Nitrogen removal characteristics of heterotrophic nitrification-aerobic denitrification by Alcaligenes faecalis C16

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.

Metagenomic analysis revealed the evolution of microbial communities, metabolic pathways, and functional genes in the heterotrophic nitrification-aerobic denitrification process under La3+ stress

Trivalent lanthanum (La3+) exists widely in ammonia nitrogen (NH4+-N) tailing water from ionic rare earth mines; however, its effect on heterotrophic nitrification-aerobic denitrification (HN-AD) is unknown, thereby limiting the application of the HN-AD process in this field. In this study, we conducted an HN-AD process using a sequencing batch reactor (5 L) that was continuously operated to directly treat acidic (NH4)2SO4 wastewater (influent NH4+-N concentration of approximately 110 mg/L and influent pH of 5) containing different La3+ concentrations (0-100 mg/L). The NH4+-N removal efficiency of the reactor reached 98.25 % at a La3+ concentration of 100 mg/L. The reactor was in a neutral-to-alkaline environment, which favored La3+ precipitation and complexation. Metagenomic analysis revealed that the relative abundance of Thauera in the reactor remained high (88.62-92.27 %) under La3+ stress. The relative abundances of Pannonobacter and Hyphomonas significantly increased, whereas that of Azoarcus significantly decreased. Metabolic functions in the reactor were mainly contributed by Thauera, and the abundance of metabolic functions under low La3+ stress (≤5 mg/L) significantly differed from that under high La3+ stress (≥10 mg/L). The relative abundance of ammonia assimilation-related genes in the reactor was high and significantly correlated with ammonia removal. However, traditional ammonia oxidation genes were not annotated, and unknown ammonia oxidation pathways may have been present in the reactor. Moreover, La3+ stimulated amino acid biosynthesis and translocation, the citrate cycle, sulfur metabolism, and oxidative phosphorylation and promoted the overproduction of extracellular polymeric substances, which underwent complexation and adsorbed La3+ to reduce its toxicity. Our results showed that the HN-AD process had a strong tolerance to La3+, stable NH4+-N removal efficiency, the potential to recover La3+, and considerable application prospects in treating NH4+-N tailing water from ionic rare earth mines.

Heterotrophic nitrification and aerobic denitrification characteristics of the psychrotolerant Pseudomonas peli NR-5 at low temperatures

The nitrogen removal efficiency of heterotrophic nitrification and aerobic denitrification (HN-AD) bacteria can be seriously inhibited at low temperatures (< 15 °C). A novel psychrotolerant bacterium, Pseudomonas peli NR-5 (P. peli NR-5), with efficient HN-AD capability was isolated and screened from river sediments in cold areas. When P. peli NR-5 was aerobically cultivated for 60 h at 10 °C with NH₄⁺-N, NO₃^--N, and NO₂^--N as the sole nitrogen sources (N 105 mg/L), the nitrogen removal efficiencies were 97.3, 95.3, and 87.8%, respectively, without nitrite accumulation, and the corresponding average nitrogen removal rates were 1.71, 1.67, and 1.55 mg/L/h, respectively. Meanwhile, P. peli NR-5 exhibited excellent simultaneous nitrification and denitrification capabilities at 10 °C. Sodium succinate was the most favorable carbon substrate for bacterial growth and ammonia removal by strain NR-5. The optimal culture conditions determined by the response surface methodology model were a carbon to nitrogen ratio of 5.9, temperature of 11.5 °C, pH of 7.0, and shaking speed of 144 rpm. Under these conditions, 99.1% of the total nitrogen was removed in the verification experiments, which was not significantly different from the predicted maximum removal in the model (99.6%). Six functional genes participating in the HN-AD process were successfully obtained by polymerase chain reaction amplification, which further confirmed the HN-AD capability of P. peli NR-5 and proposed the metabolic pathway of HN-AD. The above results provide a theoretical background of psychrotolerant HN-AD bacteria in wastewater purification under low-temperature conditions.

Nitrogen removal characterization and functional enzymes identification of a hypothermia bacterium Pseudomonas fragi EH-H1

A novel hypothermic strain, Pseudomonas fragi EH-H1, was found to effectively perform heterotrophic nitrification and aerobic denitrification at 15 °C. This strain could consume 100 %, 100 % and 99.95 % of ammonium (54.90 mg∙L^-1), nitrate (56.12 mg∙L^-1) and nitrite (54.15 mg∙L^-1), accompanied by peak removal rates of 5.51, 3.63 and 3.14 mg/L/h, respectively. The ammonium was removed preferentially during simultaneous nitrification and denitrification. Notably, the elimination rate of the toxic nitrite nitrogen remained approximately 3.14 mg/L/h, whether supplemented with ammonium or not. Stepwise inhibition experiments revealed that the key enzymes of ammonia monooxygenase (AMO) and nitrite oxidoreductase (NiR) for nitrification and denitrification coexisted in strain EH-H1. AMO, nitrate reductase and NiR were successfully expressed and detected at 0.637, 0.239 and 0.018 U/mg proteins, respectively. Overall, strain EH-H1 had an outstanding ability to remove nitrogen at low temperatures and could provide guidance for cryogenic wastewater treatment.

Nitrogen removal and mechanism of an extremely high-ammonia tolerant heterotrophic nitrification-aerobic denitrification bacterium Alcaligenes faecalis TF-1

A novel heterotrophic nitrifying bacterium with high salt and high ammonia nitrogen tolerance, Alcaligenes faecalis TF-1, was isolated from the leachate of a landfill. The verification of nitrogen removal efficiency of different nitrogen sources and PCR amplification electrophoresis results showed that the HN-AD pathway of the strain TF-1 was NH₄⁺ → NH₂OH → NO → N₂O → N₂. The results of parameter optimization showed that the optimal nitrogen removal conditions were as follows: sodium citrate as carbon source, C/N = 16, pH = 7, and NH₄⁺-N loading of 808.21 mg/L. The strain TF-1 could remove about 94.60% of ammonia nitrogen (1963.94 mg/L). The salinity tolerance range of the strain TF-1 was 0-70 g/L, and the removal efficiency was 52.87% at salinity 70 g/L and NH₄⁺-N concentration 919.20 mg/L and 55.67% at pH = 10 and NH₄⁺-N concentration 994.82 mg/L. The extreme environmental adaptability and remarkable nitrogen removal performance make this strain a promising candidate in leachate treatment.

Dirammox Is Widely Distributed and Dependently Evolved in Alcaligenes and Is Important to Nitrogen Cycle

Nitrogen cycle is an essential process for environmental health. Dirammox (direct ammonia oxidation), encoded by the dnfT1RT2ABCD cluster, was a novel pathway for microbial N2 production defined in Alcaligenes ammonioxydans HO-1. Here, a copy of the cluster dnfT1RT2ABCD as a whole was proved to have existed and very conserved in all Alcaligenes genomes. Phylogenetic analyses based on 16S rRNA gene sequences and amino acid sequences of DnfAs, together with G + C content data, revealed that dnf cluster was evolved associated with the members of the genus Alcaligenes. Under 20% O2 conditions, 14 of 16 Alcaligenes strains showed Dirammox activity, which seemed likely taxon-related. However, the in vitro activities of DnfAs catalyzing the direct oxidation of hydroxylamine to N2 were not taxon-related but depended on the contents of Fe and Mn ions. The results indicated that DnfA is necessary but not sufficient for Dirammox activity. The fact that members of the genus Alcaligenes are widely distributed in various environments, including soil, water bodies (both freshwater and seawater), sediments, activated sludge, and animal–plant-associated environments, strongly suggests that Dirammox is important to the nitrogen cycle. In addition, Alcaligenes species are also commonly found in wastewater treatment plants, suggesting that they might be valuable resources for wastewater treatment.

Simultaneous Nitrification and Denitrification under Aerobic Atmosphere by Newly Isolated Pseudomona aeruginosa LS82

Discharge of wastewater contained high amount of nitrogen would cause eutrophication to water bodies. Simultaneous nitrification and denitrification (SND) has been confirmed as an effective process, the isolation of SND bacteria is crucial for its successful operation. In this study, an SND strain was isolated and identified as Pseudomona aeruginosa LS82, which exhibited a rapid growth rate (0.385 h−1) and good nitrogen removal performance (4.96 mg N·L−1·h−1). Response surface methodology was applied to optimize the TN removal conditions, at which nearly complete nitrogen (99.8 ± 0.9%) removal were obtained within 18 h at the condition: pH 8.47, 100 rpm and the C/N ratio of 19.7. The saddle-shaped contours confirmed that the interaction of pH and inoculum size would influence the removal of total nitrogen significantly. Kinetic analyses indicated that the reduction of nitrite was the rate-limiting step in the SND process. Our research suggested strain LS82 can serve as a promising candidate for the treatment of ammonium rich wastewater, and expended our understanding the nitrogen removal mechanism in the SND process.

Genetic Foundations of Direct Ammonia Oxidation (Dirammox) to N2 and MocR-like Transcriptional Regulator DnfR in Alcaligenes faecalis JQ135

Ammonia oxidation is an important process of both the natural nitrogen cycle and nitrogen removal from engineered ecosystems. Recently, a new ammonia oxidation pathway termed Dirammox (direct ammonia oxidation, NH₃→NH₂OH→N₂) has been identified in Alcaligenes ammonioxydans. However, whether Dirammox is present in other microbes and its genetic regulation remains unknown. In this study, it was found that the metabolically versatile bacterium Alcaligenes faecalis strain JQ135 could efficiently convert ammonia into N₂ via NH₂OH under aerobic conditions. Genetic deletion and complementation results suggest that dnfABC is responsible for the ammonia oxidation to N₂ in this strain. Strain JQ135 also employs aerobic denitrification, mainly producing N₂O and trace amounts of N₂ with nitrite as sole nitrogen source. Deletion of genes nirK and nosZ that are essential for denitrification did not impair the capability of JQ135 to oxidize ammonia to N₂ (i.e., Dirammox is independent of denitrification). Furthermore, it was also demonstrated that pod (which encodes pyruvic oxime dioxygenase) was not involved in Dirammox and AFA_16745 (which was previously annotated as ammonia monooxygenase and is widespread in heterotrophic bacteria) was not an ammonia monooxygenase. The MocR-family transcriptional regulator DnfR was characterized as an activator of the dnfABC operon with the binding motif 5'-TGGTCTGT-3' in the promotor region. Bioinformatic survey showed that homologs to dnf genes are widely distributed in heterotrophic bacteria. In conclusion, this work demonstrates that besides A. ammonioxydans, Dirammox also occurs in other bacteria, and is regulated by the MocR-family transcriptional regulator DnfR. Importance Microbial ammonia oxidation is a key and rate-limiting step of the nitrogen cycle. Three previous known ammonia oxidation pathways (i.e., nitrification, anaerobic ammonia oxidation (Anammox), and complete ammonia oxidation (Comammox)) are mediated by autotrophic microbes. However, the genetic foundations of ammonia oxidation by heterotrophic microorganisms have not been investigated in depth. Recently, a previously unknown pathway, termed direct ammonia oxidation to N₂ (Dirammox), has been identified in the heterotrophic bacterium Alcaligenes ammonioxydans HO-1. This paper shows that in the metabolically versatile bacterium Alcaligenes faecalis JQ135, the Dirammox pathway is mediated by dnf genes, which are independent of the denitrification pathway. Bioinformatic survey suggests that homologs to dnf genes are widely distributed in bacteria. These findings enhance the understanding of the molecular mechanisms of heterotrophic ammonia oxidation to N₂.

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.

Heterotrophic nitrification and related functional gene expression characteristics of Alcaligenes faecalis SDU20 with the potential use in swine wastewater treatment

A new heterotrophic nitrifying bacterium was isolated from the compost of swine manure and rice husk and identified as Alcaligenes faecalis SDU20. Strain SDU20 had heterotrophic nitrification potential and could remove 99.7% of the initial NH₄⁺-N. Nitrogen balance analysis revealed that 15.9 and 12.3% of the NH₄⁺-N were converted into biological nitrogen and nitrate nitrogen, respectively. The remaining 71.44% could be converted into N₂ or N₂O. Single-factor experiments showed that the optimal conditions for ammonium removal were the carbon source of sodium succinate, C/N ratio 10, initial pH 8.0, and temperature 30 °C. Nitrification genes were determined to be upregulated when sodium succinate was used as the carbon source analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). Strain SDU20 could tolerate 4% salinity and show resistance to some heavy metal ions. Strain SDU20 removed 72.6% high concentrated NH₄⁺-N of 2000 mg/L within 216 h. In a batch experiment, the highest NH₄⁺-N removal efficiency of 98.7% and COD removal efficiency of 93.7% were obtained in the treatment of unsterilized swine wastewater. Strain SDU20 is promising in high-ammonium wastewater treatment.

Nitrogen removal characteristics of a novel heterotrophic nitrification and aerobic denitrification bacteria, Alcaligenes faecalis strain WT14

Alcaligenes faecalis strain WT14 is heterotrophic nitrification and aerobic denitrification bacterium, newly isolated from a constructed wetland, and its feasibility in nitrogen removal was investigated. The result showed sodium citrate was more readily utilized by WT14 as a carbon source. The response surface methodology model revealed the highest total nitrogen removal by WT14 occurred at 20.3 °C, 113.5 r·min^-1, C/N 10.8, and pH 8.4. Under adapted environmental conditions, up to 55.9 mg·L^-1·h^-1 of ammonium nitrogen (NH₄⁺-N) was removed by WT14, and its NH₄⁺-N tolerance ability reached 2000 mg·L^-1. In addition to the reported high NH₄⁺-resistance of Alcaligenes faecalis, WT14 multiplied fast and had strong nitrate or nitrite removal capacity when high strength nitrate or nitrite was provided as the single nitrogen source; which differed from other Alcaligenes faecalis species. These results show WT14 is a novel strain of Alcaligenes faecalis and its nitrogen removal pathway will be carried out in the further study.

Heterotrophic nitrification and biomineralization potential of Pseudomonas sp. HXF1 for the simultaneous removal of ammonia nitrogen and fluoride from groundwater

Pseudomonas sp. HXF1, a strain capable of heterotrophic nitrification, aerobic denitrification (HNAD), and biomineralization was identified and employed for the simultaneous removal of ammonia nitrogen (NH₄⁺-N) and fluoride (F^-). It removed 99.2% of NH₄⁺-N without accumulation of nitrous nitrogen (NO₂^--N) and nitrate nitrogen (NO₃^--N), while removed 87.3% of F^-. Response surface methodology (RSM) was used to study the best removal conditions for NH₄⁺-N and F^-. The results of nitrogen balance experiments with NH₄Cl, NaNO₂, and NaNO₃ as single nitrogen sources and amplification experiments of denitrification genes proved that the bacterial strains may remove NH₄⁺-N through HNAD. The experimental results of Scanning electron microscope (SEM), X-ray photoelectron spectroscopy (XPS), and X-ray diffractometer (XRD) indicated that the way of F^- removal may be adsorption and co-precipitation. The results demonstrated that the strain HXF1 has great potential in the biological denitrification and F^- removal of groundwater.

Simultaneous nitrification-denitrification by phosphate accumulating microorganisms

Nitrogen and phosphorous are important inorganic water pollutants that pose a major threat to the environment and health of both humans and animals. The physical and chemical ways to remove these pollutants from water and soil are expensive and harsh, so biological removal becomes the method of choice to alleviate the problem without any side effects. The identification of microorganisms capable of simultaneous heterotrophic nitrification and aerobic denitrification has greatly simplified the sequestration of nitrogen from ammonium (NH₄⁺) into dinitrogen (N₂). Further, the discovery of phosphorous accumulating organisms offers greater economic benefits because these organisms can favourably and simultaneously remove both nitrogen and phosphorous from wastewaters hence reducing the nutrient burden. The stability of the system and removal efficiency of inorganic pollutants can be enhanced by the use of immobilized organisms. However, limited work has been done so far in this direction and there is a need to further the efforts towards refining process efficiency by testing low-cost substrates and diverse microbial populations for the total eradication of these contaminants from wastewaters.

Nitrogen removal characteristics of a versatile heterotrophic nitrifying-aerobic denitrifying bacterium, Pseudomonas bauzanensis DN13-1, isolated from deep-sea sediment

A heterotrophic nitrifying-aerobic denitrifying bacterium isolated from deep-sea sediment was identified as Pseudomonas bauzanensis DN13-1. Nitrogen (N) removal capability and relative expression of nitrification and denitrification genes of this strain were investigated. The NO2--N, NO3--N and NH4+-N removal efficiencies were 98.82%, 65.87% and 98.89%, respectively, and strain DN13-1 could efficiently remove mixed N. Meanwhile, other inorganic N was not accumulated during these N removal processes. Genomic analysis indicated that genes nirS, norB, nosZ, nasA and putative amo were identified. The relative expression of functional genes by real-time PCR (qPCR) further confirmed nitrite, nitrate and ammonium removal pathways of strain DN13-1 under aerobic condition. Especially, the ammonium removal pathway of this strain was achieved through heterotrophic ammonium nitrification coupled with fast nitrite denitrification directly. Taken together, strain DN13-1 possesses particularity to efficiently remove N, which guarantees its promising application in aquaculture wastewater treatment.

Carbon selection for nitrogen degradation pathway by Stenotrophomonas maltophilia: Based on the balances of nitrogen, carbon and electron

A novel strain DQ01 capable of simultaneous removal of nitrate and ammonium under the aerobic condition was isolated from the landfill leachate and identified as Stenotrophomonas maltophilia. The result showed that S. maltophilia had carbon selection for the nitrogen removal pathway, and preferred to utilize carboxylate rather than carbohydrate, as carboxylate could directly participate in TCA cycle without Embden Meyerhof Parmas (EMP). Nitrogen and carbon balances confirmed that the ammonium assimilation was the main or even sole removal pathway for S. maltophilia, and carboxylate was more conducive to heterotrophic nitrification-aerobic denitrification (HN-AD) process due to the serious self-alkalization and higher reduction potential of carboxylate, which followed: NH₄⁺ → NO₂^- → NO₃^- → NO₂^- → NO due to the lack of nor and nos. Meanwhile, the higher C/N and nitrate could generate a more powerful ion transport driving force to accelerate the electron transfer in the denitrifying respiratory chain.

Identification and Characterization of Janthinobacterium svalbardensis F19, a Novel Low-C/N-Tolerant Denitrifying Bacterium

Herein, we isolated Janthinobacterium svalbardensis F19 from sludge sediment. Strain F19 can simultaneously execute heterotrophic nitrification and aerobic denitrification under aerobic conditions. The organism exhibited efficient nitrogen removal at a C/N ratio of 2:1, with an average removal rate of 0.88 mg/L/h, without nitrite accumulation. At a C/N ratio of 2, an initial pH of 10.0, a culturing temperature of 25 °C, and sodium acetate as the carbon source, the removal efficiencies of ammonium, nitrate, nitrite, and hydroxylamine were 96.44%, 92.32%, 97.46%, and 96.69%, respectively. The maximum removal rates for domestic wastewater treatment for ammonia and total nitrogen were 98.22% and 92.49%, respectively. Gene-specific PCR amplification further confirmed the presence of napA, hao, and nirS genes, which may contribute to the heterotrophic nitrification and aerobic denitrification capacity of strain F19. These results indicate that this bacterium has potential for efficient nitrogen removal at low C/N ratios from domestic wastewater.

Nitrogen Removal Characteristics of Pseudomonas putida Y-9 Capable of Heterotrophic Nitrification and Aerobic Denitrification at Low Temperature

The cold-adapted bacterium Pseudomonas putida Y-9 was investigated and exhibited excellent capability for nitrogen removal at 15°C. The strain capable of heterotrophic nitrification and aerobic denitrification could efficiently remove ammonium, nitrate, and nitrite at an average removal rate of 2.85 mg, 1.60 mg, and 1.83 mg NL^-1h^-1, respectively. Strain Y-9 performed nitrification in preference to denitrification when ammonium and nitrate or ammonium and nitrite coexisted in the solution. Meantime, the presence of nitrate had no effect on the ammonium removal rate of strain Y-9, and yet the presence of high concentration of nitrite would inhibit the cell growth and decrease the nitrification rate. The experimental results indicate that P. putida Y-9 has potential application for the treatment of wastewater containing high concentrations of ammonium along with its oxidation products at low temperature.

An integrated biological approach for treatment of cyanidation wastewater

The cyanidation process has been, and still remains, a profitable and highly efficient process for the recovery of precious metals from ores. However, this process has contributed to environmental deterioration and potable water reserve contamination due to the discharge of poorly treated, or untreated, cyanide containing wastewater. The process produces numerous cyanide complexes in addition to the gold cyanocomplex. Additionally, the discharge constituents also include hydrogen cyanide (HCN) - metallic complexes with iron, nickel, copper, zinc, cobalt and other metals; thiocyanate (SCN); and cyanate (CNO). The fate of these complexes in the environment dictates the degree to which these species pose a threat to living organisms. This paper reviews the impact that the cyanidation process has on the environment, the ecotoxicology of the cyanidation wastewater and the treatment methods that are currently utilised to treat cyanidation wastewater. Furthermore, this review proposes an integrated biological approach for the treatment of the cyanidation process wastewater using microbial consortia that is insensitive and able to degrade cyanide species, in all stages of the proposed process.

Molecular phylogeny of heterotrophic nitrifiers and aerobic denitrifiers and their potential role in ammonium removal

To investigate the physiology and taxonomic composition of the key players of nitrification and denitrification processes in paddy fields, culture dependent and independent studies have been carried out. A total of 28 bacterial strains have been screened in which six were capable of reducing nitrate and nitrite as well as having significant ammonium removal potential. 16S rRNA-PCR-DGGE-based molecular typing of enriched batch culture was done with time duration to explore and identify dominant and stable soil denitrifiers. Notably, three isolates namely PDN3, PDN19, PDN14 were found to be efficiently involved in the removal of 70.32, 71.46, and 81.50% of NH4 (+) and showed closest similarity (>98%) with Bacillus cereus, Bacillus subtilis, and Pseudomonas aeruginosa strains, respectively. The bacterial strain PDN14 showed maximum growth with highest ammonium removal rate (2.78 gN/(m(3) ·h) has also been characterized based on nosZ gene which showed similarity to uncultured γ- Proteobacteria, P. aeruginosa sp. B3. Median joining (MJ) network and rRNA secondary structure have been analyzed for their detailed taxonomic diversity and derived haplotype-based co-occurrence. Results demonstrated that such strains can serve as good candidate for in situ nitrogen transformation in paddy soils and improvingly characterized by physiological and detailed phylogenetic approaches.