Nitrite-oxidizing bacteria (NOB) are key players in the second step of nitrification, which is an important process in the soil nitrogen (N) cycle. However, the ecology of nitrite oxidizers and their ...response to disturbances such as long-term fertilization practices are scarcely known in agricultural ecosystems. We used samples from a Red soil subject to a long-term chemical and organic fertilization experiment, including control without fertilizer (CK), swine manure (M), chemical fertilization (NPK), and chemical/manure combined fertilization (MNPK) treatment, to explore how agricultural practices impact the community structure, abundance, and potential activity of nitrite oxidizers (PNO). The abundance of Nitrobacter was significantly increased in the M and MNPK plots, whereas the abundance of Nitrospira was significantly reduced in the M and NPK treatment plots and less inhibited in the MNPK treatment. The PNO showed a similar trend to that for Nitrobacter abundance. The diversity of Nitrobacter increased in the M-treated plots, while that of Nitrospira increased in the M and MNPK plots and decreased in the NPK plots. Non-metric multidimensional scaling (NMDS) revealed that the Nitrobacter- and Nitrospira-like NOB community was shift in these four fertilization treatments. Redundancy analysis showed that pH+SOC (soil organic carbon) and pH+TN (total nitrogen) significantly explained the variation in the composition of Nitrobacter and Nitrospira, respectively. In addition, the Nitrospira/Nitrobacter abundance ratio and community structure of Nitrobacter- and Nitrospira-like NOB are responsible for the changes of soil PNO. Collectively, these data suggest that the nitrite-oxidation process in the red soil is possibly controlled by both Nitrospira and Nitrobacter-like NOB, which were shaped by pH+TN and pH+SOC, respectively.
•Fertilizer significantly increased soil nitrite oxidizing potential (PNO).•Fertilizer significantly affected the abundances of Nitrobacter and Nitrospira.•PNO was strongly correlated with Nitrobacter but not Nitrospira abundance.•Fertilizer exerted significant impacts on the Nitrobacter and Nitrospira community.•Soil pH was the major driver influencing the Nitrobacter and Nitrospira community.
Carbonaceous materials are soil conditioners that affect nitrogen cycles. However, how carbonaceous materials influence nitrite-oxidizing bacteria (NOB) is yet unclear. In this study, we investigated ...the NOB community and its potential activities under different treatments (control, biochar, straw, limestone, biochar + limestone, and straw + limestone) in an Alfisol, a type of arable soil depleted in calcium carbonate but enriched in aluminum- and iron-bearing minerals. Treatments with limestone increased soil pH, and straw inputs caused an increment of available potassium (AK). Ammonia (NH4+) was inversely changed under the straw and biochar + limestone amendments. None of the treatments significantly impacted the abundance of Nitrobacter (nxrA) or the potential nitrite oxidation activity (PNO). The abundance of Nitrospira (nxrB) increased in the biochar + limestone-treated samples and was significantly correlated with PNO, pH, and AK. High-throughput sequencing results showed that the α-diversity of NOB did not change in response to the treatments. The dominant Nitrobacter OTUs were affiliated within the Clusters 3, 4, 8, and 9 (a new cluster named in this study), while those of Nitrospira were in the lineage II and Namibian soil cluster 2. The limited compositional variation for Nitrobacter was explained by pH, and that for Nitrospira by pH, TN, and NH4+. Among all available data in this study, the richness of Nitrospira was the most important predictor (73%) for PNO. Therefore, we assumed that the community of nitrite oxidizers (Nitrospira) could be relatively redundant in function, supported by the observation that the carbonaceous inputs did not impact either the potential activity or the α-diversity but did affect the abundance and community composition.
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•PNO did not change in response to carbonaceous material amendments.•Treatments with limestone increased soil pH, leading to Nitrobacter shift.•Nitrospira was more sensitive to the treatments than Nitrobacter.•Changes in pH, NH4+ and AK correlated with the variability of Nitrospira.•Nitrospira richness supported the functional redundancy of nitrite oxidation.
How nitrite-oxidizing bacteria (NOB) respond to long-term fertilization and variations in soil aggregate levels remains unclear. In this study, the potential nitrite oxidation activity (PNO), ...abundance, diversity, and community compositions of Nitrobacter- and Nitrospira-like NOB were examined in three aggregate fractions (2000–250, macroaggregate; 250–53, microaggregate; <53 μm, silt + clay) of a Mollisol under four fertilization regimes. NOB abundances were higher in macro- and micro-aggregates, and best explained by aggregate size variation. The PNO, Shannon diversity index and community composition of NOB were more affected by the fertilization regimes. We found PNO significantly correlated with the structure of Nitrospira-like NOB, followed by the abundances and Shannon diversity indexes of NOB. Soil aggregate phosphorus level, total potassium and NH4+ were associated with the NOB community structure. Our results suggested that PNO directly link to the variations for the abundance, diversity and community structure of NOB, which are regulated by the nutrient level in the microhabitat.
•Mollisol aggregate nitrite oxidizing potential (PNO) was affected by fertilization.•Soil macroaggregates possessed higher nitrite-oxidizing bacteria (NOB) abundances.•Alpha-diversity of NOB was more influenced by fertilization.•Fertilization plays more important roles in shaping the aggregate NOB community.•Soil aggregate NOB community was associated with P, K and NH4+ contents.
Nitrite oxidation, driven by nitrite-oxidizing bacteria, is an important step of nitrification and thus plays a vital role in biogeochemical nitrogen cycling in agricultural ecosystems. Although ...biochar has been widely recognized as a promising material for use in vegetable fields to slowly release nutrients, the current understanding of how nitrite oxidizers respond to the application of biochar in a plastic greenhouse vegetable field is very limited. A soil incubation experiment showed that soil nitrite oxidation was increased by 13.0%, 35.0% and 64.2% (P < 0.05) with the application of 0.5% (C0.5), 1.5% (C1.5), and 4.0% (C4.0) biochar (mass ratio), respectively. Methods including qPCR and Illumina MiSeq sequencing were also used to explore the impact of biochar on functional communities involved in nitrite oxidation. Nitrobacter and Nitrospira were the main genera of the nitrite-oxidizing bacteria and were assumed to be very important in the soil environment. Moreover, the increases in soil nitrite oxidation were positively correlated with the abundance of Nitrobacter-like NOB (P < 0.05) but not the Nitrospira-like NOB gene abundance. Furthermore, biochar application combined with nitrogen fertilizer had a significant effect on the Nitrobacter community composition, with lineages such as Nitrobacter alkalicus and Nitrobacter vulgaris being significantly enriched. Redundancy analysis indicated that the observed variations in the Nitrobacter community structure were associated with changes in soil microbial biomass nitrogen and nitrate nitrogen induced by biochar. These results implied that Nitrobacter rather than Nitrospira was significantly improved by biochar added to the soil for vegetable production.
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•Biochar stimulated the soil nitrite oxidizing potential.•Biochar significantly increased the relative abundance of Nitrobacter compared with Nitrospira.•Nitrobacter variations were significantly associated with available nitrogen.•The most impacted Nitrobacter lineages were N. vulgaris and N. alkalicus.
•Straw input and rice-growing stimulate soil nitrite oxidizing potential (NO).•Soil NO is related to a shift in Nitrospira-like NOB community structure.•Nitrospira community shift was significantly ...affected by pH, NH4+ and moisture.•Nitrobacter-like NOB was just not significantly affected in this system.•Nitrospira are more sensitive to straw input and rice-growing than Nitrobacter.
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Nitrite oxidation is recognized as an essential process of biogeochemical nitrogen cycling in agricultural ecosystems. How nitrite-oxidizing bacteria (NOB) respond to land managements (the effect from the long-term straw incorporation and environmental variability caused by the shift from the upland stage to the paddy stage) in a rapeseed-rice rotation field remains unclear. We found the nitrite oxidation (NO) in soils increased from the upland stage to the paddy stage. An inhibitory effect of the long-term straw incorporation on NO was detectable in the upland stage. The abundance of Nitrospira was always greater than Nitrobacter, and it was affected by the rice-growing and straw incorporation while Nitrobacter was not. NO correlated positively with the abundance of Nitrospira and with soluble sulfate (SO42−), soil moisture, pH and NH4+. The high-throughput sequencing analysis of the nitrite oxidoreductase nxrA and nxrB genes for Nitrobacter- and Nitrospira-like NOB was performed respectively. The dominating (relative abundance>1%) operational taxonomic units (OTUs) from Nitrobacter were closely related to Nitrobacter hamburgensis, whereas those from Nitrospira were affiliated with or related to lineage II, lineage V and several unknown groups. Heatmap analysis showed that a few dominant Nitrobacter OTUs were affected by the straw treatment or the rice-growing, and half of the dominant Nitrospira ones were explained by at least one of the variables. Multi-response permutation procedure (MRPP) and redundancy analyses showed that the Nitrospira-like NOB community changes were significantly shaped by the land managements and the soil chemical properties, including pH, moisture and NH4+, whereas that of the Nitrobacter-like NOB community was not. These results suggested that Nitrospira are more sensitive than Nitrobacter to land management in acid and fertilized soils of a rapeseed-rice rotation field trial.
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•Coupling PNA and SAD in a single reactor could achieve up to 89.6 ± 3.6 % of TNRE.•Anammox contributed to about 89.0% of nitrogen removal in the system.•Sulfide reduced nitrite ...oxidizing bacteria activity by approximately 88.2%.•Nitrosomonas, Ca. Kuenenia and Thiobacillus were functional genera.
The partial nitrification-anammox (PNA) process, as a new “green” biological nitrogen removal technology, is completely autotrophic and has great economic and environmental benefits. However, the applied bottleneck of this process is the inability to inhibit nitrite oxidizing bacteria (NOB) activity and the low total nitrogen removal efficiency (TNRE) due to nitrate accumulation. In this study, the addition of sulfide was utilized to selectively screen NOB while promoting the sulfur autotrophic denitrification (SAD) process in one sequencing batch biofilter granular reactor. The results showed that when the influent concentration of NH4+-N and S2− were 184.6 ± 4.4 mg/L and 153.9 ± 3.1 mg/L, the average TNRE reached 89.6 ± 3.6 %. At this stage, aerobic ammonia oxidizing bacteria (AOB) and anaerobic ammonium oxidation bacteria (AnAOB) showed good activities (specific oxygen uptake rate of AOB and specific anammox activity could reach to 0.09 ± 0.00 mg O2/g SS/h and 0.47 ± 0.06 mg TN/g SS/h, respectively), while NOB activity was significantly suppressed by sulfide, with specific oxygen uptake rate of 0.003 ± 0.00 mg O2/g SS/h, which further demonstrating the feasibility and long-term application of this sustainable and efficient process. Anammox was the predominant nitrogen removal pathway contributing approximately 89.0 % of nitrogen removal. Typical AOB (Nitrosomonas), AnAOB (Candidatus Kuenenia), and SAD bacteria (Thiobacillus, Pseudoxanthomonas, and Limobacter) coexisted in the PNA-SAD system. The syntrophic interactions among sulfur-oxidizing, sulfate-reducing, and anammox bacterial populations of this system were revealed by PICRUST2 and network analysis. Sulfides were most likely oxidized to biologically produced elemental sulfur first and then converted to sulfate via the Sox system. Our study provided a new reaction scheme and theoretical reference for efficient nitrogen and sulfur removal in a single reactor.
Nitrite (NO2−) oxidation is an essential step of biological nitrogen cycling in natural ecosystems, and is performed by chemolithoautotrophic nitrite-oxidizing bacteria (NOB). Although Nitrobacter ...and Nitrospira are regarded as representative NOB in nitrification systems, little attention has focused on kinetic characterisation of the coexistence of Nitrobacter and Nitrospira at various pH values. Here, we evaluate the substrate kinetics, biological mechanism and microbial community dynamics of an enrichment culture including Nitrobacter (17.5 ± 0.9%) and Nitrospira (7.2 ± 0.6%) in response to various pH constrains. Evaluation of the Monod equation at pH 6.0, 6.5, 7.0, 7.5, 8.0 and 8.5 showed that the enrichment had maximum rate (rmax) and maximum substrate affinity (KS) for NO2− oxidation at pH 7.0, which was also supported by the largest absolute abundance of Nitrobacter nxrA (5.26 × 107 copies per g wet sludge) and Nitrospira nxrB (1.975 × 109 copies per g wet sludge) genes. Moreover, the predominant species for the Nitrobacter-like nxrA were N. vulgaris and N. winogradskyi, while for the Nitrospira-like nxrB, the predominant species were N. japonica, N. calida and Ca. N. bockiana. Furthermore, the rmax was strongly and positively correlated with the abundance of the Nitrobacter nxrA or Nitrospira nxrB genes, or N. winogradsk, whereas KS was positively correlated with the abundance of Nitrobacter nxrA or Nitrospira nxrB genes or Ca. N. bockiana. Overall, this study could improve basis kinetic parameters and biological mechanism of NO2− oxidation in WWTPs.
•Biological kinetics of coexisting Nitrobacter and Nitrospira to pH was evaluated.•PH exposure has significant impact on the activity and nitrite affinity of NOB.•The pH dependence of NOB was species abundance, rather than microbial composition.•The rmax was strongly positively related with nxrA, nxrB genes and N. winogradsk.•The KS was positively correlated with nxrA, nxrB genes, Ca.N.bockiana.
The nitritation–anammox process is an efficient and cost‐effective approach for biological nitrogen removal, but its application in treating mainstream wastewater remains a great challenge. ...Mainstream nitritation–anammox processes could create opportunities for achieving energy self‐sufficient, or energy‐generating water resource recovery facilities. Significant advancements have been achieved via pilot‐ and full‐scale trials to overcome the major obstacles under mainstream conditions, such as repression of nitrite‐oxidizing bacteria, limiting the overgrowth of denitrifiers, and effective selection and retention of ammonia‐oxidizing bacteria and anammox bacteria. This review paper intends to provide a detailed update of research progress on mainstream nitritation–anammox processes, discuss metabolic interactions, and examine major challenges and possible solutions towards the future development.
Ammonia-oxidizing microorganisms, including AOA (ammonia-oxidizing archaea), AOB (ammonia-oxidizing bacteria), and Comammox (complete ammonia oxidization) Nitrospira, have been reported to possess ...the capability for the biotransformation of sulfonamide antibiotics. However, given that nitrifying microorganisms coexist and operate as communities in the nitrification process, it is surprising that there is a scarcity of studies investigating how their interactions would affect the biotransformation of sulfonamide antibiotics. This study aims to investigate the sulfamonomethoxine (SMM) removal efficiency and mechanisms among pure cultures of phylogenetically distinct nitrifiers and their combinations. Our findings revealed that AOA demonstrated the highest SMM removal efficiency and rate among the pure cultures, followed by Comammox Nitrospira, NOB, and AOB. However, the biotransformation of SMM by AOA N. gargensis is reversible, and the removal efficiency significantly decreased from 63.84 % at 167 h to 26.41 % at 807 h. On the contrary, the co-culture of AOA and NOB demonstrated enhanced and irreversible SMM removal efficiency compared to AOA alone. Furthermore, the presence of NOB altered the SMM biotransformation of AOA by metabolizing TP202 differently, possibly resulting from reduced nitrite accumulation. This study offers novel insights into the potential application of nitrifying communities for the removal of sulfonamide antibiotics (SAs) in engineered ecosystems.
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•AOA demonstrated the highest SMM removal efficiency among nitrifiers.•The biotransformation of SMM by AOA N. gargensis is reversible.•The coculture of AOA and NOB enhanced irreversible SMM removal.•NOB altered the SMM biotransformation of AOA.
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•NOB adapted to free-ammonia (FA) sludge treatment via community shift•The NOB population adapted to FA has higher growth rate and survival chances•NOB adapted to low dissolved oxygen ...(DO) by obtaining higher oxygen affinity•Incorporation of nitrite-scavengers (anammox) overcame FA- and low DO-adaptation•The combo-strategy delivered stable mainstream nitrogen removal via PN/A.
Stable suppression of nitrite-oxidizing bacteria (NOB) is still a major challenge for the implementation of partial nitritation and anammox (PN/A) in mainstream treatment. Despite numerous suppression strategies demonstrated, it is increasingly recognized that NOB could develop resistance to these strategies, threatening the long-term stability of the mainstream PN/A process. This study aims to understand adaption mechanisms and develop counter-strategies to overcome the adaptation. To this end, three previously-demonstrated suppression strategies, including NOB inactivation via side stream sludge treatment with free ammonia (FA), the use of low dissolved oxygen (DO), and the use of anammox to scavenge nitrite, were stepwise applied, over a period of 800 days, to a laboratory-scale reactor treating effluent from a high-rate activated sludge (HRAS) plant. FA sludge treatment alone sustained nitrite accumulation for about two months, after which NOB adaptation occurred causing PN to fail. The FA adaptation was induced by a shift in the NOB community from Nitrospira to Ca. Nitrotoga. The latter was found to have higher resistance to FA and also a higher maximum specific growth rate. Low DO at 0.2–0.4 mg O2 L−1 was then applied, in conjunction with FA treatment, which successfully eliminated Ca. Nitrotoga and re-established PN. However, new and unidentified NOB with a higher apparent oxygen affinity emerged in three months, again leading to PN failure. Lastly, as the third strategy for NOB suppression, anammox was introduced as an in-situ nitrite-scavenger. The combo-strategy delivered reliable NOB suppression with no further adaptation in the remaining experimental period (eight months). The resulted one-stage PN/A reactor achieved a nitrogen removal efficiency of 84.2 ± 5.37%. A control reactor, operated in parallel under the same conditions but without FA treatment, only achieved 10.4 ± 4.6% nitrogen removal, with anammox completely outcompeted by NOB in the last phase.
