. However, none of these metagenome surveys has considered the viability of constituent microorganisms when inferring impact on human health. RESULTS Reported here are the results of a viability-linked metagenomics assay, which (1) unveil a remarkably complex community profile for bacteria, fungi, and viruses and (2) bolster the detection of underrepresented taxa by eliminating biases resulting from extraneous DNA. This approach enabled, for the first time ever, the elucidation of viral genomes from a cleanroom environment. Upon comparing the viable biomes and distribution of phylotypes within a cleanroom and adjoining (uncontrolled) gowning enclosure, the rigorous cleaning and stringent control countermeasures of the former were observed to select for a greater presence of anaerobes and spore-forming microflora. Sequence abundance and correlation analyses suggest that the viable indoor microbiome is influenced by both the human microbiome and the surrounding ecosystem(s). CONCLUSIONS The findings of this investigation constitute the literature's first ever account of the indoor metagenome derived from DNA originating solely from the potential viable microbial population. Results presented in this study should prove valuable to the conceptualization and experimental design of future studies on indoor microbiomes aimed at inferring impact on human health.
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Affiliation(s)
- Thomas Weinmaier
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
| | - Alexander J Probst
- Department of Earth and Planetary Science, University of California, Berkeley, Berkeley, CA, USA.
| | - Myron T La Duc
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
- Precis Scientific, Scottsdale, AZ, USA.
| | | | | | | | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, USA.
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Checinska A, Probst AJ, Vaishampayan P, White JR, Kumar D, Stepanov VG, Fox GE, Nilsson HR, Pierson DL, Perry J, Venkateswaran K. Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities. MICROBIOME 2015; 3:50. [PMID: 26502721 PMCID: PMC4624184 DOI: 10.1186/s40168-015-0116-3] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 09/28/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND The International Space Station (ISS) is a unique built environment due to the effects of microgravity, space radiation, elevated carbon dioxide levels, and especially continuous human habitation. Understanding the composition of the ISS microbial community will facilitate further development of safety and maintenance practices. The primary goal of this study was to characterize the viable microbiome of the ISS-built environment. A second objective was to determine if the built environments of Earth-based cleanrooms associated with space exploration are an appropriate model of the ISS environment. RESULTS Samples collected from the ISS and two cleanrooms at the Jet Propulsion Laboratory (JPL, Pasadena, CA) were analyzed by traditional cultivation, adenosine triphosphate (ATP), and propidium monoazide-quantitative polymerase chain reaction (PMA-qPCR) assays to estimate viable microbial populations. The 16S rRNA gene Illumina iTag sequencing was used to elucidate microbial diversity and explore differences between ISS and cleanroom microbiomes. Statistical analyses showed that members of the phyla Actinobacteria, Firmicutes, and Proteobacteria were dominant in the samples examined but varied in abundance. Actinobacteria were predominant in the ISS samples whereas Proteobacteria, least abundant in the ISS, dominated in the cleanroom samples. The viable bacterial populations seen by PMA treatment were greatly decreased. However, the treatment did not appear to have an effect on the bacterial composition (diversity) associated with each sampling site. CONCLUSIONS The results of this study provide strong evidence that specific human skin-associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth-based cleanrooms. For example, Corynebacterium and Propionibacterium (Actinobacteria) but not Staphylococcus (Firmicutes) species are dominant on the ISS in terms of viable and total bacterial community composition. The results obtained will facilitate future studies to determine how stable the ISS environment is over time. The present results also demonstrate the value of measuring viable cell diversity and population size at any sampling site. This information can be used to identify sites that can be targeted for more stringent cleaning. Finally, the results will allow comparisons with other built sites and facilitate future improvements on the ISS that will ensure astronaut health.
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Affiliation(s)
- Aleksandra Checinska
- Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 89-2 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Alexander J Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA
| | - Parag Vaishampayan
- Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 89-2 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | | | - Deepika Kumar
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Henrik R Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | - Jay Perry
- Marshall Space Flight Center, Huntsville, AL, USA
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, Biotechnology and Planetary Protection Group, California Institute of Technology, M/S 89-2 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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Benbow ME, Pechal JL, Lang JM, Erb R, Wallace JR. The Potential of High-throughput Metagenomic Sequencing of Aquatic Bacterial Communities to Estimate the Postmortem Submersion Interval. J Forensic Sci 2015; 60:1500-10. [DOI: 10.1111/1556-4029.12859] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 11/10/2014] [Accepted: 11/14/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Mark Eric Benbow
- Department of Entomology; Michigan State University; East Lansing MI 48824
| | - Jennifer L. Pechal
- Department of Entomology; Michigan State University; East Lansing MI 48824
| | - Jennifer M. Lang
- Department of Biology; University of Dayton; Dayton OH 45469-2320
| | - Racheal Erb
- Department of Biology; Millersville University; Millersville PA 17551
| | - John R. Wallace
- Department of Biology; Millersville University; Millersville PA 17551
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Mahnert A, Vaishampayan P, Probst AJ, Auerbach A, Moissl-Eichinger C, Venkateswaran K, Berg G. Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes. PLoS One 2015; 10:e0134848. [PMID: 26273838 PMCID: PMC4537314 DOI: 10.1371/journal.pone.0134848] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/14/2015] [Indexed: 11/18/2022] Open
Abstract
Cleanrooms have been considered microbially-reduced environments and are used to protect human health and industrial product assembly. However, recent analyses have deciphered a rather broad diversity of microbes in cleanrooms, whose origin as well as physiological status has not been fully understood. Here, we examined the input of intact microbial cells from a surrounding built environment into a spacecraft assembly cleanroom by applying a molecular viability assay based on propidium monoazide (PMA). The controlled cleanroom (CCR) was characterized by ~6.2*103 16S rRNA gene copies of intact bacterial cells per m2 floor surface, which only represented 1% of the total community that could be captured via molecular assays without viability marker. This was in contrast to the uncontrolled adjoining facility (UAF) that had 12 times more living bacteria. Regarding diversity measures retrieved from 16S rRNA Illumina-tag analyzes, we observed, however, only a minor drop in the cleanroom facility allowing the conclusion that the number but not the diversity of microbes is strongly affected by cleaning procedures. Network analyses allowed tracking a substantial input of living microbes to the cleanroom and a potential enrichment of survival specialists like bacterial spore formers and archaeal halophiles and mesophiles. Moreover, the cleanroom harbored a unique community including 11 exclusive genera, e.g., Haloferax and Sporosarcina, which are herein suggested as indicators of cleanroom environments. In sum, our findings provide evidence that archaea are alive in cleanrooms and that cleaning efforts and cleanroom maintenance substantially decrease the number but not the diversity of indoor microbiomes.
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Affiliation(s)
- Alexander Mahnert
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, California, United States of America
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, California, United States of America
| | - Alexander J. Probst
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
| | - Anna Auerbach
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Christine Moissl-Eichinger
- Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
- Medical University Graz, Department of Internal Medicine, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, California, United States of America
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- * E-mail:
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Hospital-associated microbiota and implications for nosocomial infections. Trends Mol Med 2015; 21:427-32. [PMID: 25907678 DOI: 10.1016/j.molmed.2015.03.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/23/2022]
Abstract
The rise of high-throughput sequencing technologies and culture-independent microbial surveys has the potential to revolutionize our understanding of how microbes colonize, move about, and evolve in hospital environments. Genome analysis of individual organisms, characterization of population dynamics, and microbial community ecology are facilitating the identification of novel pathogens, the tracking of disease outbreaks, and the study of the evolution of antibiotic resistance. Here we review the recent applications of these methods to microbial ecology studies in hospitals and discuss their potential to influence hospital management policy and practice and to reduce nosocomial infections and the spread of antibiotic resistance.
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Muster N, Derecho I, Dallal F, Alvarez R, McCoy KB, Mogul R. Purification, biochemical characterization, and implications of an alkali-tolerant catalase from the spacecraft-associated and oxidation-resistant Acinetobacter gyllenbergii 2P01AA. ASTROBIOLOGY 2015; 15:291-300. [PMID: 25826195 DOI: 10.1089/ast.2014.1242] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Herein, we report on the purification, characterization, and sequencing of catalase from Acinetobacter gyllenbergii 2P01AA, an extremely oxidation-resistant bacterium that was isolated from the Mars Phoenix spacecraft assembly facility. The Acinetobacter are dominant members of the microbial communities that inhabit spacecraft assembly facilities and consequently may serve as forward contaminants that could impact the integrity of future life-detection missions. Catalase was purified by using a 3-step chromatographic procedure, where mass spectrometry provided respective subunit and intact masses of 57.8 and 234.6 kDa, which were consistent with a small-subunit tetrameric catalase. Kinetics revealed an extreme pH stability with no loss in activity between pH 5 and 11.5 and provided respective kcat/Km and kcat values of ∼10(7) s(-1) M(-1) and 10(6) s(-1), which are among the highest reported for bacterial catalases. The amino acid sequence was deduced by in-depth peptide mapping, and structural homology suggested that the catalases from differing strains of A. gyllenbergii differ only at residues near the subunit interfaces, which may impact catalytic stability. Together, the kinetic, alkali-tolerant, and halotolerant properties of the catalase from A. gyllenbergii 2P01AA are significant, as they are consistent with molecular adaptations toward the alkaline, low-humidity, and potentially oxidizing conditions of spacecraft assembly facilities. Therefore, these results support the hypothesis that the selective pressures of the assembly facilities impact the microbial communities at the molecular level, which may have broad implications for future life-detection missions.
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Affiliation(s)
- N Muster
- California State Polytechnic University , Pomona, California
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44
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Zhang H, Huang T, Chen S. Ignored sediment fungal populations in water supply reservoirs are revealed by quantitative PCR and 454 pyrosequencing. BMC Microbiol 2015; 15:44. [PMID: 25886005 PMCID: PMC4349462 DOI: 10.1186/s12866-015-0379-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 02/10/2015] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The sediment hosts a variety of fungal species in water supply reservoirs; however, the taxonomically and functionally diverse fungal populations have remained vastly unexplored. Here, quantitative PCR (qPCR) and recently developed high-throughput 454 GS FLX pyrosequencing were combined to investigate the abundance and diversity of sediment fungal communities in three water supply reservoirs. RESULTS These results revealed 1991, 2473, and 2610 copies of the 18S rRNA gene in the sediments from the ZC, SBY, and JP reservoirs, respectively. The fungal abundance in JP reservoir was 1.31 times higher than that of the ZC reservoir. In general, 43123 reads were recovered, corresponding to 945 distinct molecular operational taxonomic units (OTUs, 97% similarity cut-off level). The majority of the fungal nuclear ribosomal internal transcribed spacer (ITS) region sequences were affiliated with Ascomycota, Chytridiomycota, Basidiomycota, Glomeromycota, and Mucoromycotina. The highest Chao 1 index (962) was observed in the JP reservoir, and this value was 5.66 times greater than that of the SBY reservoir. Heat map analysis showed that Rhizophydium (relative frequency 30.98%), Placidium (20.20%), Apophysomyces (8.43%), Allomyces (6.26%), and Rhodotorula (6.01%) were the dominant genera in the JP reservoir, while Elaphomyces (20.0%) was the dominant genus in the ZC reservoir and Rhizophydium (30.98%) and Mattirolomyces (39.40%) were the most abundant in the JP and SBY reservoirs. Glomus sp. was only found in the JP reservoir. Furthermore, the larger proportions of "unassigned fungi" call for crafting International Nucleotide Sequence Database. Principle component analysis (PCA) and network analysis also suggested that tremendously diverse functional fungal populations were resident in the sediments of the three water supply reservoirs. CONCLUSIONS Thus, the results of this research suggest that the combination of high-throughput Roche 454 GS FLX pyrosequencing and qPCR is successfully employed to decrypt reservoir sediment fungal communities. Diverse fungi occur widely in the sediments of water supply reservoirs. These findings will undoubtedly broaden our understanding of reservoir sediment fungal species harbored in this freshwater stressful environmental condition. Future research should be conducted to determine the potential for fungi to degrade complex pollutants and their secondary metabolites related to the water quality.
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Affiliation(s)
- Haihan Zhang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, Shaanxi Province, P. R. China.
| | - Tinglin Huang
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, Shaanxi Province, P. R. China.
| | - Shengnan Chen
- School of Environmental and Municipal Engineering, Xi'an University of Architecture and Technology, Xi'an, 710055, Shaanxi Province, P. R. China.
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Stevenson A, Hallsworth JE. Water and temperature relations of soil Actinobacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:744-55. [PMID: 25132485 DOI: 10.1111/1758-2229.12199] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/31/2014] [Indexed: 05/22/2023]
Abstract
Actinobacteria perform essential functions within soils, and are dependent on available water to do so. We determined the water-activity (aw ) limits for cell division of Streptomyces albidoflavus, Streptomyces rectiviolaceus, Micromonospora grisea and Micromonospora (JCM 3050) over a range of temperatures, using culture media supplemented with a biologically permissive solute (glycerol). Each species grew optimally at 0.998 aw (control; no added glycerol) and growth rates were near-optimal in the range 0.971-0.974 (1 M glycerol) at permissive temperatures. Each was capable of cell division at 0.916-0.924 aw (2 M glycerol), but only S. albidoflavus grew at 0.895 or 0.897 aw (3 M glycerol, at 30 and 37°C respectively). For S. albidoflavus, however, no growth occurred on media at ≤ 0.870 (4 M glycerol) during the 40-day assessment period, regardless of temperature, and a theoretical limit of 0.877 aw was derived by extrapolation of growth curves. This level of solute tolerance is high for non-halophilic bacteria, but is consistent with reported limits for the growth and metabolic activities of soil microbes. The limit, within the range 0.895-0.870 aw , is very much inferior to those for obligately halophilic bacteria and extremely halophilic or xerophilic fungi, and is inconsistent with earlier reports of cell division at 0.500 aw . These findings are discussed in relation to planetary protection policy for space exploration and the microbiology of arid soils.
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Affiliation(s)
- Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast, BT9 7BL, UK
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Derecho I, McCoy KB, Vaishampayan P, Venkateswaran K, Mogul R. Characterization of hydrogen peroxide-resistant Acinetobacter species isolated during the Mars Phoenix spacecraft assembly. ASTROBIOLOGY 2014; 14:837-847. [PMID: 25243569 DOI: 10.1089/ast.2014.1193] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The microbiological inventory of spacecraft and the associated assembly facility surfaces represent the primary pool of forward contaminants that may impact the integrity of life-detection missions. Herein, we report on the characterization of several strains of hydrogen peroxide-resistant Acinetobacter, which were isolated during the Mars Phoenix lander assembly. All Phoenix-associated Acinetobacter strains possessed very high catalase specific activities, and the specific strain, A. gyllenbergii 2P01AA, displayed a survival against hydrogen peroxide (no loss in 100 mM H2O2 for 1 h) that is perhaps the highest known among Gram-negative and non-spore-forming bacteria. Proteomic characterizations reveal a survival mechanism inclusive of proteins coupled to peroxide degradation (catalase and alkyl hydroperoxide reductase), energy/redox management (dihydrolipoamide dehydrogenase), protein synthesis/folding (EF-G, EF-Ts, peptidyl-tRNA hydrolase, DnaK), membrane functions (OmpA-like protein and ABC transporter-related protein), and nucleotide metabolism (HIT family hydrolase). Together, these survivability and biochemical parameters support the hypothesis that oxidative tolerance and the related biochemical features are the measurable phenotypes or outcomes for microbial survival in the spacecraft assembly facilities, where the low-humidity (desiccation) and clean (low-nutrient) conditions may serve as selective pressures. Hence, the spacecraft-associated Acinetobacter, due to the conferred oxidative tolerances, may ultimately hinder efforts to reduce spacecraft bioburden when using chemical sterilants, thus suggesting that non-spore-forming bacteria may need to be included in the bioburden accounting for future life-detection missions.
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Affiliation(s)
- I Derecho
- 1 California State Polytechnic University , Pomona, California
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Nilsson RH, Hyde KD, Pawłowska J, Ryberg M, Tedersoo L, Aas AB, Alias SA, Alves A, Anderson CL, Antonelli A, Arnold AE, Bahnmann B, Bahram M, Bengtsson-Palme J, Berlin A, Branco S, Chomnunti P, Dissanayake A, Drenkhan R, Friberg H, Frøslev TG, Halwachs B, Hartmann M, Henricot B, Jayawardena R, Jumpponen A, Kauserud H, Koskela S, Kulik T, Liimatainen K, Lindahl BD, Lindner D, Liu JK, Maharachchikumbura S, Manamgoda D, Martinsson S, Neves MA, Niskanen T, Nylinder S, Pereira OL, Pinho DB, Porter TM, Queloz V, Riit T, Sánchez-García M, de Sousa F, Stefańczyk E, Tadych M, Takamatsu S, Tian Q, Udayanga D, Unterseher M, Wang Z, Wikee S, Yan J, Larsson E, Larsson KH, Kõljalg U, Abarenkov K. Improving ITS sequence data for identification of plant pathogenic fungi. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0291-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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48
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International Space Station environmental microbiome - microbial inventories of ISS filter debris. Appl Microbiol Biotechnol 2014; 98:6453-66. [PMID: 24695826 DOI: 10.1007/s00253-014-5650-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 02/25/2014] [Accepted: 02/26/2014] [Indexed: 01/03/2023]
Abstract
Despite an expanding array of molecular approaches for detecting microorganisms in a given sample, rapid and robust means of assessing the differential viability of the microbial cells, as a function of phylogenetic lineage, remain elusive. A propidium monoazide (PMA) treatment coupled with downstream quantitative polymerase chain reaction (qPCR) and pyrosequencing analyses was carried out to better understand the frequency, diversity, and distribution of viable microorganisms associated with debris collected from the crew quarters of the International Space Station (ISS). The cultured bacterial counts were more in the ISS samples than cultured fungal population. The rapid molecular analyses targeted to estimate viable population exhibited 5-fold increase in bacterial (qPCR-PMA assay) and 25-fold increase in microbial (adenosine triphosphate assay) burden than the cultured bacterial population. The ribosomal nucleic acid-based identification of cultivated strains revealed the presence of only four to eight bacterial species in the ISS samples, however, the viable bacterial diversity detected by the PMA-pyrosequencing method was far more diverse (12 to 23 bacterial taxa) with the majority consisting of members of actinobacterial genera (Propionibacterium, Corynebacterium) and Staphylococcus. Sample fractions not treated with PMA (inclusive of both live and dead cells) yielded a great abundance of highly diverse bacterial (94 to 118 taxa) and fungal lineages (41 taxa). Even though deep sequencing capability of the molecular analysis widened the understanding about the microbial diversity, the cultivation assay also proved to be essential since some of the spore-forming microorganisms were detected only by the culture-based method. Presented here are the findings of the first comprehensive effort to assess the viability of microbial cells associated with ISS surfaces, and correlate differential viability with phylogenetic affiliation.
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Brooks B, Firek BA, Miller CS, Sharon I, Thomas BC, Baker R, Morowitz MJ, Banfield JF. Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. MICROBIOME 2014; 2:1. [PMID: 24468033 PMCID: PMC4392516 DOI: 10.1186/2049-2618-2-1] [Citation(s) in RCA: 235] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 11/28/2013] [Indexed: 05/16/2023]
Abstract
BACKGROUND The source inoculum of gastrointestinal tract (GIT) microbes is largely influenced by delivery mode in full-term infants, but these influences may be decoupled in very low birth weight (VLBW, <1,500 g) neonates via conventional broad-spectrum antibiotic treatment. We hypothesize the built environment (BE), specifically room surfaces frequently touched by humans, is a predominant source of colonizing microbes in the gut of premature VLBW infants. Here, we present the first matched fecal-BE time series analysis of two preterm VLBW neonates housed in a neonatal intensive care unit (NICU) over the first month of life. RESULTS Fresh fecal samples were collected every 3 days and metagenomes sequenced on an Illumina HiSeq2000 device. For each fecal sample, approximately 33 swabs were collected from each NICU room from 6 specified areas: sink, feeding and intubation tubing, hands of healthcare providers and parents, general surfaces, and nurse station electronics (keyboard, mouse, and cell phone). Swabs were processed using a recently developed 'expectation maximization iterative reconstruction of genes from the environment' (EMIRGE) amplicon pipeline in which full-length 16S rRNA amplicons were sheared and sequenced using an Illumina platform, and short reads reassembled into full-length genes. Over 24,000 full-length 16S rRNA sequences were produced, generating an average of approximately 12,000 operational taxonomic units (OTUs) (clustered at 97% nucleotide identity) per room-infant pair. Dominant gut taxa, including Staphylococcus epidermidis, Klebsiella pneumoniae, Bacteroides fragilis, and Escherichia coli, were widely distributed throughout the room environment with many gut colonizers detected in more than half of samples. Reconstructed genomes from infant gut colonizers revealed a suite of genes that confer resistance to antibiotics (for example, tetracycline, fluoroquinolone, and aminoglycoside) and sterilizing agents, which likely offer a competitive advantage in the NICU environment. CONCLUSIONS We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut.
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Affiliation(s)
- Brandon Brooks
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA
| | - Brian A Firek
- University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Christopher S Miller
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of Colorado Denver, Denver, CO 80202, USA
| | - Itai Sharon
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA
| | - Brian C Thomas
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA
| | - Robyn Baker
- Division of Newborn Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15224, USA
| | | | - Jillian F Banfield
- Department of Earth and Planetary Sciences, University of California Berkeley, Berkeley, CA 94720, USA
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La Duc MT, Venkateswaran K, Conley CA. A genetic inventory of spacecraft and associated surfaces. ASTROBIOLOGY 2014; 14:15-23. [PMID: 24432775 DOI: 10.1089/ast.2013.0966] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Terrestrial organisms or other contaminants that are transported to Mars could interfere with efforts to study the potential for indigenous martian life. Similarly, contaminants that make the round-trip to Mars and back to Earth could compromise the ability to discriminate an authentic martian biosignature from a terrestrial organism. For this reason, it is important to develop a comprehensive inventory of microbes that are present on spacecraft to avoid interpreting their traces as authentic extraterrestrial biosignatures. Culture-based methods are currently used by NASA to assess spacecraft cleanliness but deliberately detect only a very small subset of total organisms present. The National Research Council has recommended that molecular (DNA)-based identification techniques should be developed as one aspect of managing the risk that terrestrial contamination could interfere with detection of life on (or returned from) Mars. The current understanding of the microbial diversity associated with spacecraft and clean room surfaces is expanding, but the capability to generate a comprehensive inventory of the microbial populations present on spacecraft outbound from Earth would address multiple considerations in planetary protection, relevant to both robotic and human missions. To this end, a 6-year genetic inventory study was undertaken by a NASA/JPL team. It was completed in 2012 and included delivery of a publicly available comprehensive final report. The genetic inventory study team evaluated the utility of three analytical technologies (conventional cloning techniques, PhyloChip DNA microarrays, and 454 tag-pyrosequencing) and combined them with a systematic methodology to collect, process, and archive nucleic acids as the first steps in assessing the phylogenetic breadth of microorganisms on spacecraft and associated surfaces.
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Affiliation(s)
- Myron T La Duc
- 1 Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
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