The purification of ammonia monooxygenase from Paracoccus denitrificans

Fulvic acid mediated highly efficient heterotrophic nitrification-aerobic denitrification by Paracoccus denitrificans XW11 with reduced C/N ratio

Reducing the C/N ratio requirements for heterotrophic nitrification-aerobic denitrification (HNAD) is crucial for its practical application; however, it remains underexplored. In this study, a highly efficient HNAD bacterium, Paracoccus denitrificans XW11, was isolated. The HNAD characteristics of XW11 were studied, and the redox mediator fulvic acid (FA) was used to reduce the C/N requirements. Whole-genome sequencing revealed multiple denitrification genes in XW11; however, nitrification genes were not identified, because heterotrophic nitrification-related gene sequences were not included in the database. However, the nitrogen removal related enzyme activity test revealed complete nitrification and denitrification pathways. Reverse transcription PCR showed that the membrane-bound nitrate reductase (NarG), rather than the periplasmic nitrate reductase, was responsible for aerobic denitrification. The conventional nitrite reductase (NirS) also does not mediate nitrite denitrification. When the C/N ratio was 10, the ammonia removal efficiency of the Control was 71.71 % and the addition of FA increased it to 86.12 %. Transcriptomic analysis indicated electron flow from the carbon source to FA without proton transmembrane transport, and the presence of FA constructs another electron transfer system. The redox potential of oxidized FA/reduced FA is 0.3679 V, avoiding competition for electrons from Complex III. Thus, ammonia monooxygenase obtains electrons more easily, thereby promoting nitrification. The enzyme activity test of the nitrification process confirmed this view. In addition, NarG expression increased, and the denitrification process was enhanced. Overall, FA improved HNAD efficiency by facilitating electron transfer to the nitrogen dissimilation process, offering a novel approach to reduce the C/N requirement of HNAD.

Hydroxylamine production by Alcaligenes faecalis challenges the paradigm of heterotrophic nitrification

Heterotrophic nitrifiers continue to be a hiatus in our understanding of the nitrogen cycle. Despite their discovery over 50 years ago, the physiology and environmental role of this enigmatic group remain elusive. The current theory is that heterotrophic nitrifiers are capable of converting ammonia to hydroxylamine, nitrite, nitric oxide, nitrous oxide, and dinitrogen gas via the subsequent actions of nitrification and denitrification. In addition, it was recently suggested that dinitrogen gas may be formed directly from ammonium. Here, we combine complementary high-resolution gas profiles, 15N isotope labeling studies, and transcriptomics data to show that hydroxylamine is the major product of nitrification in Alcaligenes faecalis. We demonstrated that denitrification and direct ammonium oxidation to dinitrogen gas did not occur under the conditions tested. Our results indicate that A. faecalis is capable of hydroxylamine production from an organic intermediate. These results fundamentally change our understanding of heterotrophic nitrification and have important implications for its biotechnological application.

Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR)

A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.

Excess sludge-based biochar loaded with manganese enhances catalytic ozonation efficiency for landfill leachate treatment

This study developed an efficient and stable landfill leachate treatment process, which was based on the combination of biochar catalytic ozonation and activated sludge technology for intensive treatment of landfill leachate, aiming to achieve the standard discharge of leachate. The focus is to investigate the effect of manganese loading on the physicochemical properties of biochar and the mechanism of its catalytic ozonation. It was found that more surface functional groups (CO, Mn-O, etc.) and defects (ID/IG = 1.27) were exposed via the change of original carbon structure by loading Mn, which is conducive to the generation of lattice oxygen. Meanwhile, generating different valence states of Mn metal can improve the redox properties and electron migration rate, and encourage the production of reactive oxygen species (ROS) during the reaction process and enhance the catalytic efficiency. The synergistic action of microorganisms, especially denitrifying bacteria, was found to play a key role in the degradation of nitrogenous pollutants during the activated sludge process. The concentration of NH+4-N was reduced from the initial 1087.03 ± 9.56 mg/L to 9.05 ± 1.91 mg/L, while COD was reduced from 2290 ± 14.14 mg/L to 86.5 ± 2.12 mg/L, with corresponding removal rates of 99.17% and 99.20%, respectively. This method offers high efficiency and stability, achieving discharge standards for leachate (GB16889-2008). The synergy between Mn-loaded biochar and microorganisms in the activated sludge is key to effective treatment. This study offers a new approach to solving the challenge of waste leachate treatment.

Phylogenetic diversity, distribution, and gene structure of the pyruvic oxime dioxygenase involved in heterotrophic nitrification

Some heterotrophic microorganisms carry out nitrification to produce nitrite and nitrate from pyruvic oxime. Pyruvic oxime dioxygenase (POD) is an enzyme that catalyzes the degradation of pyruvic oxime to pyruvate and nitrite from the heterotrophic nitrifying bacterium Alcaligenes faecalis. Sequence similarity searches revealed the presence of genes encoding proteins homologous to A. faecalis POD in bacteria of the phyla Proteobacteria and Actinobacteria and in fungi of the phylum Ascomycota, and their gene products were confirmed to have POD activity in recombinant experiments. Phylogenetic analysis further classified these POD homologs into three groups. Group 1 POD is mainly found in heterotrophic nitrifying Betaproteobacteria and fungi, and is assumed to be involved in heterotrophic nitrification. It is not clear whether group 2 POD, found mainly in species of the Gammaproteobacteria and Actinobacteria, and group 3 POD, found simultaneously with group 1 POD, are involved in heterotrophic nitrification. The genes of bacterial group 1 POD comprised a single transcription unit with the genes related to the metabolism of aromatic compounds, and many of the genes group 2 POD consisted of a single transcription unit with the gene encoding the protein homologous to 4-hydroxy-tetrahydrodipicolinate synthase (DapA). LysR- or Cro/CI-type regulatory genes were present adjacent to or in the vicinity of these POD gene clusters. POD may be involved not only in nitrification, but also in certain metabolic processes whose functions are currently unknown, in coordination with members of gene clusters.

Rapid simultaneous removal of nitrogen and phosphorous by a novel isolated Pseudomonas mendocina SCZ-2

Nitrogen (N) and phosphorous (P) removal by a single bacterium could improve the biological reaction efficiency and reduce the operating cost and complexity in wastewater treatment plants (WWTPs). Here, an isolated strain was identified as Pseudomonas mendocina SCZ-2 and showed high performance of heterotrophic nitrification (HN) and aerobic denitrification (AD) without intermediate accumulation. During the AD process, the nitrate removal efficiency and rate reached a maximum of 100% and 47.70 mg/L/h, respectively, under optimal conditions of sodium citrate as carbon source, a carbon-to-nitrogen ratio of 10, a temperature of 35 °C, and shaking a speed of 200 rpm. Most importantly, the strain SCZ-2 could rapidly and simultaneously eliminate N and P with maximum NH₄⁺-N, NO₃^--N, NO₂^--N, and PO₄^3--P removal rates of 14.38, 17.77, 20.13 mg N/L/h, and 2.93 mg P/L/h, respectively. Both the N and P degradation curves matched well with the modified Gompertz model. Moreover, the amplification results of functional genes, whole genome sequencing, and enzyme activity tests provided theoretical support for simultaneous N and P removal pathways. This study deepens our understanding of the role of HN-AD bacteria and provides more options for simultaneous N and P removal from actual sewage.

Enhanced aerobic granular sludge by static magnetic field to treat saline wastewater via simultaneous partial nitrification and denitrification (SPND) process

Saline wastewater poses a threat to biological nitrogen removal. This study investigated whether and how static magnetic field (SMF) can improve the salt-tolerance of aerobic granular sludge (AGS) in two simultaneous partial nitrification and denitrification (SPND) reactors. Results confirmed that the SMF improved the mean size and settleability of granules, stimulated secretion of extracellular polymeric substances with high protein content, in turn enhancing the aerobic granulation. Although high salt stress inhibited functional microorganisms, the SMF maintained better SPND performance with average COD removal, TN removal and nitrite accumulation ratio finally recovering to 100%, 72.9% and 91.1% respectively. High throughput sequencing revealed that functional bacteria evolved from Paracoccus to halotolerant genera Xanthomarina, Thauera, Pseudofulvimonas and Azoarcus with stepwise increasing salinity. The enhanced salt-tolerance may be because the SMF promoted the activity of these halotolerant bacteria. Therefore, this study proposes an economic, effective and environmental biotechnology for saline wastewater treatment.

Characterization of a new heterotrophic nitrification bacterium Pseudomonas sp. strain JQ170 and functional identification of nap gene in nitrite production

Heterotrophic nitrification bacteria play a critical role in nitrogen cycling and pollution removal. However, the underlying nitrification mechanisms are diverse and have rarely been investigated at the genetic level. In this study, the new heterotrophic nitrifier Pseudomonas sp. strain JQ170 was isolated. Strain JQ170 can utilize ammonia (NH₄⁺-N), nitrite (NO₂^--N), or nitrate (NO₃^--N) as sole nitrogen sources, preferring NH₄⁺-N. A ratio of 96.4% of 1.0 mM NH₄⁺-N was removed in 24 h. The optimum pH, temperature, and carbon source for NH₄⁺-N removal were pH 7.0, 30 °C, and citrate, at a C/N ratio of 9-18, respectively. During the NH₄⁺-N removal process, only NO₂^--N but neither hydroxylamine, NO₃^--N, nor gaseous nitrogen were detected. A random transposon insertion mutagenesis library of strain JQ170 was constructed. Two NO₂^--N-production deficient mutants were screened and transposon insertion sites were located in nap genes (which encode periplasmic NO₃^--N reductase Nap). Further gene knockout and complementation of the napA gene confirmed nap as essential for NO₂^--N production. The following nitrification processes in strain JQ170 is proposed: NH₄⁺-N to NO₃^--N in the cytoplasm; then NO₃^--N to NO₂^--N in the periplasmic space by Nap; finally, NO₂^--N secreted out of cells. Overall, this paper provides new insight towards understanding heterotrophic nitrification at the genetic level.

A review of research progress of heterotrophic nitrification and aerobic denitrification microorganisms (HNADMs)

Traditional nitrogen removal relies on the autotrophic nitrification and anaerobic denitrification process. In the system, autotrophic microorganisms achieve nitrification under aerobic condition and heterotrophic microorganisms complete the denitrification in anaerobic condition. As the two types of microorganisms have different tolerance on oxygen concentration, nitrification and denitrification are normally set in two compartments for high nitrogen removal. Therefore, large land occupying is required. In fact, there is a special type of microorganism called heterotrophic nitrification & aerobic denitrification microorganisms (HNADMs) which can oxidize ammonium nitrogen, and perform denitrification in the presence of oxygen. HNADMs have been reported in many environments. It was found that HNADMs could simultaneously achieve nitrification and denitrification. In addition, some HNADMs not only have the ability to remove nitrogen, but also have the ability to remove phosphorus. It suggests that HNADMs have great potential for pollution removal from wastewater. So far, individual work on single strain was carried out. Comprehensive summary of the HNADMs would provide a better picture for understanding and directing its application. In this paper, the studies related on HNADMs were reviewed. The nitrogen metabolism pathway of HNADMs was summarized. The impact of pH, DO, carbon source, and C/N on HNADMs growth and metabolism were discussed. In addition, the extracellular polymeric substance (EPS) production, quorum sensing (QS) secretion and P removal by HNADMs were displayed.

Gene expression analysis of Alcaligenes faecalis during induction of heterotrophic nitrification

Alcaligenes faecalis is a heterotrophic nitrifying bacterium that oxidizes ammonia and generates nitrite and nitrate. When A. faecalis was cultivated in a medium containing pyruvate and ammonia as the sole carbon and nitrogen sources, respectively, high concentrations of nitrite accumulated in the medium whose carbon/nitrogen (C/N) ratio was lower than 10 during the exponential growth phase, while the accumulation was not observed in the medium whose C/N ratio was higher than 15. Comparative transcriptome analysis was performed using nitrifying and non-nitrifying cells of A. faecalis cultivated in media whose C/N ratios were 5 and 20, respectively, to evaluate the fluctuations of gene expression during induction of heterotrophic nitrification. Expression levels of genes involved in primary metabolism did not change significantly in the cells at the exponential growth phase under both conditions. We observed a significant increase in the expression levels of four gene clusters: pod cluster containing the gene encoding pyruvic oxime dioxygenase (POD), podh cluster containing the gene encoding a POD homolog (PODh), suf cluster involved in an iron-sulfur cluster biogenesis, and dnf cluster involved in a novel hydroxylamine oxidation pathway in the nitrifying cells. Our results provide valuable insight into the biochemical mechanism of heterotrophic nitrification.

Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela upwelling system host diverse microbiomes

Due to their lithotrophic metabolisms, morphological complexity and conspicuous appearance, members of the Beggiatoaceae have been extensively studied for more than 100 years. These bacteria are known to be primarily sulfur-oxidizing autotrophs that commonly occur in dense mats at redox interfaces. Their large size and the presence of a mucous sheath allows these cells to serve as sites of attachment for communities of other microorganisms. But little is known about their individual niche preferences and attached microbiomes, particularly in marine environments, due to a paucity of cultivars and their prevalence in habitats that are difficult to access and study. Therefore, in this study, we compare Beggiatoaceae strain composition, community composition, and geochemical profiles collected from sulfidic sediments at four marine stations off the coast of Namibia. To elucidate community members that were directly attached and enriched in both filamentous Beggiatoaceae, namely Ca. Marithioploca spp. and Ca. Maribeggiatoa spp., as well as non-filamentous Beggiatoaceae, Ca. Thiomargarita spp., the Beggiatoaceae were pooled by morphotype for community analysis. The Beggiatoaceae samples collected from a highly sulfidic site were enriched in strains of sulfur-oxidizing Campylobacterota, that may promote a more hospitable setting for the Beggiatoaceae, which are known to have a lower tolerance for high sulfide to oxygen ratios. We found just a few host-specific associations with the motile filamentous morphotypes. Conversely, we detected 123 host specific enrichments with non-motile chain forming Beggiatoaceae. Potential metabolisms of the enriched strains include fermentation of host sheath material, syntrophic exchange of H₂ and acetate, inorganic sulfur metabolism, and nitrite oxidation. Surprisingly, we did not detect any enrichments of anaerobic ammonium oxidizing bacteria as previously suggested and postulate that less well-studied anaerobic ammonium oxidation pathways may be occurring instead.

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.

Novel Alcaligenes ammonioxydans sp. nov. from wastewater treatment sludge oxidizes ammonia to N2 with a previously unknown pathway

Heterotrophic nitrifiers are able to oxidize and remove ammonia from nitrogen-rich wastewaters but the genetic elements of heterotrophic ammonia oxidation are poorly understood. Here, we isolated and identified a novel heterotrophic nitrifier, Alcaligenes ammonioxydans sp. nov. strain HO-1, oxidizing ammonia to hydroxylamine and ending in the production of N₂ gas. Genome analysis revealed that strain HO-1 encoded a complete denitrification pathway but lacks any genes coding for homologous to known ammonia monooxygenases or hydroxylamine oxidoreductases. Our results demonstrated strain HO-1 denitrified nitrite (not nitrate) to N₂ and N₂ O at anaerobic and aerobic conditions respectively. Further experiments demonstrated that inhibition of aerobic denitrification did not stop ammonia oxidation and N₂ production. A gene cluster (dnfT1RT2ABCD) was cloned from strain HO-1 and enabled E. coli accumulated hydroxylamine. Sub-cloning showed that genetic cluster dnfAB or dnfABC already enabled E. coli cells to produce hydroxylamine and further to ¹⁵ N₂ from (¹⁵ NH₄ )₂ SO₄ . Transcriptome analysis revealed these three genes dnfA, dnfB and dnfC were significantly upregulated in response to ammonia stimulation. Taken together, we concluded that strain HO-1 has a novel dnf genetic cluster for ammonia oxidation and this dnf genetic cluster encoded a previously unknown pathway of direct ammonia oxidation (Dirammox) to N₂ .

Identification of optimal parameters for treatment of high-strength ammonium leachate by mixed communities of heterotrophic nitrifying/aerobic denitrifying bacteria

Heterotrophic nitrifying and aerobic denitrifying bacteria (HNADB) are important for partial nitrification treatment of high strength ammonium leachate. However, conditions for their optimal performance in mixed reactor systems have yet to be determined. In this study, optimal parameters were identified and included free ammonia (FA) concentrations below 40 mg/L, a dissolved oxygen concentration of 1.2 mg/L, a carbon to nitrogen ratio of 5 and a reflux ratio of 4. These conditions were applied to a continuous anoxic/oxic membrane moving biofilm reactor treating raw incineration leachate with high total ammonium nitrogen (TAN = 1400 mg/L). Ammonium conversion and nitrogen removal efficiencies of 99% and 86% were achieved. Autotrophic ammonia oxidizing bacteria were inhibited at FA concentrations above 25 mg/L. HNADB, particularly Paracoccus species, contributed to ammonium conversion at high FA (25-40 mg/L). These results show that leachate with high TAN and FA can be treated using parameters that support the growth of HNADB.

Effects of operating conditions on microbial consortium of the heterotrophic ammonia oxidation process

This study aimed to investigate the ammonia removal by the consortium mainly comprising of ammonia-oxidizing bacteria under different initial pH, temperatures and stress of heavy metals. The results showed that the consortium exhibited a strong adaptation for broad pH ranging from 5 to 9. When the temperature dropped to 15℃, its ammonium removal and nitrate accumulation rates decreased by 72.23% and 95.12%, respectively. Meanwhile, the temperature correction coefficients of the ammonium removal and nitrate accumulation rates reached the maximum. In addition, the consortium could survive in the solutions containing 0-1.0 mg·L^-1 Cu²⁺ and 0-5.0 mg·L^-1 Fe³⁺. Moreover, the inhibition of free nitrous acid (FNA) against nitrite oxidation activity was found to be much more significant than that low-temperature treatment. Microbial diversity analysis showed that the bacterial community structure was shift significantly by the temperature drop, especially change the abundance of Nitrosomonas, Paracoccus, Pseudomonas and Nitrospirae.

Microcystis blooms aggravate the diurnal alternation of nitrification and nitrate reduction in the water column in Lake Taihu

To explore the effects of Microcystis blooms on nitrogen (N) cycling in the water column, the community structures of the Microcystis-attached and free-living bacteria in Lake Taihu were assessed and a mesocosm experiment was further conducted on the shore of Lake Taihu. The bacterial communities of Microcystis-attached and free-living bacteria were dominated by heterotrophic bacteria, such as Pseudomonas and Massilia, while the relative abundances of the genera related to traditional autotrophic nitrification were surprisingly low. However, the dramatic increase in nitrate (NO₃^-) levels at the daytime suggested that in the mesocosms nitrification did occur, during which the heterotrophic nitrifiers played a predominant role as revealed by the acetylene inhibition experiment. The ammonium (NH₄⁺) concentrations were always maintained at a low level, indicating that most of the substrates for daytime nitrification originated from organic N. The total N being removed during the experiment was much less than the sum of daily NO₃^- reduction, while the decrease in NO₃^- concentration was much higher than the increase in NH₄⁺ concentration during the night, indicating that assimilation was the main explanation for nocturnal NO₃^- reduction. Thus, the cycling of organic N (remineralization) - heterotrophic nitrification - NO₃^- assimilation (reduction) promoted by Microcystis blooms aggravates the diurnal variation of NO₃^- in the water column.

Biological nitrification inhibition in the rhizosphere: determining interactions and impact on microbially mediated processes and potential applications

Nitrification is the microbial conversion of reduced forms of nitrogen (N) to nitrate (NO3-), and in fertilized soils it can lead to substantial N losses via NO3- leaching or nitrous oxide (N2O) production. To limit such problems, synthetic nitrification inhibitors have been applied but their performance differs between soils. In recent years, there has been an increasing interest in the occurrence of biological nitrification inhibition (BNI), a natural phenomenon according to which certain plants can inhibit nitrification through the release of active compounds in root exudates. Here, we synthesize the current state of research but also unravel knowledge gaps in the field. The nitrification process is discussed considering recent discoveries in genomics, biochemistry and ecology of nitrifiers. Secondly, we focus on the 'where' and 'how' of BNI. The N transformations and their interconnections as they occur in, and are affected by, the rhizosphere, are also discussed. The NH4+ and NO3- retention pathways alternative to BNI are reviewed as well. We also provide hypotheses on how plant compounds with putative BNI ability can reach their targets inside the cell and inhibit ammonia oxidation. Finally, we discuss a set of techniques that can be successfully applied to solve unresearched questions in BNI studies.

Mechanisms of Energy Transduction by Charge Translocating Membrane Proteins

Life relies on the constant exchange of different forms of energy, i.e., on energy transduction. Therefore, organisms have evolved in a way to be able to harvest the energy made available by external sources (such as light or chemical compounds) and convert these into biological useable energy forms, such as the transmembrane difference of electrochemical potential (Δμ̃). Membrane proteins contribute to the establishment of Δμ̃ by coupling exergonic catalytic reactions to the translocation of charges (electrons/ions) across the membrane. Irrespectively of the energy source and consequent type of reaction, all charge-translocating proteins follow two molecular coupling mechanisms: direct- or indirect-coupling, depending on whether the translocated charge is involved in the driving reaction. In this review, we explore these two coupling mechanisms by thoroughly examining the different types of charge-translocating membrane proteins. For each protein, we analyze the respective reaction thermodynamics, electron transfer/catalytic processes, charge-translocating pathways, and ion/substrate stoichiometries.

Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant

The Seine-Morée wastewater treatment plant (SM_WWTP), with a capacity of 100,000 population-equivalents, was fed with raw domestic wastewater during all of its start-up phase. Its microbiome resulted from the spontaneous evolution of wastewater-borne microorganisms. This rare opportunity allowed us to analyze the sequential microbiota colonization and implantation follow up during the start-up phase of this WWTP by means of regular sampling carried out over 8 months until the establishment of a stable and functional ecosystem. During the study, biological nitrification–denitrification and dephosphatation occurred 68 days after the start-up of the WWTP, followed by flocs decantation 91 days later. High throughput sequencing of 18S and 16S rRNA genes was performed using Illumina's MiSeq and PGM Ion Torrent platforms respectively, generating 584,647 16S and 521,031 18S high-quality sequence rDNA reads. Analyses of 16S and 18S rDNA datasets show three colonization phases occurring concomitantly with nitrification, dephosphatation and floc development processes. Thus, we could define three microbiota profiles that sequentially colonized the SM_WWTP: the early colonizers, the late colonizers and the continuous spectrum population. Shannon and inverse Simpson diversity indices indicate that the highest microbiota diversity was reached at days 133 and 82 for prokaryotes and eukaryotes respectively; after that, the structure and complexity of the wastewater microbiome reached its functional stability. This study demonstrates that physicochemical parameters and microbial metabolic interactions are the main forces shaping microbial community structure, gradually building up and maintaining a functionally stable microbial ecosystem.

Nitrous oxide produced directly from ammonium, nitrate and nitrite during nitrification and denitrification

A hypothermia aerobic denitrifying bacterium, Pseudomonas taiwanensis strain J488, can effectively remove multiple nitrogen sources from wastewater at 15 °C. The ammonium, nitrate and nitrite removal efficiencies were 100 %, 92.61 % and 92.49 %, respectively. Strain J488 could survive with hydroxylamine as sole nitrogen source and its removal efficiency was 97.71 %. The removal efficiency of ammonium was 100 % even in the presence of the classical inhibitors of nitrification allylthiourea and diethyldithiocarbamate. These findings fundamentally changed the picture that the ammonia monooxygenase could be inhibited by the copper chelators of allylthiourea or diethyldithiocarbamate. Similarly, the nitrite removal capacity of strain J488 was not sensitive to inhibition by Pb²⁺, and its removal efficiency was also 100 %. Additionally, by identifying the intermediates accumulation of nitrification and denitrification, using nitrification and denitrification inhibitors, measuring enzyme activities and determining N₂O concentrations, it was demonstrated that N₂O could be produced directly from ammonium, nitrate and nitrite.

Ubiquity, diversity, and activity of comammox Nitrospira in agricultural soils

The recent discovery of complete ammonia oxidation (comammox) process in a single organism challenged the division of labor between two functional groups in the classical two-step nitrification model. However, the distribution and activity of comammox bacteria in various environments remain largely unknown. This study presented a large-scale investigation of the geographical distribution, phylogenetic diversity, and activity of comammox Nitrospira in typical agricultural soils. Among the 23 samples harvested across China, comammox Nitrospira clade A was ubiquitously detected at 4.14 × 10⁴-1.65 × 10⁷amoA gene copies/g dry soil, with 90% belonging to the subclade A2. The abundance of comammox Nitrospira clade B was two orders of magnitude lower than clade A. In all samples, comammox Nitrospira were 1-2 orders of magnitude less abundant than canonical nitrifiers, and soils with slightly high pH and C/N tended to enrich more comammox Nitrospira. Unlike canonical nitrifiers, comammox Nitrospira had sustained amoA gene transcription regardless of external ammonia supply, indicating their competitive advantage over other nitrifiers under low-ammonia conditions. When fed with 1 mM ammonium for 15 days, comammox Nitrospira in tested soils were enriched 2.36 times higher than those enriched by the same amount of nitrite, indicating their preference to utilizing ammonia as the substrate. DNA-SIP further confirmed the in situ nitrification activity of comammox Nitrospira. This study provided new insights into the broad distribution and diversity of comammox Nitrospira in agricultural soils, which could potentially play an important role in the microbial nitrogen cycle in soils.

Effect of hydraulic retention time on micropollutant biodegradation in activated sludge system augmented with acclimatized sludge treating low-micropollutants wastewater

This research investigates the effect of hydraulic retention time (HRT) on micropollutant biodegradation of two-stage activated sludge (AS) system augmented with acclimatized sludge treating low-micropollutants wastewater. The experimental wastewater was a mixture of landfill leachate and agriculture wastewater, and HRT was varied between 24, 18, and 12 h. The results showed that, under 24 h HRT, the micropollutant biodegradation efficiencies were 87-93% for bisphenol A (BPA), 2,6-di-tert-butyl-phenol (2,6-DTBP), di-butyl-phthalate (DBP), di-(ethylhexyl)-phthalate (DEHP); 75-81% for carbamazepine (CBZ), diclofenac (DCF); and 88% for N,N-diethylmeta-toluamide (DEET). The degradation efficiencies were similar under 18 h HRT: 87-93% for BPA, 2,6-DTBP, DBP, DEHP; 75-80% for CBZ, DCF; and 80% for DEET. However, the efficiencies substantially declined under 12 h HRT: 71-93%, 55-60%, and 50%, respectively. Importantly, the findings revealed that HRT plays a crucial part in micropollutant biodegradation of bioaugmented AS system. More specifically, too short an HRT (12 h) results in low micropollutant removal efficiency, and too long an HRT (24 h) contributes to low daily throughput and high treatment operation cost. As a result, moderate HRT (18 h) is operationally and economically optimal for bioaugmented AS system treating low-micropollutants wastewater.

Effect of iron and manganese on ammonium removal from micro-polluted source water by immobilized HITLi7T at 2 °C

In this study, trace metals (Fe & Mn) were applied to enhance NH₄⁺-N removal in source water at 2 °C, and 22.7% of initial 2.20 mg/L NH₄⁺-N was removed by pre-treating granular activated carbon (GAC) with Fe & Mn before immobilizing Acinetobacter harbinensis HITLi7^T to form biological activated carbon (BAC). Biomass and dehydrogenase activity (DHA) on this modified BAC were 2.80 × 10⁸ CFU/g-DW C and 0.50 mg/L/g-DW C, respectively, both the highest. Additionally, 4.76 times more biomass and 9.76 times higher DHA of HITLi7^T were observed in the cultivation with Fe & Mn dosing. Extracellular polymeric substances (EPS) measurements found Fe & Mn dosing could increase total EPS amount (44.3% higher) and polysaccharide (PS) ratio (1.50% higher) secreted by HITLi7^T. According to the results of 3D-excitation-emission matrix (3D-EEM) fluorescence spectra and infrared spectra (FTIR) analysis, Fe and Mn promoted the secretion of tryptophan-like substances and changed functional groups COH, COC, CO and COOH, which are associated with protein and PS.

Ammonium transformed into nitrous oxide via nitric oxide by Pseudomonas putida Y-9 under aerobic conditions without hydroxylamine as intermediate

Previous studies have reported that hydroxylamine (NH₂OH) is an inevitable intermediate of the ammonium (NH₄⁺) oxidation pathway under aerobic conditions. In this study, Pseudomonas putida Y-9 was found to oxidize ammonium into N₂O via NO without the accumulation of NH₂OH and NO₂^- under aerobic conditions. NH₂OH was nearly completely transformed into NO₂^- whether NH₄⁺ was present in the medium, and NH₄⁺ could accelerate the transformation of NH₂OH to NO₂^- by promoting Y-9 growth. NH₄⁺ was oxidized rapidly by Y-9 with or without the presence of NH₂OH in the medium, and the decrease of total nitrogen reached 30.65 mg/L and 39.38 mg/L, respectively, which indicates that NH₂OH inhibits the transformation efficiency of NH₄⁺ to N₂O. Gene amplification and enzyme assays demonstrated that ammonia monooxygenase doesn't exist in Y-9. All results show that NH₄⁺ can be transformed into N₂O via NO by Y-9 under aerobic conditions without NH₂OH as intermediate.

Nitrogen cycling during wastewater treatment

Many wastewater treatment plants in the world do not remove reactive nitrogen from wastewater prior to release into the environment. Excess reactive nitrogen not only has a negative impact on human health, it also contributes to air and water pollution, and can cause complex ecosystems to collapse. In order to avoid the deleterious effects of excess reactive nitrogen in the environment, tertiary wastewater treatment practices that ensure the removal of reactive nitrogen species need to be implemented. Many wastewater treatment facilities rely on chemicals for tertiary treatment, however, biological nitrogen removal practices are much more environmentally friendly and cost effective. Therefore, interest in biological treatment is increasing. Biological approaches take advantage of specific groups of microorganisms involved in nitrogen cycling to remove reactive nitrogen from reactor systems by converting ammonia to nitrogen gas. Organisms known to be involved in this process include autotrophic ammonia-oxidizing bacteria, heterotrophic ammonia-oxidizing bacteria, ammonia-oxidizing archaea, anaerobic ammonia oxidizing bacteria (anammox), nitrite-oxidizing bacteria, complete ammonia oxidizers, and dissimilatory nitrate reducing microorganisms. For example, in nitrifying-denitrifying reactors, ammonia- and nitrite-oxidizing bacteria convert ammonia to nitrate and then denitrifying microorganisms reduce nitrate to nonreactive dinitrogen gas. Other nitrogen removal systems (anammox reactors) take advantage of anammox bacteria to convert ammonia to nitrogen gas using NO as an oxidant. A number of promising new biological treatment technologies are emerging and it is hoped that as the cost of these practices goes down more wastewater treatment plants will start to include a tertiary treatment step.

The plethora of membrane respiratory chains in the phyla of life

The diversity of microbial cells is reflected in differences in cell size and shape, motility, mechanisms of cell division, pathogenicity or adaptation to different environmental niches. All these variations are achieved by the distinct metabolic strategies adopted by the organisms. The respiratory chains are integral parts of those strategies especially because they perform the most or, at least, most efficient energy conservation in the cell. Respiratory chains are composed of several membrane proteins, which perform a stepwise oxidation of metabolites toward the reduction of terminal electron acceptors. Many of these membrane proteins use the energy released from the oxidoreduction reaction they catalyze to translocate charges across the membrane and thus contribute to the establishment of the membrane potential, i.e. they conserve energy. In this work we illustrate and discuss the composition of the respiratory chains of different taxonomic clades, based on bioinformatic analyses and on biochemical data available in the literature. We explore the diversity of the respiratory chains of Animals, Plants, Fungi and Protists kingdoms as well as of Prokaryotes, including Bacteria and Archaea. The prokaryotic phyla studied in this work are Gammaproteobacteria, Betaproteobacteria, Epsilonproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Firmicutes, Actinobacteria, Chlamydiae, Verrucomicrobia, Acidobacteria, Planctomycetes, Cyanobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Aquificae, Thermotogae, Deferribacteres, Nitrospirae, Euryarchaeota, Crenarchaeota and Thaumarchaeota.

Characterizing the free ammonia exposure to the nutrients removal in activated sludge systems

As a by-product during liquid production, the liquor wastewater exhibits tremendous environmental risks and may cause undesirable effects to the biological systems due to the high concentration of ammonia.

Effects of hydraulic retention time and carbon to nitrogen ratio on micro-pollutant biodegradation in membrane bioreactor for leachate treatment

This research investigated the biodegradation of the micro-pollutants in leachate by the membrane bioreactor (MBR) system under six treatment conditions, comprising two C/N ratios (6, 10) and three hydraulic retention time (HRT) durations (6, 12, 24h). The experimental results indicated that the C/N 6 environment was more advantageous to the bacterial growth. The bacterial communities residing in the sludge were those of heterotrophic bacteria (HB), heterotrophic nitrifying bacteria (HNB) and ammonia oxidizing bacteria (AOB). It was found that HB and HNB produced phenol hydroxylase (PH), esterase (EST), phthalate dioxygenase (PDO) and laccase (LAC) and also enhanced the biodegradation rate constants (k) in the system. At the same time, AOB promoted the production of HB and HNB. The findings also revealed that the 12h HRT was the optimal condition with regard to the highest growth of the bacteria responsible for the biodegradation of phenols and phthalates. Meanwhile, the longer HRT duration (i.e. 24h) was required to effectively bio-degrade carbamazepine (CBZ), N,N-diethyl-m-toluamide (DEET) and diclofenac (DCF).

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

Kinetics of phenolic and phthalic acid esters biodegradation in membrane bioreactor (MBR) treating municipal landfill leachate

The kinetic of phenolic and phthalic acid esters (PAEs) biodegradation in membrane bioreactor (MBR) treating municipal landfill leachate was investigated. Laboratory-scale MBR was fed with mixture of fresh and stabilized landfill leachate containing carbon to nitrogen (C/N) ratio of 10, 6, 3 and operated under different solid retention time (SRT) of 90, 15 and 5 d. Batch experiments using MBR sludge obtained from each steady-state operating condition revealed highest biodegradation rate constant (k) of 0.059-0.092 h(-1) of the phenolic and PAEs compounds at C/N of 6. Heterotrophic bacteria were the major group responsible for biodegradation of compounds whereas the presence of ammonia-oxidizing bacteria (AOB) helped accelerating their removals. Heterotrophic nitrifying bacteria found under high ammonia condition had an important role in enhancing the biodegradation of phenols and PAEs by releasing phenol hydroxylase (PH), esterase (EST) and phthalate dioxygenase (PDO) enzymes and the presence of AOB helped improving biodegradation of phenolic and PAEs compounds through their co-metabolism.

Exploring membrane respiratory chains

Acquisition of energy is central to life. In addition to the synthesis of ATP, organisms need energy for the establishment and maintenance of a transmembrane difference in electrochemical potential, in order to import and export metabolites or to their motility. The membrane potential is established by a variety of membrane bound respiratory complexes. In this work we explored the diversity of membrane respiratory chains and the presence of the different enzyme complexes in the several phyla of life. We performed taxonomic profiles of the several membrane bound respiratory proteins and complexes evaluating the presence of their respective coding genes in all species deposited in KEGG database. We evaluated 26 quinone reductases, 5 quinol:electron carriers oxidoreductases and 18 terminal electron acceptor reductases. We further included in the analyses enzymes performing redox or decarboxylation driven ion translocation, ATP synthase and transhydrogenase and we also investigated the electron carriers that perform functional connection between the membrane complexes, quinones or soluble proteins. Our results bring a novel, broad and integrated perspective of membrane bound respiratory complexes and thus of the several energetic metabolisms of living systems. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date.

ANaerobic AMMonium OXidation (ANAMMOX) combined with partial nitritation has been adopted for removal of ammonium from wastewater. Here, Speth et al. describe the bacterial metagenome of a partial-nitritation/anammox (PNA) reactor, and provide 23 draft genomes, 19 of which were previously uncharacterized/sequenced/cultivated.

Ammonium removal at low temperature by a newly isolated heterotrophic nitrifying and aerobic denitrifying bacterium Pseudomonas fluorescens wsw-1001

A heterotrophic nitrifier wsw-1001 was isolated from Songhua River and identified as Pseudomonas fluorescens. Ammonium removal by the strain at low temperature was investigated. The effect of initial ammonium concentration (from 5 to 1000 mg/L) and culture temperature (from 4°C to 30°C) on ammonium removal efficiency was studied. Biodegradation product, [Formula: see text], [Formula: see text], N2, N2O and intercellular N were monitored. The results indicated that the strain had potential for water and wastewater treatment. Ammonium could be removed by the strain at low temperature. Ammonium removal efficiency increased with temperature from 4°C to 20°C and decreased with ammonium concentration from 5 to 1000 mg/L. The strain exhibited a capability of heterotrophic nitrification and aerobic denitrification using [Formula: see text] as the sole nitrogen source at 8°C. [Formula: see text] and [Formula: see text] were reduced by the strain. Nitrogen balance analysis in the presence of 39.7 mg/L [Formula: see text] indicated that 71.2% [Formula: see text] was removed by converting to N2 (46.3%) and assimilating as biomass (42.5%). Substances such as [Formula: see text], [Formula: see text] and N2O were detected at very low concentrations. Ammonium mono-oxygenase, hydroxylamine oxidase, nitrite reductase and nitrate reductase activity were measured. The ammonium removal pathway of the strain was speculated to be [Formula: see text].

Bacterial structure of aerobic granules is determined by aeration mode and nitrogen load in the reactor cycle

This study investigated how the microbial composition of biomass and kinetics of nitrogen conversions in aerobic granular reactors treating high-ammonium supernatant depended on nitrogen load and the number of anoxic phases in the cycle. Excellent ammonium removal and predomination of full nitrification was observed in the reactors operated at 1.1 kg TKN m(-3) d(-1) and with anoxic phases in the cycle. In all reactors, Proteobacteria and Actinobacteria predominated, comprising between 90.14% and 98.59% of OTUs. Extracellular polymeric substances-producing bacteria, such as Rhodocyclales, Xanthomonadaceae, Sphingomonadales and Rhizobiales, were identified in biomass from all reactors, though in different proportions. Under constant aeration, bacteria capable of autotrophic nitrification were found in granules, whereas under variable aeration heterotrophic nitrifiers such as Pseudomonas sp. and Paracoccus sp. were identified. Constant aeration promoted more even bacteria distribution among taxa; with 1 anoxic phase, Paracoccus aminophilus predominated (62.73% of OTUs); with 2 phases, Corynebacterium sp. predominated (65.10% of OTUs).

Denitrification characteristics of a newly isolated indigenous aerobic denitrifying bacterium under oligotrophic conditions

A novel indigenous bacterium, strain JM10, isolated from the oligotrophic Hei He reservoir was characterized and showed aerobic denitrification ability. JM10 was identified as Bacillus sp. by phylogenetic analysis of its 16S rRNA gene sequence. Strain JM10 displayed very high levels of activity in aerobic conditions, consuming over 94.3% NO3(-)-N (approximately 3.06 mg L(-1)) with a maximum reduction rate of 0.108 mg NO3(-)-N L(-1) h(-1). Full-factorial Box-Behnken design and response surface methodology were employed to investigate the optimal nitrate degradation conditions. The optimum conditions for nitrate degradation, at a rate of 0.140 mg L(-1) h(-1), were found to be an inoculum size of 16.3% v/v, initial pH of 7.6, C/N ratio of 7.4, and temperature of 27.4 °C, and the C/N ratio and temperature had the largest effect on the nitrate degradation rate. Strain JM10 was added into the water samples from Hei He reservoir and the total nitrogen and nitrate removal rates of the strain reached 66.5% and 100%, respectively. Therefore, our results demonstrate that the strain JM10 favored the bioremediation of the oligotrophic reservoir.

Acclimation of nitrifying biomass and its effect on 2-chlorophenol removal

The metabolic and kinetic behavior of a nitrifying sludge exposed to 2-chlorophenol (2-CP) was evaluated in batch cultures. Two kinds of nitrifying culture were used; one acclimated to 4-methylphenol (4-mp), and the other unacclimated to 4-mp. The unacclimated culture was affected adversely by the 2-CP's presence, since neither nitrification nor 2-CP oxidation was observed. Nonetheless, the acclimated culture showed metabolic capacity to nitrify and mineralize 2-CP. Ammonium removal was 100%, with a nitrifying yield of 0.92 ± 0.04 mg NO(3)(-)-N/mg NH(4)(+)-N consumed. The consumption efficiency for 2-CP was 100% and the halogenated compound was mineralized to CO2. Denaturing gradient gel electrophoresis (DGGE) patterns showed the shift in microbial community structure, indicating that microbial diversity was due to the acclimation process. This is the first evidence where nitrifying culture acclimated to 4-mp completely removed ammonium and 2-CP.

Biological removal of nitrate and ammonium under aerobic atmosphere by Paracoccus versutus LYM

The bacterium isolated from sea sludge Paracoccus versutus LYM was characterized with the ability of aerobic denitrification. Strain LYM performs perfect activity in aerobically converting over 95% NO3(-)-N (approximate 400mg L(-1)) to gaseous products via nitrite with maximum reduction rate 33 mg NO3(-)-N L(-1) h(-1). Besides characteristic of aerobic denitrification, strain LYM was confirmed in terms of the ability to be heterotrophic nitrification and aerobic denitrification (HNAD) with few accumulations of intermediates. After the nitrogen balance and enzyme assays, the putative nitrogen pathway of HNAD could be NH4(+) → NH2OH → NO2(-)→ NO3(-), then NO3(-) was denitrified to gaseous products via nitrite. N2 was sole denitrification product without any detection of N2O by gas chromatography. Strain LYM could also simultaneously remove ammonium and additional nitrate. Meanwhile, the accumulated nitrite had inhibitory effect on ammonium reduction rate.

Ammonium removal by a novel oligotrophic Acinetobacter sp. Y16 capable of heterotrophic nitrification-aerobic denitrification at low temperature

Ammonium removal from source water is usually inhibited by insufficient carbon sources and low temperature in Northeastern China. A strain Y16 was isolated from oligotrophic niche and was identified as Acinetobacter sp. Y16. It demonstrated excellent capability for ammonium removal at 2 °C, and simultaneously produced nitrogen gas as the end product. About 66% of ammonium was removed after 36 h of incubation. Only trace accumulation of nitrate was observed during the process. The utilization of nitrite and nitrate as well as the existence of napA gene further proved the aerobic denitrification ability of strain Y16. Sodium acetate was the most favorable carbon source for ammonium oxidation by strain Y16. High rotation speed was beneficial for ammonium oxidation. Furthermore, strain Y16 could efficiently remove ammonium at low C/N ratio and low temperature conditions, which was advantageous for nitrogen removal from source water under cold temperatures.

Hydroxylamine as an intermediate in ammonia oxidation by globally abundant marine archaea

The ammonia-oxidizing archaea have recently been recognized as a significant component of many microbial communities in the biosphere. Although the overall stoichiometry of archaeal chemoautotrophic growth via ammonia (NH(3)) oxidation to nitrite (NO(2)(-)) is superficially similar to the ammonia-oxidizing bacteria, genome sequence analyses point to a completely unique biochemistry. The only genomic signature linking the bacterial and archaeal biochemistries of NH(3) oxidation is a highly divergent homolog of the ammonia monooxygenase (AMO). Although the presumptive product of the putative AMO is hydroxylamine (NH(2)OH), the absence of genes encoding a recognizable ammonia-oxidizing bacteria-like hydroxylamine oxidoreductase complex necessitates either a novel enzyme for the oxidation of NH(2)OH or an initial oxidation product other than NH(2)OH. We now show through combined physiological and stable isotope tracer analyses that NH(2)OH is both produced and consumed during the oxidation of NH(3) to NO(2)(-) by Nitrosopumilus maritimus, that consumption is coupled to energy conversion, and that NH(2)OH is the most probable product of the archaeal AMO homolog. Thus, despite their deep phylogenetic divergence, initial oxidation of NH(3) by bacteria and archaea appears mechanistically similar. They however diverge biochemically at the point of oxidation of NH(2)OH, the archaea possibly catalyzing NH(2)OH oxidation using a novel enzyme complex.

Biological removal of p-cresol, phenol, p-hydroxybenzoate and ammonium using a nitrifying continuous-flow reactor

Phenolic compounds biodegradation and its effect on the nitrification process were studied. A continuous stirrer tank reactor was operated in four stages, and phenolic compounds were fed as sequential way. In the first stage, at loading rate of 220 mg NH(4)(+)-N/Ld, the consumption efficiency was of 91%, being the product, nitrate. After that, p-cresol was fed at 53 mg C/Ld, reaching removal efficiencies for both substrates higher than 90%. In the third stage, p-hydroxybenzoate was fed at 56 mg C/Ld, and the removal efficiencies for all substrates remained high. In the last stage, the reactor was fed at 54 mg C/Ld of phenol, and it caused a diminishing on the ammonium removal efficiency; however, all phenolic compounds were efficiently removed. Kinetic results showed that the presence of each phenolic compound improved the ammonium oxidizing activity, but the nitrite oxidizing activity was not affected.

Microbiology of nitrogen cycle in animal manure compost

Composting is the major technology in the treatment of animal manure and is a source of nitrous oxide, a greenhouse gas. Although the microbiological processes of both nitrification and denitrification are involved in composting, the key players in these pathways have not been well identified. Recent molecular microbiological methodologies have revealed the presence of dominant Bacillus species in the degradation of organic material or betaproteobacterial ammonia-oxidizing bacteria on nitrification on the surface, and have also revealed the mechanism of nitrous oxide emission in this complicated process to some extent. Some bacteria, archaea or fungi still would be considered potential key players, and the contribution of some pathways, such as nitrifier denitrification or heterotrophic nitrification, might be involved in composting. This review article discusses these potential microbial players in nitrification-denitrification within the composting pile and highlights the relevant unknowns through recent activities that focus on the nitrogen cycle within the animal manure composting process.

Heterotrophic nitrification-aerobic denitrification by novel isolated bacteria

Three novel strains capable of heterotrophic nitrification-aerobic denitrification were isolated from the landfill leachate treatment system. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as Agrobacterium sp. LAD9, Achromobacter sp. GAD3 and Comamonas sp. GAD4, respectively. Batch tests were carried out to evaluate the growth and the ammonia removal patterns. The maximum growth rates as determined from the growth curve were 0.286, 0.228, and 0.433 h(-1) for LAD9, GAD3 and GAD4, respectively. The maximum aerobic nitrification-denitrification rate was achieved by the strain GAD4 of 0.381 mmol/l h, followed by LAD9 of 0.374 mmol/l h and GAD3 of 0.346 mmol/l h. Moreover, hydroxylamine oxidase and periplasmic nitrate reductase were successfully expressed in all the isolates. The relationship between the enzyme activities and the aerobic nitrification-denitrification rates revealed that hydroxylamine oxidation may be the rate-limiting step in the heterotrophic nitrification-aerobic denitrification process. The study results are of great significance to the wastewater treatment systems where simultaneous removal of carbon and nitrogen is desired.

Growth of ammonia-oxidizing archaea in soil microcosms is inhibited by acetylene

Autotrophic ammonia-oxidizing bacteria were considered to be responsible for the majority of ammonia oxidation in soil until the recent discovery of the autotrophic ammonia-oxidizing archaea. To assess the relative contributions of bacterial and archaeal ammonia oxidizers to soil ammonia oxidation, their growth was analysed during active nitrification in soil microcosms incubated for 30 days at 30 degrees C, and the effect of an inhibitor of ammonia oxidation (acetylene) on their growth and soil nitrification kinetics was determined. Denaturing gradient gel electrophoresis (DGGE) analysis of bacterial ammonia oxidizer 16S rRNA genes did not detect any change in their community composition during incubation, and quantitative PCR (qPCR) analysis of bacterial amoA genes indicated a small decrease in abundance in control and acetylene-containing microcosms. DGGE fingerprints of archaeal amoA and 16S rRNA genes demonstrated changes in the relative abundance of specific crenarchaeal phylotypes during active nitrification. Growth was also indicated by increases in crenarchaeal amoA gene copy number, determined by qPCR. In microcosms containing acetylene, nitrification and growth of the crenarchaeal phylotypes were suppressed, suggesting that these crenarchaea are ammonia oxidizers. Growth of only archaeal but not bacterial ammonia oxidizers occurred in microcosms with active nitrification, indicating that ammonia oxidation was mostly due to archaea in the conditions of the present study.

Metabolism of Inorganic N Compounds by Ammonia-Oxidizing Bacteria

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N2O, NO2, and N2 can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N2O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO2 can serve as an alternative oxidant in place of O2 in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.

Microbial degradation and metabolic pathway of pyridine by a Paracoccus sp. strain BW001

A bacterial strain using pyridine as sole carbon, nitrogen and energy source was isolated from the activated sludge of a coking wastewater treatment plant. By means of morphologic observation, physiological characteristics study and 16S rRNA gene sequence analysis, the strain was identified as the species of Paracoccus. The strain could degrade 2,614 mg l(-1) of pyridine completely within 49.5 h. Experiment designed to track the metabolic pathway showed that pyridine ring was cleaved between the C2 and N, then the mineralization of the carbonous intermediate products may comply with the early proposed pathway and the transformation of the nitrogen may proceed on a new pathway of simultaneous heterotrophic nitrification and aerobic denitrification. During the degradation, NH3-N occurred and increased along with the decrease of pyridine in the solution; but the total nitrogen decreased steadily and equaled to the quantity of NH3-N when pyridine was degraded completely. Adding glucose into the medium as the extra carbon source would expedite the biodegradation of pyridine and the transformation of the nitrogen. The fragments of nirS gene and nosZ gene were amplified which implied that the BW001 had the potential abilities to reduce NO2- to NO and/or N2O, and then to N2.

The link between nitrification and biotransformation of 17alpha-ethinylestradiol

Biological treatment processes are probably important for preventing the proliferation of steroidal compounds in the environment, and a growing number of reports suggest that nitrification may play a role in removing these chemicals from wastewater. The link between nitrification and biotransformation of 17alpha-ethinylestradiol (EE2) was investigated using enriched cultures of autotrophic ammonia-oxidizers. Batch experiments showed that ring A of EE2 is the site of electrophilic initiating reactions, including conjugation and hydroxylation. Ring A was also cleaved before any of the other rings were broken, which is likely because the frontier electron density of the ring A carbon units is higher than those of rings B, C, or D. EE2 and NH3 were degraded in the presence of an ammonium monooxygenase (AMO) containing protein extract, and the reaction stoichiometry was consistent with a conceptual model involving a binuclear copper site located at the AMO active site. Continuous tests showed a linear relationship between nitrification and EE2 removal in enriched nitrifying cultures. Taken together, these results support the notion that EE2 biotransformation can be cometabolically mediated under operating conditions that allow for enrichment of nitrifiers.

Nitrogen dynamics in an Australian semiarid grassland soil

We conducted a four-week laboratory incubation of soil from a Themeda triandra Forsskal grassland to clarify mechanisms of nitrogen (N) cycling processes in relation to carbon (C) and N availability in a hot, semiarid environment. Variation in soil C and N availability was achieved by collecting soil from either under tussocks or the bare soil between tussocks, and by amending soil with Themeda litter. We measured N cycling by monitoring: dissolved organic nitrogen (DON), ammonium (NH4+), and nitrate (NO3-) contents, gross rates of N mineralization and microbial re-mineralization, NH4+ and NO3- immobilization, and autotrophic and heterotrophic nitrification. We monitored C availability by measuring cumulative soil respiration and dissolved organic C (DOC). Litter-amended soil had cumulative respiration that was eightfold greater than non-amended soil (2000 compared with 250 microg C/g soil) and almost twice the DOC content (54 compared with 28 microg C/g soil). However, litter-amended soils had only half as much DON accumulation as non-amended soils (9 compared with 17 microg N/g soil) and lower gross N rates (1-4 compared with 13-26 microg N x [g soil](-1) x d(-1)) and NO3- accumulation (0.5 compared with 22 microg N/g soil). Unamended soil from under tussocks had almost twice the soil respiration as soil from between tussocks (300 compared with 175 microg C/g soil), and greater DOC content (33 compared with 24 microg C/g soil). However, unamended soil from under tussocks had lower gross N rates (3-20 compared with 17-31 microg N x [g soil](-1) d(-1)) and NO3- accumulation (18 compared with 25 microg N/g soil) relative to soil from between tussocks. We conclude that N cycling in this grassland is mediated by both C and N limitations that arise from the patchiness of tussocks and seasonal variability in Themeda litterfall. Heterotrophic nitrification rate explained >50% of total nitrification, but this percentage was not affected by proximity to tussocks or litter amendment. A conceptual model that considers DON as central to N cycling processes provided a useful initial framework to explain results of our study. However, to fully explain N cycling in this semiarid grassland soil, the production of NO3- from organic N sources must be included in this model.