Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes.
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.
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, California, United States of America.
Alexander
A
Mahnert
Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, California, United States of America.
Parag
P
Vaishampayan
Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America.
Alexander J
AJ
Probst
Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany.
Anna
A
Auerbach
Institute for Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany; Medical University Graz, Department of Internal Medicine, Graz, Austria; BioTechMed Graz, Graz, Austria.
Christine
C
Moissl-Eichinger
Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, Pasadena, California, United States of America.
Kasthuri
K
Venkateswaran
Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
Gabriele
G
Berg
D001105:Archaea / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D001386:Azides / Q000494:pharmacology; D001419:Bacteria / Q000187:drug effects / Q000235:genetics / Q000254:growth & development; D044822:Biodiversity; D015169:Colony Count, Microbial; D004780:Environment, Controlled; D014644:Genetic Variation; D006801:Humans; D008283:Maintenance; D050296:Microbial Viability / Q000187:drug effects; D064307:Microbiota / Q000187:drug effects / Q000235:genetics; D010802:Phylogeny; D011419:Propidium / Q000031:analogs & derivatives / Q000494:pharmacology; D012336:RNA, Ribosomal, 16S / Q000032:analysis / Q000235:genetics
D001386:Azides; D012336:RNA, Ribosomal, 16S; C533957:propidium monoazide; D011419:Propidium