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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

Ammonia-oxidizing microorganisms (AOM) contribute to one of the largest nitrogen fluxes in the global nitrogen budget. Four distinct lineages of AOM: ammonia-oxidizing archaea (AOA), beta- and gamma-proteobacterial ammonia-oxidizing bacteria (β-AOB and γ-AOB) and complete ammonia oxidizers (comammox), are thought to compete for ammonia as their primary nitrogen substrate. In addition, many AOM species can utilize urea as an alternative energy and nitrogen source through hydrolysis to ammonia. How the coordination of ammonia and urea metabolism in AOM influences their ecology remains poorly understood. Here we use stable isotope tracing, kinetics and transcriptomics experiments to show that representatives of the AOM lineages employ distinct regulatory strategies for ammonia or urea utilization, thereby minimizing direct substrate competition. The tested AOA and comammox species preferentially used ammonia over urea, while β-AOB favoured urea utilization, repressed ammonia transport in the presence of urea and showed higher affinity for urea than for ammonia. Characterized γ-AOB co-utilized both substrates. Furthermore, these results reveal contrasting niche adaptation and coexistence patterns among the major AOM lineages.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Floodplain nitrifiers harbor the genetic potential for utilizing a wide range of organic nitrogen compounds

Organic compounds such as urea and cyanate can serve as nitrogen (N) sources for nitrifying microorganisms, including ammonia-oxidizing archaea (AOA) and bacteria (AOB), complete ammonia-oxidizing (comammox) bacteria, and nitrite-oxidizing bacteria (NOB). Here we investigated metagenome-assembled genomes (MAGs) for all four nitrifier guilds generated from hydrologically variable floodplain sediments of the Wind River Basin (WRB; Riverton, WY, USA) for their genetic potential to utilize organic N compounds. A vast majority of WRB nitrifier MAGs harbored urease (ure) and at least one urea transporter ( utp, urt, dur3 ). AOA were the most abundant and phylogenetically diverse nitrifiers in WRB floodplain sediments. Several AOA MAGs encoded cyanase ( cynS ), nitrilase ( nit1 ), omega-amidase ( nit2 ), nitrile hydratase ( nthA ), and genes related to purine degradation, including biuret hydrolase ( biuH ), oxamic transcarbamylase ( allFGH ), and catabolic carbamate kinase ( allK ). AOA often encoded an uncharacterized amidohydrolase collocated with biuH , rather than allophanate hydrolase ( atzF ). A small number of AOA encoded atzF , functioning in an unknown pathway. AOB and comammox were of relatively low abundance and taxonomic diversity and were present only at certain depths in WRB; however, they encoded triuret/biuret degradation genes ( trtA, biuH , and atzH ), and in comammox, these genes were also collocated with allFGHK . The genetic potential of ammonia oxidizers in the WRB floodplain suggests that organic N may support nitrification in this system. The proposed pathways for utilizing purine degradation products other than urea potentially expand the known metabolic capabilities of AOA, AOB, and comammox bacteria and reveal the possibility for cryptic N cycling between microbial community members.

floodplain↗
DOE OSTI2022

Photoinhibition of comammox reaction in Nitrospira inopinata in a dose- and wavelength-dependent manner

Apparent contribution of complete ammonia-oxidizing organisms (comammox) to the global nitrogen cycle highlights the necessity for understanding niche differentiation of comammox bacteria among other ammonia oxidizers. While the high affinity for ammonia of the comammox species Nitrospira inopinata suggests their niche partitioning is expected to be centered in oligotrophic environments, their absence in nutrient-depleted environments (such as the oceans) suggests that other (abiotic) factors might control their distribution and spatial localization within microbial communities. Many ammonia- and nitrite-oxidizing organisms are sensitive to light; however, the photosensitivity of comammox has not been explored. Since comammox bacteria encode enzymatic machinery homologous to canonical ammonia-and nitrite-oxidizers, we hypothesized that comammox N. inopinata, the only available pure culture of this group of microorganisms, may be inhibited by illumination in a similar manner. We evaluated the impact of light intensity, wavelength, and duration on the degree of photoinhibition for cultures of the comammox species N. inopinata and the soil ammonia-oxidizing archaea Nitrososphaera viennensis. Both species were highly sensitive to light. Interestingly, mimicking diurnal light exposure caused an uncoupling of ammonia and nitrite oxidation in N. inopinata, indicating nitrite oxidation might be more sensitive to light exposure than ammonia oxidation. It is likely that light influences comammox spatial distribution in natural environments such as surface fresh waters according to diurnal cycles, light attenuation coefficients, and the light penetration depths. Our findings therefore provide ecophysiological insights for further studies on comammox both in field and laboratory settings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

High Synteny and Sequence Identity between Genomes of Nitrosococcus oceani Strains Isolated from Different Oceanic Gyres Reveals Genome Economization and Autochthonous Clonal Evolution

The ammonia-oxidizing obligate aerobic chemolithoautotrophic gammaproteobacterium, Nitrosococcus oceani, is omnipresent in the world’s oceans and as such important to the global nitrogen cycle. We generated and compared high quality draft genome sequences of N. oceani strains isolated from the Northeast (AFC27) and Southeast (AFC132) Pacific Ocean and the coastal waters near Barbados at the interface between the Caribbean Sea and the North Atlantic Ocean (C-27) with the recently published Draft Genome Sequence of N. oceani Strain NS58 (West Pacific Ocean) and the complete genome sequence of N. oceani C-107, the type strain (ATCC 19707) isolated from the open North Atlantic, with the goal to identify indicators for the evolutionary origin of the species. The genomes of strains C–107, NS58, C-27, and AFC27 were highly conserved in content and synteny, and these four genomes contained one nearly sequence-identical plasmid. The genome of strain AFC132 revealed the presence of genetic inventory unknown from other marine ammonia-oxidizing bacteria such as genes encoding NiFe-hydrogenase and a non-ribosomal peptide synthetase (NRPS)-like siderophore biosynthesis module. Comparative genome analysis in context with the literature suggests that AFC132 represents a metabolically more diverse ancestral lineage to the other strains with C-107 and NS58 potentially being the youngest. The results suggest that the N. oceani species evolved by genome economization characterized by the loss of genes encoding catabolic diversity while acquiring a higher redundancy in inventory dedicated to nitrogen catabolism, both of which could have been facilitated by their rich complements of CRISPR/Cas and Restriction Modification systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Manganese concentration influences nitrogen cycling in agricultural soil

Manganese (Mn) can modulate nitrogen (N) transformations in soil, yet its role in agroecosystems remains understudied. We conducted a 51-day microcosm incubation with agricultural soils differing in long-term N history (N 0 , no added N; N 1 , added 225 kg N ha −1 for a duration of 27 years) and amended with soluble Mn at 0 (M 0 ), 50 (M 1 ), or 250 (M 2 ) mg kg −1 and Glyceria striata (Lam.) residue. In N 1 soils, Mn additions (both M 1 and M 2 ) lowered total mineral N by 25 % relative to N 1 M 0 at day 51 and reduced 51-day cumulative N₂O by 32 % (N 1 M 1 ) and 42 % (N 1 M 2 ) vs. N 1 M 0 , whereas effects in N 0 were negligible. Mn also depressed ammonia-oxidizing bacterial amoA gene transcripts at day 15 in N 1 M 2 vs. N 1 M 0 (2.5 fold change). This reduction was likely due to increased N loss via complete denitrification to N₂ through microbial pathways such as nitrate/nitrite-dependent manganese oxidation (NDMO), where bacteria directly used the added Mn 2+ to reduce nitrate (NO 3 − ) and nitrite (NO 2 − ) to N 2 or as Mn dependent-ammonia oxidation (Mnammox) where bacteria oxidized ammonium (NH 4 + ) to N 2 , using Mn oxides as electron acceptors that formed from the oxidation of the added Mn. Other contributing mechanisms may include Mn-induced N immobilization, toxicity, and changes in the microbial community. These mechanistic results indicate that background Mn availability and redox dynamics can shape nitrification–denitrification pathways under N-rich conditions. In conclusion, we highlight how native Mn pools and redox state may help explain observed variability in N losses and greenhouse gas production across agricultural soils.

Decomposition↗