Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes

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.

Beyond the planetary boundary layer: Bacterial and fungal vertical biogeography at Mount Sonnblick, Austria

“…Planifilum is present in a range of bioaerosol studies from pharmaceutical indoor air and dominated other phylotypes in thermophilic composting bioaerosols (Le Goff et al, 2010;Wéry, 2014). It also occurred with high viable abundances in a controlled clean room for space craft assembly (Mahnert et al, 2015), which indicated its adaption to harsh environments.…”

“…Geobacillus is a spore-forming, gram-positive obligate thermophilic, facultative anaerobe bacterium with a growth range between 35 and 80°C (Marchant et al, 2008), most frequently isolated from hot springs (Canakci et al, 2007;Pinzón-Martínez et al, 2010) and geothermal vents (Kimura et al, 2003;Maugeri et al, 2001). However, Geobacillus has also been found in high abundances in a wide range of geographical and ecological environments, such as cold seafloor sediment (Bartholomew & Paik, 1966), Arctic soils (Marchant et al, 2002;Rahman et al, 2004), the upper troposphere (DeLeon-Rodriguez et al, 2013), the Bolivian Andes at 3,653 m asl (Marchant et al, 2002) and compost air (Le Goff et al, 2010), as well as clean rooms for space craft assembly (Mahnert et al, 2015). Zeigler (2014) attributes the ubiquitous occurrence of Geobacillus to so-called bridges in the sky, that is, airborne dispersal.…”

Characterization ofStaphylococcus epidermidisstrains isolated from industrial cleanrooms under regular routine disinfection

“…air conditioning), maintenance of partial overpressure, limited access and strict gowning protocols (Mahnert et al . ). Cleanrooms usually show a predominance of potentially human‐associated micro‐organisms (Moissl‐Eichinger et al .…”

“…Chemical disinfectant agents are usually used for regular disinfection, and these can contain different active ingredients, such as quaternary ammonium compounds, acidic compounds, hydrogen peroxide and others (Mahnert et al . ).…”

“…In the cleanroom environment, where the air supply is free of bacteria and positive pressure is maintained in the cleanest areas, the major source of contamination is people, with bacteria dispersed with skin cells, parts of skin cells or other dust particles, and through direct contact (Mahnert et al . ). El‐Din Ashour et al .…”