Complete nitrification: insights into the ecophysiology of comammox Nitrospira

Biological methane removal by groundwater trickling biofiltration for emissions reduction

Methane removal is an essential step in drinking water production from methane-rich groundwaters. Conventional aeration-based stripping results in significant direct methane emissions, contributing up to one-third of a treatment plant's total carbon footprint. To address this, a full-scale trickling filter was operated for biological methane oxidation upstream of a submerged sand filter, and its performance was compared to a conventional aeration-submerged sand filtration set-up. Full-scale data were combined with ex-situ batch assays and metagenome-resolved metaproteomics to quantify the individual contribution of the main (a)biotic processes and characterize the enriched microbial communities. Both treatment setups fully removed methane, iron, ammonium, and manganese, yet the underlying mechanisms differed significantly. Methane was completely removed from the effluent after trickling filtration, with stripping and biological oxidation each accounting for half of the removal, thereby halving overall methane emissions. Methane-oxidizing bacteria not only outcompeted nitrifiers in the trickling filter, but also likely contributed directly to ammonia oxidation. In contrast to the submerged filter preceded by methane stripping, signatures of biological iron oxidation were almost completely absent in the trickling filter, suggesting that the presence of methane directly or indirectly promotes chemical iron oxidation. All systems had similar ex-situ manganese oxidation capacities, yet removal occurred only in the submerged filters but not the trickling filter. Ultimately, our results demonstrate that trickling filtration is effective in promoting biological methane oxidation at comparable produced drinking water quality, highlighting its potential for advancing sustainable drinking water production.

A Novel Perspective on the Instability of Mainstream Partial Nitrification: The Niche Differentiation of Nitrifying Guilds

Short-cut biological nitrogen removal (sBNR) favors the paradigm shift toward energy-positive and carbon-neutral wastewater treatment processes. Partial nitrification (PN) is a key approach to provide nitrite for anammox or denitritation during sBNR, and its stability is the precondition for achieving robust nitrogen removal performance. However, maintaining a stable mainstream PN process has been a long-standing challenge. This review analyzes the mainstream PN process from a microbial ecology perspective, focusing on the niche differentiation among nitrifiers. First, we propose that mainstream PN systems are ecologically unstable, and the failure of the mainstream PN process due to the reactivation of nitrite-oxidizing bacteria (NOB) can be regarded as a behavior to restore system stabilization. Thus, maintaining mainstream PN systems primarily relies on enhancing the niche differentiation between ammonia-oxidizing bacteria (AOB) and NOB. We then summarize the realized niches of indigenous nitrifiers within nitrification systems and discuss their ecophysiological characteristics (e.g., cell structure and substrate affinity) that define their specific ecological niches. By comparing the niche breadths of AOB and NOB on various niche axes, we further discuss their niche differentiation and identify the different responses of AOB (resistance) and NOB (resilience) to exogenous perturbations. Finally, we propose outlook for achieving a stable mainstream PN process through an ecological lens. This review provides ecological insights into the instability of the mainstream PN process, which is intended to guide the derivation of optimized strategies from a single-factor approach to integrated solutions.

Exploring the ecological niche of comammox Nitrospira by in-situ enrichment within mainstream nitrification systems

Complete-ammonia-oxidization bacteria (Comammox Nitrospira) hold promising potential for reducing carbon footprint in mainstream wastewater treatment. However, the inadequate understanding of comammox Nitrospira within wastewater systems has greatly hindered the utilization of these novel microbial resources. This study explored the ecological niche of comammox Nitrospira within mainstream nitrification systems by enriching them under varied operational conditions. The joint analysis of multiple linear regression and random forest model have identified in-situ ammonium concentration and pH as the two most important parameters influencing the growth of comammox Nitrospira, followed by nitrogen loading rate, nitrogen source type, and dissolved oxygen (DO). Meanwhile, the ecological niche preference of comammox Nitrospira was revealed. The optimal ranges of in-situ ammonium concentration and pH for comammox Nitrospira was found below 0.5 mg NH4+-N/L and 6.5-7.5, respectively, indicating that low free ammonia conditions favor their growth. Furthermore, comammox Nitrospira exhibited a competitive advantage over Nitrosomonas under weakly acidic pH (6.0-6.5), and adapted to DO fluctuations by interspecies shifts, whereas Nitrosomonas preferred relatively high DO (1.5-2 mg O2/L). Comparative genomics further confirmed the above niche differentiation of two groups from reconstructed comammox Nitrospira and Nitrosomonas genomes. Overall, these findings provide guidance for the application of comammox process in wastewater treatment, thereby supporting the transition of mainstream nitrification process toward a more sustainable and energy-efficient pathway.

Spatio-temporal variability of nitrogen-cycling potentials in particle-attached and free-living microbial communities in the Yangtze River estuary and adjacent regions

Particle-attached (PA) and free-living (FL) microorganisms regulate coastal biogeochemical cycles, yet their roles in nitrogen transformation remain unclear. To address this knowledge gap, we seasonally sampled PA and FL from seawater along salinity gradients in the Yangtze River estuary (YRE) and adjacent regions to investigate the spatio-temporal variability of microbial communities, abundances of nitrogen-cycling genes, and key microbial groups affiliated with the nitrogen cycle in PA and FL. Compared to FL, the composition, structure and diversity of PA exhibited more pronounced variations in response to salinity and [NO3-]. Metagenomic analyses indicated a predominant role of denitrification in both PA and FL, with greater abundances of genes involved in most nitrogen transformation processes observed in the estuarine region. The potential for the nitrogen cycle in PA was relatively lower in May, while greater in FL, potentially due to competition for nitrogen substrates between PA and phytoplankton during spring. PERMANOVA and Mantel tests showed that gene abundances exhibited spatio-temporal dynamics and were associated with species and environmental factors. Gene-affiliated taxa identification and the Weighted Correlation Network Analysis revealed that the differences in environmental factors and taxa responsible for the nitrogen transformation drove spatio-temporal variations of the nitrogen cycle between PA and FL, and implied the significance of their interaction in nitrogen fates in coastal ecosystem. Gammaproteobacteria and Betaproteobacteria were highly affiliated with nitrogen-cycling genes, while Nitrososphaeria played an important role in nitrification and denitrification. This study offered practical insights for mitigating eutrophication through targeted regulation of microbial-mediated nitrogen fluxes.

Comammox and AOA responses to ammonia loading rate in oligotrophic environments

Nitrification is a central process in the global nitrogen cycle, yet the ecological niches and growth strategies of ammonia-oxidizing microorganisms in oligotrophic environments remain poorly understood. To investigate the ecological responses of complete ammonia oxidizers (Comammox) and ammonia-oxidizing archaea (AOA), a membrane bioreactor (MBR) system with two distinct ammonia loading rates (ALRs) was employed in this study. Metagenomic and meta-transcriptomic analyses showed that Comammox species-including Candidatus Nitrospira nitrosa and Candidatus Nitrospira inopinata-underwent a pronounced "bloom" only at high ALR, where their DNA and mRNA relative abundances reached 4.7 % and 5.63 %, respectively. Meanwhile, AOA steadily increased under both high and low ALR in oligotrophic environments. Network analysis further indicated stronger cooperative interactions between Comammox and AOA in higher ALR, highlighting distinct ecological strategies that underpin ammonia oxidation in oligotrophic environments. These findings not only support the development of low-carbon nitrogen removal processes in wastewater treatment but also clarify the impact of nitrogen loading on the distribution of ammonia-oxidizing microorganisms in natural ecosystems and provide insights into the origin and evolutionary pathways of these essential microbes.

Comparative enrichment of complete ammonium oxidation bacteria in floccular sludge reactors: Sequencing batch reactor vs. continuous stirred tank reactor

This study attempted to compare the enrichment of complete ammonium oxidation (comammox) bacteria, which are affiliated with Nitrospira and not able to generate nitrous oxide (N2O, a potent greenhouse gas) through biological pathways, in two commonly-utilized configurations of floccular sludge reactors, i.e., sequencing batch reactor (SBR) and continuous stirred tank reactor (CSTR), under the ammonium condition of mainstream wastewater (i.e., 40.0 g-N/m3). The results in terms of nitrification performance and microbial analyses during 216-d operation showed that compared with SBR offering a fluctuating but generally higher in-situ ammonium concentration (i.e., 1.0-6.0 g-N/m3) which was favorable for the growth of ammonium-oxidizing bacteria (AOB, belonging to Nitrosomonas in this study), CSTR managed to lower the in-situ ammonium level to < 2.0 g-N/m3, thus creating a competitive advantage for comammox bacteria with a highly oligotrophic lifestyle. Such an argument was further supported by dedicated batch tests which revealed that Nitrospira-dominant sludge had a lower maximum ammonium oxidation rate and lower apparent ammonium and oxygen affinity constants than Nitrosomonas-dominant sludge (i.e., 33.5 ± 2.1 mg-N/h/g-MLVSS vs. 139.9 ± 26.7 mg-N/h/g-MLVSS, 1.1 ± 0.1 g-N/m3 vs. 17.6 ± 4.6 g-N/m3, and 0.017 ± 0.002 g-O2/m3 vs. 0.037 ± 0.013 g-O2/m3, respectively), proving the nature of comammox bacteria as a K-strategist. Overall, this study not only provided useful insights into the effective enrichment of comammox bacteria in floccular sludge but also further revealed the interactions between comammox bacteria and AOB, thereby contributing to the future development of comammox-inclusive biological nitrogen removal technologies for sustainable wastewater treatment.

Investigating spatial and temporal dynamics in microbial community composition of multiple full-scale slow sand filters in drinking water treatment

Slow sand filters (SSFs) are essential for producing high-quality and sustainable drinking water, relying on chemical, physical, and microbial processes to remove nutrients, organic matter, and pathogens. Despite numerous studies on the physical and chemical mechanisms in SSFs, the microbial processes and dynamics remain poorly understood. This study bridges this knowledge gap by investigating the spatial and temporal dynamics of prokaryotic communities within SSFs, by analysing different depths and the top layer, the Schmutzdecke (SCM), over time in full-scale SSFs from different drinking water treatment plants in The Netherlands. Utilising 16S ribosomal RNA gene-targeted amplicon sequencing and quantitative PCR, we observed a horizontally uniform prokaryotic community at each depth at all analysed SSFs, suggesting effective influent water and nutrient distribution, regardless of filter size or influent inlet design. Vertically, however, the prokaryotic composition varied significantly, with the SCM showing higher biomass and diversity compared to the deeper layers. This study identified a core prokaryotic community, including the families Nitrospiraceae, Pirellulaceae, Nitrosomonadaceae, Gemmataceae, and Vicinamibacteriaceae, consistent across various depths and SSFs, and in the SCMs of different ages. Their presence suggests a central role in supporting key biological processes in SSFs such as organic matter degradation and nitrification. Additionally, the relative abundance of archaea increased with sand depth in all SSFs, suggesting their adaptation to lower-nutrient conditions found in deeper layers. Analysis of the SCM over time showed that after scraping, the prokaryotic community gradually adapted, with minimal biomass increase during the first 3.6 years, eventually evolving into a mature, diverse, and even prokaryotic community. Our findings highlight the presence of spatially distinct microbial communities at various depths of SSFs, suggesting the removal of specific compounds in distinct sand layers. Moreover, the persistence of a core prokaryotic community across different SSFs, SCM maturation stages, and even after disturbances like scraping, demonstrates that the biology in SSFs is resilient and likely ensures reliable SSF performance. It also implies possibilities for earlier SSF operational restart after cleaning than is conventionally done, but with continuous monitoring of water quality parameters to ensure microbial safety. These findings lay the groundwork for future research to focus on these microorganisms and their functional potential.

Enrichment of Nitrosocosmicus-AOA in situ and their vertical distribution characteristics in aerated biofilters

Ammonia-oxidizing archaea (AOA) are promising candidates for replacing ammonia-oxidizing bacteria in wastewater treatment. However, limited efforts have been made to enrich copiotrophic-AOA in situ competitively. To this end, two laboratory-scale intermittent aerated biofilters (upflow-aerated biofilter (R1) and downflow-aerated biofilter (R2)) were comparatively employed for the treatment of mainstream wastewater. An extended non-aerobic cycling strategy led to higher residual ammonia-nitrogen levels (0.01-18.7 mg/L), denser biofilms, and facilitated the dominance of Nitrosocosmicus-like AOA (R1: 70.31%; R2: 82.32%). Additionally, the AOA in both biofilters were the main contributors (62%-66%) to the highly efficient nitrification process. Compared with R1, R2 had a higher abundance of Nitrosomonas and Nitrospira, a lower ammonia oxidation rate, and a simpler co-occurrence network of nitrifiers. The protein content induced by intermittent aeration significantly affected the AOA community. Candidatus Brocadia (3.62%-7.82%) was also auto-enriched in both biofilters. Therefore, in situ enrichment of Nitrosocosmicus-dominant nitrifying microorganisms is conducive to developing an environment-friendly, energy-efficient, high ammonia-nitrogen removal AOA-based partial nitrification-anammox process.

Nutrient removal performance and microbial composition analysis in hybrid membrane bioreactor for municipal wastewater treatment

The removal of nutrients from wastewater to reduce the toxicity of these compounds to the environment requires more space in wastewater treatment plants to establish anaerobic, anoxic and aerobic treatment stages. To address this limitation, researchers have developed practical, intensive hybrid treatment systems that enhance nutrient removal performance while requiring less space. However, the implementation of hybrid systems within a reactor introduces the interaction between the attached and suspended growth that can influence the microbial community structure and the performance of the system, so it is crucial to understand the composition of the microbial communities involved in hybrid growth to optimize control strategies in these systems. This study investigated the microbial community structure of the integrated moving bed membrane bioreactor (IMBMBR) system and its impact on nutrient removal in municipal wastewater. The findings demonstrated that the effluent quality was improved with the IMBMBR. The efficiency of removing COD, BOD5,NH 4 + -N andPO 4 3 - -P in the IMBMBR were 91 ± 4.0%, 95 ± 4.0%, 99 ± 0.2% and 24 ± 3.0%, respectively. The IMBMBR had better nitrite oxidation and complete nitrification by increasing the diversity and abundance of effective bacteria. The abundance of Proteobacteria, Bacteroidetes and Nitrospira was enhanced in IMBMBR. Coexistence of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) in IMBMBR led to increased nutrient removal. The study results suggest that IMBMBR can be an effective process for nutrient removal, achieving quality standards that comply with legal requirements for wastewater in municipal and industries with limited space for establishing treatment facilities. Additionally, this process can be quickly implemented as an upgrade to existing wastewater treatment plants, avoiding the need to develop an entirely new system.

Nitrogen Availability and Changes in Precipitation Alter Microbially Mediated NO and N2O Emissions From a Pinyon-Juniper Dryland

Climate change is altering precipitation regimes that control nitrogen (N) cycling in terrestrial ecosystems. In ecosystems exposed to frequent drought, N can accumulate in soils as they dry, stimulating the emission of both nitric oxide (NO; an air pollutant at high concentrations) and nitrous oxide (N2O; a powerful greenhouse gas) when the dry soils wet up. Because changes in both N availability and soil moisture can alter the capacity of nitrifying organisms such as ammonia-oxidizing bacteria (AOB) and archaea (AOA) to process N and emit N gases, predicting whether shifts in precipitation may alter NO and N2O emissions requires understanding how both AOA and AOB may respond. Thus, we ask: How does altering summer and winter precipitation affect nitrifier-derived N trace gas emissions in a dryland ecosystem? To answer this question, we manipulated summer and winter precipitation and measured AOA- and AOB-derived N trace gas emissions, AOA and AOB abundance, and soil N concentrations. We found that excluding summer precipitation increased AOB-derived NO emissions, consistent with the increase in soil N availability, and that increasing summer precipitation amount promoted AOB activity. Excluding precipitation in the winter (the most extreme water limitation we imposed) did not alter nitrifier-derived NO emissions despite N accumulating in soils. Instead, nitrate that accumulated under drought correlated with high N2O emission via denitrification upon wetting dry soils. Increases in the timing and intensity of precipitation that are forecasted under climate change may, therefore, influence the emission of N gases according to the magnitude and season during which the changes occur.

Metagenome-Assembled Genomes for Oligotrophic Nitrifiers From a Mountainous Gravelbed Floodplain

Riparian floodplains are important regions for biogeochemical cycling, including nitrogen. Here, we present MAGs from nitrifying microorganisms, including ammonia-oxidising archaea (AOA) and comammox bacteria from Slate River (SR) floodplain sediments (Crested Butte, CO, US). Additionally, we explore MAGs from potential nitrite-oxidising bacteria (NOB) from the Nitrospirales. AOA diversity in SR is lower than observed in other western US floodplain sediments and Nitrosotalea-like lineages such as the genus TA-20 are the dominant AOA. No ammonia-oxidising bacteria (AOB) MAGs were recovered. Microorganisms from the Palsa-1315 genus (clade B comammox) are the most abundant ammonia-oxidizers in SR floodplain sediments. Established NOB are conspicuously absent; however, we recovered MAGs from uncultured lineages of the NS-4 family (Nitrospirales) and Nitrospiraceae that we propose as putative NOB. Nitrite oxidation may be carried out by organisms sister to established Nitrospira NOB lineages based on the genomic content of uncultured Nitrospirales clades. Nitrifier MAGs recovered from SR floodplain sediments harbour genes for using alternative sources of ammonia, such as urea, cyanate, biuret, triuret and nitriles. The SR floodplain therefore appears to be a low ammonia flux environment that selects for oligotrophic nitrifiers.

Long-term stability of comammox Nitrospira under weakly acidic conditions and their acid-adaptive mechanisms revealed by genome-centric metatranscriptomics

Despite their widespread presence in acidic environments, the stability and adaptative mechanisms of complete ammonia oxidization (comammox) bacteria remain poorly understood. In this three-year study, comammox Nitrospira consistently dominated both abundance and activity in an acidic nitrifying reactor (pH = 6.3-6.8), as revealed by metagenomic and cDNA-based 16S rRNA sequencing. Batch tests demonstrated their decent nitrification down to pH 4.7, while ceasing at pH 4.2. Genome-centric metatranscriptomics revealed that comammox Nitrospira upregulated a Rh-type ammonium transporter to enhance substrate uptake under acidic conditions. Active proton transport, mediated by NADH dehydrogenases and F-type ATPase, was identified as a primary strategy for maintaining pH homeostasis in comammox Nitrospira. Genes associated with carbon acquisition, chemotaxis, and DNA repair were upregulated at low pH, suggesting these processes play roles in acid adaptation. These findings enhance the understanding of ecological roles and adaptive mechanisms of comammox bacteria in acidic environments.

Efficient ammonia oxidation by Pseudomonas citronellolis strain YN-21 under strongly acidic conditions: Performance and mechanism

Ammonia oxidation microorganisms generally tend to have low rates of ammonia oxidation under acidic conditions, as the protonated ammonia is not a substrate for ammonia monooxygenase. In this work, heterotrophic ammonia oxidation bacteria (HAOB) Pseudomonas citronellolis strain YN-21 showed high efficiency in removing NH4+ (12.7 mg/L/h) even at initial pH 4.5. The potential acid resistance mechanisms (H+ efflux, H+ consumption, and production of alkaline substances) maintained intracellular pH neutrality. Transcriptome analysis showed that genes involved in amino acid metabolism, carbohydrate metabolism, ABC transporter and nitrogen metabolism were significantly up-regulated, which facilitated the rapid removal of NH4+ in an acidic environment. Moreover, urea could be used as an alternative nitrogen source for YN-21 in a strongly acidic environment, and the production of NH3 from urea hydrolysis provided a substrate for ammonia oxidation. These results provide new insights into efficient ammonia oxidation in acidic environments.

Distribution and key influential factors of comammox in drained and waterlogged soils of zoige plateau peatland

Peatlands are important carbon and nitrogen reservoirs, playing crucial roles in nitrogen cycling. During microbially-driven nitrogen cycling, nitrous oxide (N2O, 298 times global warming potential of CO2) can be emitted, exacerbating global warming. Complete ammonia-oxidizing bacteria (comammox), a newly discovered group of prokaryotes, can independently oxidize ammonia directly to nitrate, bypassing the nitrite stage, and thereby reducing N2O production associated with the traditional two-step nitrification process. However, information on comammox distribution and its key influential factors in plateau peatlands remains scarce. Thus, this study chose Zoige plateau peatland in China to collect soil samples from different soil types (drained and waterlogged), across different seasons (non-growing and growing), and at various depth (0-100 cm) to assess comammox abundance and community composition. Additionally, soil properties were analyzed and correlated with comammox abundance and community composition to identify the key factors affecting comammox distribution. Comammox abundance varied significantly across soil types, depth, and sampling seasons. Waterlogged soils demonstrated higher comammox abundance than drained soils. In waterlogged soils, comammox abundance showed higher during growing season than non-growing season, while the opposite trend was observed in drained soils. Regardless of soil types, comammox abundance decreased with increasing soil depth. In soils of Zoige plateau peatland, comammox clades A.1, A.2, A.3 and B.1 were identified, with clade B.1 dominating the comammox community. Both Nitrospira sp. CG24A (clade B.1) and Candidatus Nitrospira nitrificans (clade A.1) showed great seasonal variations. Soil properties, including moisture, pH, carbon, and nutrients, collectively influenced comammox abundance and diversity. Among these factors, NH4+-N was the main factor affecting comammox abundance, while moisture primarily drove community distribution. These findings provide valuable insights into comammox distribution, enhancing our understanding of its potential role in mitigating N2O emissions and thus nitrogen cycling in plateau peatland soils.

Transcriptional activity of ammonia oxidisers in response to soil temperature, moisture and nitrogen amendment

The contrasting response of AOA, AOB, and comammox Nitrospira amoA transcript abundance to temperature, moisture, and nitrogen was investigated using soil microcosms. The moisture, temperature, and nitrogen treatments were selected to represent conditions typically found in a New Zealand (NZ) dairy farm. AOB dominated all synthetic urine treated soils. Peak AOB amoA transcript abundance was positively correlated with estimated soil ammonia availability. While AOB gDNA abundance and nitrification rate trends were similar. AOA were strongly influenced by soil temperature. At 20°C, AOA amoA peak transcript abundance averaged over 1 order of magnitude higher than at 8°C. Within the AOA community a member of the Nitrosocosmicus clade was positively correlated with ammonium and estimated ammonia concentrations. The presence and relative increase of an AOA community member in a high nitrogen environment poses an interesting contrast to current scientific opinion in NZ. Comammox Nitrospira abundance showed no correlation with soil moisture. This suggests that previously found associations are more complex than originally thought. Further research is required to determine the drivers of comammox Nitrospira abundance in a high moisture environment. Overall, these results indicate that AOB are the main drivers of nitrification in New Zealand dairy farm soils.

Enrichment and identification of a moderately acidophilic nitrite-oxidizing bacterium

This study enriched a novel nitrite-oxidizing bacterium (NOB, 'Candidatus Nitrobacter acidophilus') in a laboratory reactor operating at pH 4.5 for treating low-strength ammonia wastewater. Batch experiments showed that 'Ca. N. acidophilus' oxidized nitrite to nitrate at a rate of 20.7 ± 2.3 μM/h with optimal growth at pH 5, distinguishing it from most previously known NOB strains. Phylogenetic analysis showed that this Nitrobacter strain clustered with other Nitrobacter strains obtained from acidic environments but was divergent from each other with an average nucleotide identity (ANI) below 85 %. Genomic characteristics revealed that 'Ca. N. acidophilus' possesses versatile transporter systems. They are different from previously reported Nitrobacter strains and indicate acid adaptation mechanisms. Interestingly, the mutualistic interaction with acidophilic ammonia-oxidizing archaea (AOA) Nitrosotalea markedly increased the archaeal amoA gene expression by 149 times and enhanced ammonia oxidation rates by 5 times, highlighting the NOB's role in alleviating nitrite inhibition on the acidophilic AOA. These findings expand our understanding of bacterial nitrite oxidation and provide valuable insights into an important partnership between acidophilic AOA and NOB in acidic environments.

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.

Chromolaena odorata affects soil nitrogen transformations and competition in tropical coral islands by altering soil ammonia oxidizing microbes

Invasive plants can change the community structure of soil ammonia-oxidizing microbes, affect the process of soil nitrogen (N) transformation, and gain a competitive advantage. However, the current researches on competition mechanism of Chromolaena odorata have not involved soil nitrogen transformation. In this study, we compared the microbially mediated soil transformations of invasive C. odorata and natives (Pisonia grandis and Scaevola taccada) of tropical coral islands. We assessed how differences in plant biomass and tissue N contents, soil nutrients, N transformation rates, microbial biomass and activity, and diversity and abundance of ammonia oxidizing microbes associated with these species impact their competitiveness. The results showed that C. odorata outcompeted both native species by allocating more proportionally biomass to aboveground parts in response to interspecific competition (12.92 % and 22.72 % more than P. grandis and S. taccada, respectively). Additionally, when C. odorata was planted with native plants, the available N and net mineralization rates in C. odorata rhizosphere soil were higher than in native plants rhizosphere soils. Higher abundance of ammonia-oxidizing bacteria in C. odorata rhizosphere soil confirmed this, being positively correlated with soil N mineralization rates and available N. Our findings help to understand the soil N acquisition and competition strategies of C. odorata, and contribute to improving evaluations and predictions of invasive plant dynamics and their ecological effects in tropical coral islands.

Specialists regulate microbial network and community assembly in subtropical seagrass sediments under differing land use conditions

Microorganisms in the sediment play a pivotal role in the functioning and stability of seagrass ecosystems and their dynamics are influenced by the nutrient acquisition strategies of host plants. While the distinct impacts of microbial generalists and specialists on community dynamics are recognized, their distribution patterns and ecological roles within seagrass ecosystems remain largely unexplored. To address this issue, we conducted an analysis of community assembly processes and co-occurrence relationships of both microbial generalists and specialists within sediment profiles (0-100 cm) from seagrass habitats subjected to differing land use conditions. The results revealed that seagrasses in Yifeng Estuary experienced the large proportion of cultivated land and exhibited higher organic carbon content in the 0-20 cm surface sediment layer. Nitrogen-cycling bacteria were predominantly associated with seagrasses from Yifeng Estuary, whereas Vibrio spp. was more prevalent in seagrasses from Liusha Bay. Notably, seagrass Halophia beccarii (YHB) in Yifeng Estuary harbored higher niche breadths for both microbial generalist and specialist compared to Halodule uninervis (LHU) and Halophia ovalis (LHO) from Liusha Bay. Stochastic processes were pivotal in shaping seagrass sediment microbial communities, with a higher immigration rate observed in YHB, suggesting greater microbial turnover in this area. Additionally, YHB sediment presented lower drift and higher dispersal limitation among generalists compared to LHU and LHO, whereas the pattern was reversed among specialists. Specialists were found to play a crucial role in shaping microbial interactions within YHB sediment, with genera Halioglobus identified as keystone species in the network. The specialists were further found to significantly influence microbial β-diversity in seagrass sediment directly. Overall, our findings illustrated how microbial generalists and specialists were distributed in seagrass sediments in response to land use changes and provided new insights into the potential roles of microbial regulation in degraded seagrass ecosystems.

Comammox Nitrospira was the dominant ammonia oxidizer in an acidic biofilm reactor at pH 5.5 and pH 5

Nitrification is a vital process in the biological removal of inorganic nitrogen compounds. In order to ensure the stability and effectiveness of this process, buffer solutions should be added to the system to maintain neutral to slightly alkaline conditions. With a focus on the newly discovered comammox Nitrospira, this research investigates the transition of the nitrifying community within a biofilm reactor under different acidic levels (initiated at pH 6 and gradually decreased to pH 5). During the 305-day continuous operation experiment, it was observed that responsible ammonia oxidizers transitioned from ammonia-oxidizing bacteria (AOB) during the initial stages (setup stage and early stage of pH 6) to comammox Nitrospira under pH 5.5 and pH 5. Further analysis using next-generation sequencing targeting both the 16S rRNA region and amoA region revealed a shift in the dominant cluster of both Nitrospirae and comammox Nitrospira under varying pH conditions. Our study identified a distinct cluster of comammox Nitrospira that is phylogenetically closed to sequences found in acidic environments, but exhibits dissimilarity from known comammox Nitrospira isolates and the majority of environmental sequences. This cluster was found to be prevalent in the acidic biofilm reactor studied and thrived particularly well at pH 5. These findings underscore the potential significance of this distinct, uncultivated group of comammox Nitrospira in performing ammonia oxidation under acidic conditions. KEY POINTS: • Ammonia was effectively removed under pH 5.5 and 5 in the biofilm reactor • The dominant ammonia oxidizer was comammox Nitrospira when pH was 5.5 and 5 • A potential acidophilic cluster of comammox Nitrospira was identified in this acidic biofilm reactor.

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.

Response of comammox Nitrospira clades A and B communities to long-term fertilization and rhizosphere effects and their relative contribution to nitrification in a subtropical paddy field of China

The recently discovered complete ammonia oxidation (comammox Nitrospira) containing clade A and clade B has further complemented our understanding of nitrification process. Nevertheless, understanding the community feature of comammox Nitrospira clades A and B and their relative contribution to nitrification in paddy rhizosphere are still in its infancy. In this study, we assessed the community diversity and structure of comammox Nitrospira clades A and B in paddy rhizosphere and bulk soils under thirty years of different fertilization strategies, i.e., non-fertilization control (CK), chemical fertilizers application (NPK), and NPK plus swine manure (NPKM), respectively. NPKM significantly increased the a-diversity (Chao1 and Shannon indices) of comammox Nitrospira clade A and altered the community structure (P < 0.05) but had little effect on clade B. A two-way analysis of variance (ANOVA) showed that the effect of long-term fertilization on soil comammox Nitrospira community and nitrification potential rate (PNR) was much greater than that of rhizosphere. Compared with NPK, soil PNR was greatly increased by 51.0% under the NPKM treatment in the rhizosphere (P < 0.05). Phylogenetic analysis showed that NPKM improved the relative abundances of sub-clade A.2.1 and sub-clade A.3.2 of the comammox clade A community, with an average increase of 212.2 and 210.4% in both rhizosphere and bulk soils relative to the NPK treatment. Soil organic matter, NH4+-N, and pH were significant soil drivers of comammox Nitrospira clades A and B community. Furthermore, linear regression and structural equation modeling clearly showed that comammox Nitrospira clade A a-diversity were significantly associated with soil PNR (P < 0.05). Our results suggest (i) that comammox Nitrospira clade A are sensitive to the organic fertilization; and (ii) that comammox Nitrospira clade A contribute more to nitrification than clade B under the long-term organic fertilized paddy soil.

The Effects of Mixed Robinia pseudoacacia and Quercus variabilis Plantation on Soil Bacterial Community Structure and Nitrogen-Cycling Gene Abundance in the Southern Taihang Mountain Foothills

Mixed forests often increase their stability and species richness in comparison to pure stands. However, a comprehensive understanding of the effects of mixed forests on soil properties, bacterial community diversity, and soil nitrogen cycling remains elusive. This study investigated soil samples from pure Robinia pseudoacacia stands, pure Quercus variabilis stands, and mixed stands of both species in the southern foothills of the Taihang Mountains. Utilizing high-throughput sequencing and real-time fluorescence quantitative PCR, this study analyzed the bacterial community structure and the abundance of nitrogen-cycling functional genes within soils from different stands. The results demonstrated that Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacterial groups across all three forest soil types. The mixed-forest soil exhibited a higher relative abundance of Firmicutes and Bacteroidetes, while Nitrospirae and Crenarchaeota were most abundant in the pure R. pseudoacacia stand soils. Employing FAPROTAX for predictive bacterial function analysis in various soil layers, this study found that nitrogen-cycling processes such as nitrification and denitrification were most prominent in pure R. pseudoacacia soils. Whether in surface or deeper soil layers, the abundance of AOB amoA, nirS, and nirK genes was typically highest in pure R. pseudoacacia stand soils. In conclusion, the mixed forest of R. pseudoacacia and Q. variabilis can moderate the intensity of nitrification and denitrification processes, consequently reducing soil nitrogen loss.

Microbiomes of three coral species in the Mexican Caribbean and their shifts associated with the Stony Coral Tissue Loss Disease

Stony Coral Tissue Loss Disease (SCTLD) has caused widespread coral mortality in the Caribbean Region. However, how the disease presence alters the microbiome community, their structure, composition, and metabolic functionality is still poorly understood. In this study, we characterized the microbial communities of the tissues of apparently healthy and diseased SCTLD colonies of the species Siderastrea siderea, Orbicella faveolata, and Montastraea cavernosa to explore putative changes related to the presence of SCTLD. Gammaproteobacteria, Alphaproteobacteria, and Bacteroidia were the best represented classes in the healthy tissues of all coral species, and alpha diversity did not show significant differences among the species. The microbial community structure between coral species was significantly different (PERMANOVA: F = 3.46, p = 0.001), and enriched genera were detected for each species: Vibrio and Photobacterium in S. siderea, Spirochaeta2 and Marivivens in O. faveolata and SAR202_clade and Nitrospira in M. cavernosa. Evidence of SCTLD in the microbial communities was more substantial in S. siderea, where differences in alpha diversity, beta diversity, and functional profiles were observed. In O. faveolata, differences were detected only in the community structure, while M. cavernosa samples showed no significant difference. Several microbial groups were found to have enriched abundances in tissue from SCTLD lesions from S. siderea and O. faveolata, but no dominant bacterial group was detected. Our results contribute to understanding microbial diversity associated with three scleractinian coral species and the shifts in their microbiomes associated with SCTLD in the Mexican Caribbean.

Biochar and peat amendments affect nitrogen retention, microbial capacity and nitrogen cycling microbial communities in a metal and polycyclic aromatic hydrocarbon contaminated urban soil

Soil contaminants may restrict soil functions. A promising soil remediation method is amendment with biochar, which has the potential to both adsorb contaminants and improve soil health. However, effects of biochar amendment on soil-plant nitrogen (N) dynamics and N cycling microbial guilds in contaminated soils are still poorly understood. Here, a metal- and polycyclic aromatic hydrocarbon (PAH) contaminated soil was amended with either biochar (0, 3, 6 % w/w) and/or peat (0, 1.5, 3 % w/w) in a full-factorial design and sown with perennial ryegrass in an outdoor field trial. After three months, N and the stable isotopic ratio δ15N was measured in soil, roots and leaves, along with microbial responses. Aboveground grass biomass decreased by 30 % and leaf N content by 20 % with biochar, while peat alone had no effect. Peat in particular, but also biochar, stimulated the abundance of microorganisms (measured as 16S rRNA gene copy number) and basal respiration. Microbial substrate utilization (MicroResp™) was altered differentially, as peat increased respiration of all carbon sources, while for biochar, respiration of carboxylic acids increased, sugars decreased, and was unaffected for amino acids. Biochar increased the abundance of ammonia oxidizing archaea, while peat stimulated ammonia oxidizing bacteria, Nitrobacter-type nitrite oxidizers and comB-type complete ammonia oxidizers. Biochar and peat also increased nitrous oxide reducing communities (nosZI and nosZII), while peat alone or combined with biochar also increased abundance of nirK-type denitrifiers. However, biochar and peat lowered leaf δ15N by 2-4 ‰, indicating that processes causing gaseous N losses, like denitrification and ammonia volatilization, were reduced compared to the untreated contaminated soil, probably an effect of biotic N immobilization. Overall, this study shows that in addition to contaminant stabilization, amendment with biochar and peat can increase N retention while improving microbial capacity to perform important soil functions.

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Enhanced anammox performance under lower nitrite accumulation in modified partial nitritation-anammox (PN/A) process

Higher nitrite accumulation, which is challenging to achieve reliably, is always sought to obtain better nitrogen removal performance in traditional partial nitritation-anammox (PN/A) process. This study developed a modified PN/A process by introducing nitrite-oxidizing bacteria and endogenous metabolism. Advanced nitrogen removal performance of 95.5 % was achieved at a low C/N ratio of 2.7 under nitrite accumulation ratio (NAR) fluctuations. Higher nitrate accumulation at lower NAR (70 ∼ 40 %) resulted in superior anammox contribution (60 ∼ 75 %) and nitrogen removal performance (93 ∼ 98 %). This was attributed to the higher nitrogen removal efficiency of the post-anoxic endogenous partial denitrification coupling anammox process, although the PN/A process occurring first possessed a faster anammox rate of 2.0 mg NH4+-N /(g VSS⋅h). The introduction of nitrate allowed more nitrite flow to anammox, promoting a high enrichment of anammox bacteria (Ca. Brocadia, 0.3 % to 2.8 %). This study provides new insights into the practical application of the PN/A process.

The potential linkage between sediment oxygen demand and microbes and its contribution to the dissolved oxygen depletion in the Gan River

The role of sediment oxygen demand (SOD) in causing dissolved oxygen (DO) depletion is widely acknowledged, with previous studies mainly focusing on chemical and biological SOD separately. However, the relationship between the putative functions of sediment microbes and SOD, and their impact on DO depletion in overlying water, remains unclear. In this study, DO depletion was observed in the downstream of the Gan River during the summer. Sediments were sampled from three downstream sites (YZ, Down1, and Down2) and one upstream site (CK) as a control. Aquatic physicochemical parameters and SOD levels were measured, and microbial functions were inferred from taxonomic genes through analyses of the 16S rRNA gene. The results showed that DO depletion sites exhibited a higher SOD rate compared to CK. The microbial community structure was influenced by the spatial variation of Proteobacteria, Chloroflexi, and Bacteroidota, with total organic carbon (TOC) content acting as a significant environmental driver. A negative correlation was observed between microbial diversity and DO concentration (p < 0.05). Aerobic microbes were more abundant in DO depletion sites, particularly Proteobacteria. Microbes involved in various biogeochemical cycles, such as carbon (methane oxidation, methanotrophs, and methylotrophs), nitrogen (nitrification and denitrification), sulfur (sulfide and sulfur compound oxidation), and manganese cycles (manganese oxidation), exhibited higher abundance in DO depletion sites, except for the iron cycle (iron oxidation). These processes were negatively correlated with DO concentration and positively with SOD (p < 0.05). Overall, the results highlight that aerobic bacteria's metabolic processes consume oxygen, increasing the SOD rate and contributing to DO depletion in the overlying water. Additionally, the study underscores the importance of targeting the removal of in situ microbial molecular mechanisms associated with toxic H2S and CH4 to support reoxygenation efforts in rehabilitating DO depletion sites in the Gan River, aiding in identifying factors controlling DO consumption and offering practical value for the river's restoration and management.

Metatranscriptomic Analysis Reveals Synergistic Activities of Comammox and Anammox Bacteria in Full-Scale Attached Growth Nitrogen Removal System

Leveraging comammox Nitrospira and anammox bacteria for shortcut nitrogen removal can drastically lower the carbon footprint of wastewater treatment facilities by decreasing aeration energy, carbon, alkalinity, and tank volume requirements while also potentially reducing nitrous oxide emissions. However, their co-occurrence as dominant nitrifying bacteria is rarely reported in full-scale wastewater treatment. As a result, there is a poor understanding of how operational parameters, in particular, dissolved oxygen, impact their activity and synergistic behavior. Here, we report the impact of dissolved oxygen concentration (DO = 2, 4, 6 mg/L) on the microbial community's transcriptomic expression in a full-scale integrated fixed film activated sludge (IFAS) municipal wastewater treatment facility where nitrogen removal is predominantly performed by comammox Nitrospira and anammox bacterial populations. 16S rRNA transcript compositions revealed anammox bacteria and Nitrospira were significantly more active in IFAS biofilms compared to suspended sludge biomass. In IFAS biofilms, anammox bacteria significantly increased hzo expression at lower dissolved oxygen concentrations and this increase was highly correlated with the amoA expression levels of comammox bacteria. Interestingly, the genes involved in nitrite oxidation by comammox bacteria were significantly more upregulated, relative to the genes involved in ammonia oxidation with decreasing dissolved oxygen concentrations. Ultimately, our findings suggest that comammox Nitrospira supplies anammox bacteria with nitrite via ammonia oxidation and that this synergistic behavior is dependent on dissolved oxygen concentrations.

Long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol

The discovery of complete ammonia oxidizers (comammox) has dramatically altered our perception of nitrogen (N) biogeochemistry. However, their functional importance vs. the canonical ammonia oxidizers (i.e., ammonia oxidizing-archaea (AOA) and bacteria (AOB)) in agroecosystems is still poorly understood. Accordingly, a new assay using acetylene, 3,4-dimethylpyrazole phosphate (DMPP), and 1-octyne was adopted to assess the ammonia (NH3) oxidation and nitrous oxide (N2O) production activity of these functional guilds in a subtropical Inceptisol under long-term different fertilization regimes. These regimes include CK (no fertilizer control), synthetic fertilizer only (NPK), organic manure only (M) and organic manure plus synthetic fertilizer (MNPK). AOA dominated NH3 oxidation in the M treatment, while AOB dominated both NH3 oxidation and N2O production in all treatments except M. Comammox always played a minor role in both NH3 oxidation and N2O production across all treatments. Both M and MNPK treatments significantly increased the activity and growth of comammox. Compared to NPK, comammox exhibited increases of 270 % and 326 % in the NH3 oxidation rates, and increases of 1472 % and 563 % in the N2O production rates in M and MNPK, respectively. Random forest model revealed that copper (Cu), comammox abundance, and dissolved organic nitrogen (DON) were the most important predictors for the NH3 oxidation rates of comammox. Redundancy analyses (RDA) showed that fertilizer treatments significantly altered the community composition of NH3 oxidizers, and pH was the overarching parameter underpinning the community shift of the NH3 oxidizers. Overall, this study provides evidence that comammox play a minor yet unneglectable role in the nitrification of agroecosystems, and the long-term addition of organic manure stimulates the growth and activity of comammox in a subtropical Inceptisol.

Diversity and ecology of NrfA-dependent ammonifying microorganisms

Nitrate ammonifiers are a taxonomically diverse group of microorganisms that reduce nitrate to ammonium, which is released, and thereby contribute to the retention of nitrogen in ecosystems. Despite their importance for understanding the fate of nitrate, they remain a largely overlooked group in the nitrogen cycle. Here, we present the latest advances on free-living microorganisms using NrfA to reduce nitrite during ammonification. We describe their diversity and ecology in terrestrial and aquatic environments, as well as the environmental factors influencing the competition for nitrate with denitrifiers that reduce nitrate to gaseous nitrogen species, including the greenhouse gas nitrous oxide (N2O). We further review the capacity of ammonifiers for other redox reactions, showing that they likely play multiple roles in the cycling of elements.

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.

Competitive bio-augmentation overcoming unusual direct inhibitor inefficacy in mainstream nitrite-oxidizing bacteria suppression: Unveiling the underpinnings in microbial and nitrogen metabolism aspects

The long-stabilized mainstream partial nitritation/Anammox (PN/A) process continues to encounter significant challenges from nitrite-oxidizing bacteria (NOB). Therefore, this study aimed to determine an efficient, rapid, and easily implementable strategy for inhibiting NOB. A laboratory-scale reactor was operated continuously for 325 days, experiencing NOB outbreak in mainstream and recovery with simulated sidestream support. The results show that direct inhibitory strategies including intermittent aeration and approximately 35 mg/L free ammonia had unusual weak inhibitory effects on NOB activity. Subsequently, the exogenous Anammox from sidestream employed as a competitive bio-augmentation approach rapidly inhibited NOB dynamics. Evidence suggests that the damaged hydroxyapatite granules under low pH conditions might have contributed to NOB dominance by diminishing Anammox bacteria activity, thereby creating a substrate-rich environment favoring NOB survival. In contrast, the introduction of exogenous Candidatus Kuenenia facilitated the nitrogen removal efficiency from 32.5 % to over 80 %. This coincided with a decrease in the relative abundance of Nitrospira from 16.5 % to 2.7 % and NOB activity from 0.34 to 0.07 g N/(g mixed liquor volatile suspended solid)/d. Metagenomic analysis reveals a decrease in the functional potential of most nitrite transport proteins, coupled with a significant increase in eukaryotic-like serine/threonine-protein kinase involved in cellular regulation, during the Anammox activity recovery. This study's findings reveal the feasibility of the bio-augmentation based on substrate competition, wherein sidestream processes support the mainstream PN/A integration, offering significant potential for practical applications.

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.

Contrasting response of comammox Nitrospira, ammonia oxidising bacteria, and archaea to soil pH and nitrogen inputs

This study aimed to investigate the effect of soil pH change, and nitrogen amendment on ammonia oxidiser abundance and comammox Nitrospira community composition. The experimental design used soil mesocosms placed in a temperature-controlled incubator for 90 days. A Templeton silt loam was used as its physiochemical properties are typical of the region's dairy farms. The results showed that comammox Nitrospira clade B preferred the natural (pH 6.1-6.2) soil pH with no applied nitrogen. Furthermore, synthetic urine (N700) decreased the abundance of comammox Nitrospira clade B. This may have been because the large amounts of available ammonia in the N700 treatments inhibited the growth of comammox Nitrospira. These results suggest that while comammox Nitrospira clade B are present in New Zealand dairy farm soils, but their role in nitrification in the very high nitrogen environment under a urine patch in grazed pastures may be limited. Further research is needed to confirm this. In contrast to comammox, the AOB community (dominated by Nitrosospira) responded positively to the application of synthetic urine. The response was greatest in the high pH soil (7.1), followed by the natural and then the low pH (4.9) soils. This may be due to the difference in ammonia availability. At high pH, the ammonia/ammonium equilibrium favours ammonia production. Calculated ammonia availability in the N700 treatments accurately predicted the AOB amoA gene abundance. Interestingly, the AOA community abundance (which was predominantly made up of Thaumarchaeota group I.1b clade E) seemed to prefer the natural and high pH soils over the low pH. This may be due to the specific lineage of AOA present. AOA did not respond to the application of nitrogen.

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.

Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.

Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica

Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3-) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3- via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via 13C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.

Pilot-scale investigation of performance and microbial community in a novel system combining fixed and suspended activated sludge

The conventional activated sludge (CAS) process is a widely used method for wastewater treatment due to its effectiveness and affordability. However, it can be prone to sludge abnormalities such as sludge bulking/foaming and sludge loss, which can lead to a decrease in treatment efficiency. To address these issues, a novel bag-based fixed activated sludge (BBFAS) system utilizing mesh bags to contain the sludge was developed for low carbon/nitrogen ratio wastewater treatment. Pilot-scale experiments demonstrated that the BBFAS system could successfully avoid the sludge abnormalities. Moreover, it was not affected by mass transfer resistance and exhibited significantly higher nitrogen removal efficiency, surpassing that of the CAS system by up to 78%. Additionally, the BBFAS system demonstrated comparable organic matter removal efficiency to CAS system. 16S rRNA gene high-throughput sequencing revealed that the bacterial community structure within the BBFAS system was significantly different from that of the CAS system. The bacteria associated with ammonium removal were more abundant in the BBFAS system than in the CAS system. The abundance of Nitrospira in the BBFAS could reach up to 6% and significantly higher than that in the CAS system, and they were likely responsible for both ammonia-oxidizing and nitrite-oxidizing functions. Clear stratification of microbial communities was observed from the outer to inner layers of the bag components due to the gradients of dissolved oxygen and other substrates. Overall, this study presents a promising approach for avoiding activated sludge abnormalities while maintaining high pollutant removal performance.

Altitudinal patterns of alpine soil ammonia-oxidizing community structure and potential nitrification rate

Nitrogen availability limits the net primary productivity in alpine meadows on the Qinghai-Tibetan Plateau, which is regulated by ammonia-oxidizing microorganisms. However, little is known about the elevational patterns of soil ammonia oxidizers in alpine meadows. Here, we investigated the potential nitrification rate (PNR), abundance, and community diversity of soil ammonia-oxidizing microorganisms along the altitudinal gradient between 3,200 and 4,200 m in Qinghai-Tibetan alpine meadows. We found that both PNR and amoA gene abundance declined from 3,400 to 4,200 m but lowered at 3,200 m, possibly due to intense substrate competition and biological nitrification inhibition from grasses. The primary contributors to soil nitrification were ammonia-oxidizing archaea (AOA), and their proportionate share of soil nitrification increased with altitude in comparison to ammonia-oxidizing bacteria (AOB). The alpha diversity of AOA increased by higher temperature and plant richness at low elevations, while decreased by higher moisture and low legume biomass at middle elevations. In contrast, the alpha diversity of AOB increased along elevation. The elevational patterns of AOA and AOB communities were primarily driven by temperature, soil moisture, and vegetation. These findings suggest that elevation-induced climate changes, such as shifts in temperature and water conditions, could potentially alter the soil nitrification process in alpine meadows through changes in vegetation and soil properties, which provide new insights into how soil ammonia oxidizers respond to climate change in alpine meadows.IMPORTANCEThe importance of this study is revealing that elevational patterns and nitrification contributions of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities were primarily driven by temperature, soil moisture, and vegetation. Compared to AOB, the relative contribution of AOA to soil nitrification increased at higher elevations. The research highlights the potential impact of elevation-induced climate change on nitrification processes in alpine meadows, mediated by alterations in vegetation and soil properties. By providing new insights into how ammonia oxidizers respond to climate change, this study contributes valuable knowledge to the field of microbial ecology and helps predict ecological responses to environmental changes in alpine meadows.

Competitive enrichment of comammox Nitrospira in floccular sludge

The discovery of complete ammonium oxidation (comammox) has subverted the traditional perception of two-step nitrification, which plays a key role in achieving biological nitrogen removal from wastewater. Floccular sludge-based treatment technologies are being applied at the majority of wastewater treatment plants in service where detection of various abundances and activities of comammox bacteria have been reported. However, limited efforts have been made to enrich and subsequently characterize comammox bacteria in floccular sludge. To this end, a lab-scale sequencing batch reactor (SBR) in the step-feeding mode was applied in this work to enrich comammox bacteria through controlling appropriate operational conditions (dissolved oxygen of 0.5 ± 0.1 g-O2/m3, influent ammonium of 40 g-N/m3 and uncontrolled longer sludge retention time). After 215-d operation, comammox bacteria gradually gained competitive advantages over counterparts in the SBR with a stable nitrification efficiency of 92.2 ± 2.2 %: the relative abundance of Nitrospira reached 42.9 ± 1.3 %, which was 13 times higher than that of Nitrosomonas, and the amoA gene level of comammox bacteria increased to 7.7 ± 2.1 × 106 copies/g-biomass, nearly 50 times higher than that of conventional ammonium-oxidizing bacteria. The enrichment of comammox bacteria, especially Clade A Candidatus Nitrospira nitrosa, in the floccular sludge led to (i) apparent affinity constants for ammonium and oxygen of 3.296 ± 0.989 g-N/m3 and 0.110 ± 0.004 g-O2/m3, respectively, and (ii) significantly low N2O and NO production, with emission factors being 0.136 ± 0.026 % and 0.023 ± 0.013 %, respectively.

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.

Ammonia-oxidizing bacteria and archaea exhibit differential nitrogen source preferences

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

Multiple microbial guilds mediate soil methane cycling along a wetland salinity gradient

Estuarine wetlands harbor considerable carbon stocks, but rising sea levels could affect their ability to sequester soil carbon as well as their potential to emit methane (CH4). While sulfate loading from seawater intrusion may reduce CH4 production due to the higher energy yield of microbial sulfate reduction, existing studies suggest other factors are likely at play. Our study of 11 wetland complexes spanning a natural salinity and productivity gradient across the San Francisco Bay and Delta found that while CH4 fluxes generally declined with salinity, they were highest in oligohaline wetlands (ca. 3-ppt salinity). Methanogens and methanogenesis genes were weakly correlated with CH4 fluxes but alone did not explain the highest rates observed. Taxonomic and functional gene data suggested that other microbial guilds that influence carbon and nitrogen cycling need to be accounted for to better predict CH4 fluxes at landscape scales. Higher methane production occurring near the freshwater boundary with slight salinization (and sulfate incursion) might result from increased sulfate-reducing fermenter and syntrophic populations, which can produce substrates used by methanogens. Moreover, higher salinities can solubilize ionically bound ammonium abundant in the lower salinity wetland soils examined here, which could inhibit methanotrophs and potentially contribute to greater CH4 fluxes observed in oligohaline sediments.IMPORTANCELow-level salinity intrusion could increase CH4 flux in tidal freshwater wetlands, while higher levels of salinization might instead decrease CH4 fluxes. High CH4 emissions in oligohaline sites are concerning because seawater intrusion will cause tidal freshwater wetlands to become oligohaline. Methanogenesis genes alone did not account for landscape patterns of CH4 fluxes, suggesting mechanisms altering methanogenesis, methanotrophy, nitrogen cycling, and ammonium release, and increasing decomposition and syntrophic bacterial populations could contribute to increases in net CH4 flux at oligohaline salinities. Improved understanding of these influences on net CH4 emissions could improve restoration efforts and accounting of carbon sequestration in estuarine wetlands. More pristine reference sites may have older and more abundant organic matter with higher carbon:nitrogen compared to wetlands impacted by agricultural activity and may present different interactions between salinity and CH4. This distinction might be critical for modeling efforts to scale up biogeochemical process interactions in estuarine wetlands.

How does biochar influence soil nitrification and nitrification-induced N2O emissions?

Nitrification is a major pathway of N2O production, especially in aerobic soils. The amendment of soils with biochar has been suggested as a promising solution to regulate soil N cycle and reduce N2O emissions. However, there is a lack of comprehensive and quantitative understanding of biochar impacts on soil nitrification and nitrification-induced N2O emissions. In this study, a meta-analysis was conducted using data compiled across 95 peer-reviewed studies. Results showed that biochar in general significantly increased soil nitrification rate by 56 %, with overall no significant effect on nitrification-induced N2O emissions, suggesting that biochar likely restricted the fraction of nitrified N emitted as N2O emissions. The abundance of ammonia-oxidizing bacteria (AOB) was significantly increased by 37 % following biochar addition, but that of ammonia-oxidizing archaea (AOA) did not change significantly, indicating that the impact of biochar on AOB rather than AOA may play an important role in soil nitrification. The impacts of biochar on soil nitrification processes were heterogeneous depending on soil properties. Biochar increased soil nitrification rate and AOB abundance to a larger extent in poorly pH-buffered soils such as those with acidic pH (<5), low organic carbon (<10 g kg-1), or poor texture (rich in either sand or clay), which may be attributed to the liming and structural effects of biochar that regulate soil pH and water-air status. The overall no significant effect of biochar on nitrification-induced N2O emissions was due to a positive effect in acidic soils, a negative effect in alkaline soils, and little effect in neutral soils. This study provides a comprehensive insight into how different factors mediate the response of soil nitrification processes to biochar amendment, which contributes to a new understanding of biochar function in regulating soil N2O emissions, and can assist in designing biochar projects that would benefit soil N cycle while minimizing undesirable side effects.

Temporal enrichment of comammox Nitrospira and Ca. Nitrosocosmicus in a coastal plastisphere

Plastic marine debris is known to harbor a unique microbiome (termed the "plastisphere") that can be important in marine biogeochemical cycles. However, the temporal dynamics in the plastisphere and their implications for marine biogeochemistry remain poorly understood. Here, we characterized the temporal dynamics of nitrifying communities in the plastisphere of plastic ropes exposed to a mangrove intertidal zone. The 39-month colonization experiment revealed that the relative abundances of Nitrospira and Candidatus Nitrosocosmicus representatives increased over time according to 16S rRNA gene amplicon sequencing analysis. The relative abundances of amoA genes in metagenomes implied that comammox Nitrospira were the dominant ammonia oxidizers in the plastisphere, and their dominance increased over time. The relative abundances of two metagenome-assembled genomes of comammox Nitrospira also increased with time and positively correlated with extracellular polymeric substances content of the plastisphere but negatively correlated with NH4+ concentration in seawater, indicating the long-term succession of these two parameters significantly influenced the ammonia-oxidizing community in the coastal plastisphere. At the end of the colonization experiment, the plastisphere exhibited high nitrification activity, leading to the release of N2O (2.52 ng N2O N g-1) in a 3-day nitrification experiment. The predicted relative contribution of comammox Nitrospira to N2O production (17.9%) was higher than that of ammonia-oxidizing bacteria (4.8%) but lower than that of ammonia-oxidizing archaea (21.4%). These results provide evidence that from a long-term perspective, some coastal plastispheres will become dominated by comammox Nitrospira and thereby act as hotspots of ammonia oxidation and N2O production.

Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers

Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.

Validation of key sponge symbiont pathways using genome-centric metatranscriptomics

The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.

Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy

Background

Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.

Results

We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.

Conclusions

The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.