Chemoorganoheterotrophic growth of Nitrosomonas europaea and Nitrosomonas eutropha

Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment

Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.

IMPORTANCE

Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.

Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge

This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.

Dual isotope labelling combined with multi-omics analysis revealing the N2O source evolution in aerobic biological systems driven by salinity gradient

Salinity is considered a major factor influencing nitrous oxide (N2O) emissions from biochemical treatment of high-salinity wastewater, but its mechanism has not been thoroughly investigated. In this study, we investigated the effects of salinity on N2O emissions under aerobic conditions. As salinity rose from 0.66 % to 3.66 %, N2O emission flux first increased and then decreased, while the emission factor (EF) consistently increased, likely due to significant inhibition of nitrification at 3.66 % salinity. Nitrogen‑oxygen dual isotope labeling experiments demonstrated that the dominant N2O production pathway shifted with salinity: from nitrifier nitrification (NN, 36.07 %-40.97 %) at low salinity (0.66 %, 1.66 %), to nitrification-coupled denitrification (NCD, 51.67 %) at 2.66 %, and to nitrifier denitrification (ND, up to 80.81 %) at the salinity of 3.66 %. From the changes in bacterial relative abundances and expressions of 4 key functional genes (amoA, hao, nor, and nosZ) revealed by metatranscriptomic sequencing, Nitrosomonas, unclassified Rhodospirillales, and Nitrospira were identified as key contributors to NN, NCD, and ND pathways, respectively, as salinity increased. We also found that the differential expressed genes and metabolites involved in energy metabolism, oxidative phosphorylation, and metabolism of amino acids, pyrimidines, and nucleotides may affect N-cycling bacteria, thereby influencing nitrogen conversion and salinity tolerance as well. This study sheds light on nitrification process in response to salinity stress and offers insights for mitigating greenhouse gas emissions from high-salinity wastewater treatment.

Nitrite accumulation in activated sludge through cyclic anaerobic exposure with acetate

Achieving nitrite accumulation still remains challenging for efficient short-cut biological nitrogen removal in municipal wastewater treatment. To tackle the problem of insufficient carbon in incoming wastewater for biological nutrient removal, a return activated sludge (RAS) fermentation method has been proposed and demonstrated to enable producing supplemental volatile fatty acids (VFAs) and enhance biological phosphorus removal via sludge cycling between mainstream and a sidestream anaerobic reactor. However, the impacts of long anaerobic exposure with acetate on nitrifying bacteria, known as the aerobic chemoautotrophic microorganisms, remains unexplored. In this study, the activated sludge underwent a cyclic anaerobic treatment with the addition of acetate (Ac), the effects on nitrification rate, abundance and microdiversity of nitrifying communities were comprehensively assessed. Firstly, batch activity tests proved the direct addition of high acetate (above 1000 mg/L) could cause inhibition on the nitrification rate, moreover, the inhibitory effect was stronger on nitrite-oxidizing bacteria (NOB) activity than that of ammonia-oxidizing bacteria (AOB). Then, a sequencing batch reactor (SBR) was applied to test the nitrogen conversion performance for low-strength ammonium wastewater. Nitrite accumulation could be achieved via the cyclic anaerobic exposure with 1000-5000 mg Ac/L. The maximum effluent concentration of nitrite was 40.8 ± 3.5 mg N/L with nitrite accumulation ratio (NAR) of 67.6 ± 3.5%. The decrease in NOB activity (72.7%) was greater than AOB of 42.4%, promoting nitrite accumulation via nitritation process. Furthermore, the cyclic anaerobic exposure with acetate can largely reshape the nitrifying communities. As the dominant AOB and NOB, the abundance of Nitrosomonas and Nitrospira were both decreased with species-level microdiversity in the nitrifying communities. However, the heterotrophic microorganism, Thauera, were found to be highly enriched (from 0 to 17.3%), which may act as the potential nitrite producer as proved by the increased nitrate reduction gene abundance. This study can provide new insights into achieving mainstream nitrite accumulation by involving sidestream RAS fermentation towards efficient wastewater treatment management.

Redirecting carbon to recover VFA to facilitate biological short-cut nitrogen removal in wastewater treatment: A critical review

Wastewater treatment plants (WWTPs) are facing a great challenge to transition from energy-intensive to carbon-neutral and energy-efficient systems. Biological nutrient removal (BNR) can be severely impacted by carbon limitation, particularly for wastewater with a low carbon-to-nitrogen (C/N) ratio, which can significantly increase the operational costs. Waste activated sludge (WAS) is a valuable byproduct of WWTPs, as it contains high levels of organic matter that can be utilized to improve BNR management by recovering and reusing the fermentative volatile fatty acids (VFAs). This review provides a comprehensive examination of the recovery and reuse of VFAs in wastewater management, with a particular focus on advancing the preferable biological short-cut nitrogen removal process for carbon-insufficient municipal wastewaters. First, the method of carbon redirection for recovering VFAs was reviewed. Carbon could be captured through the two-stage A/B process or via sludge fermentation with different sludge pretreatment and process control strategies to accelerate sludge hydrolysis and inhibit methanogens to enhance VFA production. Second, VFAs can support the metabolism of autotrophic N-cycling microorganisms involved in wastewater treatment, such as AOB, NOB, anammox, and comammox bacteria. However, VFAs can also cause inhibition at high concentrations, leading to the partition of AOB and NOB; and can promote partial denitrification as an efficient carbon source for heterotrophic denitrifiers. Third, the lab- and pilot-scale engineering practices with different configurations (i.e., A²O, SBR, UASB) were summarized that have shown the feasibility of utilizing the fermentate to achieve superior nitrogen removal performance without the need for external carbon addition. Lastly, the future perspectives on leveraging the relationships between mainstream and sidestream, nitrogen and phosphorus, autotrophs and heterotrophs were given for sustainable and efficient BNR management.

Deciphering nitrous oxide emissions from tropical soils of different land uses

Tropical regions are hotspots of increasing greenhouse gas emissions associated with land-use change. Although many field studies have quantified soil fluxes of nitrous oxide (N₂O; a potent greenhouse gas) from various land uses, the driving mechanisms remain uncertain. Here, we used tropical soils of diverse land uses and actively manipulated the soil moisture (35%, 60%, and 95% water-filled pore space [WFPS]) and substrate supply (control, nitrate, and nitrate plus glucose) to investigate the responses of N₂O emissions with short-term incubations. We then identified key factors regulating N₂O emissions out of a series of soil physicochemical and biological factors and explored how these factors interacted to drive N₂O emissions. Land-use changes from primary forest to oil palm or Acacia plantation risks emitting more N₂O, whereas low emissions could be maintained by conversion to Macaranga forest or Imperata grassland; these laboratory observations were corroborated by a literature synthesis of field N₂O measurements across tropical regions. Soil redox potential (Eh) and labile organic nitrogen (LON; amino acid mixture, arginine, and urea) mineralization were among the factors with greatest influence on N₂O emissions. In contrast to common understandings, the control of WFPS over N₂O emissions was largely indirect, and acted through Eh. The mineralization of LON, particularly arginine, potentially played multiple roles in N₂O production (e.g., bottlenecks of nitrifier-denitrification or simultaneous nitrification-denitrification versus substrate competition for co-denitrification). Structural equation models suggest that soil-environmental factors of different levels (from distal including land use, soil moisture, and pH to proximal such as LON mineralization) drive N₂O emissions through cascading interactions. Overall, we show that, despite identical initial soil conditions, land conversion can substantially alter the N₂O emission potential. Also, collectively considering soil-environmental regulators and their interactions associated with land conversion is crucial to predict and design mitigation strategies for N₂O emissions from land-use change.

Syringic acid from rice roots inhibits soil nitrification and N2O emission under red and paddy soils but not a calcareous soil

Syringic acid (SA) is a novel biological nitrification inhibitor (BNIs) discovered in rice root exudates with significant inhibition of Nitrosomonas strains. However, the inhibitory effect of SA on nitrification and nitrous oxide (N₂O) emissions in different soils and the environmental factors controlling the degree of inhibition have not been studied. Using 14-day microcosm incubation, we investigated the effects of different concentrations of SA on nitrification activity, abundance of ammonia-oxidizing microorganisms, and N₂O emissions in three typical agricultural soils. The nitrification inhibitory efficacy of SA was strongest in acidic red soil, followed by weakly acidic paddy soil, with no significant effect in an alkaline calcareous soil. Potential nitrification activity (PNA) were also greatly reduced by SA additions in paddy and red soil. Pearson correlation analysis showed that the inhibitory efficacy of SA might be negatively correlated with soil pH and positively correlated with clay percentage. SA treatments significantly reduced N₂O emissions by 69.1-79.3% from paddy soil and by 40.8%-46.4% from red soil, respectively, but no effect was recorded in the calcareous soil. SA addition possessed dual inhibition of both ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) abundance in paddy and red soil. Structural equation modelling revealed that soil ammonium (NH₄ ⁺) and dissolved organic carbon content (DOC) were the key variables explaining AOA and AOB abundance and subsequent N₂O emissions. Our results support the potential for the use of the BNI SA in mitigating N₂O emissions and enhancing N utilization in red and paddy soils.

Thermodynamic Analysis of Intermediary Metabolic Steps and Nitrous Oxide Production by Ammonium-Oxidizing Bacteria

Nitrous oxide (N₂O) is a greenhouse gas emitted from wastewater treatment, soils, and agriculture largely by ammonium-oxidizing bacteria (AOB). While AOB are characterized by being aerobes that oxidize ammonium (NH₄⁺) to nitrite (NO₂^-), fundamental studies in microbiology are revealing the importance of metabolic intermediates and reactions that can lead to the production of N₂O. These findings about the metabolic pathways for AOB were integrated with thermodynamic electron-equivalents modeling (TEEM) to estimate kinetic and stoichiometric parameters for each of the AOB's nitrogen (N)-oxidation and -reduction reactions. The TEEM analysis shows that hydroxylamine (NH₂OH) oxidation to nitroxyl (HNO) is the most energetically efficient means for the AOB to provide electrons for ammonium monooxygenation, while oxidations of HNO to nitric oxide (NO) and NO to NO₂^- are energetically favorable for respiration and biomass synthesis. The respiratory electron acceptor can be O₂ or NO, and both have similar energetics. The TEEM-predicted value for biomass yield, maximum-specific rate of NH₄⁺ utilization, and maximum specific growth rate are consistent with empirical observations. NO reduction to N₂O is thermodynamically favorable for respiration and biomass synthesis, but the need for O₂ as a reactant in ammonium monooxygenation likely precludes NO reduction to N₂O from becoming the major pathway for respiration.

Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.

Nitrosomonas europaea catalyzes the first step of the nitrification process (ammonia to nitrite). It has been recognized as one of the most important members of microbial communities of wastewater treatment processes. Genome-scale models are powerful tools in process optimization since they can predict the organism’s behavior under different growth conditions. The final genome-scale model of N. europaea ATCC19718, iGC535, can predict growth and oxygen uptake rates with 90.52% accuracy under chemolithotrophic and chemolitoorganotrophic conditions. Moreover, iGC535 can predict the simultaneous oxidation of ammonia and wastewater pollutants, such as benzene, toluene, phenol and, chlorobenzene. iGC535 represents the most comprehensive knowledge-base for a nitrifying organism available to date. The genome-scale model reconstructed in this work brings us closer to understanding N. europaea’s role in a community with other nitrifying bacteria.

Survival strategy of comammox bacteria in a wastewater nutrient removal system with sludge fermentation liquid as additional carbon source

Complete ammonia oxidizing (comammox) bacteria are frequently detected in wastewater biological nutrient removal (BNR) systems. This study identified "Candidatus Nitrospira nitrosa"-like comammox bacteria as the predominant ammonia oxidizers (97.5-99.4%) in a lab-scale BNR system with acetate and sludge fermentation liquid as external carbon sources. The total nitrogen and phosphorus removals of the system were 75.9% and 86.9% with minimal N₂O emission (0.27%). Low ammonia concentration, mixotrophic growth potentials and metabolic interactions with diverse heterotrophs collectively contributed to the survival of comammox bacteria in the system. The recovered draft genomes of comammox bacteria indicated their potentials in using acetate and propionate but not butyrate. Acetate and propionate indeed stimulated the transcription of comammox amoA genes (up-regulated by 4.1 folds compared with no organic addition), which was positively correlated with the ammonia oxidation rate of the community (r = 0.75, p < 0.05). Comammox bacteria could provide vitamins/cofactors (e.g., cobalamin and biotin) to heterotrophs (e.g., Burkholderiaceae), and in return receive amino acids (e.g., phenylalanine and tyrosine) from heterotrophs, which they cannot synthesize. Compared with comammox bacteria, ammonia oxidizing bacteria (AOB) exhibited lower metabolic versatility, and lacked more pathways for the synthesis of amino acids and vitamin/cofactors, leading to their washout in the studied system. BNRs with comammox bacteria as the major nitrifiers hold great potentials in achieving superior performance at low aeration cost and low N₂O emission and at full-scale plants.

Effect of carbon source on nitrous oxide emission characteristics and sludge properties during anoxic/aerobic wastewater treatment process

Carbon sources are an important parameter in wastewater treatment processes and are closely related to treatment efficiency and nitrous oxide (N₂O) emissions. In this study, three parallel sequencing batch reactors (SBRs) were processed with acetic acid, propionic acid, and a 1:1 mixture of both acids (calculated in COD) to study the effect of carbon sources on N₂O generation and sludge properties (including intracellular polymer content, extracellular polymeric substance (EPS) composition, particle size distribution, settleability, and microbial community structure). The results showed that the highest COD, NH₄⁺-N, and TP removal efficiencies (92.2%, 100%, and 82.3%, respectively) were achieved by the reactor with mixed acid as the carbon source, whereas the reactor using acetic acid had the highest TN removal rate (82.6%) and the lowest N₂O-N conversion rate (1.4%, based on TN removal). The reactor with the carbon source of mixed acid produced the highest polyhydroxyalkanoate (PHA) content, which led to an increase in N₂O generation from the aerobic denitrification pathway. The SBR with mixed acid carbon source also had the highest concentration of EPS, which resulted in the largest particle size and the lowest settleability of sludge flocs among the SBRs. Microbial analysis results revealed that the difference in carbon sources resulted in a variation in the microbial community as well as in the relative abundances of functional microbes involved in biological nitrogen removal processes. The mixed acid promoted the development of ammonia-oxidizing bacteria (AOB), which conducted the primary N₂O generation pathway of aerobic denitrification bioreactions. The carbon source of acetic acid promoted the growth of denitrifying bacteria (DNB), which led to the highest TN removal rate. This study provides a comprehensive understanding of the effects of carbon sources on N₂O generation and sludge properties for WWTPs.

Envisioning role of ammonia oxidizing bacteria in bioenergy production and its challenges: a review

Ammonia oxidizing bacteria (AOB) play a key role in the biological oxidation of ammonia to nitrite and mark their significance in the biogeochemical nitrogen cycle. There has been significant development in harnessing the ammonia oxidizing potential of AOB in the past few decades. However, very little is known about the potential applications of AOB in the bioenergy sector. As alternate sources of energy represent a thrust area for environmental sustainability, the role of AOB in bioenergy production becomes a significant area of exploration. This review highlights the role of AOB in bioenergy production and emphasizes the understanding of the genetic make-up and key cellular biochemical reactions occurring in AOB, thereby leading to the exploration of its various functional aspects. Recent outcomes in novel ammonia/nitrite oxidation steps occurring in a model AOB - Nitrosomonas europaea propel us to explore several areas of environmental implementation. Here we present the significant role of AOB in microbial fuel cells (MFC) where Nitrosomonas sp. play both anodic and cathodic functions in the generation of bioelectricity. This review also presents the potential role of AOB in curbing fuel demand by producing alternative liquid fuel such as methanol and biodiesel. Herein, the multiple roles of AOB in bioenergy production namely: bioelectricity generation, bio-methanol, and biodiesel production have been presented.

Comprehensive analysis of microbial dynamics linked with the reduction of odorous compounds in a full-scale swine manure pit recharge system with recirculation of aerobically treated liquid fertilizer

It is believed that the generation of odorous materials in manure-slurry pits during the storage can be reduced by recirculating aerobically treated liquid fertilizer (ATLF) to a manure-pit recharge system (PRS). However, the biological mechanisms for reduction of those problematic compounds remain poorly understood. In this study, the links between microbial evolution and changes in chemical composition and odorous compounds were analyzed where swine-manure slurry was stored in a full-scale PRS. Some beneficial microorganisms were successfully established in the PRS. This resulted in the accumulation of fewer undesirable chemical components and lower amounts of odorous compounds compared to those in a conventional swine-manure slurry pit (the control). Decrease in the volatile fatty acids (1387-8478 mg/L → 306-1258 mg/L) and NH₃ (3387-4300 mg/L → 85-200 mg/L) in the PRS was mainly due to the development of a key community that included a mix of aerobic, anaerobic fermentative, nitrifying (0.1-0.6%) and denitrifying (1.7-3.5%), and methanogenic microorganisms (2.1-4.2%). Meanwhile, the generation of greater amounts of H₂S (12-290 mg/L → 61-1754 mg/L) was found in the PRS, which condition was supported by the increased proportion of sulfate-reducing bacteria (0.5-3%). To the authors' best knowledge this is the first study comprehensively analyzing microbial dynamics linked with the reduction of odorous compounds in the full-scale PRS in response to recirculation of ATLF.

Estuarine microbial diversity and nitrogen cycling increase along sand-mud gradients independent of salinity and distance

Estuaries are depositional environments prone to terrigenous mud sedimentation. While macrofaunal diversity and nitrogen retention are greatly affected by changes in sedimentary mud content, its impact on prokaryotic diversity and nitrogen cycling activity remains understudied. We characterized the composition of estuarine tidal flat prokaryotic communities spanning a habitat range from sandy to muddy sediments, while controlling for salinity and distance. We also determined the diversity, abundance and expression of ammonia oxidizers and N₂ O-reducers within these communities by amoA and clade I nosZ gene and transcript analysis. Results show that prokaryotic communities and nitrogen cycling fractions were sensitive to changes in sedimentary mud content, and that changes in the overall community were driven by a small number of phyla. Significant changes occurred in prokaryotic communities and N₂ O-reducing fractions with only a 3% increase in mud, while thresholds for ammonia oxidizers were less distinct, suggesting other factors are also important for structuring these guilds. Expression of nitrogen cycling genes was substantially higher in muddier sediments, and results indicate that the potential for coupled nitrification-denitrification became increasingly prevalent as mud content increased. Altogether, results demonstrate that mud content is a strong environmental driver of diversity and N-cycling dynamics in estuarine microbial communities.

Usitatibacter rugosus gen. nov., sp. nov. and Usitatibacter palustris sp. nov., novel members of Usitatibacteraceae fam. nov. within the order Nitrosomonadales isolated from soil

Members of the metabolically diverse order Nitrosomonadales inhabit a wide range of environments. Two strains affiliated with this order were isolated from soils in Germany and characterized by a polyphasic approach. Cells of strains 0125_3^T and Swamp67^T are Gram-negative rods, non-motile, non-spore-forming, non-capsulated and divide by binary fission. They tested catalase-negative, but positive for cytochrome c-oxidase. Both strains form small white colonies on agar plates and grow aerobically and chemoorganotrophically on SSE/HD 1 : 10 medium, preferably utilizing organic acids and proteinaceous substrates. Strains 0125_3^T and Swamp67^T are mesophilic and grow optimally without NaCl addition at slightly alkaline conditions. Major fatty acids are C_16 : 1  ω7c, C_16 : 0 and C_14 : 0. The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidyglycerol. The predominant respiratory quinone is Q-8. The G+C content for 0125_3^T and Swamp67^T was 67 and 66.1 %, respectively. The 16S rRNA gene analysis indicated that the closest relatives (<91 % sequence similarity) of strain 0125_3^T were Nitrosospira multiformis ATCC 25196^T, Methyloversatilis universalis FAM5^T and Denitratisoma oestradiolicum AcBE2-1^T, while Nitrosospira multiformis ATCC 25196^T, Nitrosospira tenuis Nv1^T and Nitrosospira lacus APG3^T were closest to strain Swamp67^T. The two novel strains shared 97.4 % 16S rRNA gene sequence similarity with one another and show low average nucleotide identity of their genomes (83.8 %). Based on the phenotypic, chemotaxonomic, genomic and phylogenetic analysis, we propose the two novel species Usitatibacter rugosus sp. nov (type strain 0125_3^T=DSM 104443^T=LMG 29998^T=CECT 9241^T) and Usitatibacter palustris sp. nov. (type strain Swamp67^T=DSM 104440^T=LMG 29997^T=CECT 9242^T) of the novel genus Usitatibacter gen. nov., within the novel family Usitatibacteraceae fam. nov.

Impacts of organics on the microbial ecology of wastewater anammox processes: Recent advances and meta-analysis

Anaerobic ammonium oxidation (anammox) represents a promising technology for wastewater nitrogen removal. Organics management is critical to achieving efficient and stable performance of anammox or integrated processes, e.g., denitratation-anammox. The aim of this systematic review is to synthesize the state-of-the-art knowledge on the multifaceted impacts of organics on wastewater anammox community structure and function. Both exogenous and endogenous organics are discussed with respect to their effects on the biofilm/granule structure and function, as well as the interactions between anammox bacteria (AnAOB) and a broad range of coexisting functional groups. A global core community consisting of 19 taxa is identified and a co-occurrence network is constructed by meta-analysis on the 16S rDNA sequences of 149 wastewater anammox samples. Correlations between core taxa, keystone taxa, and environmental factors, including COD, nitrogen loading rate (NLR) and C/N ratio are obtained. This review provides a holistic understanding of the microbial responses to different origins and types of organics in wastewater anammox reactors, which will facilitate the design and operation of more efficient anammox-based wastewater nitrogen removal process.

Lost in translation: the quest for Nitrosomonas cluster 7-specific amoA primers and TaqMan probes

The choice of primer and TaqMan probes to quantify ammonia-oxidizing bacteria (AOB) in environmental samples is of crucial importance. The re-evaluation of primer pairs based on current genomic sequences used for quantification of the amoA gene revealed (1) significant misrepresentations of the AOB population in environmental samples, (2) and a lack of perfect match primer pairs for Nitrosomonas europaea and Nitrosomonas eutropha. We designed two new amoA cluster 7-specific primer pairs and TaqMan probes to quantify N. europaea (nerF/nerR/nerTaq) and N. eutropha (netF/netR/netTaq). Specificity and quantification biases of the newly designed primer sets were compared with the most popular primer pair (amoA1f/amoA2r) using DNA from various AOB cultures as individual templates as well as DNA mixtures and environmental samples. Based on the qPCR results, we found that the newly designed primer pairs and the most popular one performed similarly for individual templates but differed for the DNA mixtures and environmental samples. Using the popular primer pair introduced a high underestimation of AOB in environmental samples, especially for N. eutropha. Thus, there is a strong need for more specific primers and probes to understand the occurrence and competition between N. europaea and N. eutropha in different environments.

Nitrous oxide production by ammonia oxidizers: Physiological diversity, niche differentiation and potential mitigation strategies

Oxidation of ammonia to nitrite by bacteria and archaea is responsible for global emissions of nitrous oxide directly and indirectly through provision of nitrite and, after further oxidation, nitrate to denitrifiers. Their contributions to increasing N₂ O emissions are greatest in terrestrial environments, due to the dramatic and continuing increases in use of ammonia-based fertilizers, which have been driven by requirement for increased food production, but which also provide a source of energy for ammonia oxidizers (AO), leading to an imbalance in the terrestrial nitrogen cycle. Direct N₂ O production by AO results from several metabolic processes, sometimes combined with abiotic reactions. Physiological characteristics, including mechanisms for N₂ O production, vary within and between ammonia-oxidizing archaea (AOA) and bacteria (AOB) and comammox bacteria and N₂ O yield of AOB is higher than in the other two groups. There is also strong evidence for niche differentiation between AOA and AOB with respect to environmental conditions in natural and engineered environments. In particular, AOA are favored by low soil pH and AOA and AOB are, respectively, favored by low rates of ammonium supply, equivalent to application of slow-release fertilizer, or high rates of supply, equivalent to addition of high concentrations of inorganic ammonium or urea. These differences between AOA and AOB provide the potential for better fertilization strategies that could both increase fertilizer use efficiency and reduce N₂ O emissions from agricultural soils. This article reviews research on the biochemistry, physiology and ecology of AO and discusses the consequences for AO communities subjected to different agricultural practices and the ways in which this knowledge, coupled with improved methods for characterizing communities, might lead to improved fertilizer use efficiency and mitigation of N₂ O emissions.

Bioenergetics analysis of ammonia-oxidizing bacteria and the estimation of their maximum growth yield

The currently accepted biochemistry and bioenergetics of ammonia-oxidizing bacteria (AOB) show an inefficient metabolism: only 53.8% of the energy released when a mole of ammonia is oxidised and less than two of the electrons liberated can be directed to the autotrophic anabolism. However, paradoxically, AOB seem to thrive in challenging conditions: growing readily in virtually most aerobic environment, yet limited AOB exist in pure culture. In this study, a comprehensive model of the biochemistry of the metabolism of AOB is presented. Using bioenergetics calculations and selecting the minimum estimation for the energy dissipated in each of the metabolic steps, the model predicts the highest possible true yield of 0.16 gBio/gN and a yield of 0.13 gBio/gN when cellular maintenance is considered. Observed yields should always be lower than these values but the range of experimental values in literature vary between 0.04 and 0.45 gBio/gN. In this work, we discuss if this variance of observed values for AOB growth yield could be understood if other non-considered alternative energy sources are present in the biochemistry of AOB. We analyse how the predicted maximum growth yield of AOB changes considering co-metabolism, the use of hydroxylamine as a substrate, the abiotic oxidation of NO, energy harvesting in the monooxygenase enzyme or the use of organic carbon sources.

New pieces to the carbon metabolism puzzle of Nitrosomonas europaea: Kinetic characterization of glyceraldehyde-3 phosphate and succinate semialdehyde dehydrogenases

Nitrosomonas europaea is a chemolithotroph that obtains energy through the oxidation of ammonia to hydroxylamine while assimilates atmospheric CO₂ to cover the cell carbon demands for growth. This microorganism plays a relevant role in the nitrogen biogeochemical cycle on Earth but its carbon metabolism remains poorly characterized. Based on sequence homology, we identified two genes (cbbG and gabD) coding for redox enzymes in N. europaea. Cloning and expression of the genes in Escherichia coli, allowed the production of recombinant enzymes purified to determine their biochemical properties. The protein CbbG is a glyceraldehyde-3-phosphate (Ga3P) dehydrogenase (Ga3PDHase) catalyzing the reversible oxidation of Ga3P to 1,3-bis-phospho-glycerate (1,3bisPGA), using specifically NAD⁺/NADH as cofactor. CbbG showed ∼6-fold higher K_m value for 1,3bisPGA but ∼5-fold higher k_cat for the oxidation of Ga3P. The protein GabD irreversibly oxidizes Ga3P to 3Pglycerate using NAD⁺ or NADP⁺, thus resembling a non-phosphorylating Ga3PDHase. However, the enzyme showed ∼6-fold higher K_m value and three orders of magnitude higher catalytic efficiency with succinate semialdehyde (SSA) and NADP⁺. Indeed, the GabD protein identity corresponds to an SSA dehydrogenase (SSADHase). CbbG seems to be the only Ga3PDHase present in N. europaea; which would be involved in reducing triose-P during autotrophic carbon fixation. Otherwise, in cells grown under conditions deprived of ammonia and oxygen, the enzyme could catalyze the glycolytic step of Ga3P oxidation producing NADH. As an SSADHase, GabD would physiologically act producing succinate and preferentially NADPH over NADH; thus being part of an alternative pathway of the tricarboxylic acid cycle converting α-ketoglutarate to succinate. The properties determined for these enzymes contribute to better identify metabolic steps in CO₂ assimilation, glycolysis and the tricarboxylic acid cycle in N. europaea. Results are discussed in the framework of metabolic pathways that launch biosynthetic intermediates relevant in the microorganism to develop and fulfill its role in nature.

Metabolic and Proteomic Responses to Salinity in Synthetic Nitrifying Communities of Nitrosomonas spp. and Nitrobacter spp

Typically, nitrification is a two-stage microbial process and is key in wastewater treatment and nutrient recovery from waste streams. Changes in salinity represent a major stress factor that can trigger response mechanisms, impacting the activity and the physiology of bacteria. Despite its pivotal biotechnological role, little information is available on the specific response of nitrifying bacteria to varying levels of salinity. In this study, synthetic communities of ammonia-oxidizing bacteria (AOB Nitrosomonas europaea and/or Nitrosomonas ureae) and nitrite-oxidizing bacteria (NOB Nitrobacter winogradskyi and/or Nitrobacter vulgaris) were tested at 5, 10, and 30 mS cm^-1 by adding sodium chloride to the mineral medium (0, 40, and 200 mM NaCl, respectively). Ammonia oxidation activity was less affected by salinity than nitrite oxidation. AOB, on their own or in combination with NOB, showed no significant difference in the ammonia oxidation rate among the three conditions. However, N. winogradskyi improved the absolute ammonia oxidation rate of both N. europaea and N. ureae. N. winogradskyi’s nitrite oxidation rate decreased to 42% residual activity upon exposure to 30 mS cm^-1, also showing a similar behavior when tested with Nitrosomonas spp. The nitrite oxidation rate of N. vulgaris, as a single species, was not affected when adding sodium chloride up to 30 mS cm^-1, however, its activity was completely inhibited when combined with Nitrosomonas spp. in the presence of ammonium/ammonia. The proteomic analysis of a co-culture of N. europaea and N. winogradskyi revealed the production of osmolytes, regulation of cell permeability and an oxidative stress response in N. europaea and an oxidative stress response in N. winogradskyi, as a result of increasing the salt concentration from 5 to 30 mS cm^-1. A specific metabolic response observed in N. europaea suggests the role of carbon metabolism in the production of reducing power, possibly to meet the energy demands of the stress response mechanisms, induced by high salinity. For the first time, metabolic modifications and response mechanisms caused by the exposure to salinity were described, serving as a tool toward controllability and predictability of nitrifying systems exposed to salt fluctuations.

Ammonia oxidizers and nitrite-oxidizing bacteria respond differently to long-term manure application in four paddy soils of south of China

Nitrification plays an important role in the soil nitrogen (N) cycle, and fertilizer application may influence soil nitrifiers' abundance and composition. However, the effect of long-term manure application in paddy soils on nitrifying populations is poorly understood. We chose four long-term manure experimental fields in the south of China to study how the abundance and community structure of nitrifiers would change in response to long-term manure application using quantitative PCR and Miseq sequencing analyses. Our results showed that manure application significantly increased ammonia oxidizing archaea (AOA) abundance at the ChangSha (CS) and NanChang (NC) sites, while the abundance of ammonia oxidizing bacteria (AOB) represented 4.8- and 12.8- fold increases at the JiaXing (JX) and YingTan (YT) sites, respectively. Miseq sequencing of 16S rRNA genes indicated that manure application altered the community structure of nitrifying populations, especially at the NC and YT sites. The application of manure significantly changed AOA and nitrite oxidizing bacteria (NOB) community structures but not those of AOB, suggesting that AOA and NOB may be more sensitive to manures. Variation partitioning analysis (VPA) and redundancy analysis (RDA) indicated that soil pH, TN, NO₃^--N and water content were the main factors in shaping nitrifying communities. These findings suggest that nitrifiers respond diversely to manure application, and soil physiochemical properties play an important role in determining nitrifiers' abundance and communities with long-term manure addition.

Response and recovery of a pristine groundwater ecosystem impacted by toluene contamination - A meso-scale indoor aquifer experiment

Microbial communities are the driving force behind the degradation of contaminants like aromatic hydrocarbons in groundwater ecosystems. However, little is known about the response of native microbial communities to contamination in pristine environments as well as their potential to recover from a contamination event. Here, we used an indoor aquifer mesocosm filled with sandy quaternary calciferous sediment that was continuously fed with pristine groundwater to study the response, resistance and resilience of microbial communities to toluene contamination over a period of almost two years, comprising 132days of toluene exposure followed by nearly 600days of recovery. We observed an unexpectedly high intrinsic potential for toluene degradation, starting within the first two weeks after the first exposure. The contamination led to a shift from oxic to anoxic, primarily nitrate-reducing conditions as well as marked cell growth inside the contaminant plume. Depth-resolved community fingerprinting revealed a low resistance of the native microbial community to the perturbation induced by the exposure to toluene. Distinct populations that were dominated by a small number of operational taxonomic units (OTUs) rapidly emerged inside the plume and at the plume fringes, partially replacing the original community. During the recovery period physico-chemical conditions were restored to the pristine state within about 35days, whereas the recovery of the biological parameters was much slower and the community composition inside the former plume area had not recovered to the original state by the end of the experiment. These results demonstrate the low resilience of sediment-associated groundwater microbial communities to organic pollution and underline that recovery of groundwater ecosystems cannot be assessed solely by physico-chemical parameters.

Changing roles of ammonia-oxidizing bacteria and archaea in a continuously acidifying soil caused by over-fertilization with nitrogen

Nitrification coupled with nitrate leaching contributes to soil acidification. However, little is known about the effect of soil acidification on nitrification, especially on ammonia oxidation that is the rate-limiting step of nitrification and performed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). Serious soil acidification occurs in Chinese greenhouses due to the overuse of N-fertilizer. In the present study, greenhouse soils with 1, 3, 5, 7, and 9 years of vegetable cultivation showed a consistent pH decline (i.e., 7.0, 6.3, 5.6, 4.9, and 4.3). Across the pH gradient, we analyzed the community structure and abundance of AOB and AOA by pyrosequencing and real-time PCR techniques, respectively. The recovered nitrification potential (RNP) method was used to determine relative contributions of AOA and AOB to nitrification potential. The results revealed that soil acidification shaped the community structures of AOA and AOB. In acidifying soil, soil pH, NH3 concentration, and DOC content were critical factors shaping ammonia oxidizer community structure. AOB abundance, but not AOA, was strongly influenced by soil acidification. When soil pH was below 5.0, AOA rather than AOB were responsible for almost all of the RNP. However, when soil pH ranged from 5.6 to 7.0, AOB were the major contributors to RNP. The group I.1a-associatied AOA had more relative abundance in low pH (pH<6.3), whereas group I.1b tended to prefer neutral pH. Clusters 2, 10, and 12 in AOB were more abundant in acidic soil (pH <5.6), while Nitrosomonas-like lineage and unclassified lineage 3 were prevailing in neutral soil and slightly acidic soil (pH, 6.0-6.5), respectively. These results suggested that soil acidification had a profound impact on ammonia oxidation and more specific lineages in AOB occupying different pH-associated niches required further investigation.

Influence of Temperature and Copper on Oxalobacteraceae in Soil Enrichments

β-Proteobacteria is one of the most abundant phylum in soils, including autotrophic and heterotrophic ammonium-consumers with relevance in N circulation in soils. The effects of high-temperature events and phytosanitary treatments, such as copper amendments, on soil bacterial communities relevant to N-cycling remain to be studied. As an example, South Portugal soils are seasonally exposed to high-temperature periods, the temperature at the upper soil layers can reach over 40 °C. Here, we evaluated the dynamics of mesophilic and thermophilic bacteria from a temperate soil, in particular of heterotrophic β-Proteobacteria, regarding the ammonium equilibrium, as a function of temperature and copper treatment. Soil samples were collected from an olive orchard in southern Portugal. Selective enrichments were performed from samples under different conditions of temperature (30 and 50 °C) and copper supplementation (100 and 500 µM) in order to mime seasonal variations and phytosanitary treatments. Changes in the microbial communities under these conditions were examined by denaturing gradient gel electrophoresis, a molecular fingerprint technique. At moderate temperature--30 °C--either without or with copper addition, dominant members were identified as different strains belonging to genus Massilia, a genus of the Oxalobacteraceae (β-Proteobacteria), while at 50 °C, members of the Brevibacillus genus, phylum Firmicutes were also represented. Ammonium production during bacterial growth at moderate and high temperatures was not affected by copper addition. Results indicate that both copper and temperature selected specific tolerant bacterial strains with consequences for N-cycling in copper-treated orchards.

Characterizing the metabolic trade-off in Nitrosomonas europaea in response to changes in inorganic carbon supply

The link between the nitrogen and one-carbon cycles forms the metabolic basis for energy and biomass synthesis in autotrophic nitrifying organisms, which in turn are crucial players in engineered nitrogen removal processes. To understand how autotrophic nitrifying organisms respond to inorganic carbon (IC) conditions that could be encountered in engineered partially nitrifying systems, we investigated the response of one of the most extensively studied model ammonia oxidizing bacteria, Nitrosomonas europaea (ATCC19718), to three IC availability conditions: excess gaseous and excess ionic IC supply (40× stoichiometric requirement), excess gaseous IC supply (4× stoichiometric requirement in gaseous form only), and limiting IC supply (0.25× stoichiometric requirement). We found that, when switching from excess gaseous and excess ionic IC supply to excess gaseous IC supply, N. europaea chemostat cultures demonstrated an acclimation period that was characterized by transient decreases in the ammonia removal efficiency and transient peaks in the specific oxygen uptake rate. Limiting IC supply led to permanent reactor failures (characterized by biomass washout and failure of ammonia removal) that were preceded by similar decreases in the ammonia removal efficiency and peaks in the specific oxygen uptake rate. Notably, both excess gaseous IC supply and limiting IC supply elicited a previously undocumented increase in nitric and nitrous oxide emissions. Further, gene expression patterns suggested that excess gaseous IC supply and limiting IC supply led to consistent up-regulation of ammonia respiration genes and carbon assimilation genes. Under these conditions, interrogation of the N. europaea proteome revealed increased levels of carbon fixation and transport proteins and decreased levels of ammonia oxidation proteins (active in energy synthesis pathways). Together, the results indicated that N. europaea mobilized enhanced IC scavenging pathways for biosynthesis and turned down respiratory pathways for energy synthesis, when challenged with excess gaseous IC supply and limiting IC supply.

Metaphylogenomic and potential functionality of the limpet Patella pellucida's gastrointestinal tract microbiome

This study investigated the microbial diversity associated with the digestive tract of the seaweed grazing marine limpet Patella pellucida. Using a modified indirect DNA extraction protocol and performing metagenomic profiling based on specific prokaryotic marker genes, the abundance of bacterial groups was identified from the analyzed metagenome. The members of three significantly abundant phyla of Proteobacteria, Firmicutes and Bacteroidetes were characterized through the literature and their predicted functions towards the host, as well as potential applications in the industrial environment assessed.

Quantitative response of nitrifying and denitrifying communities to environmental variables in a full-scale membrane bioreactor

The abundance and transcription levels of specific gene markers of total bacteria, ammonia-oxidizing Betaproteobacteria, nitrite-oxidizing bacteria (Nitrospira-like) and denitrifiers (N2O-reducers) were analyzed using quantitative PCR (qPCR) and reverse-transcription qPCR during 9 months in a full-scale membrane bioreactor treating urban wastewater. A stable community of N-removal key players was developed; however, the abundance of active populations experienced sharper shifts, demonstrating their fast adaptation to changing conditions. Despite constituting a small percentage of the total bacterial community, the larger abundances of active populations of nitrifiers explained the high N-removal accomplished by the MBR. Multivariate analyses revealed that temperature, accumulation of volatile suspended solids in the sludge, BOD5, NH4(+) concentration and C/N ratio of the wastewater contributed significantly (23-38%) to explain changes in the abundance of nitrifiers and denitrifiers. However, each targeted group showed different responses to shifts in these parameters, evidencing the complexity of the balance among them for successful biological N-removal.

Nitrogen removal via the nitrite pathway during wastewater co-treatment with ammonia-rich landfill leachates in a sequencing batch reactor

The biological treatment of ammonia-rich landfill leachates due to an inadequate C to N ratio requires expensive supplementation of carbon from an external carbon source. In an effort to reduce treatment costs, the objective of the study was to determine the feasibility of nitrogen removal via the nitrite pathway during landfill leachate co-treatment with municipal wastewater. Initially, the laboratory-scale sequencing batch reactor (SBR) was inoculated with nitrifying activated sludge and fed only raw municipal wastewater (RWW) during a start-up period of 9 weeks. Then, in the co-treatment period, consisting of the next 17 weeks, the system was fed a mixture of RWW and an increasing quantity of landfill leachates (from 1 to 10% by volume). The results indicate that landfill leachate addition of up to 10% (by volume) influenced the effluent quality, except for BOD5. During the experiment, a positive correlation (r(2) = 0.908) between ammonia load in the influent and nitrite in the effluent was observed, suggesting that the second step of nitrification was partially inhibited. The partial nitrification (PN) was also confirmed by fluorescence in situ hybridisation (FISH) analysis of nitrifying bacteria. Nitrogen removal via the nitrite pathway was observed when the oxygen concentration ranged from 0.5 to 1.5 mg O2/dm(3) and free ammonia (FA) ranged from 2.01 to 35.86 mg N-NH3/dm(3) in the aerobic phase. Increasing ammonia load in wastewater influent was also correlated with an increasing amount of total nitrogen (TN) in the effluent, which suggested insufficient amounts of assimilable organic carbon to complete denitrification. Because nitrogen removal via the nitrite pathway is beneficial for carbon-limited and highly ammonia-loaded mixtures, obtaining PN can lead to a reduction in the external carbon source needed to support denitrification.

L-Malate dehydrogenase activity in the reductive arm of the incomplete citric acid cycle of Nitrosomonas europaea

The autotrophic nitrifying bacterium Nitrosomonas europaea does not synthesize 2-oxoglutarate (α-ketoglutarate) dehydrogenase under aerobic conditions and so has an incomplete citric acid cycle. L-malate (S-malate) dehydrogenase (MDH) from N. europaea was predicted to show similarity to the NADP(+)-dependent enzymes from chloroplasts and was separated from the NAD(+)-dependent proteins from most other bacteria or mitochondria. MDH activity in a soluble fraction from N. europaea ATCC 19718 was measured spectrophotometrically and exhibited simple Michaelis-Menten kinetics. In the reductive direction, activity with NADH increased from pH 6.0 to 8.5 but activity with NADPH was consistently lower and decreased with pH. At pH 7.0, the K m for oxaloacetate was 20 μM; the K m for NADH was 22 μM but that for NADPH was at least 10 times higher. In the oxidative direction, activity with NAD(+) increased with pH but there was very little activity with NADP(+). At pH 7.0, the K m for L-malate was 5 mM and the K m for NAD(+) was 24 μM. The reductive activity was quite insensitive to inhibition by L-malate but the oxidative activity was very sensitive to oxaloacetate. MDH activity was not strongly activated or inhibited by glycolytic or citric acid cycle metabolites, adenine nucleotides, NaCl concentrations, or most metal ions, but increased with temperature up to about 55 °C. The reductive activity was consistently 10-20 times higher than the oxidative activity. These results indicate that the L-malate dehydrogenase in N. europaea is similar to other NAD(+)-dependent MDHs (EC 1.1.1.37) but physiologically adapted for its role in a reductive biosynthetic sequence.

Long-term low DO enriches and shifts nitrifier community in activated sludge

In the activated sludge process, reducing the operational dissolved oxygen (DO) concentration can improve oxygen transfer efficiency, thereby reducing energy use. The low DO, however, may result in incomplete nitrification. This research investigated the long-term effect of low DO on the nitrification performance of activated sludge. Results indicated that, for reactors with 10 and 40 day solids retention times (SRTs), complete nitrification was accomplished after a long-term operation with a DO of 0.37 and 0.16 mg/L, respectively. Under long-term low DO conditions, nitrite oxidizing bacteria (NOB) became a better oxygen competitor than ammonia oxidizing bacteria (AOB) and, as a result, no nitrite accumulated. Real-time PCR assays indicated that the long-term low DO enriched both AOB and NOB in activated sludge, increasing the sludge nitrification capacity and diminishing the adverse effect of low DO on the overall nitrification performance. The increase in the population size of nitrifiers was likely resulted from the reduced nitrifier endogenous decay rate by a low DO. Under long-term low DO conditions, Nitrosomonas europaea/eutropha remained as the dominant AOB, whereas the number of Nitrospira-like NOB became much greater than Nitrobacter-like NOB, especially for the 40 day SRT sludge. The enrichment and shift of the nitrifier community reduced the adverse effect of low DO on nitrification; therefore, low DO operation of a complete nitrification process is feasible.

Probing the stoichiometry of the nitrification process using the respirometric approach

Quantifying oxygen demand and nitrifier yield are important in the design and operation of advanced wastewater treatment systems. However, the accurate stoichiometry of the autotrophic nitrification process has not been fully developed. In this research, stoichiometric links between nitrifier yield, ammonia and nitrite oxidization, ammonia assimilation, and oxygen uptake for each step of the nitrification process were determined. A pulse-flow respirometer was used to measure the oxygen uptake for complete nitrification and nitrite oxidation reactions. Results indicated that the specific oxygen uptake was 4.23 mg-O(2)/mg-N oxidized for complete nitrification, with 3.17 mg-O(2)/mg-N oxidized for ammonia oxidation (first step nitrification) and 1.06 mg-O(2)/mg-N oxidized for nitrite oxidation (second step nitrification). For the complete nitrification, fractions of ammonia used for electron donation, synthesis of ammonia oxidizers, and synthesis of nitrite oxidizers were 97.1%, 2.2%, and 0.7%, respectively. The fractions of electrons transferred into cell synthesis were approximately 7.5% for ammonia oxidation and 7.3% for nitrite oxidation. Biomass yield coefficients for ammonia oxidizers and nitrite oxidizers were 0.18 and 0.06 g-VSS/g-N oxidized, respectively. These parameters are critical when calculating oxygen needs and nitrifier biomass concentrations during the design of advanced wastewater treatment processes.

Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

Nitrous oxide (N(2)O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N(2)O is formed biologically from the oxidation of hydroxylamine (NH(2)OH) or the reduction of nitrite (NO(-) (2)) to NO and further to N(2)O. Our review of the biological pathways for N(2)O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO(-) (2) to NO and the further reduction of NO to N(2)O, while N(2)O formation from NH(2)OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N(2)O formation due to the reactivity of NO(-) (2), NH(2)OH, and nitroxyl (HNO). Moreover, biological N(2)O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N(2)O build-up are key to understand mechanisms of N(2)O release. Here, we discuss novel technologies that allow experiments on NO and N(2)O formation at high temporal resolution, namely NO and N(2)O microelectrodes and the dynamic analysis of the isotopic signature of N(2)O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N(2)O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N(2)O build-up.

Insights into glycogen metabolism in chemolithoautotrophic bacteria from distinctive kinetic and regulatory properties of ADP-glucose pyrophosphorylase from Nitrosomonas europaea

Nitrosomonas europaea is a chemolithoautotroph that obtains energy by oxidizing ammonia in the presence of oxygen and fixes CO(2) via the Benson-Calvin cycle. Despite its environmental and evolutionary importance, very little is known about the regulation and metabolism of glycogen, a source of carbon and energy storage. Here, we cloned and heterologously expressed the genes coding for two major putative enzymes of the glycogen synthetic pathway in N. europaea, ADP-glucose pyrophosphorylase and glycogen synthase. In other bacteria, ADP-glucose pyrophosphorylase catalyzes the regulatory step of the synthetic pathway and glycogen synthase elongates the polymer. In starch synthesis in plants, homologous enzymes play similar roles. We purified to homogeneity the recombinant ADP-glucose pyrophosphorylase from N. europaea and characterized its kinetic, regulatory, and oligomeric properties. The enzyme was allosterically activated by pyruvate, oxaloacetate, and phosphoenolpyruvate and inhibited by AMP. It had a broad thermal and pH stability and used different divalent metal ions as cofactors. Depending on the cofactor, the enzyme was able to accept different nucleotides and sugar phosphates as alternative substrates. However, characterization of the recombinant glycogen synthase showed that only ADP-Glc elongates the polysaccharide, indicating that ATP and glucose-1-phosphate are the physiological substrates of the ADP-glucose pyrophosphorylase. The distinctive properties with respect to selectivity for substrates and activators of the ADP-glucose pyrophosphorylase were in good agreement with the metabolic routes operating in N. europaea, indicating an evolutionary adaptation. These unique properties place the enzyme in a category of its own within the family, highlighting the unique regulation in these organisms.

Archaeal and bacterial ammonia-oxidisers in soil: the quest for niche specialisation and differentiation

Autotrophic archaeal and bacterial ammonia-oxidisers (AOA and AOB) drive soil nitrification. Ammonia limitation, mixotrophy, and pH have been suggested as factors providing niche specialisation and differentiation between soil AOA and AOB. However, current data from genomes, cultures, field studies, and microcosms suggest that no single factor discriminates between AOA and AOB. In addition, there appears to be sufficient physiological diversity within each group for growth and activity in all soils investigated, with the exception of acidic soils (pH <5.5), which are dominated by AOA. Future investigation of niche specialisation in ammonia-oxidisers, and other microbial communities, requires characterisation of a wider range of environmentally representative cultures, emphasis on experimental studies rather than surveys, and greater consideration of small-scale soil heterogeneity.

Expression, and molecular and enzymatic characterization of Cu-containing nitrite reductase from a marine ammonia-oxidizing gammaproteobacterium, Nitrosococcus oceani

Ammonia-oxidizing bacteria (AOB) remove intracellular nitrite to prevent its toxicity by a nitrifier denitrification pathway involving two denitrifying enzymes, nitrite reductase and nitric oxide reductase. Here, a Cu-containing nitrite reductase from Nitrosococcus oceani strain NS58, a gammaproteobacterial marine AOB, was expressed in Escherichia coli and purified to homogeneity. Sequence homology analysis indicated that the nitrite reductase from N. oceani was phylogenetically closer to its counterparts from denitrifying bacteria than that of the betaproteobacterium Nitrosomonas europaea. The recombinant enzyme was a homotrimer of a 32 kDa subunit molecule. The enzyme was green in the oxidized state with absorption peaks at 455 nm and 575 nm. EPR spectroscopy indicated the presence of type 2 Cu. Molecular activities and the affinity constant for the nitrite were determined to be 1.6×10(3) s(-1) and 52 μM, respectively.

Low-dissolved-oxygen nitrifying systems exploit ammonia-oxidizing bacteria with unusually high yields

In wastewater treatment plants, nitrifying systems are usually operated with elevated levels of aeration to avoid nitrification failures. This approach contributes significantly to operational costs and the carbon footprint of nitrifying wastewater treatment processes. In this study, we tested the effect of aeration rate on nitrification by correlating ammonia oxidation rates with the structure of the ammonia-oxidizing bacterial (AOB) community and AOB abundance in four parallel continuous-flow reactors operated for 43 days. Two of the reactors were supplied with a constant airflow rate of 0.1 liter/min, while in the other two units the airflow rate was fixed at 4 liters/min. Complete nitrification was achieved in all configurations, though the dissolved oxygen (DO) concentration was only 0.5 ± 0.3 mg/liter in the low-aeration units. The data suggest that efficient performance in the low-DO units resulted from elevated AOB levels in the reactors and/or putative development of a mixotrophic AOB community. Denaturing gel electrophoresis and cloning of AOB 16S rRNA gene fragments followed by sequencing revealed that the AOB community in the low-DO systems was a subset of the community in the high-DO systems. However, in both configurations the dominant species belonged to the Nitrosomonas oligotropha lineage. Overall, the results demonstrated that complete nitrification can be achieved at low aeration in lab-scale reactors. If these findings could be extended to full-scale plants, it would be possible to minimize the operational costs and greenhouse gas emissions without risk of nitrification failure.

A conceptual ecosystem model of microbial communities in enhanced biological phosphorus removal plants

The microbial populations in 25 full-scale activated sludge wastewater treatment plants with enhanced biological phosphorus removal (EBPR plants) have been intensively studied over several years. Most of the important bacterial groups involved in nitrification, denitrification, biological P removal, fermentation, and hydrolysis have been identified and quantified using quantitative culture-independent molecular methods. Surprisingly, a limited number of core species was present in all plants, constituting on average approx. 80% of the entire communities in the plants, showing that the microbial populations in EBPR plants are rather similar and not very diverse, as sometimes suggested. By focusing on these organisms it is possible to make a comprehensive ecosystem model, where many important aspects in relation to microbial ecosystems and wastewater treatment can be investigated. We have reviewed the current knowledge about these microorganisms with focus on key ecophysiological factors and combined this into a conceptual ecosystem model for EBPR plants. It includes the major pathways of carbon flow with specific organic substances, the dominant populations involved in the transformations, interspecies interactions, and the key factors controlling their presence and activity. We believe that the EBPR process is a perfect model system for studies of microbial ecology in water engineering systems and that this conceptual model can be used for proposing and testing theories based on microbial ecosystem theories, for the development of new and improved quantitative ecosystem models and is beneficial for future design and management of wastewater treatment systems.

Diversity, abundance and distribution of amoA-encoding archaea in deep-sea methane seep sediments of the Okhotsk Sea

The ecological characteristics of amoA-encoding archaea (AEA) in deep-sea sediments are largely unsolved. This paper aimed to study the diversity, structure, distribution and abundance of the archaeal community and especially its AEA components in the cold seep surface sediments of the Okhotsk Sea, a marginal sea harboring one of the largest methane hydrate reservoirs in the world. Diverse archaeal 16S rRNA gene sequences were identified, with the majority being related to sequences from other cold seep and methane-rich sediment environments. However, the AEA diversity and abundance were quite low as revealed by amoA gene analyses. Correlation analysis indicates that the abundance of the archaeal amoA genes was correlated with the sediment organic matter content. Thus, it is possible that the amoA-carrying archaea here might utilize organic matter for a living. The affiliation of certain archaeal amoA sequences to the GenBank sequences originally obtained from deep-sea hydrothermal vent environments indicated that the related AEA either have a wide range of temperature adaptation or they have a thermophilic evolutionary history in the modern cold deep-sea sediments of the Okhotsk Sea. The dominance of ammonia-oxidizing bacteria over AEA may indicate that bacteria play a significant role in nitrification in the Okhotsk Sea cold seep sediments.

Homologues of nitrite reductases in ammonia-oxidizing archaea: diversity and genomic context

Ammonia-oxidizing archaea are frequent and ubiquitous inhabitants of terrestrial and marine environments. As they have only recently been detected, most aspects of their metabolism are yet unknown. Here we report on the occurrence of genes encoding potential homologues of copper-dependent nitrite reductases (NirK) in ammonia-oxidizing archaea of soils and other environments using metagenomic approaches and PCR amplification. Two pairs of highly overlapping 40 kb genome fragments, each containing nirK genes of archaea, were isolated from a metagenomic soil library. Between 68% and 85% of the open reading frames on these genome fragments had homologues in the genomes of the marine archaeal ammonia oxidizers Nitrosopumilus maritimus and Cenarchaeum symbiosum. Extensions of NirK homologues with C-terminal fused amicyanin domains were deduced from two of the four fosmids indicating structural variation of these multicopper proteins in archaea. Phylogenetic analyses including all major groups of currently known NirK homologues revealed that the deduced protein sequences of marine and soil archaea were separated into two highly divergent lineages that did not contain bacterial homologues. In contrast, another separated lineage contained potential multicopper oxidases of both domains, archaea and bacteria. More nirK gene variants directly amplified by PCR from several environments indicated further diversity of the gene and a widespread occurrence in archaea. Transcription of the potential archaeal nirK in soil was demonstrated at different water contents, but no significant increase in transcript copy number was observed with increased denitrifying activity.