More Like this

1. Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

   LaSarre, B; Morlen, R; Neumann, GC; Harwood, CS; McKinlay, JB (September 2023, bioRxiv)

   Denitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one, or some, of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here we tested the denitrifying capabilities of two purple nonsulfur bacteria, Rhodopseudomonas palustris CGA0092 and Rhodobacter capsulatus SB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2- to N2 and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used for both electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in the dark. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3- served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter we found that NO3- acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2-, but not NO3-, activated N2O reduction but NO2- was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. 

   more » « less
2. Non‐denitrifier nitrous oxide reductases dominate marine biomes

   https://doi.org/10.1111/1758-2229.12879  

   Bertagnolli, Anthony_D; Konstantinidis, Konstantinos_T; Stewart, Frank_J (September 2020, Environmental Microbiology Reports)

   Summary Microbial enzymes often occur as distinct variants that share the same substrate but differ in substrate affinity, sensitivity to environmental conditions, or phylogenetic ancestry. Determining where variants occur in the environment helps identify thresholds that constrain microbial cycling of key chemicals, including the greenhouse gas nitrous oxide (N₂O). To understand the enzymatic basis of N₂O cycling in the ocean, we mined metagenomes to characterize genes encoding bacterial nitrous oxide reductase (NosZ) catalyzing N₂O reduction to N₂. We examined data sets from diverse biomes but focused primarily on those from oxygen minimum zones where N₂O levels are often elevated. With few exceptions, marinenosZdata sets were dominated by ‘atypical’ clade II gene variants. AtypicalnosZhas been associated with low oxygen, enhanced N₂O affinity, and organisms lacking enzymes for complete denitrification, i.e., non‐denitrifiers. AtypicalnosZ often occurred in metagenome‐assembled genomes (MAGs) with nitrate or nitrite respiration genes, although MAGs with genes for complete denitrification were rare. We identified atypicalnosZ in several taxa not previously associated with N₂O consumption, in addition to known N₂O‐associated groups. The data suggest that marine environments generally select for high N₂O‐scavenging ability across diverse taxa and have implications for how N₂O concentration may affect N₂O removal rates. 

   more » « less
3. Impacts of Climate Change and Agricultural Practices on Nitrogen Processes, Genes, and Soil Nitrous Oxide Emissions: A Quantitative Review of Meta-Analyses

   https://doi.org/10.3390/agriculture14020240  

   Hui, Dafeng; Ray, Avedananda; Kasrija, Lovish; Christian, Jaekedah (February 2024, Agriculture)

   Microbial-driven processes, including nitrification and denitrification closely related to soil nitrous oxide (N2O) production, are orchestrated by a network of enzymes and genes such as amoA genes from ammonia-oxidizing bacteria (AOB) and archaea (AOA), narG (nitrate reductase), nirS and nirK (nitrite reductase), and nosZ (N2O reductase). However, how climatic factors and agricultural practices could influence these genes and processes and, consequently, soil N2O emissions remain unclear. In this comprehensive review, we quantitatively assessed the effects of these factors on nitrogen processes and soil N2O emissions using mega-analysis (i.e., meta-meta-analysis). The results showed that global warming increased soil nitrification and denitrification rates, leading to an overall increase in soil N2O emissions by 159.7%. Elevated CO2 stimulated both nirK and nirS with a substantial increase in soil N2O emission by 40.6%. Nitrogen fertilization amplified NH4+-N and NO3−-N contents, promoting AOB, nirS, and nirK, and caused a 153.2% increase in soil N2O emission. The application of biochar enhanced AOA, nirS, and nosZ, ultimately reducing soil N2O emission by 15.8%. Exposure to microplastics mostly stimulated the denitrification process and increased soil N2O emissions by 140.4%. These findings provide valuable insights into the mechanistic underpinnings of nitrogen processes and the microbial regulation of soil N2O emissions. 

   more » « less
4. Bacterial denitrification drives elevated N ₂ O emissions in arid southern California drylands

   https://doi.org/10.1126/sciadv.adj1989  

   Krichels, Alexander H; Jenerette, G Darrel; Shulman, Hannah; Piper, Stephanie; Greene, Aral C; Andrews, Holly M; Botthoff, Jon; Sickman, James O; Aronson, Emma L; Homyak, Peter M (December 2023, Science Advances)

   Soils are the largest source of atmospheric nitrous oxide (N₂O), a powerful greenhouse gas. Dry soils rarely harbor anoxic conditions to favor denitrification, the predominant N₂O-producing process, yet, among the largest N₂O emissions have been measured after wetting summer-dry desert soils, raising the question: Can denitrifiers endure extreme drought and produce N₂O immediately after rainfall? Using isotopic and molecular approaches in a California desert, we found that denitrifiers produced N₂O within 15 minutes of wetting dry soils (site preference = 12.8 ± 3.92 per mil, δ¹⁵N^bulk= 18.6 ± 11.1 per mil). Consistent with this finding, we detected nitrate-reducing transcripts in dry soils and found that inhibiting microbial activity decreased N₂O emissions by 59%. Our results suggest that despite extreme environmental conditions—months without precipitation, soil temperatures of ≥40°C, and gravimetric soil water content of <1%—bacterial denitrifiers can account for most of the N₂O emitted when dry soils are wetted. 

   more » « less
5. Isotopic signals in an agricultural watershed suggest denitrification is locally intensive in riparian areas but extensive in upland soils

   https://doi.org/10.1007/s10533-022-00898-9  

   Sigler, W. A.; Ewing, S. A.; Wankel, S. D.; Jones, C. A.; Leuthold, S.; Brookshire, E. N.; Payn, R. A. (March 2022, Biogeochemistry)

   Abstract Nitrogen loss from cultivated soils threatens the economic and environmental sustainability of agriculture. Nitrate (NO 3 − ) derived from nitrification of nitrogen fertilizer and ammonified soil organic nitrogen may be lost from soils via denitrification, producing dinitrogen gas (N 2 ) or the greenhouse gas nitrous oxide (N 2 O). Nitrate that accumulates in soils is also subject to leaching loss, which can degrade water quality and make NO 3 − available for downstream denitrification. Here we use patterns in the isotopic composition of NO 3 − observed from 2012 to 2017 to characterize N loss to denitrification within soils, groundwater, and stream riparian corridors of a non-irrigated agroecosystem in the northern Great Plains (Judith River Watershed, Montana, USA). We find evidence for denitrification across these domains, expressed as a positive linear relationship between δ 15 N and δ 18 O values of NO 3 − , as well as increasing δ 15 N values with decreasing NO 3 − concentration. In soils, isotopic evidence of denitrification was present during fallow periods (no crop growing), despite net accumulation of NO 3 − from the nitrification of ammonified soil organic nitrogen. We combine previous results for soil NO 3 − mass balance with δ 15 N mass balance to estimate denitrification rates in soil relative to groundwater and streams. Substantial denitrification from soils during fallow periods may be masked by nitrification of ammonified soil organic nitrogen, representing a hidden loss of soil organic nitrogen and an under-quantified flux of N to the atmosphere. Globally, cultivated land spends ca. 50% of time in a fallow condition; denitrification in fallow soils may be an overlooked but globally significant source of agricultural N 2 O emissions, which must be reduced along-side other emissions to meet Paris Agreement goals for slowing global temperature increase. 

   more » « less