Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Development of a nitrifying bacterial community for a low temperature recirculating aquaculture system

Two separate ammonia- and nitrite-oxidizing bacterial communities were developed to operate in a low temperature closed recirculating aquaculture system. These communities were cultivated via batch culture using an inorganic nutrient medium containing ammonia or nitrite. Subsequently, a unique closed recirculating culture system was developed, and enrichment culture was performed in an inorganic nutrient medium containing 1 mM ammonia. Through this approach, a bacterial community was developed that can efficiently nitrify 1 mM ammonia within 1 day at 15 °C. Amplicon sequencing revealed Nitrosomonadaceae and Nitrospirales, were the key groups responsible for ammonia and nitrite oxidation. The bacterial community was introduced into microbial tanks for the rearing of Oryzias latipes var. himedaka and Lefua echigonia (Hotokedojo) at 15 °C, where regular measurements confirmed the effective removal of ammonia and nitrite. However, nitrate accumulation occurred, which was mitigated by the introduction of Epipremnum aureum (Pothos) into the tank. This system provides a sustainable solution for the closed recirculating aquaculture of cold-water fish species.

Comparative analysis of niche adaptation strategies of AOA, AOB, and comammox along a gate-controlled river-estuary continuum

Ammonia oxidizers are key players in the biogeochemical nitrogen cycle. However, in critical ecological zones such as estuaries, especially those affected by widespread anthropogenic dam control, our understanding of their occurrence, ecological performance, and survival strategies remains elusive. Here, we sampled sediments along the Haihe River-Estuary continuum in China, controlled by the Haihe Tidal Gate, and employed a combination of biochemical and metagenomic approaches to investigate the abundance, activity, and composition of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (comammox). We also conducted an extensive comparison of the salinity adaptation mechanisms of different ammonia oxidizers. We found that AOB (57.55 ± 11.46 %) dominated the nitrification process upstream of the tidal gate, while comammox (68.22 ± 14.42 %) played the major role downstream. Redundancy analysis results showed that total nitrogen, ammonium, and salinity were the primary factors influencing the abundance, activity, and contribution of ammonia oxidizers. The abundance and activity of AOB were significantly positively correlated with ammonium. KEGG annotation results showed that AOA Nitrososphaera, AOB Nitrosomonas, and comammox Nitrospira had 7, 31, and 22 genes associated to salinity adaptation, respectively, and were capable of employing both the "salt-in" and "salt-out" strategies. Metagenome assembly results indicated that comammox outperformed AOA primarily in compatible solute accumulation; AOA can synthesize glutamate, whereas comammox Nitrospira can additionally synthesize glycine betaine, choline, and trehalose. The tidal gate caused sharp shifts in ammonium (from 4.10 ± 3.28 mg·kg-1 to 0.45 ± 0.10 mg·kg-1) and salinity (from 1.64 ± 0.48 ppt to 3.26 ± 0.89 ppt), playing a dominant role in driving niche differentiation of ammonia oxidizers along the Haihe River-Estuary continuum. These findings provide profound insights into the nitrogen cycle in freshwater-saltwater transition zones, especially in today's world where estuaries are widely controlled by tidal gates.

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.

Metagenomic insights into the influence of pH on antibiotic removal and antibiotic resistance during nitritation: Regulations on functional genus and genes

The changes in pH and the resulting presence of free nitrous acid (FNA) or free ammonia (FA) often inhibit antibiotic biodegradation during nitritation. However, the specific mechanisms through which pH, FNA and FA influence antibiotic removal and the fate of antibiotic resistance genes (ARGs) are not yet fully understood. In this study, the effects of pH, FNA, and FA on the removal of cefalexin and amoxicillin during nitritation were investigated. The results revealed that the decreased antibiotic removal under both acidic condition (pH 4.5) and alkaline condition (pH 9.5) was due to the inhibition of the expression of amoA in ammonia-oxidizing bacteria and functional genes (hydrolase-encoding genes, transferase-encoding genes, lyase-encoding genes, and oxidoreductase-encoding genes) in heterotrophs. Furthermore, acidity was the primary inhibitor of antibiotic removal at pH 4.5, followed by FNA. Antibiotic removal was primarily inhibited by alkalinity at pH 9.5, followed by FA. The proliferation of ARGs mediated by mobile genetic element was promoted under both acidic and alkaline conditions, attributed to the promotion of FNA and FA, respectively. Overall, this study highlights the inhibitory effects of acidity and alkalinity on antibiotic removal during nitritation.

Achieving nitrite shunt using in-situ free ammonia enriched by natural zeolite: Pilot-scale mainstream anammox with flexible nitritation strategy

The mainstream partial nitritation/anammox (PN/A) process represents a significant innovation in decarbonizing municipal wastewater treatment. However, its implementation is considerably hampered by the challenge of stable nitrite supply. In this study, a pilot-scale PN/A system receiving real sewage (20 m3) was operated at room temperature for nearly one year. Remarkable PN performance with relatively high nitrite accumulation ratio of 75.04 ± 10.05 % was obtained via in-situ free ammonia (FA) strategy. The ammonium concentration enriched in the zeolite increased significantly by 548.8 times compared to that in the aqueous phase by ion exchange. This substantial increase robustly inhibited nitrite-oxidizing bacteria (NOB), resulting in high relative abundance ratio of ammonia-oxidizing bacteria (AOB) to NOB of 37.93 ± 12.61 in the zeolite biofilm, compared to 10.22 ± 1.67 in suspended floc sludge. The significant differences in FA concentrations between zeolite biofilm and suspended floc sludge resulted in distinct spatial distribution disparities of AOB and NOB, which were central to achieving stable nitrite accumulation without complex multiple selective pressures. Consequently, compliant effluent with total nitrogen of 10.91 ± 4.23 mg N/L was achieved at 10.4-31.1 °C without external carbon source addition. The biocarriers in the anammox process played a key role in enhancing functional genes and electron flow, supporting anammox-dominated nitrogen removal. This study presents a flexible and adaptable strategy for mainstream nitrite shunting, highlighting its potential for large-scale implementation of mainstream anammox treatment.

Response of nitrifiers to gradually increasing pH conditions in a membrane nitrification bioreactor: Microbial dynamics and alkali-resistant mechanism

Nitrification and nitrifiers are pH-sensitive especially under the alkaline environment in the activated sludge system. However, it is unclear how nitrifiers and nitrification respond to long-term alkaline environment. This study employed a continuous flow membrane nitrification bioreactor to investigate the dynamics of nitrification efficiency and microbial community adaptation under a 320-day alkaline operation. Results showed that activated sludge adapted remarkably to a progressive increase in pH from 7.5 to 10.0, achieving robust nitrification with average ammonia removal efficiencies of 96.6 ± 2.2%. Subsequently, an integrated alkali-resistant mechanism of nitrifiers was proposed. Specifically, under the long-term operation of pH 10.0, certain bacteria secreted enhanced extracellular acidic polysaccharides (i.e., up to 10.95 ± 0.27 mg·g-1 MLVSS in soluble extracellular polymeric substances (EPS)) and acidic organic compounds (e.g., humic acids increased by 1.47-fold in tightly bounded EPS) to neutralize external alkalinity. Moreover, significant enrichments in both the ammonia oxidizing bacteria Nitrosomonas (by 1.3%) and the nitrite oxidizing bacteria Nitrospira (by 5.4%) were observed in a 170-day operation of pH 10.0 condition. Meanwhile, norank_f__JG30-KF-CM45 (2.0%) and Rhodobacter (0.9%) also contributed to ammonia removal at pH 10.0. On the cellular-level, bacteria enabled to maintain intracellular pH stabilization primarily through cation/proton antiporters, evidenced by significant increases in NhaA, TrkA and KefB activities by 98.0%, 151.7% and 115.2%, respectively. A 43.1% increase in carbonic anhydrase activity also facilitated consumption of aqueous OH- ions through biomineralization, leading to CaCO3 deposition on microbial surface. These findings further enhanced understandings of physiological adaptation of nitrifiers in the long-term alkaline activated sludge system.

Acidophilic partial nitrification (pH<6) facilitates ultra-efficient short-flow nitrogen transformation: Experimental validation and genomic insights

Partial nitrification (PN) represents an energy-efficient bioprocess; however, it often confronts challenges such as unstable nitrite accumulation, nitrite oxidizing bacteria shocks, and slow reaction rate. This study established an acidophilic PN with self-sustained pH as low as 5.36. Over 120-day monitoring, nitrite accumulation rate (NAR) was stabilized at more than 97.9 %, and an ultra-high ammonia oxidation rate of 0.81 kg/m3·d was achieved. Notably, least NAR of 77.8 % persisted even under accidental nitrite oxidizing bacteria invasion, aeration delay, alkalinity fluctuations, and cooling shocks. During processing, despite detrimental effects on bacterial diversity, there was a discernible increase in acid-tolerant bacteria responsible for nitrification. Candidatus Nitrosoglobus, gradually dominated in nitrifying guild (2.15 %), with the substantially reduction or disappearance of typical nitrifying microorganisms. Acidobacteriota, a key player in nitrogen cycling of soil, significantly increased from 0.45 % to 9.98 %, and its associated nitrogen metabolism genes showed a substantial 215 % rise. AmoB emerged as the most critical functional gene influencing acidophilic PN, exhibiting significantly higher unit gene expression than other nitrification genes. Blockade tricarboxylic acid cycle, DNA damage, and presence of free nitrous acid exert substantial effects on nitrite-oxidizing bacteria (NOB), serving as internal driving forces for acidophilic PN. This highlights the reliable potential for shortening nitrogen transformation process.

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.

An abundant bacterial phylum with nitrite-oxidizing potential in oligotrophic marine sediments

Nitrite-oxidizing bacteria (NOB) are important nitrifiers whose activity regulates the availability of nitrite and dictates the magnitude of nitrogen loss in ecosystems. In oxic marine sediments, ammonia-oxidizing archaea (AOA) and NOB together catalyze the oxidation of ammonium to nitrate, but the abundance ratios of AOA to canonical NOB in some cores are significantly higher than the theoretical ratio range predicted from physiological traits of AOA and NOB characterized under realistic ocean conditions, indicating that some NOBs are yet to be discovered. Here we report a bacterial phylum Candidatus Nitrosediminicolota, members of which are more abundant than canonical NOBs and are widespread across global oligotrophic sediments. Ca. Nitrosediminicolota members have the functional potential to oxidize nitrite, in addition to other accessory functions such as urea hydrolysis and thiosulfate reduction. While one recovered species (Ca. Nitrosediminicola aerophilus) is generally confined within the oxic zone, another (Ca. Nitrosediminicola anaerotolerans) additionally appears in anoxic sediments. Counting Ca. Nitrosediminicolota as a nitrite-oxidizer helps to resolve the apparent abundance imbalance between AOA and NOB in oxic marine sediments, and thus its activity may exert controls on the nitrite budget.

Differential effects of winter cold stress on soil bacterial communities, metabolites, and physicochemical properties in two varieties of Tetrastigma hemsleyanum Diels & Gilg in reclaimed land

Tetrastigma hemsleyanum Diels & Gilg (TDG) has been recently planted in reclaimed lands in Zhejiang Province, China, to increase reclaimed land use. Winter cold stress seriously limits the growth and development of TDG and has become the bottleneck limiting the TDG planting industry. To investigate the defense mechanisms of TDG toward winter cold stress when grown on reclaimed land, a combined analysis of soil bacterial communities, metabolites, and physicochemical properties was conducted in this study. Significant differences were observed in the composition of soil bacterial communities, metabolites, and properties in soils of a cold-tolerant variety (A201201) compared with a cold-intolerant variety (B201810). The fresh weight (75.8% of tubers) and dry weight (73.6%) of A201201 were significantly higher than those of B201810. The 16S rRNA gene amplicon sequencing of soil bacteria showed that Gp5 (25.3%), Gemmatimonas (19.6%), Subdivision3 (16.7%), Lacibacterium (11.9%), Gp4 (11.8%), Gp3 (10.4%), Gp6 (7.0%), and WPS-1 (1.2%) were less common, while Chryseolinea (10.6%) were more common in A201201 soils than B201810 soils. Furthermore, linear discriminant analysis of effect size identified 35 bacterial biomarker taxa for both treatments. Co-occurrence network analyses also showed that the structures of the bacterial communities were more complex and stable in A201201 soils compared to B201810 soils. In addition, ultra-high-performance liquid chromatography coupled to mass spectrometry analysis indicated the presence of significantly different metabolites in the two soil treatments, with 10 differentially expressed metabolites (DEMs) (8 significantly upregulated by 9.2%-391.3% and 2 significantly downregulated by 25.1%-73.4%) that belonged to lipids and lipid-like molecules, organic acids and derivatives, and benzenoids. The levels of those DEMs were significantly correlated with the relative abundances of nine bacterial genera. Also, redundancy discriminant analysis revealed that the main factors affecting changes in the bacterial community composition were available potassium (AK), microbial biomass nitrogen (MBN), microbial biomass carbon (MBC), alkaline hydrolysis nitrogen (AHN), total nitrogen (TN), available phosphorus (AP), and soil organic matter (SOM). The main factors affecting changes in the metabolite profiles were AK, MBC, MBN, AHN, pH, SOM, TN, and AP. Overall, this study provides new insights into the TDG defense mechanisms involved in winter cold stress responses when grown on reclaimed land and practical guidelines for achieving optimal TDG production.IMPORTANCEChina has been undergoing rapid urbanization, and land reclamation is regarded as a viable option to balance occupation and compensation. In general, the quality of reclaimed land cannot meet plant or even cultivation requirements due to poor soil fertility and high gravel content. However, Tetrastigma hemsleyanum Diels & Gilg (TDG), extensively used in Chinese herbal medicine, can grow well in stony soils with few nutrients. So, to increase reclaimed land use, TDG has been cultivated on reclaimed lands in Zhejiang Province, China, recently. However, the artificial cultivation of TDG is often limited by winter cold stress. The aim of this study was to find out how TDG on reclaimed land deal with winter cold stress by looking at the bacterial communities, metabolites, and physicochemical properties of the soil, thereby guiding production in practice.

Spatio-temporal structuring and assembly of abundant and rare bacteria in the benthic compartment of a marginally eutrophic lagoon

The investigations on ecological processes that structure abundant and rare sub-communities are limited from the benthic compartments of tropical brackish lagoons. We examined the spatial and temporal patterns in benthic bacterial communities of a brackish lagoon; Chilika. Abundant and rare bacteria showed differences in niche specialization but exhibited similar distance-decay patterns. Abundant bacteria were mostly habitat generalists due to their broader niche breadth, environmental response thresholds, and greater functional redundancy. In contrast, rare bacteria were mostly habitat specialists due to their narrow niche breadth, lower environmental response thresholds, and functional redundancy. The spatial patterns in abundant bacteria were largely shaped by stochastic processes (88.7 %, mostly dispersal limitation). In contrast, rare bacteria were mostly structured by deterministic processes (56.4 %, mostly heterogeneous selection). These findings provided a quantitative assessment of the different forces namely spatial, environmental, and biotic that together structured bacterial communities in the benthic compartment of a marginally eutrophic lagoon.

Potential stimulation of nitrifying bacteria activities and genera by landfill leachate

With the increasing complexity of influent composition in wastewater treatment plants, the potential stimulating effects of refractory organic matter in wastewater on growth characteristics and genera conversion of nitrifying bacteria (ammonium-oxidizing bacteria [AOB] and nitrite-oxidizing bacteria [NOB]) need to be further investigated. In this study, domestic wastewater was co-treated with landfill leachate in the lab-scale reactor, and the competition and co-existence of NOB genera Nitrotoga and Nitrospira were observed. The results demonstrated that the addition of landfill leachate could induce the growth of Nitrotoga, whereas Nitrotoga populations remain less competitive in domestic wastewater operation. In addition, the refractory organic matter in the landfill leachate also would have a potential stimulating effect on the maximum specific growth rate of AOB genus Nitrosomonas (μmax, aob). The μmax, aob of Nitrosomonas in the control group was estimated to be 0.49 d-1 by fitting the ASM model, and the μmax, aob reached 0.66-0.71 d-1 after injection of refractory organic matter in the landfill leachate, while the maximum specific growth rate of NOB (μmax, nob) was always in the range of 1.05-1.13 d-1. These findings have positive significance for the understanding of potential stimulation on nitrification processes and the stable operation of innovative wastewater treatment process.

Role of plant metabolites in the formation of bacterial communities in the rhizosphere of Tetrastigma hemsleyanum

Tetrastigma hemsleyanum Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of SYQ. In the plant growth related researches, rhizosphere microbiome has gained significant attention. However, the role of bacterial communities in the accumulation of metabolites in plants have not been investigated. Herein, the composition of bacterial communities in the rhizosphere soils and the metabolites profile of different SYQ cultivars' roots were analyzed. It was found that the composition of microbial communities varied in the rhizosphere soils of different SYQ cultivars. The high abundance of Actinomadura, Streptomyces and other bacteria was found to be associated with the metabolites profile of SYQ roots. The findings suggest that the upregulation of rutin and hesperetin may contribute to the high bioactive constituent in SYQ roots. These results provide better understanding of the metabolite accumulation pattern in SYQ, and also provide a solution for enhancing the quality of SYQ by application of suitable microbial consortia.

Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales

Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named "Ca. Nitronereus thalassa", represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, "Ca. Nitronereus thalassa" harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, "Ca. Nitronereus thalassa" appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.

Microbial community and gene dynamics response to high concentrations of gadolinium and sulfamethoxazole in biological nitrogen removal system

The impact of high antibiotic and heavy metal pollution levels on biological nitrogen removal in wastewater treatment plants (WWTPs) remains poorly understood, posing a global concern regarding the issue spread of antibiotic resistance induced by these contaminants. Herein, we investigated the effects of gadolinium (Gd) and sulfamethoxazole (SMX), commonly found in medical wastewater, on biological nitrogen removal systems and microbial characteristics, and the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). Our findings indicated that high SMX and Gd(III) concentrations adversely affected nitrification and denitrification, with Gd(III) exerting a strong inhibitory effect on microbial activity. Metagenomic analysis revealed that high SMX and Gd(III) concentrations could reduce microbial diversity, with Thauera and Pseudomonas emerging as dominant genera across all samples. While the relative abundance of most ARGs decreased under single Gd(III) stress, MRGs increased, and nitrification functional genes were inhibited. Conversely, combined SMX and Gd(III) pollution increased the relative abundance of intl1. Correlation analysis revealed that most genera could host ARGs and MRGs, indicating co-selection and competition between these resistance genes. However, most denitrifying functional genes exhibited a positive correlation with MRGs. Overall, our study provides novel insights into the impact of high concentrations of antibiotics and heavy metal pollution in WWTPs, and laying the groundwork for the spread and proliferation of resistance genes under combined SMX and Gd pollution.

Nitrification in acidic and alkaline environments

Aerobic nitrification is a key process in the global nitrogen cycle mediated by microorganisms. While nitrification has primarily been studied in near-neutral environments, this process occurs at a wide range of pH values, spanning ecosystems from acidic soils to soda lakes. Aerobic nitrification primarily occurs through the activities of ammonia-oxidising bacteria and archaea, nitrite-oxidising bacteria, and complete ammonia-oxidising (comammox) bacteria adapted to these environments. Here, we review the literature and identify knowledge gaps on the metabolic diversity, ecological distribution, and physiological adaptations of nitrifying microorganisms in acidic and alkaline environments. We emphasise that nitrifying microorganisms depend on a suite of physiological adaptations to maintain pH homeostasis, acquire energy and carbon sources, detoxify reactive nitrogen species, and generate a membrane potential at pH extremes. We also recognize the broader implications of their activities primarily in acidic environments, with a focus on agricultural productivity and nitrous oxide emissions, as well as promising applications in treating municipal wastewater.

Rapid nitrification involving comammox and canonical Nitrospira at extreme pH in saline-alkaline lakes

Nitrite-oxidizing bacteria (NOB) catalyse the second nitrification step and are the main biological source of nitrate. The most diverse and widespread NOB genus is Nitrospira, which also contains complete ammonia oxidizers (comammox) that oxidize ammonia to nitrate. To date, little is known about the occurrence and biology of comammox and canonical nitrite oxidizing Nitrospira in extremely alkaline environments. Here, we studied the seasonal distribution and diversity, and the effect of short-term pH changes on comammox and canonical Nitrospira in sediments of two saline, highly alkaline lakes. We identified diverse canonical and comammox Nitrospira clade A-like phylotypes as the only detectable NOB during more than a year, suggesting their major importance for nitrification in these habitats. Gross nitrification rates measured in microcosm incubations were highest at pH 10 and considerably faster than reported for other natural, aquatic environments. Nitrification could be attributed to canonical and comammox Nitrospira and to Nitrososphaerales ammonia-oxidizing archaea. Furthermore, our data suggested that comammox Nitrospira contributed to ammonia oxidation at an extremely alkaline pH of 11. These results identify saline, highly alkaline lake sediments as environments of uniquely strong nitrification with novel comammox Nitrospira as key microbial players.

Rapid establishment of algal-bacterial granular sludge system by applying mycelial pellets in a lab-scale photo-reactor under low aeration conditions: Performance and mechanism analysis

Light-driven algal-bacterial granular sludge (ABGS) is an innovative low-carbon technology with significant merits in treating municipal wastewater, but how to shorten the photogranulation process, especially under low aeration conditions, is largely unknown. Herein, two strategies were proposed to accelerate the start-up of the ABGS system in photo-sequencing batch reactors (PSBRs) with a low superficial gas velocity of 0.5 cm/s. Compared to directly dosing mycelial pellets (MPs), applying MPs to flocculate algae and using the formed algal-mycelial pellets (AMPs) as carriers enhanced the establishment of the algal-bacterial symbiosis. The ABGS system developed rapidly within 20 days, with a large particle diameter (mean diameter of 321 μm) and excellent settleability (SVI₃₀ of 55.4 mL/g). More importantly, this system could be stably operated for at least 100 days, mainly attributed to the reinforced secretion of protein with unique secondary structure and elevated hydrophobic functional groups. As for the reactor performance, the average removal efficiencies of the ABGS system were 97.8% for organic matter, 80.0% for total nitrogen, and 84.4% for phosphorus. The enrichment of functional bacteria and algae, and the up-regulation of functional genes and enzymes involved in electron production and transport processes likely drove the transformation of the pollutants, underlining the inherent mechanism for the excellent nutrient removal performance. This study provides a promising approach to solve the problem of a long ABGS start-up period and unstable granular structure under low aeration conditions, which is significant for achieving effective wastewater treatment without energy intensive aeration.

Reactive and microbial inhibitory mechanisms depicting the panoramic view of pH stress effect on common biological nitrification

pH is a crucial factor of microbial nitrification, which often combines with high-strength ammonium to influence nitrogen removal pathway in wastewater treatment. However, the detailed inhibitory mechanisms of pH stress are not sufficiently disclosed yet. In this study, the pH stress effect on nitrification was comprehensively studied by a set of experiments which identified the reactivity of nitrification processes and activity of nitrifiers, the time dependence of inhibition effect and the hybrid pH stress effect with ammonium. The results revealed two distinct inhibitory mechanisms dominating in alkaline and acid ranges. In alkaline range (pH > 8), pH stress causes physiological damages on microorganisms which is named as microbial inhibition. It has the features of less recoverability of nitrifiers, time-dependent inhibition effect and low pH-tolerance of nitrite oxidation bacteria. Free ammonia enhanced microbial inhibition and greatly promoted nitrite accumulation. A novel reactive inhibition mechanism dominated in acid range (pH < 7) was disclosed. It only impedes ammonia oxidation process (AOP) but not impair microbial activity obviously and the effect is time-independent. The mechanism was clarified from H⁺ transport because AOP involved H⁺ production. The H⁺ transport was impeded under acid stress owing to the decrease of pH gradient across cell membrane. The two mechanisms formed a panoramic view of pH stress effect on nitrification advancing the understanding of nitrifier adaptability and nitritation regulation in wastewater treatment processes.

How methanotrophs respond to pH: A review of ecophysiology

Varying pH globally affects terrestrial microbial communities and biochemical cycles. Methanotrophs effectively mitigate methane fluxes in terrestrial habitats. Many methanotrophs grow optimally at neutral pH. However, recent discoveries show that methanotrophs grow in strongly acidic and alkaline environments. Here, we summarize the existing knowledge on the ecophysiology of methanotrophs under different pH conditions. The distribution pattern of diverse subgroups is described with respect to their relationship with pH. In addition, their responses to pH stress, consisting of structure-function traits and substrate affinity traits, are reviewed. Furthermore, we propose a putative energy trade-off model aiming at shedding light on the adaptation mechanisms of methanotrophs from a novel perspective. Finally, we take an outlook on methanotrophs' ecophysiology affected by pH, which would offer new insights into the methane cycle and global climate change.

Microplastics drive nitrification by enriching functional microorganisms in aquaculture pond waters

The plastisphere refers to biofilm formation on the microplastic (MP) surface, but its subsequent functions, especially driving the nitrogen biogeochemical cycle, are rarely studied. Here, MPs were incubated in the pelagic water and benthic water-sediment interface of an aquaculture pond, and the two corresponding microcosms amended with incubated plastisphere were simulated. The results showed decreased ammonia concentrations and increased nitrification rates in microcosms with either pelagic or benthic plastispheres. To uncover the possible mechanisms, the community structure and function of the plastisphere were investigated. As clarified by 16S rRNA, the community diversity of the pelagic plastisphere was significantly higher than that of the corresponding hydrosphere. Plastisphere communities, especially those incubated in pelagic water, were separated from the hydrosphere. Moreover, the abundance of Proteobacteria increased while the abundance of Cyanobacteria decreased in both plastispheres. Metagenome further revealed that the abundance of amoA and annotated Nitrososphaeraceae_archaeon and hao and affiliated Nitrosomonas_europaea, which contributed to ammonia oxidation to nitrite, was higher in the benthic plastisphere. Comparing the pelagic plastisphere with the corresponding hydrosphere, however, the abundance of nxrA and annotated Nitrobacter hamburgensis and nxrB and the affiliated Nitrospira moscoviensis, which are involved in nitrite oxidation, was more abundant in the plastisphere. These findings suggest that the plastisphere might selectively enrich functional microorganisms and genes in a habitat-dependent manner to promote nitrification in aquaculture ponds.

A nitrite-oxidising bacterium constitutively consumes atmospheric hydrogen

Chemolithoautotrophic nitrite-oxidising bacteria (NOB) of the genus Nitrospira contribute to nitrification in diverse natural environments and engineered systems. Nitrospira are thought to be well-adapted to substrate limitation owing to their high affinity for nitrite and capacity to use alternative energy sources. Here, we demonstrate that the canonical nitrite oxidiser Nitrospira moscoviensis oxidises hydrogen (H2) below atmospheric levels using a high-affinity group 2a nickel-iron hydrogenase [Km(app) = 32 nM]. Atmospheric H2 oxidation occurred under both nitrite-replete and nitrite-deplete conditions, suggesting low-potential electrons derived from H2 oxidation promote nitrite-dependent growth and enable survival during nitrite limitation. Proteomic analyses confirmed the hydrogenase was abundant under both conditions and indicated extensive metabolic changes occur to reduce energy expenditure and growth under nitrite-deplete conditions. Thermodynamic modelling revealed that H2 oxidation theoretically generates higher power yield than nitrite oxidation at low substrate concentrations and significantly contributes to growth at elevated nitrite concentrations. Collectively, this study suggests atmospheric H2 oxidation enhances the growth and survival of NOB amid variability of nitrite supply, extends the phenomenon of atmospheric H2 oxidation to an eighth phylum (Nitrospirota), and reveals unexpected new links between the global hydrogen and nitrogen cycles. Long classified as obligate nitrite oxidisers, our findings suggest H2 may primarily support growth and survival of certain NOB in natural environments.

Effects of agricultural land use on the differentiation of nitrifier communities and functional patterns from natural terrestrial ecosystems

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such variation is mostly limited to ammonia oxidizers (AO) in local fields, excluding soil heterogeneity and nitrite-oxidizing bacteria (NOB); the variation under diverse climatic and soil conditions is not comprehensively understood. We conducted a large-scale survey of 131 cropland and natural sites in China. The community patterns of ammonia-oxidizing bacteria (AOB) and NOB differed significantly between croplands and some natural ecosystems, whereas ammonia-oxidizing archaea (AOA) were not affected by ecosystem type. The AOB population and nitrification potential (NP) were significantly higher in agroecosystems than in natural systems except wetlands. Fewer co-occurrence interactions involving nitrifiers were observed in croplands than in natural ecosystems except forests, systematically indicating the ecological diversification of nitrifiers in potential microbial associations among these habitats. Ecosystem type, pH, organic matter (OM), total phosphorus (TP), mean annual temperature (MAT) and mean annual precipitation (MAP) were primary drivers of nitrifier community and functional shifts. This study provides the first large-scale evidence of overall nitrifier community (i.e., AOA, AOB and NOB) and potential functional shifts between agroecosystems and natural environments, enabling predictions of terrestrial N cycle under foreseeable natural land use conversions and global climate change.

Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge

Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.

Effects of long-term exposure to the herbicide nicosulfuron on the bacterial community structure in a factory field

This study aims to investigate the effects of long-term nicosulfuron residue on an herbicide factory ecosystem. High-throughput sequencing was used to investigate the environmental microbial community structure and interactions. The results showed that the main contributor to the differences in the microbial community structure was the sample type, followed by oxygen content, pH and nicosulfuron residue concentration. Regardless of the presence or absence of nicosulfuron, soil, sludge, and sewage were dominated by groups of Bacteroidetes, Actinobacteria, and Proteobacteria. Long-term exposure to nicosulfuron increased alpha diversity of bacteria and archaea but significantly decreased the abundance of Bacteroidetes and Acidobateria compared to soils without nicosulfuron residue. A total of 81 possible nicosulfuron-degrading bacterial genera, e.g., Rhodococcus, Chryseobacterium, Thermomonas, Stenotrophomonas, and Bacillus, were isolated from the nicosulfuron factory environmental samples through culturomics. The co-occurrence network analysis indicated that the keystone taxa were Rhodococcus, Stenotrophomonas, Nitrospira, Terrimonas, and Nitrosomonadaceae_MND1. The strong ecological relationship between microorganisms with the same network module was related to anaerobic respiration, the carbon and nitrogen cycle, and the degradation of environmental contaminants. Synthetic community (SynCom), which provides an effective top-down approach for the critical degradation strains obtained, enhanced the degradation efficiency of nicosulfuron. The results indicated that Rhodococcus sp. was the key genus in the environment of long-term nicosulfuron exposure.

Influence of ammonia and NaCl on nitrifying community and activity: Implications for formulating nitrifying culture augmentation

Bioaugmentation of nitrifying cultures can accelerate nitrification during startup and transition periods of recirculating aquaculture system (RAS) operations. To formulate nitrifying cultures for RASs, impacts of ammonia and salinity (NaCl) on culturing nitrifying microorganisms were comprehensively investigated by including currently known groups of nitrifying microorganisms (ammonia oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), comammox, Nitrospira, and Nitrobacter). By varying ammonia loading rate (ALRs of 1.6, 8, 20, 40, 60 and 150 mgN/L/d) of continuous-flow bioreactors fed with inorganic medium experimented for culture preparation, cultures containing distinct patterns of nitrifying communities were produced. Operating the reactors at the ALRs of ≤40 mgN/L/d, resulting in the effluent total ammonia nitrogen (TAN) and nitrite concentrations of ≤2.64 and ≤0.53 mgN/L, respectively, delivered the consortia consisting of a broad spectrum of substrate affinity nitrifying microorganisms. At the lower ranges of these ALRs (≤8 mgN/L/d), the most desirable consortia comprising comparable numbers of AOB, AOA, and comammox could be produced (the effluent TAN concentrations of ≤0.20 mgN/L), which would be resilient for applying in various RAS types. Enriching the cultures at the ALRs of ≥60 mgN/L/d allowed only the nitrifying microorganisms with low substrate affinity to dominate, incongruent with the consortia found in actual RASs. AOB were adaptable at all salinity studied (2, 15, and 30 g/L), while AOA and comammox were sensitive to elevated salinity (15 and 30 g/L, respectively). The ammonia removal rate of a culture prepared at 2 g/L salinity decreased largely when applied at 15 and 30 g/L. In contrast, those prepared at 15 and 30 g/L were more robust to different salinity. Separately preparing the cultures at different salinity for uses in freshwater-low salinity and brackish-marine RASs is recommended. The findings of this work enhance our understanding on how to formulate nitrifying culture augmentation for used in different RAS types.

Microbial community structures and their driving factors in a typical gathering area of antimony mining and smelting in South China

This study investigated soil microbial community in a typical gathering area of antimony mining and smelting in South China. The physical and chemical properties of different soils (mining waste dumps, flotation tailings, and smelting slag) and depths (0-20 cm, 40-60 cm, and 80-100 cm) were compared. The results showed that antimony (Sb) and arsenic (As) were the main pollutants, and their concentrations were 5524.7 mg/kg and 3433.7 mg/kg, respectively. Xanthates were found in the flotation tailings and smelting slag, and the highest concentration was 585.1 mg/kg. The microbial communities were analyzed by high-throughput sequencing, and it was shown that Proteobacteria, Acidobacteria, Chlorobacterium, Bacteroides, and Actinomycetes were the dominant taxa at the phylum level. There were obvious differences in microbial community structure in different sites. The dominant microorganism in the mining site was Chujaibacter. Subgroup_2_unclassified and Gemmatimonadaceae_unclassified were the prevalent microorganisms in the flotation and smelting sites, respectively. As, Sb, and xanthates were the main factors affecting the diversity and composition of bacteria in the flotation tailings and smelting slag areas. Therefore, this study provides experimental guidance and a theoretical basis for soil antimony pollution quality assessment, biological treatment, and environmental remediation.

Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.

Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors

Aerobic ammonia and nitrite oxidation reactions are fundamental biogeochemical reactions contributing to the global nitrogen cycle. Although aerobic nitrite oxidation yields 4.8-folds less Gibbs free energy (∆G_r ) than aerobic ammonia oxidation in the NH₄ ⁺ -feeding marine recirculating trickling biofilter reactors operated in the present study, nitrite-oxidizing and not ammonia-oxidizing Nitrospira (sublineage IV) outnumbered ammonia-oxidizing Nitrosomonas (relative abundance; 53.8% and 7.59% respectively). CO₂ assimilation efficiencies during ammonia or nitrite oxidation were 0.077 μmol-¹⁴ CO₂ /μmol-NH₃ and 0.053-0.054 μmol-¹⁴ CO₂ /μmol-NO₂ ^- respectively, and the difference between ammonia and nitrite oxidation was much smaller than the difference of ∆G_r . Free-energy efficiency of nitrite oxidation was higher than ammonia oxidation (31%-32% and 13% respectively), and high CO₂ assimilation and free-energy efficiencies were a determinant for the dominance of Nitrospira over Nitrosomonas. Washout of Nitrospira and Nitrosomonas from the trickling biofilter reactors was also examined by quantitative PCR assay. Normalized copy numbers of Nitrosomonas amoA were 1.5- to 1.7-folds greater than Nitrospira nxrB and 16S rRNA gene in the reactor effluents. Nitrosomonas was more susceptible for washout than Nitrospira in the trickling biofilter reactors, which was another determinant for the dominance of Nitrospira in the trickling biofilter reactors.

Metabacillus dongyingensis sp. nov. Is Represented by the Plant Growth-Promoting Bacterium BY2G20 Isolated from Saline-Alkaline Soil and Enhances the Growth of Zea mays L. under Salt Stress

A novel plant growth-promoting rhizobacterium (PGPR), which was designated strain BY2G20, was isolated from saline-alkaline soil in Dongying, China. Strain BY2G20 can grow at a NaCl range from 0 to 7% and a pH range from 7 to 9 and can prevent the growth of the phytopathogen Ralstonia solanacearum. Based on its phenotypic and genomic characteristics and phylogenetic analysis, strain BY2G20 represents a novel species of the genus Metabacillus, for which the name Metabacillus dongyingensis sp. nov. is proposed. Comparative genomic analysis of strain BY2G20 with its closely related species exhibited a high level of evolutionary plasticity derived by horizontal gene transfer, which facilitated adaptative evolution. Different evolutionary constraints have operated on the diverse functions of BY2G20, with the gene adapted to saline-alkaline ecosystems experiencing functional constraints. We determined the genetic properties of saline-alkaline tolerance and plant growth promotion, such as cation-proton antiporters, cation transporters, osmoprotectant synthesis and transport, H⁺-transporting F₁F₀-ATPase, indole-3-acetic acid production, and secondary metabolite synthesis. We also evaluated the effects of strain BY2G20 on the growth of Zea mays L. (maize) under salt stress. The physiological parameters of maize such as plant height, stem diameter, dry biomass, and fresh biomass were significantly higher after inoculating strain BY2G20 under salt stress, indicating that inoculation with BY2G20 enhanced the growth of maize in saline areas. This study demonstrates that M. dongyingensis sp. nov. BY2G20 is a potential candidate for organic agriculture biofertilizers in saline-alkaline areas.

IMPORTANCE Plant growth and yield are adversely affected by soil salinity. PGPRs can promote plant growth and enhance plant tolerance to salt stress. In this study, a saline-alkaline tolerant PGPR strain BY2G20 was isolated from the rhizosphere of Ulmus pumila in Dongying, China. Strain BY2G20 represents a novel species within the genus Metabacillus based on phenotypic, genomic, and phylogenetic analysis. Genomic components have undergone different functional constraints, and the disparity in the evolutionary rate may be associated with the adaptation to a specific niche. Genomic analysis revealed numerous adaptive features of strain BY2G20 to a saline-alkaline environment and rhizosphere, especially genes related to salt tolerance, pH adaptability, and plant growth promotion. Our work also exhibited that inoculation of strain BY2G20 enhanced the growth of maize under salt stress. This study demonstrates that PGPRs play an important role in stimulating salt tolerance in plants and can be used as biofertilizers to enhance the growth of crops in saline-alkaline areas.

Effects of Waterlogging on Soybean Rhizosphere Bacterial Community Using V4, LoopSeq, and PacBio 16S rRNA Sequence

Waterlogging causes a significant reduction in soil oxygen levels, which in turn negatively affects soil nutrient use efficiency and crop yields. Rhizosphere microbes can help plants to better use nutrients and thus better adapt to this stress, while it is not clear how the plant-associated microbes respond to waterlogging stress. There are also few reports on whether this response is influenced by different sequencing methods and by different soils. In this study, using partial 16S rRNA sequencing targeting the V4 region and two full-length 16S rRNA sequencing approaches targeting the V1 to V9 regions, the effects of waterlogging on soybean rhizosphere bacterial structure in two types of soil were examined. Our results showed that, compared with the partial 16S sequencing, full-length sequencing, both LoopSeq and Pacific Bioscience (PacBio) 16S sequencing, had a higher resolution. On both types of soil, all the sequencing methods showed that waterlogging significantly affected the bacterial community structure of the soybean rhizosphere and increased the relative abundance of Geobacter. Furthermore, modular analysis of the cooccurrence network showed that waterlogging increased the relative abundance of some microorganisms related to nitrogen cycling when using V4 sequencing and increased the microorganisms related to phosphorus cycling when using LoopSeq and PacBio 16S sequencing methods. Core microorganism analysis further revealed that the enriched members of different species might play a central role in maintaining the stability of bacterial community structure and ecological functions. Together, our study explored the role of microorganisms enriched at the rhizosphere under waterlogging in assisting soybeans to resist stress. Furthermore, compared to partial and PacBio 16S sequencing, LoopSeq offers improved accuracy and reduced sequencing prices, respectively, and enables accurate species-level and strain identification from complex environmental microbiome samples. IMPORTANCE Soybeans are important oil-bearing crops, and waterlogging has caused substantial decreases in soybean production all over the world. The microbes associated with the host have shown the ability to promote plant growth, nutrient absorption, and abiotic resistance. High-throughput sequencing of partial 16S rRNA is the most commonly used method to analyze the microbial community. However, partial sequencing cannot provide correct classification information below the genus level, which greatly limits our research on microbial ecology. In this study, the effects of waterlogging on soybean rhizosphere microbial structure in two soil types were explored using partial 16S rRNA and full-length 16S gene sequencing by LoopSeq and Pacific Bioscience (PacBio). The results showed that full-length sequencing had higher classification resolution than partial sequencing. Three sequencing methods all indicated that rhizosphere bacterial community structure was significantly impacted by waterlogging, and the relative abundance of Geobacter was increased in the rhizosphere in both soil types after suffering waterlogging. Moreover, the core microorganisms obtained by different sequencing methods all contain species related to nitrogen cycling. Together, our study not only explored the role of microorganisms enriched at the rhizosphere level under waterlogging in assisting soybean to resist stress but also showed that LoopSeq sequencing is a less expensive and more convenient method for full-length sequencing by comparing different sequencing methods.

Sodium Energetic Cycle in the Natronophilic Bacterium Thioalkalivibrio versutus

As inhabitants of soda lakes, Thioalkalivibrio versutus are halo- and alkaliphilic bacteria that have previously been shown to respire with the first demonstrated Na⁺-translocating cytochrome-c oxidase (CO). The enzyme generates a sodium-motive force (Δs) as high as −270 mV across the bacterial plasma membrane. However, in these bacteria, operation of the possible Δs consumers has not been proven. We obtained motile cells and used them to study the supposed Na⁺ energetic cycle in these bacteria. The resulting motility was activated in the presence of the protonophore 2-heptyl-4-hydroxyquinoline N-oxide (HQNO), in line with the same effect on cell respiration, and was fully blocked by amiloride—an inhibitor of Na⁺-motive flagella. In immotile starving bacteria, ascorbate triggered CO-mediated respiration and motility, both showing the same dependence on sodium concentration. We concluded that, in T. versutus, Na⁺-translocating CO and Na⁺-motive flagella operate in the Na⁺ energetic cycle mode. Our research may shed light on the energetic reason for how these bacteria are confined to a narrow chemocline zone and thrive in the extreme conditions of soda lakes.

Salt tolerance-based niche differentiation of soil ammonia oxidizers

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined ¹³C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of active ammonia oxidizers in a saline-sodic (solonetz) soil with high salinity and pH (20.9 cmol_c exchangeable Na⁺ kg^-1 soil and pH 9.64). Both ammonia-oxidizing archaea (AOA) and bacteria (AOB) exhibited strong nitrification activities, although AOB performed most of the ammonia oxidation observed in the solonetz soil and in the farmland soil converted from solonetz soil. Members of the Nitrosococcus, which are more often associated with aquatic habitats, were identified as the dominant ammonia oxidizers in the solonetz soil with the first direct labeling evidence, while members of the Nitrosospira were the dominant ammonia oxidizers in the farmland soil, which had much lower salinity and pH. Metagenomic analysis of "Candidatus Nitrosococcus sp. Sol14", a new species within the Nitrosococcus lineage, revealed multiple genomic adaptations predicted to facilitate osmotic and pH homeostasis in this extreme habitat, including direct Na⁺ extrusion/H⁺ import and the ability to increase intracellular osmotic pressure by accumulating compatible solutes. Comparative genomic analysis revealed that variation in salt-tolerance mechanisms was the primary driver for the niche differentiation of ammonia oxidizers in saline-sodic soils. These results demonstrate how ammonia oxidizers can adapt to saline-sodic soil with excessive Na⁺ content and provide new insights on the nitrogen cycle in extreme terrestrial ecosystems.

Metagenomics insights into the selective inhibition of NOB and comammox by phenacetin: Transcriptional activity, nitrogen metabolism and mechanistic understanding

Phenacetin (PNCT), a common antipyretic and analgesic drug, is often used to treat fever and headache. However, the effect of PNCT on nitrifiers in wastewater treatment processes remains unclear. The practicability of attaining partial nitrification (PN) through inhibitor-PNCT was investigated in this study. The optimal treatment conditions of soaking once for 18 h with 2.50 × 10^-3 g PNCT/(g MLSS) were applied to the PN stability experiment. The results showed that ammonia oxidation activity recovered quickly after 3 cycles of operation, while nitrite oxidation activity was suppressed steadily. In addition, average ammonium removal efficiency and nitrite accumulation ratio during 138 cycles could reach 94.94% and 85.38%, respectively. Complimentary DNA high-throughput sequencing and oligotyping analysis showed that the activity of Nitrosomonas would gradually surpass Nitrospira after PNCT treatment only once. The decrease of Nitrospira activity was accompanied by the simplification of oligotypes after PNCT treatment, while Nitrosomonas could adapt to PNCT stress by reducing the differences between oligotypes. Metagenomics revealed that the decrease in the number of NXR in the nitrogen metabolism pathways was the key reason for achieving PN. The potential mechanisms might be that the dominant nitrite-oxidizing bacteria and complete ammonia oxidizers were bio-killed by PNCT.

Nitrogen Kinetic Isotope Effects of Nitrification by the Complete Ammonia Oxidizer Nitrospira inopinata

Analysis of nitrogen isotope fractionation effects is useful for tracing biogeochemical nitrogen cycle processes. Nitrification can cause large nitrogen isotope effects through the enzymatic oxidation of ammonia (NH₃) via nitrite (NO₂⁻) to nitrate (NO₃⁻) (¹⁵ε_NH4+→NO2- and ¹⁵ε_NO2-→NO3-). The isotope effects of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and of nitrite-oxidizing bacteria (NOB) have been analyzed previously. Here, we studied the nitrogen isotope effects of the complete ammonia oxidizer (comammox) Nitrospira inopinata that oxidizes NH₃ to NO₃⁻. At high ammonium (NH₄⁺) availability (1 mM) and pH between 6.5 and 8.5, its ¹⁵ε_NH4+→NO2- ranged from −33.1 to −27.1‰ based on substrate consumption (residual substrate isotopic composition) and −35.5 to −31.2‰ based on product formation (cumulative product isotopic composition), while the ¹⁵ε_NO2-→NO3- ranged from 6.5 to 11.1‰ based on substrate consumption. These values resemble isotope effects of AOB and AOA and of NOB in the genus Nitrospira, suggesting the absence of fundamental mechanistic differences between key enzymes for ammonia and nitrite oxidation in comammox and canonical nitrifiers. However, ambient pH and initial NH₄⁺ concentrations influenced the isotope effects in N. inopinata. The ¹⁵ε_NH4+→NO2- based on product formation was smaller at pH 6.5 (−31.2‰) compared to pH 7.5 (−35.5‰) and pH 8.5 (−34.9‰), while ¹⁵ε_NO2-→NO3- was smaller at pH 8.5 (6.5‰) compared to pH 7.5 (8.8‰) and pH 6.5 (11.1‰). Isotopic fractionation via ¹⁵ε_NH4+→NO2- and ¹⁵ε_NO2-→NO3- was smaller at 0.1 mM NH₄⁺ compared to 0.5 to 1.0 mM NH₄⁺. Environmental factors, such as pH and NH₄⁺ availability, therefore need to be considered when using isotope effects in ¹⁵N isotope fractionation models of nitrification.

IMPORTANCE Nitrification is an important nitrogen cycle process in terrestrial and aquatic environments. The discovery of comammox has changed the view that canonical AOA, AOB, and NOB are the only chemolithoautotrophic organisms catalyzing nitrification. However, the contribution of comammox to nitrification in environmental and technical systems is far from being completely understood. This study revealed that, despite a phylogenetically distinct enzymatic repertoire for ammonia oxidation, nitrogen isotope effects of ¹⁵ε_NH4+→NO2- and ¹⁵ε_NO2-→NO3- in comammox do not differ significantly from those of canonical nitrifiers. Thus, nitrogen isotope effects are not suitable indicators to decipher the contribution of comammox to nitrification in environmental samples. Moreover, this is the first systematic study showing that the ambient pH and NH₄⁺ concentration influence the isotope effects of nitrifiers. Hence, these key parameters should be considered in comparative analyses of isotope effects of nitrifiers across different growth conditions and environmental samples.

Salinity gradients shape the nitrifier community composition in Nanliu River Estuary sediments and the ecophysiology of comammox Nitrospira inopinata

The recent discovery of complete ammonia oxidizers (comammox), which convert ammonia to nitrate in a single organism, revolutionized the conventional understanding that two types of nitrifying microorganisms have to be involved in the nitrification process for more than 100 years. However, how different types of nitrifiers in response to salinity change remains largely unclear. This study not only investigated nitrifier community (including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), comammox and nitrite-oxidizing Nitrospira) in the Nanliu estuary to find the ecological relationship between salinity and functional communities and also studied the physiology of a typical comammox Nitrospira inopinata in response to a salinity gradient. Based on sequences retrieved with four sets of functional gene primes, comammox Nitrospira was in general, mainly composed of clade A, with a clear separation of clade A1 subgroup in all samples and clade A2 subgroup in low salinity ones. As expected, group I.1b and group I.1a AOA dominated the AOA community in low- and high-salinity samples, respectively. Nitrosomonas-AOB were detected in all samples while Nitrosospira-AOB were mainly found in relatively high-salinity samples. Regarding general Nitrospira, lineages II and IV were the major groups in most of the samples, while lineage I Nitrospira was only detected in low-salinity samples. Furthermore, the comammox pure culture of N. inopinata showed an optimal salinity at 0.5‰ and ceased to grow at 12.8‰ for ammonia oxidation, but remained active for nitrite oxidation. These results show new evidence regarding niche specificity of different nitrifying microorganisms modulated mainly by salinity, and also a clear response by comammox N. inopinata to a wide range of simulated salinity levels.

Activity-Based Cell Sorting Reveals Resistance of Functionally Degenerate Nitrospira during a Press Disturbance in Nitrifying Activated Sludge

Managing and engineering activated sludge wastewater treatment microbiomes for low-energy nitrogen removal requires process control strategies to stop the oxidation of ammonium at nitrite. Our ability to out-select nitrite-oxidizing bacteria (NOB) from activated sludge is challenged by their metabolic and physiological diversity, warranting measurements of their in situ physiology and activity under selective growth pressures. Here, we examined the stability of nitrite oxidation in activated sludge during a press disturbance induced by treating a portion of return activated sludge with a sidestream flow containing free ammonia (FA) at 200 mg NH₃-N/liter. The nitrite accumulation ratio peaked at 42% by day 40 in the experimental bioreactor with the press disturbance, while it did not increase in the control bioreactor. A subsequent decrease in nitrite accumulation within the experimental bioreactor coincided with shifts in dominant Nitrospira 16S rRNA amplicon sequence variants (ASVs). We applied bioorthogonal noncanonical amino acid tagging (BONCAT) coupled with fluorescence-activated cell sorting (FACS) to investigate changes in the translational activity of NOB populations throughout batch exposure to FA. BONCAT-FACS confirmed that the single Nitrospira ASV washed out of the experimental bioreactor had reduced translational activity following exposure to FA, whereas the two Nitrospira ASVs that emerged after process acclimation were not impacted by FA. Thus, the coexistence of functionally degenerate and physiologically resistant Nitrospira populations provided resilience to the nitrite-oxidizing function during the press disturbance. These results highlight how BONCAT-FACS can resolve ecological niche differentiation within activated sludge and inform strategies to engineer and control microbiome function.

IMPORTANCE Nitrogen removal from activated sludge wastewater treatment systems is an energy-intensive process due to the large aeration requirement for nitrification. This energy footprint could be minimized with engineering control strategies that wash out nitrite-oxidizing bacteria (NOB) to limit oxygen demands. However, NOB populations can have a high degree of physiological diversity, and it is currently difficult to decipher the behavior of individual taxa during applied selective pressures. Here, we utilized a new substrate analog probing approach to measure the activity of NOB at the cellular translational level in the face of a press disturbance applied to the activated sludge process. Substrate analog probing corroborated the time series reactor sampling, showing that coexisting and functionally degenerate Nitrospira populations provided resilience to the nitrite oxidation process. Taken together, these results highlight how substrate analog approaches can illuminate in situ ecophysiologies within shared niches, and can inform strategies to improve microbiome engineering and management.

Response of activity and community composition of nitrite-oxidizing bacteria to partial substitution of chemical fertilizer by organic fertilizer

Nitrite oxidation as the second step of nitrification can become the determining step in disturbed soil systems. As a beneficial fertilization practice to maintain high crop yield and soil fertility, partial substitution of chemical fertilizer (CF) by organic fertilizer (OF) may exert a notable disturbance to soil systems. However, how nitrite oxidation responds to different proportions of CF to OF is still unclear. We sampled soils from a 4-year field experiment subject to a gradient of increasing proportions of OF to CF application. Activity, size, and structure of Nitrospira-like and Nitrobacter-like nitrite-oxidizing bacteria (NOB) community were measured. The results revealed that with increasing proportion of OF to CF application, potential nitrite oxidation activity (PNO) showed a marked decreasing trend. PNO was significantly correlated with the abundance of Nitrobacter-like but not Nitrospira-like NOB. The abundance of Nitrobacter-like was significantly influenced by soil organic matter, organic nitrogen (N), and available N. In addition, PNO was also affected by the structure of Nitrobacter-like NOB. The relative abundance of Nitrobacter hamburgensis, alkalicus, winogradskyi, and vulgaris responded differently to the proportions of OF to CF application. Organic N, organic matter, and available N were the main factor shaping their community structure. Overall, Nitrobacter-like NOB is more sensitive and plays a more important role than Nitrospira-like NOB in responding to different proportions of OF to CF application.

Metabolic versatility of the nitrite-oxidizing bacterium Nitrospira marina and its proteomic response to oxygen-limited conditions

The genus Nitrospira is the most widespread group of nitrite-oxidizing bacteria and thrives in diverse natural and engineered ecosystems. Nitrospira marina Nb-295^T was isolated from the ocean over 30 years ago; however, its genome has not yet been analyzed. Here, we investigated the metabolic potential of N. marina based on its complete genome sequence and performed physiological experiments to test genome-derived hypotheses. Our data confirm that N. marina benefits from additions of undefined organic carbon substrates, has adaptations to resist oxidative, osmotic, and UV light-induced stress and low dissolved pCO₂, and requires exogenous vitamin B₁₂. In addition, N. marina is able to grow chemoorganotrophically on formate, and is thus not an obligate chemolithoautotroph. We further investigated the proteomic response of N. marina to low (∼5.6 µM) O₂ concentrations. The abundance of a potentially more efficient CO₂-fixing pyruvate:ferredoxin oxidoreductase (POR) complex and a high-affinity cbb₃-type terminal oxidase increased under O₂ limitation, suggesting a role in sustaining nitrite oxidation-driven autotrophy. This putatively more O₂-sensitive POR complex might be protected from oxidative damage by Cu/Zn-binding superoxide dismutase, which also increased in abundance under low O₂ conditions. Furthermore, the upregulation of proteins involved in alternative energy metabolisms, including Group 3b [NiFe] hydrogenase and formate dehydrogenase, indicate a high metabolic versatility to survive conditions unfavorable for aerobic nitrite oxidation. In summary, the genome and proteome of the first marine Nitrospira isolate identifies adaptations to life in the oxic ocean and provides insights into the metabolic diversity and niche differentiation of NOB in marine environments.

Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification

The recent discovery of bacteria within the genus Nitrospira capable of complete ammonia oxidation (comammox) demonstrated that the sequential oxidation of ammonia to nitrate via nitrite can also be performed within a single bacterial cell. Although comammox Nitrospira exhibit a wide distribution in natural and engineered ecosystems, information on their physiological properties is scarce due to the limited number of cultured representatives. Additionally, most available genomic information is derived from metagenomic sequencing and high-quality genomes of Nitrospira in general are limited. In this study, we obtained a high (90%) enrichment of a novel comammox species, tentatively named "Candidatus Nitrospira kreftii", and performed a detailed genomic and physiological characterization. The complete genome of "Ca. N. kreftii" allowed reconstruction of its basic metabolic traits. Similar to Nitrospira inopinata, the enrichment culture exhibited a very high ammonia affinity (K_{m(app)_NH3} ≈ 0.040 ± 0.01 µM), but a higher nitrite affinity (K_{m(app)_NO2}- = 12.5 ± 4.0 µM), indicating an adaptation to highly oligotrophic environments. Furthermore, we observed partial inhibition of ammonia oxidation at ammonium concentrations as low as 25 µM. This inhibition of "Ca. N. kreftii" indicates that differences in ammonium tolerance rather than affinity could potentially be a niche determining factor for different comammox Nitrospira.

Nitrospira as versatile nitrifiers: Taxonomy, ecophysiology, genome characteristics, growth, and metabolic diversity

The global nitrogen cycle is of paramount significance as it affects important processes like primary productivity and decomposition. Nitrification, the oxidation of ammonia to nitrate via nitrite, is a key process in the nitrogen cycle. The knowledge about nitrification has been challenged during the last few decades with inventions like anaerobic ammonia oxidation, ammonia-oxidizing archaea, and recently the complete ammonia oxidation (comammox). The discovery of comammox Nitrospira has made a paradigm shift in nitrification, before which it was considered as a two-step process, mediated by chemolithoautotrophic ammonia oxidizers and nitrite oxidizers. The genome of comammox Nitrospira equipped with molecular machineries for both ammonia and nitrite oxidation. The genus Nitrospira is ubiquitous, comes under phylum Nitrospirae, which comprises six sublineages consisting of canonical nitrite oxidizers and comammox. The single-step nitrification is energetically more feasible; furthermore, the existence of diverse metabolic pathways in Nitrospira is critical for its establishment in various habitats. The present review discusses the taxonomy, ecophysiology, isolation, identification, growth, and metabolic diversity of the genus Nitrospira; compares the genomes of canonical nitrite-oxidizing Nitrospira and comammox Nitrospira, and analyses the differences of Nitrospira with other nitrifying bacteria.