Nitrite Control over Dissimilatory Nitrate/Nitrite Reduction Pathways in Shewanella loihica Strain PV-4

Abstract

؊ as a relevant modulator of NO 3 ؊ fate in S. loihica strain PV-4, and, by extension, suggest that NO 2 ؊ is a relevant determinant for N retention (i.e., ammonification) versus N loss and greenhouse gas emission (i.e., denitrification). T wo major dissimilatory pathways determine the fate of nitrate (NO 3Ϫ ) in anoxic environments: denitrification and respiratory ammonification (1, 2). In denitrification, NO 3 Ϫ is stepwise reduced via nitrite (NO 2 Ϫ ), nitric oxide (NO), and nitrous oxide (N 2 O) to dinitrogen (N 2 ). In respiratory ammonification, NO 3 Ϫ is reduced via NO 2 Ϫ to ammonium (NH 4 ϩ ). Nitrite is the common intermediate of the two pathways and the branching point for both dissimilatory pathways. In the presence of NH 4 ϩ , NO 2 Ϫ also can serve as the electron acceptor for anaerobic ammonium oxidation (anammox) (3); however, in soil environments this process appears to be less relevant than the other two processes (4). The fate of NO 2 Ϫ via denitrification or respiratory ammonification has great environmental impact. Denitrification forms gaseous products (N 2 O, N 2 ), which are emitted from the soil, resulting in N loss, whereas respiratory ammonification generates NH 4 ϩ leading to N retention (5, 6). Atmospheric N 2 O is a potent greenhouse gas and an ozone-depleting agent (7,8). Therefore, knowledge of the environmental factors that control these NO 2 Ϫ reduction pathways is needed to estimate, predict, and possibly manipulate N loss versus N retention.The major sources of NO 2 Ϫ in the environment include NH 4 ϩ oxidation performed by nitrosifiers and NO 3 Ϫ reduction. In these conversions, NO 2 Ϫ accumulates when its production is kinetically faster than NO 2 Ϫ consumption (9, 10). Nitrite accumulation had been thought to occur rarely in the environment (11); however, recent observations suggested that NO 2 Ϫ formation can occur as a result of NO 3 Ϫ reduction and NH 4 ϩ oxidation under conditions that favor NO 2 Ϫ production over consumption (12)(13)(14)(15)(16). For example, high pH and abundance of NH 4 ϩ and hydroxylamine (NH 2 OH) affect NO 2 Ϫ oxidizers, causing NO 2 Ϫ accumulation from nitrosification (15), while oxygen intrusion and/or electron donor limitations may cause NO 2 Ϫ accumulation from denitrification (12). In pure-culture studies, several denitrifiers and respiratory ammonifiers were found to reduce NO 3 Ϫ at a higher rate than NO 2 Ϫ , causing dynamic changes of the NO 2 Ϫ :NO 3 Ϫ ratios in the medium (10). Additional NO 2 Ϫ may be generated by NO 3 Ϫ -to-NO 2 Ϫ reducers sensu stricto, which generate NO 2 Ϫ as an end product (12). For example, in activated sludge, the activity of NO 3 Ϫ -to-NO 2 Ϫ reducers leads to NO 2 Ϫ formation; however, the contribution of NO 3 Ϫ -to-NO 2 Ϫ reducers to NO 2 Ϫ accumulation in natural environments is uncertain (17,18).Even though NO 2 Ϫ formation occurs in diverse environments (12,19), information regarding the impact of NO 2 Ϫ on dissimilatory NO 3 Ϫ /NO 2 Ϫ reduction pathways is scarce. Increased NO 2 Ϫ concentrations and respi...

Nitrous Oxide Reduction Kinetics Distinguish Bacteria Harboring Clade I NosZ from Those Harboring Clade II NosZ

“…The measurements were adjusted for the weight of the salts in the culture medium that stayed on the membrane filter after filtration. This adjustment was necessary because media with different ionic strengths were used for the cultivation of the microorganisms (30).…”

“…A Henry's constant of 2.21 was used to correct for the ionic strength effects in the saline medium used for culturing S. loihica (28)(29)(30). OD 600 measurements were performed with a Spectronic 20Dϩ spectrophotometer (Thermo Scientific, Waltham, MA) using disposable plastic cuvettes with a 1-cm path length.…”

Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon

“…However, comparison of lake parameters to DEA results (phenotype) and qPCR on N cycling genes (genotype) confirmed the lack of influence of nutrient inflow on the microbial community. It is possible the spatial distribution of microorganisms is not controlled by the amount of either organic carbon or nitrogen alone, but by their ratio in the sediments (Dang et al, 2009; Yoon et al, 2015a,b). Correlations also suggest that DEA results are unlikely to be influenced by any measured physical factors.…”

Dissimilatory nitrogen reduction in intertidal sediments of a temperate estuary: small scale heterogeneity and novel nitrate-to-ammonium reducers

“…coli , differential expression of nrfA and nirB under low and high nitrate concentrations respectively was observed (Wang and Gunsalus, 2000 ). DNRA-related ecophysiology, enzymology, gene expression and regulation have been extensively studied in model organisms like E. coli, W. succinogenes , and B. subtilis (Cole, 1996 ; Nakano and Zuber, 1998 ; Simon, 2002 ), and more recently also in B. vireti (Mania et al, 2014 ) and Shewanella loihica (Yoon et al, 2015a , b ). Whole genome sequence analyses, however, demonstrated that DNRA, similar to denitrification, is phylogenetically very widespread, and can be found in members of Bacteroidetes (Mohan et al, 2004 ), Proteobacteria ( Gamma -, Delta -, and Epsilon ; Smith et al, 2007 ), Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi , and Planctomycetes (Welsh et al, 2014 ).…”

“…Some DNRA bacteria have furthermore been shown to contain partial or complete suites of genes for both DNRA and denitrification in their genome (Heylen and Keltjens, 2012 ; Sanford et al, 2012 ; Yoon et al, 2013 ; Mania et al, 2014 ). Functional capacity to carry out both nitrate reducing processes and the environmental drivers of nitrate partitioning to either process, like carbon-to-nitrogen ratios and nitrite concentrations, have thus far only been demonstrated for the marine strain Shewanella loihica PV-4 (Yoon et al, 2015a , b ). In addition to pure culture experiments, natural prokaryotic communities have also been used for examining these environmental drivers (Kraft et al, 2014 ; Van Den Berg et al, 2015 ).…”