Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira

The functional dominance and metabolic diversity of comammox Nitrospira in recirculating aquaculture systems

As a newly discovered group of ammonia-oxidizing microorganisms, complete ammonia oxidizing (comammox) Nitrospira has been widely found in various oligotrophic ecosystems. However, their activity and ecological niche is still unclear in recirculating aquaculture systems (RAS). This study aimed to compare the abundance and activity of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), and elucidate metabolic versatility of comammox Nitrospira in RAS. Quantitative PCR (qPCR) results showed that either comammox Nitrospira or AOB numerically predominated, while comammox Nitrospira and AOA shared similar low ammonia niches. Specifically, DNA-based stable isotope probing in conjunction with high-throughput 16S rRNA gene amplicon sequencing revealed that comammox Nitrospira accounted for 79.1 %, 97.5 %, 91.9 % and 97.6 % in the active ammonia-oxidizing community in four selected typical samples representing high abundance of comammox, AOA, and AOB, respectively. Phylogenetic analysis of heavy fraction DNA further identified novel comammox species from Nitrospira nitrificans cluster and clade A.2 acting as active species in different freshwater aquariums. Moreover, metagenome-assembled genome analysis revealed them as novel species with stress resistance and metabolic diversity compared with known comammox Nitrospira. This study underscores the dominant role of comammox Nitrospira as active ammonia-oxidizers in RAS and presents two novel comammox MAGs with metabolic flexibility, enriching our understanding of the nitrification process in oligotrophic artificial ecosystems.

Comammox Nitrospira are the dominant ammonia oxidizers in the Yangtze estuarine biofilms

Biofilms are indispensable ecological habitats for microbes that have garnered global attention and play a potential role in influencing the biogeochemical cycling of nitrogen. However, the biogeochemical significance of biofilms and the mechanisms by which they regulate nitrogen cycling remain elusive. In this study, we utilized DNA-stable isotope probing (DNA-SIP) labelling techniques in conjunction with metagenomics to reveal a nitrifying ecological niche in biofilms taken from the Yangtze Estuary, with those from sediment and water samples for comparison. Quantitative analysis showed that the amoA gene abundance of comammox Nitrospira (2.3 × 103 copies ng-1 DNA) was significantly higher than that of ammonia-oxidizing archaea (AOA-amoA, 62.4 copies ng-1 DNA) and ammonia-oxidizing bacteria (AOB-amoA, 218.1 copies ng-1 DNA) in biofilms, and the average abundance of comammox Nitrospira showed the following order: water > biofilm > sediment. Moreover, the NOB nxrB gene was more abundant than the amoA gene of ammonia oxidizers in all three media. DNA-SIP further revealed that the active comammox Nitrospira clade A mediates the nitrification process in biofilms with peak abundance at a buoyant density of 1.715 g mL-1. Active nitrifying bacteria exhibit metabolic diversity in both biofilms and sediments, and occupy unique nitrifying ecological niches. Additionally, the co-occurrence network showed that chlorophyll a, NO3- and salinity emerged as the predominant physicochemical factors affecting the nitrogen transformation genes in biofilms. Taken together, this study indicates that biofilms constitute an emerging nitrifying ecological niche in estuarine environments and deepens our understanding of the mechanisms by which biofilms function in marine biogeochemistry.

Exploring the enzymatic repertoires of Bacteria and Archaea and their associations with metabolic maps

The evolution, survival, and adaptation of microbes are consequences of gene duplication, acquisition, and divergence in response to environmental challenges. In this context, enzymes play a central role in the evolution of organisms, because they are fundamental in cell metabolism. Here, we analyzed the enzymatic repertoire in 6,467 microbial genomes, including their abundances, and their associations with metabolic maps. We found that the enzymes follow a power-law distribution, in relation to the genome sizes. Therefore, we evaluated the total proportion enzymatic classes in relation to the genomes, identifying a descending-order proportion: transferases (EC:2.-), hydrolases (EC:3.-), oxidoreductases (EC:1.-), ligases (EC:6.-), lyases (EC:4.-), isomerases (EC:5.-), and translocases (EC:7-.). In addition, we identified a preferential use of enzymatic classes in metabolism pathways for xenobiotics, cofactors and vitamins, carbohydrates, amino acids, glycans, and energy. Therefore, this analysis provides clues about the functional constraints associated with the enzymatic repertoire of functions in Bacteria and Archaea.

Microbial and mineralogical characterization of the alkaline Chae Son hot spring, Northern Thailand

Early characterizations by morphological identification through light microscopy only revealed the presence of a few microbial lineages and the majority of microbial community at the Chae Son hot spring remains uncharacterized. Therefore, this study aims to examine thermophilic microbial communities at the Chae Son hot spring using next-generation sequencing, including investigating hot spring mineralogy. Results suggest that the Chae Son hot spring (49-75 °C, pH = 6.5-7.0) precipitates digitate structures which comprise mainly silica, and that microbial permineralization is primarily through silicification. Alternating layers of mineralized microbial biofilms and silica were observed in digitate sinter cross-sections, contributing to the build-up of microstromatolites. Molecular results revealed that phylogenetically distinct members of photoautotrophic taxa, Chloroflexota and Cyanobacteriota, dominated spring microbial communities (63.19% relative abundance). Potential primary production processes were mainly through photoautotrophy, with minor lithoautotrophic activities (e.g., sulfur cycling and nitrogen cycling). Moreover, overall microbial community and Cyanobacteriota population alpha diversities significantly decreased with increased temperatures. However, no significant correlation was identified between Chloroflexota population diversity and temperatures. This study provides an update on the microbial community using a high-throughput next-generation sequencing technology, including the mineralogy of the Chae Son hot spring, Northern Thailand.

Enhancing Photosynthetic Carbon Transport in Rice Plant Optimizes Rhizosphere Bacterial Community in Saline Soil

Saline soils exert persistent salt stress on plants that inhibits their ability to carry out photosynthesis and leads to photosynthetic carbon (C) scarcity in plant roots and the rhizosphere. However, it remains unclear how a rhizosphere environment is shaped by photosynthetic C partitioning under saline conditions. Given that sucrose is the primary form of photosynthetic C transport, we, respectively, created sucrose transport distorted (STD) and enhanced (STE) rice lines through targeted mutation and overexpression of the sucrose transporter gene OsSUT5. This approach allowed us to investigate different scenarios of photosynthate partitioning to the rhizosphere. Compared to the non-saline soil, we found a significant decrease in soil dissolved organic carbon (DOC) in the rhizosphere, associated with a reduction in bacterial diversity when rice plants were grown under moderate saline conditions. These phenomena were sharpened with STD plants but were largely alleviated in the rhizosphere of STE plants, in which the rhizosphere DOC, and the diversity and abundances of dominant bacterial phyla were measured at comparable levels to the wildtype plants under non-saline conditions. The complexity of bacteria showed a greater level in the rhizosphere of STE plants grown under saline conditions. Several salt-tolerant genera, such as Halobacteroidaceae and Zixibacteria, were found to colonize the rhizosphere of STE plants that could contribute to improved rice growth under persistent saline stresses, due to an increase in C deposition.

Comprehensive evaluation of primer pairs targeting the ammonia monooxygenase subunit A gene of complete ammonia-oxidizing Nitrospira

Since the discovery of complete ammonia oxidizers (comammox) within the genus Nitrospira, their distribution and abundance across habitats have been intensively studied to better understand their ecological significance. Many primers targeting their ammonia monooxygenase subunit A gene (amoA) have been designed to detect and quantify comammox bacteria and to describe their community structure. We identified 38 published primers, but only few had high coverage and specificity for all known comammox Nitrospira or one of the two described subclades. For each target group, we comprehensively evaluated selected primer pairs using in silico analyses, endpoint PCRs, qPCRs, and amplicon sequencing on samples from various environments. Endpoint PCRs and qPCRs showed that the most commonly used primer pairs (comaA-244F/659R, comaB-244F/659R, and Ntsp-amoA162F/359R) produced several bands, which likely inflated quantifications via qPCR. In contrast, the recently published primer combinations CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R resulted mostly in a single band. Furthermore, amplicon sequencing demonstrated that these primer combinations also captured the highest richness of comammox Nitrospira. Taken together, our results indicate that few existing comammox amoA primer combinations have both high specificity and coverage and that the choice of these high-specificity and high-coverage primer pairs substantially impacts the accurate detection, quantification, and community description of comammox bacteria. We, therefore, recommend using the CA377F/C576R, CB377F/C576R, and CA-CB377F/C576R primer pairs.IMPORTANCEBacteria that can fully convert ammonia via nitrite to nitrate, the complete ammonia oxidizers (comammox), were recently discovered and are found in many natural and engineered environments. PCR-based tools to study their abundance and diversity were rapidly developed, resulting in a plethora of primers available, many of which are widely used. The presence of comammox bacteria in an environment can, however, only be correctly determined if the used primers detect all members of this group while not detecting any other guilds. This study assesses the coverage and specificity of existing primers targeting comammox bacteria using both computational and standard molecular techniques, revealing large differences in their performance. The uniform usage of well-performing primers across studies could aid in generating comparable and generalizable data to better understand the importance of comammox bacteria in the environment.

Comammox rather than AOB dominated the efficient autotrophic nitrification-denitrification process in an extremely oxygen-limited environment

The discovery of complete ammonia oxidizer (comammox) has challenged the traditional understanding of the two-step nitrification process. However, their functions in the oxygen-limited autotrophic nitrification-denitrification (OLAND) process remain unclear. In this study, OLAND was achieved using comammox-dominated nitrifying bacteria in an extremely oxygen-limited environment with a dissolved oxygen concentrations of 0.05 mg/L. The ammonia removal efficiency exceeded 97 %, and the total nitrogen removal efficiency reached 71 % when sodium bicarbonate was used as the carbon source. The pseudo-first- and second-order models were found to best fit the ammonia removal processes under low and high loads, respectively, suggesting distinct ammonia removal pathways. Full-length 16S rRNA gene sequencing and metagenomic results revealed that comammox-dominated under different oxygen levels, in conjunction with anammox and heterotrophic denitrifiers. The abundance of enzymes involved in energy metabolism indicates the coexistence of anammox and autotrophic nitrification-heterotrophic denitrification pathways. The binning results showed that comammox bacteria engaged in horizontal gene transfer with nitrifiers, anammox bacteria, and denitrifiers to adapt to an obligate environments. Therefore, this study demonstrated that comammox, anammox, and heterotrophic denitrifiers play important roles in the OLAND process and provide a reference for further reducing aeration energy in the autotrophic nitrogen removal process.

In-situ rapid cultivation of aerobic granular sludge in A/O bioreactor by using Ca(ClO)2 pretreating sludge

The efficient utilization of residual sludge and the rapid cultivation of aerobic granular sludge in continuous-flow engineering applications present significant challenges. In this study, aerobic granular cultivation was fostered in a continuous-flow system using Ca(ClO)2-sludge carbon (Ca-SC). Ca-SC retained the original sludge properties, contributing to granular growth in an A/O bioreactor. By day 40, the granule diameters increased to 0.8 mm with the SVI30 decreased by 2.7 times. Moreover, Ca-SC facilitated protein secretion, reaching 98.06 mg/g VSS and enhanced the hydrophobicity to 68.4 %. The continuous-flow aerobic granular sludge exhibited a nutrient removal rate above 90 %. Furthermore, Tessaracoccus and Nitrospira were enriched to promote granular formation and nitrogen removal. The residual sludge was carbonized and reused in the traditional wastewater treatment process to culture granular sludge in situ, aiming to achieve "self-production and self-consumption" of sludge and promote the innovative model of "treating waste with waste" in urban sewage environmental restoration.

Role of comammox bacteria in granular bioreactor for nitrogen removal via partial nitritation/anammox

In this study, two bioprocess models were first constructed with the newly-discovered comammox process described as one-step and two-step nitrification and evaluated against relevant experimental data. The validated models were then applied to reveal the potential effect of comammox bacteria on the granular bioreactor particularly suitable for undertaking partial nitritation/anammox (PN/A) under different operating conditions of bulk dissolved oxygen (DO) and influent NH4+. The results showed although comammox bacteria-based PN/A could achieve > 80.0 % total nitrogen (TN) removal over a relatively wider range of bulk DO and influent NH4+ (i.e., 0.25-0.40 g-O2/m3 and 470-870 g-N/m3, respectively) without significant nitrous oxide (N2O) production (< 0.1 %), the bulk DO should be finely controlled based on the influent NH4+ to avoid the undesired full nitrification by comammox bacteria. Comparatively, conventional ammonium-oxidizing bacteria (AOB)-based PN/A not only required higher bulk DO to achieve > 80.0 % TN removal but also suffered from 1.7 %∼2.8 % N2O production.

A critical review of comammox and synergistic nitrogen removal coupling anammox: Mechanisms and regulatory strategies

Nitrification is highly crucial for both anammox systems and the global nitrogen cycle. The discovery of complete ammonia oxidation (comammox) challenges the inherent concept of nitrification as a two-step process. Its wide distribution, adaptability to low substrate environments, low sludge production, and low greenhouse gas emissions may make it a promising new nitrogen removal treatment process. Meanwhile, anammox technology is considered the most suitable process for future wastewater treatment. The diverse metabolic capabilities and similar ecological niches of comammox bacteria and anammox bacteria are expected to achieve synergistic nitrogen removal within a single system. However, previous studies have overlooked the existence of comammox, and it is necessary to re-evaluate the conclusions drawn. This paper outlined the ecophysiological characteristics of comammox bacteria and summarized the environmental factors affecting their growth. Furthermore, it focused on the enrichment, regulatory strategies, and nitrogen removal mechanisms of comammox and anammox, with a comparative analysis of hydroxylamine, a particular intermediate product. Overall, this is the first critical overview of the conclusions drawn from the last few years of research on comammox-anammox, highlighting possible next steps for research.

Genotypic Identification of Trees Using DNA Barcodes and Microbiome Analysis of Rhizosphere Microbial Communities

DNA barcodes can provide accurate identification of plants. We used previously reported DNA primers targeting the internal transcribed spacer (ITS1) region of the nuclear ribosomal cistron, internal transcribed spacer (ITS2), and chloroplast trnL (UAA) intron to identify four trees at Bergen Community College. Two of the four trees were identified as Acer rubrum and Fagus sylvatica. However, Quercus was only identified at the genus level, and the fourth tree did not show similar identification between barcodes. Next-generation sequencing of 16S rRNA genes showed that the predominant bacterial communities in the rhizosphere mainly consisted of the Pseudomonadota, Actinomycetota, Bacteroidota, and Acidobacteriota. A. rubrum showed the most diverse bacterial community while F. sylvatica was less diverse. The genus Rhodoplanes showed the highest relative bacterial abundance in all trees. Fungal ITS sequence analysis demonstrated that the communities predominantly consisted of the Ascomycota and Basidiomycota. Quercus showed the highest fungi diversity while F. sylvatica showed the lowest. Russula showed the highest abundance of fungi genera. Average similarity values in the rhizosphere for fungi communities at the phylum level were higher than for bacteria. However, at the genus level, bacterial communities showed higher similarities than fungi. Similarity values decreased at lower taxonomical levels for both bacteria and fungi, indicating each tree has selected for specific bacterial and fungal communities. This study confirmed the distinctiveness of the microbial communities in the rhizosphere of each tree and their importance in sustaining and supporting viability and growth but also demonstrating the limitations of DNA barcoding with the primers used in this study to identify genus and species for some of the trees. The optimization of DNA barcoding will require additional DNA sequences to enhance the resolution and identification of trees at the study site.

Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil

Introduction

Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study.

Methods

The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing.

Results and Discussion

The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.

Abundance, diversity and physiological preferences of comammox Nitrospira in urban groundwater

Complete ammonia oxidizer (comammox Nitrospira), catalyze complete nitrification process in a single organism, are frequently detected in groundwater ecosystem. However, the ecological niches and environmental driving factors of comammox Nitrospira in urban groundwater are largely unknown. Here we investigated the communities of ammonia oxidizers in urban groundwater located in Shanghai city, China. Quantitative analysis demonstrated the dominance of comammox Nitrospira over classical ammonia oxidizers (ammonia-oxidizing archaea and bacteria, AOA and AOB). Phylogenetic analysis showed clades B and A2 comprise the majority of comammox Nitrospira groups. Temperature was one of the most vital factors affecting comammox Nitrospira community. Furthermore, clade A comammox Nitrospira can be enriched by urea substrate, which was in line with the ability of utilizing urea by the pure clade A comammox culture Nitrospira inopinata. In addition, we observed that relatively low temperature (<20 °C) and high copper levels (>0.04 mg L-1) can stimulate the growth of comammox Nitrospira. Overall, this study revealed the presence, diversity and physiological preferences of comammox Nitrospira in urban groundwater nitrification, shedding insights on the ecological roles of comammox Nitrospira in subsurface environment.

Differential contribution of nitrifying prokaryotes to groundwater nitrification

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX ammonia monooxygenase sub-unit A (amoA) genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

Influence of double-layer filling structure on nitrogen removal and internal microbial distribution in bioretention cells

The nitrogen removal effect of traditional bioretention cells on runoff rainwater is not stable. The nitrogen removal effect of bioretention cells can be improved by setting up a layered filling structure, but the effect of changes in filling structure on the nitrogen removal process and microbial community characteristics is still unclear. Two types of porosity fillers were set up in the experiment, and a homogeneous bioretention cell and three bioretention cells with layered fillers were constructed by changing the depth range of the upper and lower layers to analyze the influence of the pore variation of different depth fillers on the nitrogen removal process and microbial community characteristics. The experimental results showed that, compared with the homogeneous filing structure, the layered filling structure can strengthen the adsorption of NH₄⁺-N and the conversion of NO₃^--N, so as to increase the removal rates of NH₄⁺-N and NO₃^--N by 20.71-81.56% and 9.25%-78.19%, respectively. Although the low porosity filler structure will reduce the nitrification activity and urease activity by 48.63%-66.68% and 8.00%-20.64% respectively, it can increase the denitrification activity by 19.14%-31.92%, thus significantly reducing the nitrate content in the filler. The low porosity filler structure can affect the growth and reproduction of various phylum bacteria such as Proteobacteria, Chloroflexi, Acidobacteria, and genus bacteria such as Nitrospira, Ellin6067, Rhizobacter, Pseudomonas, which can improve the diversity and richness of microorganisms.

Manganese-mediated ammonium removal by a bacterial consortium from wastewater: Experimental proof and biochemical mechanisms

Manganese-redox-mediated nitrogen transformation is promising for ammonium wastewater treatment. However, due to the limited contact between insoluble Mn and the microbe, extracellular electron transfer (EET) inefficiencies become a technical bottleneck in the technical practical application. To overcome this obstacle, humic acid (HA) was introduced to synthesize manganese-humic acid complex (Mn-HA) to increase Mn solubility. The TIN (Total Inorganic Nitrogen) removal rate constant k was 3.18, 1.08, 3.56, 1.13 and 1.05 times higher than CK (Control group) at 10, 15, 20, 40 and 60 mg/L influent nitrate in the MH group, respectively. Mn-HA was inferred to stimulated the nitrogen removal by providing more reaction active sites, bridging Mn-O bonds to transfer electrons and playing a redox role in the respiratory chain. A Mnammox-NDMO (manganese oxide reduction-coupled ammonium oxidation - nitrate/nitrite- dependent manganese oxidation) bacteria consortium was enriched in MH group, containing Mnammox bacteria Geothrix, Geobacter and NDMO bacteria Pseudomonas and Bacillus.

Ubiquitous occurrence and functional dominance of comammox Nitrospira in full-scale wastewater treatment plants

The recent discovery of complete ammonia oxidation (comammox) bacteria has fundamentally upended the traditional two-step nitrification conception, but their functional importance in wastewater treatment plants (WWTPs) is still poorly understood. This study investigated distributions of comammox Nitrospira, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in activated sludge samples collected from 25 full-scale WWTPs. Using quantitative PCR (qPCR) and 16S rRNA gene amplicon sequencing, our results revealed that comammox Nitrospira ubiquitously occurred in all of 25 WWTPs and even outnumbered AOB and AOA with an average abundance of 1∼183 orders of magnitude higher in 19 WWTPs. Moreover, DNA-based stable isotope probing (DNA-SIP) assays validated that comammox Nitrospira actively participated in ammonia oxidation in the three microcosms seeding with activated sludge from three typical WWTPs, in which the ratios of comammox amoA to AOB amoA were at the range of 1∼10, 10∼100 and >100, respectively. Phylogenetic analysis in heavy fractions further indicated that Nitrospira nitrosa (N. nitrosa) was the dominant and active species. We quantified the contribution of ammonia oxidizers based on the currently available kinetic parameters of the representative species and found that comammox made major contributions to ammonia oxidation than other nitrifiers (5 ∼ 106 times that of AOB). The findings not only demonstrate the ubiquitous occurrence of comammox, but also highlight their functional dominance in ammonia oxidation in WWTPs.

Replicated life-history patterns and subsurface origins of the bacterial sister phyla Nitrospirota and Nitrospinota

The phyla Nitrospirota and Nitrospinota have received significant research attention due to their unique nitrogen metabolisms important to biogeochemical and industrial processes. These phyla are common inhabitants of marine and terrestrial subsurface environments and contain members capable of diverse physiologies in addition to nitrite oxidation and complete ammonia oxidation. Here, we use phylogenomics and gene-based analysis with ancestral state reconstruction and gene-tree-species-tree reconciliation methods to investigate the life histories of these two phyla. We find that basal clades of both phyla primarily inhabit marine and terrestrial subsurface environments. The genomes of basal clades in both phyla appear smaller and more densely coded than the later-branching clades. The extant basal clades of both phyla share many traits inferred to be present in their respective common ancestors, including hydrogen, one-carbon, and sulfur-based metabolisms. Later-branching groups, namely the more frequently studied classes Nitrospiria and Nitrospinia, are both characterized by genome expansions driven by either de novo origination or laterally transferred genes that encode functions expanding their metabolic repertoire. These expansions include gene clusters that perform the unique nitrogen metabolisms that both phyla are most well known for. Our analyses support replicated evolutionary histories of these two bacterial phyla, with modern subsurface environments representing a genomic repository for the coding potential of ancestral metabolic traits.

Diversity of the Hydroxylamine Oxidoreductase (HAO) Gene and Its Enzyme Active Site in Agricultural Field Soils

Nitrification is a key process in the biogeochemical nitrogen cycle and a major emission source of the greenhouse gas nitrous oxide (N2O). The periplasmic enzyme hydroxylamine oxidoreductase (HAO) is involved in the oxidation of hydroxylamine to nitric oxide in the second step of nitrification, producing N2O as a byproduct. Its three-dimensional structure demonstrates that slight differences in HAO active site residues have inhibitor effects. Therefore, a more detailed understanding of the diversity of HAO active site residues in soil microorganisms is important for the development of novel nitrification inhibitors using structure-guided drug design. However, this has not yet been examined. In the present study, we investigated hao gene diversity in beta-proteobacterial ammonia-oxidizing bacteria (β-AOB) and complete ammonia-oxidizing (comammox; Nitrospira spp.) bacteria in agricultural fields using a clone library ana-lysis. A total of 1,949 hao gene sequences revealed that hao gene diversity in β-AOB and comammox bacteria was affected by the fertilizer treatment and field type, respectively. Moreover, hao sequences showed the almost complete conservation of the six HAO active site residues in both β-AOB and comammox bacteria. The diversity of nitrifying bacteria showed similarity between hao and amoA genes. The nxrB amplicon sequence revealed the dominance of Nitrospira cluster II in tea field soils. The present study is the first to reveal hao gene diversity in agricultural soils, which will accelerate the efficient screening of HAO inhibitors and evaluations of their suppressive effects on nitrification in agricultural soils.