Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

ABSTRACT 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 populati...

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Autores principales:	Ganesh Babu Malli Mohan, Ceth W. Parker, Camilla Urbaniak, Nitin K. Singh, Anthony Hood, Jeremiah J. Minich, Rob Knight, Michelle Rucker, Kasthuri Venkateswaran
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	extravehicular activity Analog habitat microbiome microbial diversity functional metagenomics spacecraft microbiome Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/51accbf5dc5c4df08805182a96044f85
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spelling	oai:doaj.org-article:51accbf5dc5c4df08805182a96044f852021-12-02T19:47:35ZMicrobiome and Metagenome Analyses of a Closed Habitat during Human Occupation10.1128/mSystems.00367-202379-5077https://doaj.org/article/51accbf5dc5c4df08805182a96044f852020-08-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00367-20https://doaj.org/toc/2379-5077ABSTRACT 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.Ganesh Babu Malli MohanCeth W. ParkerCamilla UrbaniakNitin K. SinghAnthony HoodJeremiah J. MinichRob KnightMichelle RuckerKasthuri VenkateswaranAmerican Society for Microbiologyarticleextravehicular activityAnalog habitatmicrobiomemicrobial diversityfunctional metagenomicsspacecraft microbiomeMicrobiologyQR1-502ENmSystems, Vol 5, Iss 4 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	extravehicular activity Analog habitat microbiome microbial diversity functional metagenomics spacecraft microbiome Microbiology QR1-502
spellingShingle	extravehicular activity Analog habitat microbiome microbial diversity functional metagenomics spacecraft microbiome Microbiology QR1-502 Ganesh Babu Malli Mohan Ceth W. Parker Camilla Urbaniak Nitin K. Singh Anthony Hood Jeremiah J. Minich Rob Knight Michelle Rucker Kasthuri Venkateswaran Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation
description	ABSTRACT 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.
format	article
author	Ganesh Babu Malli Mohan Ceth W. Parker Camilla Urbaniak Nitin K. Singh Anthony Hood Jeremiah J. Minich Rob Knight Michelle Rucker Kasthuri Venkateswaran
author_facet	Ganesh Babu Malli Mohan Ceth W. Parker Camilla Urbaniak Nitin K. Singh Anthony Hood Jeremiah J. Minich Rob Knight Michelle Rucker Kasthuri Venkateswaran
author_sort	Ganesh Babu Malli Mohan
title	Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation
title_short	Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation
title_full	Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation
title_fullStr	Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation
title_full_unstemmed	Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation
title_sort	microbiome and metagenome analyses of a closed habitat during human occupation
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/51accbf5dc5c4df08805182a96044f85
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Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation

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