An official website of the United States government
Nitrous oxide (N2O) is a potent greenhouse gas and a major cause of ozone depletion. One-third of atmospheric N2O originates in aquatic environments. Reduction of N2O to dinitrogen gas (N2) requires the nitrous oxide reductase enzyme, which is encoded by the genenosZ. Organisms that containnosZare the only known biological sinks of N2O and are found in diverse genera and a wide range of environments. The two clades ofnosZ(Clade I and II) contain great diversity, making it challenging to study the population structure and distribution ofnosZcontaining organisms in the environment. A database of over 11,000nosZsequences was compiled from NCBI (representing diverse aquatic environments) and unpublished sequences and metagenomes (primarily from oxygen minimum zones, OMZs, where N2O levels are often elevated). Sequences were clustered into archetypes based on DNA and amino acid sequence identity and their clade, phylogeny, and environmental source were determined. Further analysis of the source and environmental distribution of the sequences showed strong habitat separation between clades and phylogeny. Although there are more Clade InosZgenes in the compilation, Clade II is more diverse phylogenetically and has a wider distribution across environmental sources. On the other hand, Clade InosZgenes are predominately found within marine sediment and are primarily from the phylum Pseudonomonadota. The majority of the sequences analyzed from marine OMZs represented distinct phylotypes between different OMZs showing that thenosZgene displays regional and environmental separation. This study expands the known diversity ofnosZgenes and provides a clearer picture of how the clades and phylogeny ofnosZorganisms are distributed across diverse environments.
more »
« less
This content will become publicly available on September 17, 2026
Aquatic copper-containing nitrite reductase gene (nirK) phylogeny and environmental distribution
Nitrite reduction is an essential step in the oceanic Nitrogen cycle. Nitrite reductase genes, mainlynirSandnirK, are found in dozens of phyla, are often associated with denitrifiers, ammonia- and nitrite-oxidizing bacteria (AOB and NOB) as well as ammonia-oxidizing archaea (AOA).nirKis found throughout the ocean, including in oxygenated surface water as well as in oxygen minimum zones (OMZs). The diverse and complex evolutionary history of thenirKgenes makes it challenging to study the population structure and distribution ofnirKcontaining organisms in the environment. The organisms containingnirKplay key roles in the global nitrogen cycle, including the loss of fixed N, and have the potential to influence nitrous oxide (N2O) emissions via multiple pathways. This study surveyed the phylogeny and environmental distribution of over 12,000nirKgenes, focusing on those originating from marine and aquatic sources. Sequences were clustered into OTUs based on DNA sequence identity and their phylogeny and environmental sources were examined. The distribution of the sequences showed habitat separation within taxonomic groups, i.e., the majority of the OTUs were associated with only one environmental source. BacterialnirKis more diverse phylogenetically and has a wider distribution across environmental sources than archaealnirK. Most of the bacterial sequences were obtained from marine sediments, but there was variation in the dominant environmental source across phyla and classes. Archaeal sequences demonstrated niche separation between phyla as sequences from the more phylogenetically diverse phylum, Euryarchaeota, were all isolated from hypersaline environments while Nitrososphaerota sequences came from a wider range of environmental sources. This study expands the known diversity ofnirKgenes and provides a clearer picture of hownirKorganisms are distributed across diverse environments.
more »
« less
- Award ID(s):
- 1946516
- PAR ID:
- 10636495
- Publisher / Repository:
- Frontiers of Micrdobiology
- Date Published:
- Journal Name:
- Frontiers in Microbiology
- Volume:
- 16
- ISSN:
- 1664-302X
- Page Range / eLocation ID:
- 16:1635656.
- Subject(s) / Keyword(s):
- nitrite reduction nirK oxygen minimum zone nitrogen cycling denitrification AOA ammonia oxidizing archaea nitrification
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Abstract Hopanoid lipids, bacteriohopanols and bacteriohopanepolyols, are membrane components exclusive to bacteria. Together with their diagenetic derivatives, they are commonly used as biomarkers for specific bacterial groups or biogeochemical processes in the geologic record. However, the sources of hopanoids to marine and freshwater environments remain inadequately constrained. Recent marker gene studies suggest a widespread potential for hopanoid biosynthesis in marine bacterioplankton, including nitrifying (i.e., ammonia‐ and nitrite‐oxidizing) bacteria. To explore their hopanoid biosynthetic capacities, we studied the distribution of hopanoid biosynthetic genes in the genomes of cultivated and uncultivated ammonia‐oxidizing (AOB), nitrite‐oxidizing (NOB), and complete ammonia‐oxidizing (comammox) bacteria, finding that biosynthesis of diverse hopanoids is common among seven of the nine presently cultivated clades of nitrifying bacteria. Hopanoid biosynthesis genes are also conserved among the diverse lineages of bacterial nitrifiers detected in environmental metagenomes. We selected seven representative NOB isolated from marine, freshwater, and engineered environments for phenotypic characterization. All tested NOB produced diverse types of hopanoids, with some NOB producing primarily diploptene and others producing primarily bacteriohopanepolyols. Relative and absolute abundances of hopanoids were distinct among the cultures and dependent on growth conditions, such as oxygen and nitrite limitation. Several novel nitrogen‐containing bacteriohopanepolyols were tentatively identified, of which the so called BHP‐743.6 was present in all NOB. Distinct carbon isotopic signatures of biomass, hopanoids, and fatty acids in four tested NOB suggest operation of the reverse tricarboxylic acid cycle inNitrospiraspp. andNitrospina gracilisand of the Calvin–Benson–Bassham cycle for carbon fixation inNitrobacter vulgarisandNitrococcus mobilis. We suggest that the contribution of hopanoids by NOB to environmental samples could be estimated by their carbon isotopic compositions. The ubiquity of nitrifying bacteria in the ocean today and the antiquity of this metabolic process suggest the potential for significant contributions to the geologic record of hopanoids.more » « less
-
Abstract Complete ammonia oxidizing bacteria coexist with canonical ammonia and nitrite oxidizing bacteria in a wide range of environments. Whether this is due to competitive or cooperative interactions, or a result of niche separation is not yet clear. Understanding the factors driving coexistence of nitrifiers is critical to manage nitrification processes occurring in engineered and natural ecosystems. In this study, microcosm-based experiments were used to investigate the impact of nitrogen source and loading on the population dynamics of nitrifiers in drinking water biofilter media. Shotgun sequencing of DNA followed by co-assembly and reconstruction of metagenome assembled genomes revealed clade A2 comammox bacteria were likely the primary nitrifiers within microcosms and increased in abundance over Nitrosomonas-like ammonia and Nitrospira-like nitrite oxidizing bacteria irrespective of nitrogen source type or loading. Changes in comammox bacterial abundance did not correlate with either ammonia or nitrite oxidizing bacterial abundance in urea-amended systems, where metabolic reconstruction indicated potential for cross-feeding between strict ammonia and nitrite oxidizers. In contrast, comammox bacterial abundance demonstrated a negative correlation with nitrite oxidizers in ammonia-amended systems. This suggests potentially weaker synergistic relationships between strict ammonia and nitrite oxidizers might enable comammox bacteria to displace strict nitrite oxidizers from complex nitrifying communities.more » « less
-
ABSTRACT Ammonia availability due to chloramination can promote the growth of nitrifying organisms, which can deplete chloramine residuals and result in operational problems for drinking water utilities. In this study, we used a metagenomic approach to determine the identity and functional potential of microorganisms involved in nitrogen biotransformation within chloraminated drinking water reservoirs. Spatial changes in the nitrogen species included an increase in nitrate concentrations accompanied by a decrease in ammonium concentrations with increasing distance from the site of chloramination. This nitrifying activity was likely driven by canonical ammonia-oxidizing bacteria (i.e., Nitrosomonas ) and nitrite-oxidizing bacteria (i.e., Nitrospira ) as well as by complete-ammonia-oxidizing (i.e., comammox) Nitrospira -like bacteria. Functional annotation was used to evaluate genes associated with nitrogen metabolism, and the community gene catalogue contained mostly genes involved in nitrification, nitrate and nitrite reduction, and nitric oxide reduction. Furthermore, we assembled 47 high-quality metagenome-assembled genomes (MAGs) representing a highly diverse assemblage of bacteria. Of these, five MAGs showed high coverage across all samples, which included two Nitrosomonas, Nitrospira, Sphingomonas , and Rhizobiales -like MAGs. Systematic genome-level analyses of these MAGs in relation to nitrogen metabolism suggest that under ammonia-limited conditions, nitrate may be also reduced back to ammonia for assimilation. Alternatively, nitrate may be reduced to nitric oxide and may potentially play a role in regulating biofilm formation. Overall, this study provides insight into the microbial communities and their nitrogen metabolism and, together with the water chemistry data, improves our understanding of nitrogen biotransformation in chloraminated drinking water distribution systems. IMPORTANCE Chloramines are often used as a secondary disinfectant when free chlorine residuals are difficult to maintain. However, chloramination is often associated with the undesirable effect of nitrification, which results in operational problems for many drinking water utilities. The introduction of ammonia during chloramination provides a potential source of nitrogen either through the addition of excess ammonia or through chloramine decay. This promotes the growth of nitrifying microorganisms and provides a nitrogen source (i.e., nitrate) for the growth for other organisms. While the roles of canonical ammonia-oxidizing and nitrite-oxidizing bacteria in chloraminated drinking water systems have been extensively investigated, those studies have largely adopted a targeted gene-centered approach. Further, little is known about the potential long-term cooccurrence of complete-ammonia-oxidizing (i.e., comammox) bacteria and the potential metabolic synergies of nitrifying organisms with their heterotrophic counterparts that are capable of denitrification and nitrogen assimilation. This study leveraged data obtained for genome-resolved metagenomics over a time series to show that while nitrifying bacteria are dominant and likely to play a major role in nitrification, their cooccurrence with heterotrophic organisms suggests that nitric oxide production and nitrate reduction to ammonia may also occur in chloraminated drinking water systems.more » « less
-
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
