Reconnaissance of Oxygenic Denitrifiers in Agriculturally Impacted Soils.

Row crop production in the agricultural Midwest pollutes waterways with nitrate, and exacerbates climate change through increased emissions of nitrous oxide and methane. Oxygenic denitrification processes in agricultural soils mitigate nitrate and nitrous oxide pollution by short-circuiting the canonical pathway to avoid nitrous oxide formation. Furthermore, many oxygenic denitrifiers employ a nitric oxide dismutase (nod) to create molecular oxygen that is used by methane monooxygenase to oxidize methane in otherwise anoxic soils. The direct investigation of nod genes that could facilitate oxygenic denitrification processes in agricultural sites is limited, with no prior studies investigating nod genes at tile drainage sites. Thus, we performed a reconnaissance of nod genes at variably saturated surface sites, and within a variably to fully saturated soil core in Iowa to expand the known distribution of oxygenic denitrifiers. We identified new nod gene sequences from agricultural soil and freshwater sediments in addition to identifying nitric oxide reductase (qNor) related sequences. Surface and variably saturated core samples displayed a nod to 16S rRNA gene relative abundance of 0.004% to 0.1% and fully saturated core samples had relative nod gene abundance of 1.2%. The relative abundance of the phylum Methylomirabilota increased from 0.6% and 1% in the variably saturated core samples to 3.8% and 5.3% in the fully saturated core samples. The more than 10-fold increase in relative nod abundance and almost 9-fold increase in relative Methylomirabilota abundance in fully saturated soils suggests that potential oxygenic denitrifiers play a greater nitrogen cycling role under these conditions. IMPORTANCE The direct investigation of nod genes in agricultural sites is limited, with no prior studies investigating nod genes at tile drains. An improved understanding of nod gene diversity and distribution is significant to the field of bioremediation and ecosystem services. The expansion of the nod gene database will advance oxygenic denitrification as a potential strategy for sustainable nitrate and nitrous oxide mitigation, specifically for agricultural sites.

Motility of Shewanella oneidensis MR-1 Allows for Nitrate Reduction in the Toxic Region of a Ciprofloxacin Concentration Gradient in a Microfluidic Reactor.

Subsurface environments often contain mixtures of contaminants in which the microbial degradation of one pollutant may be inhibited by the toxicity of another. Agricultural settings exemplify these complex environments, where antimicrobial leachates may inhibit nitrate bioreduction, and are the motivation to address this fundamental ecological response. In this study, a microfluidic reactor was fabricated to create diffusion-controlled concentration gradients of nitrate and ciprofloxacin under anoxic conditions in order to evaluate the ability of Shewanella oneidenisis MR-1 to reduce the former in the presence of the latter. Results show a surprising ecological response, where swimming motility allow S. oneidensis MR-1 to accumulate and maintain metabolic activity for nitrate reduction in regions with toxic ciprofloxacin concentrations (i.e., 50× minimum inhibitory concentration, MIC), despite the lack of observed antibiotic resistance. Controls with limited nutrient flux and a nonmotile mutant (Δ flag) show that cells cannot colonize antibiotic rich microenvironments, and this results in minimal metabolic activity for nitrate reduction. These results demonstrate that under anoxic, nitrate-reducing conditions, motility can control microbial habitability and metabolic activity in spatially heterogeneous toxic environments.