Quo vadis? Microbial profiling revealed strong effects of cleanroom maintenance and routes of contamination in indoor environments

Abstract

Space agencies maintain highly controlled cleanrooms to ensure the demands of planetary protection. To study potential effects of microbiome control, we analyzed microbial communities in two particulate-controlled cleanrooms (ISO 5 and ISO 8) and two vicinal uncontrolled areas (office, changing room) by cultivation and 16S rRNA gene amplicon analysis (cloning, pyrotagsequencing, and PhyloChip G3 analysis). Maintenance procedures affected the microbiome on total abundance and microbial community structure concerning richness, diversity and relative abundance of certain taxa. Cleanroom areas were found to be mainly predominated by potentially human-associated bacteria; archaeal signatures were detected in every area. Results indicate that microorganisms were mainly spread from the changing room (68%) into the cleanrooms, potentially carried along with human activity. The numbers of colony forming units were reduced by up to ~400 fold from the uncontrolled areas towards the ISO 5 cleanroom, accompanied with a reduction of the living portion of microorganisms from 45% (changing area) to 1% of total 16S rRNA gene signatures as revealed via propidium monoazide treatment of the samples. Our results demonstrate the strong effects of cleanroom maintenance on microbial communities in indoor environments and can be used to improve the design and operation of biologically controlled cleanrooms.

Endophytes-assisted biocontrol: novel insights in ecology and the mode of action of Paenibacillus

“…Different lichen species were shown to harbor rather small proportions of Paenibacillus (0.01-0.04 %; Grube et al 2015). In contrast, high Paenibacillus abundance was found in cleanrooms (0.1-4.0 %; Moissl-Eichinger et al 2015). These artificial habitats are repeatedly exposed to decontamination-related stress, and therefore sporeforming bacteria may have better chances of survival or at least be more persistent.…”

“…In order to gain greater insight into the relative abundance of Paenibacillus we have analyzed 17 publicly available datasets(Delmotte et al 2009;Knief et al 2011;Köberl et al 2011;Grube et al 2015;Moissl- Eichinger et al 2015) including our own datasets from the metagenomes of seven plant habitats, four soils, and three lichens, and compared them with three indoor habitats (Supplementary…”

Characterization ofStaphylococcus epidermidisstrains isolated from industrial cleanrooms under regular routine disinfection

“…Cleanrooms usually show a predominance of potentially human‐associated micro‐organisms (Moissl‐Eichinger et al . ).…”

“…Bacteria of the Staphylococcus and Microbacterium genera (Moissl‐Eichinger et al . ) have been identified as the prevalent bacteria isolated from air and surface samples in cleanroom environments. When analysing contaminated samples from environmental monitoring in pharmaceutical units that process mesenchymal stem cells for clinical use, Gálvez Martín et al .…”

Bacillus safensisFO-36b andBacillus pumilusSAFR-032: A Whole Genome Comparison of Two Spacecraft Assembly Facility Isolates

“…Microbial persistence in built environments such as spacecraft cleanroom facilities [2][3][4] is often characterized by their unusual resistances to different physical and chemical factors [2,[5][6][7][8].…”