Ammonia-oxidizing Archaea Research Articles

"Ca. Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres.

Ammonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the "Ca. Nitrosocosmicus" clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that "Ca. Nitrosocosmicus" may be an important clade of AOA with potential AOA-plant interaction.

Growth of soil ammonia-oxidizing archaea on air-exposed solid surface.

Soil microorganisms often thrive as microcolonies or biofilms within pores of soil aggregates exposed to the soil atmosphere. However, previous studies on the physiology of soil ammonia-oxidizing microorganisms (AOMs), which play a critical role in the nitrogen cycle, were primarily conducted using freely suspended AOM cells (planktonic cells) in liquid media. In this study, we examined the growth of two representative soil ammonia-oxidizing archaea (AOA), Nitrososphaera viennensis EN76 and "Nitrosotenuis chungbukensis" MY2, and a soil ammonia-oxidizing bacterium, Nitrosomonas europaea ATCC 19718 on polycarbonate membrane filters floated on liquid media to observe their adaptation to air-exposed solid surfaces. Interestingly, ammonia oxidation activities of N. viennensis EN76 and "N. chungbukensis" MY2 were significantly repressed on floating filters compared to the freely suspended cells in liquid media. Conversely, the ammonia oxidation activity of N. europaea ATCC 19718 was comparable on floating filters and liquid media. N. viennensis EN76 and N. europaea ATCC 19718 developed microcolonies on floating filters. Transcriptome analysis of N. viennensis EN76 floating filter-grown cells revealed upregulation of unique sets of genes for cell wall and extracellular polymeric substance biosynthesis, ammonia oxidation (including ammonia monooxygenase subunit C (amoC3) and multicopper oxidases), and defense against H2O2-induced oxidative stress. These genes may play a pivotal role in adapting AOA to air-exposed solid surfaces. Furthermore, the floating filter technique resulted in the enrichment of distinct soil AOA communities dominated by the "Ca. Nitrosocosmicus" clade. Overall, this study sheds light on distinct adaptive mechanisms governing AOA growth on air-exposed solid surfaces.

Activity of novel virus families infecting soil nitrifiers is concomitant with host niche differentiation.

Chemolithoautotrophic nitrifiers are model groups for linking phylogeny, evolution, and ecophysiology. Ammonia-oxidising bacteria (AOB) typically dominate the first step of ammonia oxidation at high ammonium supply rates, ammonia-oxidising archaea (AOA) and complete ammonia-oxidising Nitrospira (comammox) are often active at lower supply rates or during AOB inactivity, and nitrite-oxidising bacteria (NOB) complete canonical nitrification. Soil virus communities are dynamic but contributions to functional processes are largely undetermined. In addition, characterising viruses infecting hosts with low relative abundance, such as nitrifiers, may be constrained by vast viral diversity, partial genome recovery, and difficulties in host linkage. Here, we describe a targeted incubation study that aimed to determine whether growth of different nitrifier groups in soil is associated with active virus populations and if process-focussed analyses facilitate characterisation of high-quality virus genomes. dsDNA viruses infecting different nitrifier groups were enriched in situ via differential host inhibition. Growth of each nitrifier group was consistent with predicted inhibition profiles and concomitant with the abundance of their viruses. These included 61 high-quality/complete virus genomes 35-173kb in length with minimal similarity to validated families. AOA viruses lacked ammonia monooxygenase sub-unit C (amoC) genes found in marine AOA viruses but some encoded AOA-specific multicopper oxidase type 1 (MCO1), previously implicated in copper acquisition, and suggesting a role in supporting energy metabolism of soil AOA. Findings demonstrate focussed incubation studies facilitate characterisation of active host-virus interactions associated with specific processes and viruses of soil AOA, AOB and NOB are dynamic and potentially influence nitrogen cycling processes.

Effects of Vegetable Planting Ages on Community Structure of Ammonia-oxidizing Archaea and Ammonia-oxidizing Bacteria in Greenhouse Vegetable Fields

The ammonia oxidation process driven by microorganisms is a dominant source for nitrous oxide （N2O） emissions. Here, we examined the influence of greenhouse vegetable planting ages on soil ammonia-oxidizing archaea （AOA） and ammonia-oxidizing bacteria （AOB）, which is of great significance for assessing the soil quality status and greenhouse gas transformations. A field study was conducted at different times （1, 5, 10, and 20 a） in greenhouse vegetable soils of Gaoyi, Hebei Province. Chemical analysis and Illumina NovaSeq high-throughput sequencing were used to analyze the soil physicochemical properties and community structures and diversity of AOA and AOB. The variation in AOA and AOB communities and the driving factors in greenhouse soils at different ages were also investigated. The results showed that the contents of total nitrogen, organic matter, alkali-hydrolyzable nitrogen, available phosphorus, and available potassium first increased and then decreased with the prolongation of growth. The contents of nitrate nitrogen, ammonium nitrogen, and electrical conductivity first decreased and then increased with the prolongation of growth. The pH value of soils decreased with the prolongation of growth. The abundance and diversity index of AOA and AOB first decreased and then increased with the prolongation of growth. Nitrososphaeria, unclassified Thaumarchaeota, and Candidatus Nitrosocaldus were the dominant species of AOA, while Betaproteobacteria and Nitrosospira were the dominant species of AOB. The composition of the soil AOA community varied greatly compared to that of AOB with the prolongation of growth. Correlation analysis showed that the changes in soil nutrient factors had a significant correlation with AOA and AOB communities. Redundancy analysis indicated that ammonium nitrogen, alkali-hydrolyzable nitrogen, and nitrate nitrogen were key factors of AOA communities, while electrical conductivity, available potassium, and nitrate nitrogen were key factors for AOB. In summary, long-term planting of greenhouse vegetables significantly affected the abundance and composition of soil AOA and AOB communities. Our results provide a theoretical basis for further studies on the greenhouse gas transformation and microbial mechanisms of the nitrogen cycle in greenhouse soils.

Shore-to-water spatial variations of complete ammonia oxidizers in a lake in Wuhan, China

Complete ammonia oxidizers (comammox bacteria) can convert ammonia into nitric acid through single-step nitrification. This study explored the spatial variations of comammox bacteria in the lakeshore area of the Houguan Lake in Wuhan, China. The abundance of the two comammox bacteria clades and two traditional ammonia-oxidizing microorganisms, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), generally showed a gradually decreasing trend from the shore to the water. Moreover, a similar decreasing trend was observed for the respective and total nitrification rate of three types of ammonia-oxidizing microorganisms. The average nitrification rate of AOA, AOB and comammox bacteria was 0.568, 0.718, and 0.935 mg N kg−1 d−1, respectively. Besides, comammox bacteria exhibited a high biological diversity, with clade A and clade B and three subclades of clade A all present. Among different clades, clade B played a dominant role in the ammonia oxidation process. Both the abundance and nitrification rate of comammox bacteria were significantly positively correlated with total carbon and total nitrogen, indicating that these two nutrient substances are important factors influencing this microorganism. Our results demonstrate that the spatial variations of environmental elements in the lakeshore area lead to gradual decreases of comammox bacteria from the shore to the water.

Adaptive traits of Nitrosocosmicus clade ammonia-oxidizing archaea.

Nitrification is a vital process within the global biogeochemical nitrogen cycle but plays a significant role in the eutrophication of aquatic ecosystems and the production of the greenhouse gas nitrous oxide (N2O) from industrial agriculture ecosystems. While various types of ammonia-oxidizing microorganisms play a critical role in the N cycle, ammonia-oxidizing archaea (AOA) are often the most abundant nitrifiers in natural environments. Members of the genus Nitrosocosmicus are one of the prevalent AOA groups detected in undisturbed terrestrial ecosystems and have previously been reported to possess a range of physiological characteristics that set their physiology apart from other AOA species. This study provides significant progress in understanding these unique physiological traits and their genetic drivers. Our results highlight how physiological studies based on comparative genomics-driven hypotheses can contribute to understanding the unique niche of Nitrosocosmicus AOA.

Maize–peanut intercropping and N fertilization changed the potential nitrification rate by regulating the ratio of AOB to AOA in soils

Maize–peanut intercropping could potentially mitigate nitrogen (N) loss from the soil, a process primarily governed by the net nitrification rate. However, the impact of maize–peanut intercropping on the potential nitrification rate (PNR) and its relationships with key players, such as ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), are not well understood. Herein, we conducted a field experiment involving two management systems and two crops, namely, maize (MPm) and peanut (MPp) intercropping, maize monoculture (MM), and peanut monoculture (PM), under three N fertilization rates (no N fertilization, 150 kg N ha−1, and 300 kg N ha−1). Under intercropping (MPm and MPp), the abundance of AOA amoA gene increased by 64.8% and 60.3% and the abundance of AOB amoA gene increased by 63.2% and 68.2% compared to the MM and PM monoculture systems, respectively. Furthermore, the abundances of AOA and AOB decreased in MPp and MM, while AOB increased in MPm and PM across the N fertilization gradient. The PNR increased corresponding to the N fertilization rates, with intercropping enhancing the PNR in peanut-planted soil but reducing the PNR in maize-planted soil compared to monocropping. Notably, no significant positive relationship between the abundances of AOA or AOB and the PNR. Random forest analysis indicated that the AOB/AOA ratio was an important predictor of the PNR. N fertilization and intercropping regulated the AOB/AOA ratio mainly through controlling the ammonia content and the soil C/N, respectively. These findings highlight the substantial impacts of N fertilization and intercropping on PNR, with the AOB/AOA ratio emerging as a valuable predictive indicator for the PNR.

Contrasting nitrogen dynamics across the Mid‐Atlantic Bight shelfbreak front: Insights from nitrate dual isotopes and nitrifier gene abundance

AbstractObservations and model studies suggest that front dynamics can enhance phytoplankton productivity. This study tested whether frontal systems also increase the abundance of nitrifying microbes and nitrogen recycling during repeat sampling transects across the Mid‐Atlantic Bight shelfbreak in July 2019. We measured ammonium concentrations, nitrate dual isotopes (δ15N, δ18O), and ammonia monooxygenase subunit A (amoA) genes of ammonia‐oxidizing archaea (AOA) and bacteria (AOB). In subsurface shelf waters, ammonium concentrations exceeded 2 μmol L−1, due to a temporary imbalance in regeneration from sinking particles and subsequent nitrification. The inverse correlation between nitrate δ15N values and ammonium concentrations confirmed nitrate was partially or entirely from local nitrification on the shelf. In contrast, the shelfbreak frontal zone and slope sea subsurface waters had much lower ammonium concentrations (0.1–0.2 μmol L−1) due to tight coupling between ammonium regeneration and nitrification. The deviation of nitrate δ15N and δ18O from algal uptake‐driven 1 : 1 ratio suggests concurrent nitrification in the euphotic zone. The shelfbreak front acted as an ecological boundary where AOA and AOB amoA gene numbers were partitioned, with AOAs abounding in slope waters and AOBs in shelf waters, likely due to ammonium availability. At certain slope stations, deep‐water nutrient inputs via isopycnal lifting induced by Gulf Stream intrusions caused unexpectedly high phytoplankton biomass, which doubled nitrifier abundance and potentially stimulated both ammonium regeneration and nitrification. These findings demonstrate distinct distributions of nitrifying microbes along the salinity gradient from shelf to slope and highlight the significant influence of coastal ocean‐western boundary current interactions on nitrogen biogeochemistry.

Organic fertilizer significantly mitigates N2O emissions while increase contributed of comammox Nitrospira in paddy soils

Nitrification is the dominant process for nitrous oxide (N2O) production under aerobic conditions, but the relative contribution of the autotrophic nitrifiers (the ammonia-oxidising archaea (AOA), the ammonia-oxidising bacteria (AOB) and the comammox) to this process is still unclear in some soil types. This is particularly the case in paddy soils under different fertilization regimes. We investigated active nitrifiers and their contribution to nitrification and N2O production in a range of unfertilized and fertilized paddy soils, using 13CO2-DNA based stable isotope probing (SIP) technique combined with a series of specific nitrification inhibitors, including acetylene (C2H2), 3, 4-dimethylpyrazole phosphate (DMPP) and 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide (PTIO). The soils had a long-term history of fertilizer application, including chemical fertilizer only, a mixture of chemical fertilizers (70 %) and chicken manure (30 %) or a mixture of rice straw and chemical fertilizers. 13CO2-DNA-SIP and Illumina MiSeq sequencing demonstrated that comammox clades A.1 and B were active nitrifiers in all fertilized paddy soils. Inhibitor experiment showed that AOB largely contributed to nitrification activity and N2O emission in all paddy soils, while comammox contribution was more significant than AOA. Fertilization considerably altered nitrifiers' relative contribution to nitrification activity and N2O emissions. Applying organic fertilizers significantly decreased the N2O emissions but increased the contribution of comammox to the process. These findings expand the functional ecological niche of comammox, revealing their nitrification role and N2O production in other ecosystems than oligotrophic habitats.

The herbicidal activity of pre-emergence herbicide cinmethylin and its potential risks on soil ecology: pH, enzyme activities and bacterial community

BackgroundThe herbicide cinmethylin, which was originally registered for use in rice fields, has the potential to control grass weeds in wheat fields before the emergence of wheat. However, its herbicidal activity against various troublesome grass weeds that infest wheat fields in China and its relationships with soil pH, soil enzymes and soil bacteria are not well known. Here, the effects of applying cinmethylin on the soil surface were tested on six grass weeds, and its impacts on soil characteristics, including the soil pH, soil enzymes and bacterial community, were evaluated.ResultsAlopecurus aequalis, A. japonicus and A. myosuroides were highly sensitive to cinmethylin, with GR50 values of 78.77, 61.49 and 119.67 g a.i. ha− 1, respectively. The half-lives of cinmethylin at 1-, 10- and 100-fold the recommended rates were estimated at 26.46 − 52.33 d. Cinmethylin significantly increased the soil pH but decreased the activities of soil sucrase and urease. At 10- and 100-fold the recommended rate of cinmethylin, the bacterial abundance and diversity significantly decreased at 30 and 60 days after cinmethylin treatment. Cinmethylin at 100-fold the recommended rates largely promoted bacterial co-occurrence network complexity. Cinmethylin at high concentrations temporarily inhibited the abundance of the Nitrospira genus, as indicated by the copy numbers of the ammonia-oxidising archaea (AOA) amoA and ammonia-oxidising bacteria (AOB) amoA genes. Further analysis revealed that soil pH was negatively related to soil urease, and a significantly positive correlation was detected between soil urease and soil nitrification.ConclusionCollectively, the application of cinmethylin at the recommended field dose had nearly no effect on the soil ecosystem, but its potential risks at high concentrations deserve further attention.

Nitrous oxide production and consumption by marine ammonia-oxidizing archaea under oxygen depletion.

Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle and among the most abundant microorganisms in the ocean, thriving even in oxygen-depleted ecosystems. AOA produce the greenhouse gas nitrous oxide (N2O) as a byproduct of ammonia oxidation. Additionally, the recent discovery of a nitric oxide dismutation pathway in the AOA isolate Nitrosopumilus maritimus points toward other N2O production and consumption pathways in AOA. AOA that perform NO dismutation when exposed to oxygen depletion, produce oxygen and dinitrogen as final products. Based on the transient accumulation of N2O coupled with oxygen accumulation, N2O has been proposed as an intermediate in this novel archaeal pathway. In this study, we spiked N2O to oxygen-depleted incubations with pure cultures of two marine AOA isolates that were performing NO dismutation. By using combinations of N compounds with different isotopic signatures (15NO2 - pool +44N2O spike and 14NO2 - pool +46N2O spike), we evaluated the N2O spike effects on the production of oxygen and the isotopic signature of N2 and N2O. The experiments confirmed that N2O is an intermediate in NO dismutation by AOA, distinguishing it from similar pathways in other microbial clades. Furthermore, we showed that AOA rapidly reduce high concentrations of spiked N2O to N2. These findings advance our understanding of microbial N2O production and consumption in oxygen-depleted settings and highlight AOA as potentially important key players in N2O turnover.

Metabolic activities of marine ammonia-oxidizing archaea orchestrated by quorum sensing.

Ammonia-oxidizing archaea (AOA) play crucial roles in marine carbon and nitrogen cycles by fixing inorganic carbon and performing the initial step of nitrification. Evaluation of carbon and nitrogen metabolism popularly relies on functional genes such as amoA and accA. Increasing studies suggest that quorum sensing (QS) mainly studied in biofilms for bacteria may serve as a universal communication and regulatory mechanism among prokaryotes; however, this has yet to be demonstrated in marine planktonic archaea. To bridge this knowledge gap, we employed a combination of metabolic activity markers (amoA, accA, and grs) to elucidate the regulation of AOA-mediated nitrogen, carbon processes, and their interactions with the surrounding heterotrophic population. Through co-transcription investigations linking metabolic markers to potential key QS genes, we discovered that QS molecules could regulate AOA's carbon, nitrogen, and lipid metabolisms under different conditions. Interestingly, specific AOA ecotypes showed a preference for employing distinct QS systems and a distinct QS circuit involving a typical population. Overall, our data demonstrate that QS orchestrates nitrogen and carbon metabolism, including the exchange of organic metabolites between AOA and surrounding heterotrophic bacteria, which has been previously overlooked in marine AOA research.

Impact of nitrogen and phosphorus amendments on nitrogen‐cycling microbial abundances and potentials: A meta‐analysis

AbstractThe rapid increase in nitrogen (N) and phosphorus (P) availabilities in terrestrial ecosystems has led to sustained shifts in soil microbial communities and microbially‐mediated N‐cycling. However, the specific effects of N and P amendments on N‐cycling microbes are poorly understood. This meta‐analysis synthesizes the effects of N and/or P amendments on the abundances and functional potentials of N‐cycling genes involved in N₂ fixation, organic N mineralization, nitrification, and denitrification across natural ecosystems and diverse soil conditions in China. Our findings indicate that ammonia‐oxidizing bacteria (AOB) showed greater responsiveness to N amendment than ammonia‐oxidizing archaea (AOA), and AOB amoA abundance increased while AOA amoA abundance decreased with P amendments. Additionally, the abundance of nirS declined, while nirK abundance remained unresponsive to both N and P amendments. These findings highlight the distinct ecological niches occupied by microbial groups with equivalent functions in response to N and P amendments. Moreover, our findings indicate that soil N and P availabilities, along with soil acidification induced by N additions and microbial biomass carbon content, are key factors regulating N‐cycling gene abundances and potentials. The driving mechanisms for N‐cycling genes and their corresponding potentials appear to be distinct, with gene abundance showing only a limited influence on functional potentials. This suggests that factors such as soil properties and microbial community compositions may be more critical determinants of N‐cycling processes than functional gene abundances with regard to scenarios of increasing N and P deposition.

Environmental Adaptability and Roles in Ammonia Oxidation of Aerobic Ammonia-Oxidizing Microorganisms in the Surface Sediments of East China Sea.

This study investigated the community characteristics and environmental influencing factors of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the surface sediments of the East China Sea. The research found no consistent pattern in the richness and diversity of AOA and AOB with respect to the distance from the shore, indicating a complex interplay of factors. The expression levels of AOA amoA gene and AOB amoA gene in the surface sediments of the East China Sea ranged from 4.49 × 102 to 2.17 × 106 copies per gram of sediment and from 6.6 × 101 to 7.65 × 104 copies per gram of sediment, respectively. Salinity (31.77 to 34.53 PSU) and nitrate concentration (1.51 to 10.12 μmol/L) were identified as key environmental factors significantly affecting the AOA community, while salinity and temperature (13.71 to 19.50°C) were crucial for the AOB community. The study also found that AOA, dominated by the Nitrosopumilaceae family, exhibited higher gene expression levels than AOB, suggesting a more significant role in ammonia oxidation. The expression of AOB was sensitive to multiple environmental factors, indicating a responsive role in nitrogen cycles and ecosystem health. The findings contribute to a better understanding of the biogeochemical processes and ecological roles of ammonia-oxidizing microorganisms in marine sediments.

Microbiome signature of different stages of hypoxia event in Wonmun Bay

We investigated how microbial communities associated with different hypoxic stages respond to environmental changes across three water depths in Wonmun Bay, South Korea. Analysis of temperature, salinity, dissolved oxygen (DO), and nutrient concentrations revealed prominent seasonal shifts and strong stratification during summer hypoxia. Metabarcoding of prokaryotic 16 S rRNA genes and phototrophic eukaryotic chloroplasts along with quantitative PCR (qPCR) revealed variations in the abundance and composition of these communities. Chloroplast 16 S sequences in May were dominated by land plants (93% of Embryophyta), contrasting with the diverse phytoplankton taxa detected in other months. The water communities in May also had higher total microbial abundance than other months but significantly lower alpha diversity. These results suggest a major influence of freshwater discharge on water communities, pre-conditioning for hypoxia events by promoting organic matter decomposition coupled with DO consumption in bottom water. Subsequently, distinct microbial communities were observed across depths during hypoxia in June and July, while less variability was detected among different depths in September and later months when hypoxia events disappeared. Principal Coordinate analysis (PCoA) demonstrated the distinct patterns of microbial communities in May, June, and July from other months. Both sulfur-oxidizing and sulfate-reducing bacteria (SRB) were prevalent in June while the increase of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) was observed in mid and bottom water in July. This data suggests the intricate interaction between sulfur and nitrogen-cycling microbes during the hypoxia events in Wonmun Bay. In conclusion, this study provides valuable insights into the microbial community responses to the varying environmental conditions at different stages of hypoxia events in eutrophic coastal ecosystems.

Impacts of Biochar and Gypsum on Ammonia-Oxidizing Microorganisms in Coastal Saline Soil

Nitrification is the core step of the soil nitrogen cycle and directly affects the nitrogen use efficiency in agricultural systems. Biochar and gypsum are two important soil amendments widely used in coastal saline farmland. However, little is known about their effects on nitrification and ammonia-oxidizing microorganisms. A one-year pot experiment with three treatments including biochar application (BC), gypsum application (SG), and no amendment (CK) was conducted, and the responses of the nitrification rate, amoA gene copies, and the diversity and community structure of ammonia-oxidizing archaea (AOA) and bacteria (AOB) to biochar and gypsum were evaluated. The results indicated that biochar and gypsum application both resulted in alterations to the soil properties. They both had inhibiting effects on nitrification and AOB amoA gene copies, whereas they had no significant effect on AOA amoA gene copies. Biochar had no significant effect on the diversity indexes of AOA, but it significantly reduced the Shannon index of AOB. Meanwhile, gypsum had no significant influence on the diversity indexes of both AOA and AOB. Biochar and gypsum did not significantly affect the community structure of AOA but did induce changes in that of AOB. In detail, biochar significantly enhanced the relative abundance of the dominant cluster Nitrosospira, whereas gypsum led to a notable increase in the relative abundance of unclassified_o_Nitrosomonadales. The Shannon index of AOB had a significant negative correlation with soil TOC, TN, and NH4+ content, and soil pH was the first primary environmental factor that affected the AOB community structure. In conclusion, biochar and gypsum inhibited nitrification by suppressing the activities of AOB and changed the diversities and community structure of AOB by altering related soil properties.

Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers.

Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.

Dynamics and activity of an ammonia-oxidizing archaea bloom in South San Francisco Bay.

Transient or recurring blooms of ammonia-oxidizing archaea (AOA) have been reported in several estuarine and coastal environments, including recent observations of AOA blooms in South San Francisco Bay (SFB). Here, we measured nitrification rates, quantified AOA abundance, and analyzed both metagenomic and metatranscriptomic data to examine the dynamics and activity of nitrifying microorganisms over the course of an AOA bloom in South SFB during the autumn of 2018 and seasonally throughout 2019. Nitrification rates were correlated with AOA abundance in qPCR data and both increased several orders of magnitude between the autumn AOA bloom and spring and summer seasons. From bloom samples, we recovered an extremely abundant, high-quality Ca. Nitrosomarinus catalina-like AOA metagenome-assembled genome (MAG) that had high transcript abundance during the bloom and expressed >80% of genes in its genome. We also recovered a putative nitrite-oxidizing bacteria (NOB) MAG from within the Nitrospinaceae that was of much lower abundance and had lower transcript abundance than AOA. During the AOA bloom, we observed increased transcript abundance for nitrogen uptake and oxidative stress genes in non-nitrifier MAGs. This study confirms AOA are not only abundant, but also highly active during blooms oxidizing large amounts of ammonia to nitrite - a key intermediate in the microbial nitrogen cycle - and producing reactive compounds that may impact other members of the microbial community.

Community Composition and Functional Characterization of Microorganisms in Surface Sediment of the New Britain Trench.

The deep-sea harbors abundant prokaryotic biomass is a major site of organic carbon remineralization and long-term carbon burial in the ocean. Deep-sea trenches are the deepest part of the ocean, and their special geological and morphological features promoting the accumulation of organic matter and active organic carbon turnover. Despite the expanding reports about the organic matter inputs, limited information is known regarding microbial processes in deep-sea trenches. In this study, we investigated the species composition and metabolic potential in surface sediment of the New Britain Trench (NBT), using a metagenomic approach. The predominant microbial taxa in NBT sediment include Proteobacteria, Acidobacteria, Planctomycetes, Actinobacteria and Chloroflexota. The microbial communities showed highly diverse metabolic potentials. Particularly, genes encoding enzymes for degradation of aromatic compounds, as well as those encoding haloalkane dehalogenase and haloacetate dehalogenase were annotated in the NBT surface sediment, which indicate the potential of microorganisms to degrade different types of refractory organic matter. The functional genes encoding enzymes for dissimilatory nitrate reduction, denitrification, and nitrification were also represented in the NBT metagenome. Overall, the microbial communities show high diversity of heterotrophic lineages and metabolic features, supporting their potential contributions in organic carbon metabolism. Meanwhile, Nitrosopumilus, a dominant genus in the surface sediment of the NBT, is a typical ammonia-oxidizing archaea (AOA), with autotrophic CO2 fixation pathways including the 3-hydroxypropionate/4-hydroxybutylate (3HP/4HB) cycle, the reductive TCA (rTCA) cycle. The results demonstrate that autotrophic metabolic processes also play an important role in the surface sediment, by providing newly synthesized organic matter.

Comammox Nitrospira among dominant ammonia oxidizers within aquarium biofilter microbial communities.

Nitrification is a crucial process that converts toxic ammonia waste into less harmful nitrate that occurs in aquarium biofilters. Prior research found that ammonia-oxidizing archaea (AOA) were dominant over ammonia-oxidizing bacteria (AOB) in freshwater aquarium biofilters. Our study profiled microbial communities of aquarium biofilters and quantified the abundance of all currently known groups of aerobic ammonia oxidizers. The findings reveal that complete ammonia-oxidizing (comammox) Nitrospira were present in all freshwater aquarium biofilter samples in high abundance, challenging our previous understanding of aquarium nitrification. We also highlight niche adaptation of ammonia oxidizers based on salinity. The network analysis of freshwater biofilter microbial communities revealed significant positive correlations among nitrifiers and other community members, suggesting intricate interactions within biofilter communities. Overall, this study expands our understanding of nitrification in aquarium biofilters, emphasizes the role of comammox Nitrospira, and highlights the value of aquaria as microcosms for studying nitrifier ecology.