Antibiotics in soils may affect the structure and function of microbial communities. In this study, we investigated the acute effects of tetracycline on soil microbial community composition and production of nitrous oxide (N₂O) and dinitrogen (N₂) as the end-products of denitrification. Grassland soils were pre-incubated with and without tetracycline for 1-week prior to measurements of N₂O and N₂ production in soil slurries along with the analysis of prokaryotic and fungal communities by quantitative polymerase chain reaction (qPCR) and next-generation sequencing. Abundance and taxonomic composition of bacteria carrying two genotypes of N₂O reductase genes (nosZ-I and nosZ-II) were evaluated through qPCR and metabolic inference. Soil samples treated with tetracycline generated 12 times more N₂O, but N₂ production was reduced by 84% compared to the control. In parallel with greater N₂O production, we observed an increase in the fungi:bacteria ratio and a significant decrease in the abundance of nosZ-II carrying bacteria; nosZ-I abundance was not affected. NosZ-II-carrying Bacillus spp. (Firmicutes) and Anaeromyxobacter spp. (Deltaproteobacteria) were particularly susceptible to tetracycline and may serve as a crucial N₂O sink in grassland soils. Our study indicates that the introduction of antibiotics to agroecosystems may promote higher N₂O production due to the inhibitory effects on nosZ-II-carrying communities.

Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O₂-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O₂-deficient mesopelagic layer with high concentrations of nitrate (NO₃^–). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO₃^– concentrations and negatively correlated with temperature and O₂, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.

The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the abundance of the clinical class 1 integron-integrase gene (intI1) through qPCR as a secondary marker of anthropogenic contamination. Abundance and diversity of ARGs were substantially higher in the impacted tidal creek, especially near the wastewater discharge. Abundances of ARGs conferring resistance to macrolides, tetracyclines, and streptogramins were also higher in the impacted creek than the reference creek. From the N cycling genes detected in the metagenomes, nrfA, the genetic marker for dissimilatory nitrate reduction to ammonia (DNRA), had the strongest positive relationship with the total abundance of ARGs, which may indicate an increased potential of eutrophication in ARG-impacted ecosystems due to nitrogen retention. This study demonstrates that wastewater discharge from a poultry processing plant can increase the spread of ARGs, which may result in negative impacts on ecosystem health.