Abundance and Functional Importance of Complete Ammonia Oxidizers and Other Nitrifiers in a Riparian Ecosystem

Metagenomic insights into effects of carbon/nitrogen ratio on microbial community and antibiotic resistance in moving bed biofilm reactor

This study investigated the effects of carbon/nitrogen (C/N) ratio on microbial community in moving bed biofilm reactor (MBBR) using metagenomic analysis, and the dynamic changes of relevant antibiotic resistance genes (ARGs) were also analyzed. The results showed that under low C/N ratio, MBBR exhibited average removal rates of 98.41 % for ammonia nitrogen and 75.79 % for total nitrogen. Metagenomic analysis showed low C/N ratio altered the structure of biofilm and water microbiota, resulting in the detachment of bacteria such as Actinobacteria from biofilm into water. Furthermore, sulfamethazine (SMZ)-resistant bacteria and related ARGs were released into water under low C/N ratio, which lead to the increase of SMZ resistance rate to 90%. Moreover, most dominant genera are potential hosts for both nitrogen cycle related genes and ARGs. Specifically, Nitrosomonas that carried gene sul2 might be released from biofilm into water. These findings implied the risks of antibiotic resistance dissemination in MBBR under low C/N ratio.

Journey of the swift nitrogen transformation: Unveiling comammox from discovery to deep understanding

COMplete AMMonia OXidizer (comammox) refers to microorganisms that have the function of oxidizing NH4+ to NO3- alone. The discovery of comammox overturned the two-step theory of nitrification in the past century and triggered many important scientific questions about the nitrogen cycle in nature. This comprehensive review delves into the origin and discovery of comammox, providing a detailed account of its detection primers, clades metabolic variations, and environmental factors. An in-depth analysis of the ecological niche differentiation among ammonia oxidizers was also discussed. The intricate role of comammox in anammox systems and the relationship between comammox and nitrogen compound emissions are also discussed. Finally, the relationship between comammox and anammox is displayed, and the future research direction of comammox is prospected. This review reveals the metabolic characteristics and distribution patterns of comammox in ecosystems, providing new perspectives for understanding nitrogen cycling and microbial ecology. Additionally, it offers insights into the potential application value and prospects of comammox.

Urban and agricultural land use led to niche differentiation of AOA, AOB and comammox along the Beiyun River continuum

River ecological health has been severely threatened by anthropogenic land-use pressures. Here, by combining remote sensing and molecular biology methods, we evaluated the impact of land-use activities on nitrification, a fundamental ecological process in rivers, which is conducted by ammonia-oxidising archaea (AOA) and ammonia-oxidising bacteria (AOB), or the newly discovered complete ammonia oxidisers (comammox). We explored the relationships of the abundance, activity, and diversity of AOA, AOB, and comammox in river sediments with land-use pressure by proposing a quantitative land use pattern index (LPI) over a 184 km continuum along the Beiyun River in North China. We found that comammox dominated nitrification in the forestry upstream (67.07 % in summer, 56.40 % in winter), while AOB became the major player in the urban middle (56.51 % in summer, 53.08 % in winter) and agricultural downstream reaches (62.98 % in summer, 50.74 % in winter). In addition, urban and agricultural land use lowered the α diversity of AOA and comammox, as well as simplified their co-occurrence networks, but promoted AOB diversity and complicated their networks. The structural equation model illustrated that the key drivers affecting the key taxa and activities were ammonia, and C/N for AOB, and total organic matter, and pH for comammox. We thus conclude that watershed urban and agricultural land use drive the niche differentiation of AOA, AOB, and comammox, specifically leading to a robust AOB community but weakened AOA and comammox communities. Our study connects the macro and micro worlds and provides a new paradigm for studying the variation in microbial communities as well as the potential ecological consequences under the increased anthropogenic land-use pressures in the Anthropocene.

The significant contribution of comammox bacteria to nitrification in a constructed wetland revealed by DNA-based stable isotope probing

The discovery of Comammox bacteria (CMX) has changed our traditional concept towards nitrification, yet its role in constructed wetlands (CWs) remains unclear. This study investigated the contributions of CMX and two canonical ammonia-oxidizing microorganisms, ammonia-oxidizing bacteria (AOB) and archaea to nitrification in four regions (sediment, shoreside, adjacent soil, and water) of a typical CW using DNA-based stable isotope probing. The results revealed that CMX not only widely occurred in sediment and shoreside zones with high abundance (5.08 × 104 and 6.57 × 104 copies g-1 soil, respectively), but also actively participated in ammonia oxidation, achieving ammonia oxidation rates of 1.43 and 2.00 times that of AOB in sediment and shoreside, respectively. Phylogenetic analysis indicated that N. nitrosa was the dominant and active CMX species. These findings uncovered the crucial role of CMX in nitrification of sediment and shoreside, providing a new insight into nitrogen cycle of constructed wetlands.

Metabolic Profiles and Microbial Synergy Mechanism of Anammox Biomass Enrichment and Membrane Fouling Alleviation in the Anammox Dynamic Membrane Bioreactor

The anammox dynamic membrane bioreactor (DMBR) is promising in applications with enhanced anammox biomass enrichment and fouling alleviation. However, the metabolic mechanism underlying the functional features of anammox sludge and the biofilm membrane is still obscure. We investigated the metabolic networks of anammox sludge and membrane biofilm in the DMBR. The cooperation between anammox and dissimilatory nitrate reduction to ammonium processes favored the robust anammox process in the DMBR. The rapid bacterial growth occurred in the DMBR sludge with 1.33 times higher biomass yield compared to the MBR sludge, linked to the higher activities of lipid metabolism, nucleotide metabolism, and B vitamin-related metabolism of the DMBR sludge. The metabolism of the DMBR biofilm microbial community benefited the fouling alleviation that the abundant fermentative bacteria and their cooperation with the anammox sludge microbial community promoted organics degradation. The intensified degradation of foulants by the DMBR biofilm community was further evidenced by the active carbohydrate metabolism and the upregulated vitamin B intermediates in the biofilms of the DMBR. Our findings provide insights into key metabolic mechanisms for enhanced biomass enrichment and fouling control of the anammox DMBR, guiding manipulations and applications for overcoming anammox biomass loss in the treatment of wastewater under detrimental environmental conditions.

Effect of tillage state of paddy soils with heavy metal pollution on the nosZ gene of N2O reductase

Paddy soils are an important source of atmospheric nitrous oxide (N2O). However, numerous studies have focused on N2O production during the soil tillage period, neglecting the N2O production during the dry fallow period. In this study, we conducted an incubation experiment using the acetylene inhibition technique to investigate N2O emission and reduction rates of paddy soil profiles (0-1 m) from Guangdong Province and Jinlin Province in China, with different heavy-metal pollution levels. The abundance and community structures of denitrifying bacteria were determined via quantitative-PCR and Illumina MiSeq sequencing of nosZ, nirK, and nirS genes. Our results showed that the potential N2O emission rate, N2O production rate, and denitrification rate have decreased with increasing soil vertical depth and heavy-metal pollution. More importantly, we found that the functional gene type of N2O reductase switched with the tillage state of paddy soils, which clade Ⅱ nosZ genes were the dominant gene during the tillage period, while clade Ⅰ nosZ genes were the dominant gene during the dry fallow period. The heavy-metal pollution has less effect on the niche differentiation of the nosZ gene. The N2O emission rate was significantly regulated by the genus Bradyhizobium, which contains both N2O reductase and nitrite reductase genes. Our findings suggests that the nosZ gene of N2O reductase can significantly impact the N2O emission from paddy soils.

Multidrug-resistant plasmid RP4 inhibits the nitrogen removal capacity of ammonia-oxidizing archaea, ammonia-oxidizing bacteria, and comammox in activated sludge

In wastewater treatment plants (WWTPs), ammonia oxidation is primarily carried out by three types of ammonia oxidation microorganisms (AOMs): ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and comammox (CMX). Antibiotic resistance genes (ARGs), which pose an important public health concern, have been identified at every stage of wastewater treatment. However, few studies have focused on the impact of ARGs on ammonia removal performance. Therefore, our study sought to investigate the effect of the representative multidrug-resistant plasmid RP4 on the functional microorganisms involved in ammonia oxidation. Using an inhibitor-based method, we first evaluated the contributions of AOA, AOB, and CMX to ammonia oxidation in activated sludge, which were determined to be 13.7%, 41.1%, and 39.1%, respectively. The inhibitory effects of C2H2, C8H14, and 3,4-dimethylpyrazole phosphate (DMPP) were then validated by qPCR. After adding donor strains to the sludge, fluorescence in situ hybridization (FISH) imaging analysis demonstrated the co-localization of RP4 plasmids and all three AOMs, thus confirming the horizontal gene transfer (HGT) of the RP4 plasmid among these microorganisms. Significant inhibitory effects of the RP4 plasmid on the ammonia nitrogen consumption of AOA, AOB, and CMX were also observed, with inhibition rates of 39.7%, 36.2%, and 49.7%, respectively. Moreover, amoA expression in AOB and CMX was variably inhibited by the RP4 plasmid, whereas AOA amoA expression was not inhibited. These results demonstrate the adverse environmental effects of the RP4 plasmid and provide indirect evidence supporting plasmid-mediated conjugation transfer from bacteria to archaea.

The abundance of comammox bacteria was higher than that of ammonia-oxidizing archaea and bacteria in rhizosphere of emergent macrophytes in a typical shallow lake riparian

Complete ammonia oxidation (comammox) bacteria can complete the whole nitrification process independently, which not only challenges the classical two-step nitrification theory but also updates long-held perspective of microbial ecological relationship in nitrification process. Although comammox bacteria have been found in many ecosystems in recent years, there is still a lack of research on the comammox process in rhizosphere of emergent macrophytes in lakeshore zone. Sediment samples were collected in this study from rhizosphere, far-rhizosphere, and non-rhizosphere of emergent macrophytes along the shore of Lake Liangzi, a shallow lake. The diversity of comammox bacteria and amoA gene abundance of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) in these samples were measured. The results showed that comammox bacteria widely existed in the rhizosphere of emergent macrophytes and fell into clade A.1, clade A.2, and clade B, and clade A was the predominant community in all sampling sites. The abundance of comammox amoA gene (6.52 × 106-2.45 × 108 copies g-1 dry sediment) was higher than that of AOB amoA gene (6.58 × 104-3.58 × 106 copies g-1 dry sediment), and four orders of magnitude higher than that of AOA amoA gene (7.24 × 102-6.89 × 103 copies g-1 dry sediment), suggesting that the rhizosphere of emergent macrophytes is more favorable for the growth of comammox bacteria than that of AOB and AOA. Our study indicated that the comammox bacteria may play important roles in ammonia-oxidizing processes in all different rhizosphere regions.

Unraveling microbial characteristics of simultaneous nitrification, denitrification and phosphorus removal in a membrane-aerated biofilm reactor

This study describes the simultaneous removal of carbon, ammonium, and phosphate from domestic wastewater by a membrane-aerated biofilm reactor (MABR) which was operated for 360 days. During the operation, the maximum removal efficiencies of chemical oxygen demand (COD), total nitrogen (TN) and total phosphorus (TP) reached 93.1%, 83.98%, and 96.41%, respectively. Statistical analysis showed that the MABR could potentially treat wastewater with a high ammonium concentration and a relatively low C/N ratio. Dissolved oxygen and multiple pollutants, including ammonium, carbon, phosphate, and sulfate, shaped the structure of the microbial community in the MABR. High throughput sequencing uncovered the crucial microbiome in ammonium transformation in MABR. Phylogenetic analysis of the ammonia monooxygenase (amoA) genes revealed an important role for comammox Nitrospira in the nitrification process. Diverse novel phosphate-accumulating organisms (Thauera, Bacillus, and Pseudomonas) and sulfur-oxidizing bacteria (Thiobacillus, Thiothrix and Sulfurimonas) were potentially involved in denitrification in MABR. The results from this study suggested that MABR could be a feasible system for the simultaneous removal of nitrogen, carbon, phosphorus, and sulfur from sewage water.

Non-rhizosphere reinforces the contributions of Feammox and anammox to nitrogen loss than rhizosphere in riparian zones

The emergence of anaerobic ammonium oxidation (anammox) coupled to iron reduction (named Feammox) refreshes the microbial pathways for nitrogen (N) loss. However, the ecological role of Feammox, compared with conventional denitrification and anammox, in microbial N attenuation in ecosystems remains unclear. Here, the specific contribution of Feammox to N loss and the underlying microbiome interactive characteristics in a riparian ecosystem were investigated through 15N isotope tracing and molecular analysis. Feammox was highlighted in the riparian interface soils and maximally contributed 14.2% of N loss. Denitrification remained the dominant contributor to N loss (68.0%-95.3%), followed by anammox (5.7%-19.1%) and Feammox (0-14.2%). The rates of Feammox and anammox significantly decreased in rhizosphere soils (0.15 ± 0.08 μg N g-1 d -1 for Feammox, 0.80 ± 0.39 μg N g-1 d -1 for anammox) compared with those in non-rhizosphere soils; however, the activities of denitrification remarkably increased in the rhizosphere (13.17 ± 3.71 μg N g-1 d -1). In rhizosphere soils, the competition between bioavailable organic matter (e.g., amino acids and carbohydrates) and ammonium for electron acceptor [i.e., Fe(III)] was the vital inducement for restricted Feammox, while the nitrite consumption boosted by heterotrophic denitrifiers was responsible for weakened anammox. The functional gene of autotrophic Acidimicrobiaceae bacterium A6, instead of heterotrophic Geobacteraceae spp., was significantly positively correlated with Feammox activity. Rare iron-reducing bacteria showed higher node degrees in the non-rhizosphere network than in the rhizosphere network. A syntrophic relationship was found between iron-reducing bacteria (e.g., Anaeromyxobacter, Geobacter) and iron-oxidizing bacteria (e.g., Sideroxydans) in the non-rhizosphere network and facilitated the Feammox pathway. This study provides an in-depth exploration of microbial driven N loss in a riparian ecosystem and introduces new insights into riparian management practices toward high-efficient N pollution alleviation.

Abundance, community and driving factor of nitrifiers in western China plateau

Complete ammonia oxidation (comammox) is one of the most important biogeochemical processes, with recent studies showing that comammox process dominates nitrification in many ecosystems. However, the abundance, community and driving factor of comammox bacteria and other nitrifying microorganisms in plateau wetland is still unclear. Here, the abundances and community features of comammox bacteria, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the wetland sediments of western China plateaus were examined using qPCR and high-throughput sequencing. The results indicate that comammox bacteria were more abundant than AOA and AOB, and dominated the nitrification process. Compared with low-elevation samples (below 3000 m: samples 6-10, 12, 13, 15, 16), the abundance of comammox bacteria was much higher at high-elevation samples (above 3000 m: samples 1-5, 11, 14, 17, 18). The key species of AOA, AOB, and comammox bacteria were Nitrososphaera viennensis, Nitrosomonas europaea, and Nitrospira nitrificans, respectively. The key factor affecting comammox bacteria community was elevation. Elevation could increase the interaction links of key species Nitrospira nitrificans, resulting in high comammox bacterial abundance. The results of this study advance our knowledge of comammox bacteria in natural ecosystems.

Community assembly of comammox Nitrospira in coastal wetlands across southeastern China

Complete ammonia oxidizers (comammox Nitrospira) are ubiquitous in coastal wetland sediments and play an important role in nitrification. Our study examined the impact of habitat modifications on comammox Nitrospira communities in coastal wetland sediments across tropical and subtropical regions of southeastern China. Samples were collected from 21 coastal wetlands in five provinces where native mudflats were invaded by Spartina alterniflora and subsequently converted to aquaculture ponds. The results showed that comammox Nitrospira abundances were mainly influenced by sediment grain size rather than by habitat modifications. Compared to S. alterniflora marshes and native mudflats, aquaculture pond sediments had lower comammox Nitrospira diversity, lower clade A.1 abundance, and higher clade A.2 abundance. Sulfate concentration was the most important factor controlling the diversity of comammox Nitrospira. The response of comammox Nitrospira community to habitat change varied significantly by location, and environmental variables accounted for only 11.2% of the variations in community structure across all sites. In all three habitat types, dispersal limitation largely controlled the comammox Nitrospira community assembly process, indicating the stochastic nature of these sediment communities in coastal wetlands. IMPORTANCE Comammox Nitrospira have recently gained attention for their potential role in nitrification and nitrous oxide (N2O) emissions in soil and sediment. However, their distribution and assembly in impacted coastal wetland are poorly understood, particularly on a large spatial scale. Our study provides novel evidence that the effects of habitat modification on comammox Nitrospira communities are dependent on the location of the wetland. We also found that the assembly of comammox Nitrospira communities in coastal wetlands was mainly governed by stochastic processes. Nevertheless, sediment grain size and sulfate concentration were identified as key variables affecting comammox Nitrospira abundance and diversity in coastal sediments. These findings are significant as they advance our understanding of the environmental adaptation of comammox Nitrospira and how future landscape modifications may impact their abundance and diversity in coastal wetlands.

Shifts of soil archaeal nitrification and methanogenesis with elevation in water level fluctuation zone of the three Gorges Reservoir, China

The water level fluctuation zone is a unique ecological zone exposed to long-term drying and flooding and plays a critical role in the transport and transformation of carbon and nitrogen materials in reservoir-river systems. Archaea are a vital component of soil ecosystems in the water level fluctuation zones, however, the distribution and function of archaeal communities in responde to long-term wet and dry alternations are still unclear. The community structure of archaea in the drawdown areas at various elevations of the Three Gorges Reservoir was investigated by selecting surface soils (0-5 cm) of different inundation durations at three sites from upstream to downstream according to the flooding pattern. The results revealed that prolonged flooding and drying increased the community diversity of soil archaea, with ammonia-oxidizing archaea being the dominant species in non-flooded regions, while methanogenic archaea were abundant in soils that had been flooded for an extended period of time. Long-term alternation of wetting and drying increases methanogenesis but decreases nitrification. It was determined that soil pH, NO3--N, TOC and TN are significant environmental factors affecting the composition of soil archaeal communities (P = 0.02). Long-term flooding and drying changed the community composition of soil archaea by altering environmental factors, which in turn influenced nitrification and methanogenesis in soils at different elevations. These findings contribute to our understanding of soil carbon and nitrogen transport transformation processes in the water level fluctuation zone as well as the effects of long-term wet and dry alternation on soil carbon and nitrogen cycles. The results of this study can provide a basis for ecological management, environmental management, and long-term operation of reservoirs in water level fluctuation zones.

Anthropogenic land-use activities within watersheds reduce comammox activity and diversity in rivers

Nitrogen cycling plays a key role in maintaining river ecological functions which are threatened by anthropogenic activities. The newly discovered complete ammonia oxidation, comammox, provides novel insights into the ecological effects of nitrogen on that it oxidizes ammonia directly to nitrate without releasing nitrite as canonical ammonia oxidization conducted by AOA or AOB which is believed to play an important role in greenhouse gas generation. Theoretically, contribution of commamox, AOA and AOB to ammonia oxidization in rivers might be impacted by anthropogenic land-use activities through alterations in flow regime and nutrient input. While how land use pattern affects comammox and other canonical ammonia oxidizers remains elusive. In this study, we examined the ecological effects of land use practices on the activity and contribution of three distinctive groups of ammonia oxidizers (AOA, AOB, comammox) as well as the composition of comammox bacterial communities from 15 subbasins covering an area of 6166 km² in North China. The results showed that comammox dominated nitrification (55.71%-81.21%) in less disturbed basins characterized by extensive forests and grassland, while AOB became the major player (53.83%-76.43%) in highly developed basins with drastic urban and agricultural development. In addition, increasing anthropogenic land use activities within the watershed lowered the alpha diversity of comammox communities and simplified the comammox network. Additionally, the alterations of NH₄⁺-N, pH and C/N induced by land use change were found to be crucial drivers in determining the distribution and activity of AOB and comammox. Together, our findings cast a new light on aquatic-terrestrial linkages from the view of microorganism-mediated nitrogen cycling and can further be applied to target watershed land use management.

Community composition and abundance of complete ammonia oxidation (comammox) bacteria in the Lancang River cascade reservoir

The construction of the reservoir has changed the nitrogen migration and transformation processes in the river, and a large amount of sediment deposition in the reservoir may also lead to the spatial differentiation of complete ammonia oxidation (comammox) bacteria. The study investigated the abundance and diversity of comammox bacteria in the sediments of three cascade reservoirs, namely, Xiaowan, Manwan, and Nuozhadu on the Lancang River in China. In these reservoirs, the average amoA gene abundance of clade A and clade B of comammox bacteria, ammonia-oxidizing archaea (AOA), and ammonia-oxidizing bacteria (AOB) was 4.16 ± 0.85 × 10⁵, 1.15 ± 0.33 × 10⁵, 7.39 ± 2.31 × 10⁴, and 3.28 ± 0.99 × 10⁵ copies g^-1, respectively. The abundance of clade A was higher than that of other ammonia oxidizing microorganisms. The spatial variation of comammox bacteria abundance differed among different reservoirs, but the spatial variation trends of the two clades of comammox bacteria in the same reservoir were similar. At each sampling point, clade A1, clade A2, and clade B coexisted, and clade A2 was usually the dominant species. The connection between comammox bacteria in the pre-dam sediments was looser than that in non-pre-dam sediments, and comammox bacteria in pre-dam sediments exhibited a simpler network structure. The main factor affecting comammox bacteria abundance was NH₄⁺-N, while altitude, temperature, and conductivity of overlying water were the main factors affecting comammox bacteria diversity. Environmental changes caused by differences in the spatial distribution of these cascade reservoirs may be the main driver of the changes of community composition and abundance of comammox bacteria. This study confirms that the construction of cascade reservoirs results in niche spatial differentiation of comammox bacteria.

Complete ammonia oxidization in agricultural soils: High ammonia fertilizer loss but low N2 O production

The contribution of agriculture to the sustainable development goals requires climate-smart and profitable farm innovations. Increasing the ammonia fertilizer applications to meet the global food demands results in high agricultural costs, environmental quality deterioration, and global warming, without a significant increase in crop yield. Here, we reported that a third microbial ammonia oxidation process, complete ammonia oxidation (comammox), is contributing to a significant ammonia fertilizer loss (41.9 ± 4.8%) at the rate of 3.53 ± 0.55 mg N kg^-1 day^-1 in agricultural soils around the world. The contribution of comammox to ammonia fertilizer loss, occurring mainly in surface agricultural soil profiles (0-0.2 m), was equivalent to that of bacterial ammonia oxidation (48.6 ± 4.5%); both processes were significantly more important than archaeal ammonia oxidation (9.5 ± 3.6%). In contrast, comammox produced less N₂ O (0.98 ± 0.44 μg N kg^-1 day^-1 , 11.7 ± 3.1%), comparable to that produced by archaeal ammonia oxidation (16.4 ± 4.4%) but significantly lower than that of bacterial ammonia oxidation (72.0 ± 5.1%). The efficiency of ammonia conversion to N₂ O by comammox (0.02 ± 0.01%) was evidently lower than that of bacterial (0.24 ± 0.06%) and archaeal (0.16 ± 0.04%) ammonia oxidation. The comammox rate increased with increasing soil pH values, which is the only physicochemical characteristic that significantly influenced both comammox bacterial abundance and rates. Ammonia fertilizer loss, dominated by comammox and bacterial ammonia oxidation, was more intense in soils with pH >6.5 than in soils with pH <6.5. Our results revealed that comammox plays a vital role in ammonia fertilizer loss and sustainable development in agroecosystems that have been previously overlooked for a long term.

Co-Occurrence and Cooperation between Comammox and Anammox Bacteria in a Full-Scale Attached Growth Municipal Wastewater Treatment Process

Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems, including synthetic community constructs; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase, with minimal contribution by ammonia-oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2 - 6 mg/L) setpoints indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed the high abundance (relative abundance 6.53 ± 0.34%) of two Brocadia-like anammox populations, while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37 ± 0.03%) and Nitrosomonas-like ammonia oxidizers were even lower (0.12 ± 0.02%). Collectively, our study reports for the first time the co-occurrence and cooperation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.

Effects of dam building on the occurrence and activity of comammox bacteria in river sediments and their contribution to nitrification

The recent discovery of complete ammonia oxidizers (comammox) has fundamentally changed our understanding of nitrification. However, studies on the occurrence and activity of comammox bacteria and their contribution to nitrification remain unclear. Here, we investigated the abundance, activity, and diversity of comammox bacteria and their contribution to nitrification in sediments from dammed rivers in winter and summer. Our results indicated that comammox clade A was ubiquitous in all sediment samples and the community structure in comammox varied between the upper and lower reaches, but not on the time scale (winter and summer). Comammox activity in the dammed river sediments in summer was prominently higher than in winter (summer: 1.08 ± 0.52; winter: 0.197 ± 0.148 mg N kg-1 day-1). Furthermore, the activity of comammox bacteria in summer appeared higher in the vicinity of the dammed river and in the Sanjiang estuary, which is located downstream of the dammed river. The activity of ammonia-oxidizing bacteria (AOB) (0.77 ± 0.478 mg N kg-1 day-1) was higher compared to comammox (0.639 ± 0.588 mg N kg-1 day-1) and ammonia-oxidizing archaea (AOA) (0.026 ± 0.022 mg N kg-1 day-1) in both winter and summer. In terms of contribution to the nitrification process, AOB (winter: 67.13 ± 12.21 %; summer: 50.57 ± 16.14 %) outperformed comammox (winter: 28.59 ± 12.51 %; summer: 48.38 ± 16.62 %) and AOA (winter: <7.39 %; summer: <2.09 %). These findings indicated that the nitrification process in dammed river sediments was mainly dominated by AOB. Additionally, comammox activity was significantly affected by temperature and NH4+, suggesting that these variables were key determinants of the niche partitioning of comammox. Collectively, our findings provide novel perspectives into the widespread distribution and contribution of comammox to nitrification in dammed river ecosystems, thus broadening our understanding of the nitrification processes.

Discrepant Effects of Flooding on Assembly Processes of Abundant and Rare Communities in Riparian Soils

Numerous rare species coexist with a few abundant species in microbial communities and together play an essential role in riparian ecosystems. Relatively little is understood, however, about the nature of assembly processes of these communities and how they respond to a fluctuating environment. In this study, drivers controlling the assembly of abundant and rare subcommunities for bacteria and archaea in a riparian zone were determined, and their resulting patterns on these processes were analyzed. Abundant and rare bacteria and archaea showed a consistent variation in the community structure along the riparian elevation gradient, which was closely associated with flooding frequency. The community assembly of abundant bacteria was not affected by any measured environmental variables, while soil moisture and ratio of submerged time to exposed time were the two most decisive factors determining rare bacterial community. Assembly of abundant archaeal community was also determined by these two factors, whereas rare archaea was significantly associated with soil carbon-nitrogen ratio and total carbon content. The assembly process of abundant and rare bacterial subcommunities was driven respectively by dispersal limitation and variable selection. Undominated processes and dispersal limitation dominated the assembly of abundant archaea, whereas homogeneous selection primarily driven rare archaea. Flooding may therefore play a crucial role in determining the community assembly processes by imposing disturbances and shaping soil niches. Overall, this study reveals the assembly patterns of abundant and rare communities in the riparian zone and provides further insight into the importance of their respective roles in maintaining a stable ecosystem during times of environmental perturbations.

Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira

BACKGROUND

The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete.

RESULTS

In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification.

CONCLUSIONS

Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.

Towards a more labor-saving way in microbial ammonium oxidation: A review on complete ammonia oxidization (comammox)

In the Anthropocene, nitrogen pollution is becoming an increasing challenge for both mankind and the Earth system. Microbial nitrogen cycling begins with aerobic nitrification, which is also the key rate-limiting step. For over a century, it has been accepted that nitrification occurs sequentially involving ammonia oxidation, which produces nitrite followed by nitrite oxidation, generating nitrate. This perception was changed by the discovery of comammox Nitrospira bacteria and their metabolic pathway. In addition, this also provided us with new knowledge concerning the complex nitrogen cycle network. In the comammox process, ammonia can be completely oxidized to nitrate in one cell via the subsequent activity of the enzyme complexes, ammonia monooxygenase, hydroxylamine dehydrogenase, and nitrite oxidodreductase. Over the past five years, research on comammox made great progress. However, there still exist a lot of questions, including how much does comammox contribute to nitrification? How large is the diversity and are there new strains to be discovered? Do comammox bacteria produce the greenhouse gas N₂O, and how or to which extent may they contribute to global climate change? The above four aspects are of great significance on the farmland nitrogen management, aquatic environment restoration, and mitigation of global climate change. As large number of comammox bacteria and pathways have been detected in various terrestrial and aquatic ecosystems, indicating that the comammox process may exert an important role in the global nitrogen cycle.

Niche differentiation of comammox Nitrospira in sediments of the Three Gorges Reservoir typical tributaries, China

Complete ammonia oxidizer (Comammox) can complete the whole nitrification process independently, whose niche differentiation is important guarantee for its survival and ecological function. This study investigated the niche differentiation of comammox Nitrospira in the sediments of three typical tributaries of the Three Gorges Reservoir (TGR). Clade A and clade B of comammox Nitrospira coexisted in all sampling sites simultaneously. The amoA gene abundance of clade A and B was gradually increased or decreased along the flow path of the three tributaries with obvious spatial differentiation. The amoA gene abundance of comammox Nitrospira clade A (6.36 × 10³ - 5.06 × 10⁴ copies g^-1 dry sediment) was higher than that of clade B (6.26 × 10² - 6.27 × 10³ copies g^-1 dry sediment), and the clade A amoA gene abundance was one order of magnitude higher than that of AOA (7.24 × 10² - 6.89 × 10³ copies g^-1 dry sediment) and AOB (1.44 × 10² - 1.46 × 10³ copies g^-1 dry sediment). A significant positive correlation was observed between comammox Nitrospira clade A amoA gene abundance and flow distance (P < 0.05). The number of operational taxonomic units (OTUs) in two sub-clades of clade A accounted for the majority in different tributaries, indicating that clade A also had population differentiation among different tributaries. This study revealed that comammox Nitrospira in the sediments of TGR tributaries have niche differentiation and clade A.2 played a more crucial role in comammox Nitrospira community.

Comammox activity dominates nitrification process in the sediments of plateau wetland

The recent discovery of complete ammonia oxidation (comammox) has increased our understanding of nitrification. Although comammox has been shown to play an important role in plain wetland ecosystems, studies of comammox contribution are still limited in plateau wetland ecosystems. Here, we analyzed the abundance, activity, community and biogeochemical mechanisms of the comammox bacteria in Yunnan-kweichow and Qinghai-Tibet plateau wetlands from elevations of 1000-5000 m. Comammox bacteria were widely distributed in all 16 sediment samples with abundances higher than 0.96 ± 0.26 × 10⁷ copies g^-1 (n = 16). Comammox showed high activity (1.18 ± 0.17 to 1.98 ± 0.08 mg N kg^-1 d^-1) at high-elevation (3000-5000 m) and dominated the nitrification process (activity contribution: 37.20 - 60.62%). The activity contribution of ammonia-oxidizing bacteria (1.07 ± 0.08 to 2.79 ± 0.35 mg N kg^-1 d^-1) dominated the nitrification process (44.55 - 64.15%) in low-elevation (1000-3000 m) samples. All detected comammox Nitrospira belonged to clade A, while clade B was not detected. Elevation always had a strongest effect on key comammox species. Thus, we infer that elevation may drive the high relative abundance of the species Candidatus Nitrospira nitrificans (avg. 12.40%) and the low relative abundance of the species Nitrospira sp. SG-bin2 (avg. 4.75%) in high-elevation samples that showed a high comammox activity (avg. 1.62 mg N kg^-1 d^-1) and high contribution (avg. 46.08%) to the nitrification process. These results indicate that comammox may be an important and currently underestimated microbial nitrification process in plateau wetland ecosystems.