The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome.

The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.

Ozone inactivation of airborne influenza and lack of resistance of respiratory syncytial virus to aerosolization and sampling processes.

Influenza and RSV are human viruses responsible for outbreaks in hospitals, long-term care facilities and nursing homes. The present study assessed an air treatment using ozone at two relative humidity conditions (RHs) in order to reduce the infectivity of airborne influenza. Bovine pulmonary surfactant (BPS) and synthetic tracheal mucus (STM) were used as aerosols protectants to better reflect the human aerosol composition. Residual ozone concentration inside the aerosol chamber was also measured. RSV's sensitivity resulted in testing its resistance to aerosolization and sampling processes instead of ozone exposure. The results showed that without supplement and with STM, a reduction in influenza A infectivity of four orders of magnitude was obtained with an exposure to 1.70 ± 0.19 ppm of ozone at 76% RH for 80 min. Consequently, ozone could be considered as a virucidal disinfectant for airborne influenza A. RSV did not withstand the aerosolization and sampling processes required for the use of the experimental setup. Therefore, ozone exposure could not be performed for this virus. Nonetheless, this study provides great insight for the efficacy of ozone as an air treatment for the control of nosocomial influenza A outbreaks.

Microbial communities and biogenic Mn-oxides in an on-site biofiltration system for cold Fe-(II)- and Mn(II)-rich groundwater treatment.

This study investigated relationships between microbial communities, groundwater chemistry, and geochemical and mineralogical characteristics in field-aged biofilter media from a two-stage, pilot-scale, flow-through biofiltration unit designed to remove Fe(II) and Mn(II) from cold groundwater (8 to 15 °C). High-throughput 16S rRNA gene amplicon sequencing of influent groundwater and biofilter samples (solids, effluents, and backwash water) revealed significant differences in the groundwater, Fe filter, and Mn filter communities. These community differences reflect conditions in each filter that select for populations that biologically oxidize Fe(II) and Mn(II) in the two filters, respectively. Genera identified in both filters included relatives of known Fe(II)-oxidizing bacteria (FeOB), Mn(II)-oxidizing bacteria (MnOB), and ammonia-oxidizing bacteria (AOB). Relatives of AOB and nitrite-oxidizing bacteria were abundant in sequencing reads from both filters. Relatives of FeOB in class Betaproteobacteria dominated the Fe filter. Taxa related to Mn-oxidizing organisms were minor members of the Mn-filter communities; intriguingly, while Alphaproteobacteria dominated (40 ± 10% of sequencing reads) the Mn filter community, these Alphaproteobacteria did not classify as known MnOB. Isolates from Fe and Mn filter backwash enrichment studies provide insight on the identity of MnOB in this system. Novel putative MnOB isolates included Azospirillum sp. CDMB, Solimonas soli CDMK, and Paenibacillus sp. CDME. The isolate Hydrogenophaga strain CDMN can oxidize Mn(II) at 8 °C; this known FeOB is likely capable of Mn(II) oxidation in this system. Synchrotron-based X-ray near-edge spectroscopy (XANES) coupled with electron paramagnetic resonance (EPR) revealed the dominant Mn-oxide that formed was biogenic birnessite. Co-existence of amorphous and crystallized Mn-oxide surface morphologies on the Mn-filter media suggest occurrence of both biological and autocatalytic Mn(II) oxidation in the biofilter. This study provides evidence that biofiltration is a viable approach to remove iron, manganese, and ammonia in cold groundwater systems, and that mineralogical and microbiological approaches can be used to monitor biofiltration system efficacy and function.

Hunting for a viral proxy in bioaerosols of swine buildings using molecular detection and metagenomics.

There are limited biosecurity measures directed at preventing airborne transmission of viruses in swine. The effectiveness of dust mitigation strategies such as oil sprinkling, to decrease risk of airborne virus transmission are unknown. Metagenomics and qPCR for common fecal viruses were used to hunt for a ubiquitous virus to serve as a proxy when evaluating the efficiency of mitigation strategies against airborne viral infectious agents. Air particles were collected from swine buildings using high-volume air samplers. Extracted DNA and RNA were used to perform specific RT-qPCR and qPCR and analyzed by high-throughput sequencing. Porcine astroviruses group 2 were common (from 102 to 105 genomic copies per cubic meter of air or gc/m3, 93% positivity) while no norovirus genogroup II was recovered from air samples. Porcine torque teno sus virus were detected by qPCR in low concentrations (from 101 to 102 gc/m3, 47% positivity). Among the identified viral families by metagenomics analysis, Herelleviridae, Microviridae, Myoviridae, Podoviridae, and Siphoviridae were dominant. The phage vB_AviM_AVP of Aerococcus was present in all air samples and a newly designed qPCR revealed between 101 and 105 gc/m3 among the samples taken for the present study (97% positivity) and banked samples from 5- and 15-year old studies (89% positivity). According to the present study, both the porcine astrovirus group 2 and the phage vB_AviM_AVP of Aerococcus could be proxy for airborne viruses of swine buildings.