Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation.

Ganesh Babu Malli Mohan,Michelle Rucker,Camilla Urbaniak,Kasthuri Venkateswaran,Nitin K Singh,Anthony Hood,Rob Knight,Jeremiah J Minich,Ceth W Parker,Naseer Sangwan

doi:10.1128/msystems.00367-20

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.

Highlights

Over the few decades the National Aeronautics and Space Administration (NASA), along with international partners, has planned to begin the expansion of human space exploration beyond low Earth orbit, to the Moon and on to Mars
Among the locations sampled (n=12) and controls (n=4) there is distinctive grouping noticed based on material type
Cultivable population from the Analog habitat surfaces ranged from 4.0 x 100 to 1.8 x 105 colony forming units (CFU)/25 cm2 except in samples collected from the location (Wet porch table top) or location (Bottom of top bunk above pillow)

Summary

Introduction

Over the few decades the National Aeronautics and Space Administration (NASA), along with international partners, has planned to begin the expansion of human space exploration beyond low Earth orbit, to the Moon and on to Mars. This endeavor will entail a variety of new space habitats designed for both interplanetary travel and surface habitation [1, 2]. Humans host an intricate microbiome consisting of numerous microorganisms that live on and within us [5] Most of these microorganisms are either benign and pose no danger to the inhabitant, or are beneficial and perform necessary roles like protection from pathogens or conversion of nutrients into more readily absorbed compounds in our gut. Similar to recent trends in hospital and medical instrument design, engineering mechanisms into habitat construction to manage microbial ecology while continuously monitoring the remaining microbial populations will be critical to future space mission success [7, 8]

Objectives

Methods

Results

Discussion

Conclusion