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1. Sustained bacterial N2O reduction at acidic pH

   https://doi.org/10.1038/s41467-024-48236-x  

   He, Guang; Chen, Gao; Xie, Yongchao; Swift, Cynthia M.; Ramirez, Diana; Cha, Gyuhyon; Konstantinidis, Konstantinos T.; Radosevich, Mark; Löffler, Frank E. (May 2024, Nature Communications)

   Abstract Nitrous oxide (N₂O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N₂O to dinitrogen (N₂) is the major consumption process but microbial N₂O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbornosZgenes encoding N₂O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N₂O at pH 4.5. The co-culture exhibits bimodal growth with aSerratiasp. fermenting pyruvate followed by hydrogenotrophic N₂O reduction by aDesulfosporosinussp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermentingSerratiasp. supplying amino acids as essential growth factors to the N₂O-reducingDesulfosporosinussp. Thus, we demonstrate growth-linked N₂O reduction between pH 4.5 and 6, highlighting microbial N₂O reduction potential in acidic soils. 

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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. 

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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. 

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4. Phylogenomic analysis of novel Diaforarchaea is consistent with sulfite but not sulfate reduction in volcanic environments on early Earth

   https://doi.org/10.1038/s41396-020-0611-9  

   Colman, Daniel R.; Lindsay, Melody R.; Amenabar, Maximiliano J.; Fernandes-Martins, Maria C.; Roden, Eric R.; Boyd, Eric S. (February 2020, The ISME Journal)

   Abstract The origin(s) of dissimilatory sulfate and/or (bi)sulfite reducing organisms (SRO) remains enigmatic despite their importance in global carbon and sulfur cycling since at least 3.4 Ga. Here, we describe novel, deep-branching archaeal SRO populations distantly related to other Diaforarchaea from two moderately acidic thermal springs. Dissimilatory (bi)sulfite reductase homologs, DsrABC, encoded in metagenome assembled genomes (MAGs) from spring sediments comprise one of the earliest evolving Dsr lineages. DsrA homologs were expressed in situ under moderately acidic conditions. MAGs lacked genes encoding proteins that activate sulfate prior to (bi)sulfite reduction. This is consistent with sulfide production in enrichment cultures provided sulfite but not sulfate. We suggest input of volcanic sulfur dioxide to anoxic spring-water yields (bi)sulfite and moderately acidic conditions that favor its stability and bioavailability. The presence of similar volcanic springs at the time SRO are thought to have originated (>3.4 Ga) may have supplied (bi)sulfite that supported ancestral SRO. These observations coincide with the lack of inferred SO42− reduction capacity in nearly all organisms with early-branching DsrAB and which are near universally found in hydrothermal environments. 

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5. Novel metagenome-assembled genomes involved in the nitrogen cycle from a Pacific oxygen minimum zone

   https://doi.org/10.1038/s43705-021-00030-2  

   Sun, Xin; Ward, Bess B. (December 2021, ISME Communications)

   null (Ed.)

   Abstract Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N 2 O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life. 

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