Longitudinal survey of total airborne bacterial and archaeal concentrations and bacterial diversity in enriched colony housing and aviaries for laying hens.

Conventional cages for laying hens will be banned in Canada as of 2036, and the egg industry is transitioning toward enriched colony housing and aviaries. While higher concentrations of particulate matter have been previously reported in aviaries and other cage-free housing systems, concentrations of total bacteria and archaea suspended in the air are still uncharacterized in Canadian enriched colonies and aviaries. The aim of the present study was to conduct a longitudinal survey of airborne total bacteria and of airborne total archaea in twelve enriched colonies and twelve aviaries in Eastern Canada during a whole laying period.

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes.

Background: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown.

Into the darkness of the microbial dark matter activities through expression profiles of populations.

form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 populations in brackish microbial mats to test whether our understanding of metabolism allows the extrapolation of their activities.

Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia.

DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function.