Effects of allylthiourea, salinity, and pH on ammonia/ammonium-oxidizing prokaryotes in mangrove sediment incubated in laboratory microcosms

Study on the mechanism of Phoslock's impact on nitrogen migration at the sediment-water interface

Phoslock has a wide range of applications in regulating the release of endogenous phosphorus. Nevertheless, the knowledge regarding its influence on the nitrogen migration process at the sediment-water interface (SWI) remains rather limited. Therefore, this study explores Phoslock's impact on NO3--N and NH4+-N migration at the SWI in Lake Xuanwu and Lake Li using DGT and Rhizon samplers. The results revealed that at 30 °C, Phoslock increased bioavailable NO3--N concentrations in the overlying water compared to the control group in both lakes. However, there were no significant differences in bioavailable NH4+-N concentrations between experimental and control groups in the overlying water at different temperatures. At 30 °C, the downward diffusion intensity of bioavailable NO3--N in the overlying waters of Lake Xuanwu was about 41.59% and 45.76% higher under aerobic and anaerobic conditions (p < 0.05), respectively, and 10.64% and 184.33% higher in Lake Li, compared to the control group. At 15 °C, compared to the control groups, the overall diffusion intensity in the experimental groups of both lakes showed an increasing trend, but the differences were not significant. Phoslock reduced the upward diffusion flux of bioavailable NH4+-N at the SWI of Lake Xuanwu and Lake Li. The inhibitory effect on the release flux of bioavailable NH4+-N increased as the temperature decreased, but the impact on dissolved oxygen (DO) was minimal. For example, at 30 °C, the addition of Phoslock in Lake Xuanwu reduced the upward diffusion flux of bioavailable NH4+-N by approximately 23.4% and 22.01% under aerobic and anaerobic conditions, respectively. At 15 °C, the reduction was approximately 33.52% and 36.25%, respectively. Phoslock also decreased the abundance of sediment nitrification functional genes (AOA and AOB) and enhanced the ability of sediments to replenish bioavailable NO3--N into interstitial water, while the ability to replenish bioavailable NH4+-N decreased. According to the diffusion direction and intensity of bioavailable NO3--N and NH4+-N at the SWI, the addition of Phoslock makes more bioavailable nitrogen in the overlying water accumulate in the sediments.

Simultaneous Removal of Ammonium and Cr(VI) by the Newly Isolated Marine Bacterium Sulfitobacter dubius PT04 in Tannery Wastewater

Biological ammonium nitrogen removal in tannery wastewater is significantly hindered by hexavalent chromium (Cr(VI)) and high salinity. In this study, Sulfitobacter dubius PT04, a newly isolated, salt-tolerant marine bacterium from deep-sea hydrothermal vent sediment in the South Atlantic Ocean, was characterized for its ability to simultaneously remove total ammonia nitrogen (TAN) and Cr(VI). This strain demonstrated effective removal across a pH range of 6-8, temperatures of 25-35 °C, and salinity levels of 0-6%.Optimal conditions identified using Response Surface Methodology (RSM) were pH 6.92, 27.69 °C, and 3.78% salinity. Most TAN was assimilated into biological nitrogen, effectively reducing inorganic nitrogen pollutants. Additionally, Cr(VI) removal was facilitated by enzymatic reactions with reduction activity predominantly in the cell membrane, followed by extracellular release of Cr(III) with minimal surface adsorption. After 7 days of treatment, strain PT04 achieved removal rates of 90.66% for TAN and 74.81% for Cr(VI), highlighting its bioremediation potential for TAN and Cr(VI) in tannery wastewater.

Outstanding enrichment of ladderane lipids in anammox bacteria: Overlooked effect of pH

Ladderane lipids synthesised by anammox bacteria hold significant potential for applications in jet fuel, drug delivery, and optoelectronics. Despite the widespread use of anammox bacteria in nitrogen removal from wastewater, the optimal conditions for maximising ladderane production remain unclear, limiting their broader application. To address this, we operated a fed-batch bioreactor with anammox bacteria, gradually adjusting the pH from 6.5 to 7.5 while regularly sampling for microbial community composition (Illumina sequencing), proteins, and ladderane lipids (UHPLC-HRMS). Our findings reveal that ladderane production positively correlates with rising pH increasing nearly fivefold as pH rose from 6.5 to 7.5, with a notable shift towards lipids containing two ladderane alkyl chains at higher pH. However, the conditions at an alkaline pH range also induced mild stress in anammox bacteria, as evidenced by our proteomic and microbial community data. Therefore, we propose maintaining a pH above 7.5 to enrich ladderane-rich anammox biomass but emphasise the need for gradual adaptation. This approach could optimise anammox installations for producing high-value ladderane lipids from wastewater.

Research on intensive nitrogen removal of municipal sewage by mainstream anaerobic ammonia oxidation process

The anaerobic ammonia oxidation (anammox) process is a pivotal nitrogen removal technique, playing a significant role in the field of wastewater treatment. The paper commences by delineating the merits of the anammox process in comparison to conventional nitrification-denitrification techniques. Subsequently, it delves into the characteristics of different sludge morphologies process of the behavior of anammox bacteria and their reactions to environmental factors. Revising the issues associated with managing urban sewage in mainstream areas., it discusses the issues faced by the anammox process under reduced nitrogen loads, such as restricted activity due to decreased the levels of ammonia nitrogen and nitrite concentrations, as well as the impact of environmental factors like low temperature, organic matter, and sulfur ions. Following this, a comprehensive review of various types of coupled anammox processes is provided, highlighting the advantages and characteristics of partial nitrification (PN), partial denitrification (PD), methane-dependent nitrite/nitrate reduction (DAMO), sulfur-driven autotrophic denitrification (SAD), iron ammonia oxidation (feammox) and algae photoautotrophy coupling techniques, emphasizing their significance in system stability and resource utilization efficiency. Future research directions include exploring the applicability of the anammox process under various temperature conditions and addressing NO3--N issues in effluent. The findings from these studies will offer valuable insights for further enhancing the optimization of the anammox process in mainstream urban wastewater treatment.

Potential electron acceptors for ammonium oxidation in wastewater treatment system under anoxic condition: A review

Anaerobic ammonium oxidation has been considered as an environmental-friendly and energy-efficient biological nitrogen removal (BNR) technology. Recently, new reaction pathway for ammonium oxidation under anaerobic condition had been discovered. In addition to nitrite, iron trivalent, sulfate, manganese and electrons from electrode might be potential electron acceptors for ammonium oxidation, which can be coupled to traditional BNR process for wastewater treatment. In this paper, the pathway and mechanism for ammonium oxidation with various electron acceptors under anaerobic condition is studied comprehensively, and the research progress of potentially functional microbes is summarized. The potential application of various electron acceptors for ammonium oxidation in wastewater is addressed, and the N2O emission during nitrogen removal is also discussed, which was important greenhouse gas for global climate change. The problems remained unclear for ammonium oxidation by multi-electron acceptors and potential interactions are also discussed in this review.

Impact of salinity and organic matter on the ammonia-oxidizing archaea and bacteria in treating hypersaline industrial wastewater: amoA gene abundance and ammonia removal contributions

Studies published recently proposed that ammonia-oxidizing archaea (AOA) may be beneficial for hypersaline (salinity > 50 g NaCl L-1) industrial wastewater treatment. However, knowledge of AOA activity in hypersaline bioreactors is limited. This study investigated the effects of salinity, organic matter, and practical pickled mustard tuber wastewater (PMTW) on AOA and ammonia-oxidizing bacteria (AOB) in two sequencing batch biofilm reactors (SBBRs). Results showed that despite observed salinity inhibition (p < 0.05), both AOA and AOB contributed to high ammonia removal efficiency at a salinity of 70 g NaCl L-1 in the two SBBRs. The ammonia removal efficiency of SBBR2 did not significantly differ from that of SBBR1 in the absence of organic matter (p > 0.05). Batch tests and quantitative real-time PCR (qPCR) reveal that salinity and organic matter inhibition resulted in a sharp decline in specific ammonia oxidation rates and amoA gene copy numbers of AOA and AOB (p < 0.05). AOA demonstrated higher abundance and more active ammonia oxidation activity in hypersaline and high organic matter environments. Salinity was positively correlated with the potential ammonia oxidation contribution of AOA (p < 0.05), resulting in a potential transition from AOB dominance to AOA dominance in SBBR1 as salinity levels rose. Moreover, autochthonous AOA in PMTW promoted the abundance and ammonia oxidation activities of AOA in SBBR2, further elevating the nitrification removal efficiency after feeding the practical PMTW. AOA demonstrates greater tolerance to the challenging hypersaline environment, making it a valuable candidate for the treatment of practical industrial wastewater with high salinity and organic content.

Global landfill leachate characteristics: Occurrences and abundances of environmental contaminants and the microbiome

Landfill leachates are complex mixtures containing very high concentrations of biodegradable and recalcitrant toxic compounds. Understanding the major contaminant components and microbial community signatures in global landfill leachates is crucial for timely decision-making regarding contaminant management and treatment. Therefore, this study analyzed leachate data from 318 landfill sites primarily used for municipal solid waste disposal, focusing on their chemical and microbiological characteristics. The most prevalent and dominant components in landfill leachates are the chemical oxygen demand (COD, 3.7-75.9 × 103 mg/L) and NH4+ (0.03-0.81 × 104 mg/L), followed by salt species such as SO42- (0.03-5.25 × 103 mg/L), Cl- (3.2-7.8 × 103 mg/L), K+ (0.58-4.20 × 103 mg/L), Na+ (1.3-13.0 × 103 mg/L) and Ca2+ (2.35-230.23 × 103 mg/L), which exhibit significant fluctuations. Heavy metals and metalloids are widely distributed in most landfill leachates but at relatively low concentrations (<182.8 mg/L) compared to conventional parameters. Importantly, there is a distinct global variation in the occurrence of emerging environmental contaminants (ECs). Among these compounds, perfluorooctanoic acid (PFOA, 0.02-7.50 × 103 μg/L) of per- and poly-fluoroalkyl substances (PFAS), bisphenol A (BPA, 0.01-33.46 × 103 μg/L) belonged to endocrine-disrupting compounds (EDCs), together with di-ethyltoluamide (DEET, 1.0-1.0 × 103 μg/L) affiliated to pharmaceuticals and personal care products (PPCPs) are the most frequently detected in landfill leachates. Additionally, the microbial community compositions in most leachates are primarily dominated by Proteobacteria, Bacteroidota, Firmicutes, and Chloroflexi, and some of their abundances are correlated with the concentrations of NH4+, NO3-, Cl-, Na+ and Cr. Notably, the leading microbes driving advanced removal of inorganic nitrogen in the treatment systems are Candidatus Brocadia (anammox), denitrifying Thauera, nitrite-oxidizing bacteria Nitrospira, along with ammonia-oxidizing bacteria Nitrosomonas and Nitrosospira. The findings of this work provide a deeper insight into the leachate characteristics and the sustainable management of landfill leachates, especially presenting a snapshot of the global distribution of pollutants and also the microbiome.

A comprehensive insight into the abundance and community of anammox bacteria in sediments of Hangzhou Bay, China

A total of 13 surface sediments were collected from Hangzhou Bay (HZB) for an investigation into the distribution and influencing factors of anammox bacterial community. The anammox bacterial 16S rRNA and hzo genes ranged between 2.34 × 105 to 9.22 × 105 copies/g and 3.68 × 105 to 1.70 × 106 copies/g, respectively. The results of high throughput sequencing (HTS) revealed that the obtained OTUs were affiliated with five known genera, named Ca. Scalindua, Ca. Jettenia, Ca. Brocadia, Ca. Kuenenia and Ca. Anammoxoglobus. RDA analysis indicated that salinity, pH, and water depth influenced the anammox bacterial community. Furthermore, network analysis identified Ca. Scalindua as a key genus. Neutral community model (NCM) and modified stochasticity ratio (MST) indicated that the deterministic process dominated the anammox bacterial community assembly. Overall, this study offers a more comprehensive understanding of the abundance and community of anammox bacteria in the sediments of HZB.

Improved regression model for anaerobic ammonium oxidation by repeated and prolonged batch assay under stressful salinity and pH conditions

The aim of this study was to propose repeated and prolonged batch (RPB) assay as a promising specific anammox activity (SAA) methodology assessing the anammox activity under stressed salinity and pH conditions. Response surface analysis (RSA) was used as a regression tool to evaluate statistical significance. The feasibility of RPB was investigated at 0 to 15 g-NaCl/L of salinity and pH 6 to 8 with reflecting the results of preliminary SAA. As a result, conventional SAA was statistically insignificant. In addition, the RSA results obtained from repeated batch did not meet the statistical significance despite ten times iterative reaction. Interestingly, the RPB assay (i.e., applied both repeated and prolonged reaction) was effective to obtain the reliable results. Candidadus Brocadia and Candidadus Jettenia were functional anammox microbiome during RPB. Outcomes of this study suggest that RPB assay can be applied to accurately determine the anammox activity under various stressful conditions.

Response mechanisms of bacterial communities and nitrogen cycle functional genes in millet rhizosphere soil to chromium stress

Introduction

A growing amount of heavy metal contamination in soil disturbs the ecosystem's equilibrium, in which microbial populations play a key role in the nutrient cycle of soils. However, given the different sensitivity of microbial communities to different spatial and temporal scales, microbial community structure and function also have varied response mechanisms to different heavy metal contaminated habitats.

Methods

In this study, samples were taken prior to Cr stress (CK) and 6 h and 6 days after Cr stress (Cr_6h, Cr_6d) in laboratory experiments. High-throughput sequencing revealed trends in the structure and diversity of the bacterial communities, and real-time fluorescence quantitative polymerase chain reaction (qPCR) was used to analyze trends in nitrogen cycle functional genes (AOA-amoA, AOB-amoA, narG, nirK, and nifH).

Results

The findings showed that (1) the composition structure of the soil bacterial community changed considerably in Cr-stressed soils; α-diversity showed significant phase transition characteristic from stress to stability (p < 0.05). (2) With an overall rising tendency, the abundance of the nitrogen cycle functional genes (AOA-amoA and AOB-amoA) decreased considerably before increasing, and α-diversity dramatically declined (p < 0.05). (3) The redundancy analysis (RDA) and permutational multivariate analysis of variance (PERMANOVA) tests results showed that the soil physicochemical parameters were significantly correlated with the nitrogen cycle functional genes (r: 0.4195, p < 0.01). Mantel analysis showed that available nitrogen (N), available potassium (K), and available phosphorus (P) were significantly correlated with nifH (p = 0.006, 0.008, 0.004), and pH was highly significantly correlated with nifH (p = 0.026). The PLS-ME (partial least squares path model) model further demonstrated a significant direct effect of the soil physicochemical parameters on the nitrogen cycling functional genes.

Discussion

As a result, the composition and diversity of the bacterial community and the nitrogen cycle functional genes in Cr-stressed agricultural soils changed considerably. However, the influence of the soil physicochemical parameters on the functional genes involved in the nitrogen cycle was greater than that of the bacterial community. and Cr stress affects the N cycling process in soil mainly by affecting nitrification. This research has significant practical ramifications for understanding the mechanisms of microbial community homeostasis maintenance, nitrogen cycle response mechanisms, and soil remediation in heavy metal-contaminated agricultural soils.

Integrated moving bed biofilm reactor with partial denitrification-anammox for promoted nitrogen removal: Layered biofilm structure formation and symbiotic functional microbes

Partial denitrification/anaerobic ammonia oxidation (anammox) (PD/A) is currently an advanced nitrogen removal process. This study developed a PD/A system in a moving bed biofilm reactor. Results showed that the nitrogen removal efficiency reached 76.60% with a COD/NO₃-N of 2.0, and the contribution of anammox was 88.01%. Further analysis showed that the biocarriers could form layered pH and dissolved oxygen structures to promote the aggregation of different functional bacteria at various depths, thus stabilizing the coupled process. Microbial structure analysis showed that the abundance of Saccharimonadales, responsible for denitrification, increased from 0% to 36.27% between day 0 and day 120, while the abundance of Candidatus Jettenia, responsible for anammox, decreased from 10.41% to 2.20%. The synergistic effect of Saccharimonadales and Candidatus Jettenia enabled stable and efficient removal of nitrogen. This study proposed a novel configuration of the PD/A process and provided a theoretical basis for its promotion and application.

Evaluation of PCR primers for detecting the distribution of nitrifiers in mangrove sediments

Ammonia-oxidizing archaea and ammonia-oxidizing bacteria (AOA and AOB), complete ammonia oxidizers (Comammox), and nitrite-oxidizing bacteria (NOB) play a crucial role in the nitrification process during the nitrogen cycle. However, their occurrence and diversity in mangrove ecosystems are still not fully understood. Here, a total of 11 pairs of PCR primers were evaluated to study the distribution and abundances of these nitrifiers in rhizosphere and non-rhizosphere sediments of a mangrove ecosystem. The amplification efficiency of these 11 pairs of primers was first evaluated and their performances were found to vary considerably. The CamoA-19F/CamoA-616R primer pair was suitable for the amplification of AOA in mangrove sediments, especially on the surface of rhizosphere sediments. Primer pair amoA1F/amoA2R was better for the characterization of novel AOB in the bacterial community of non-rhizosphere sediments of mangroves. In contrast, primer nxrB169F/nxrB638R showed a low abundance of NOB in mangrove sediments (except for R1). Comammox bacteria were abundant and diverse in mangrove sediments, as indicated by both the amoB gene for Comammox clade A and the amoA gene for Comammox Nitrospira clade B. However, the amoA gene for Comammox Nitrospira clade A was not successful in detecting them in the mangrove sediments. Furthermore, 568 operational taxonomic units (OTUs) were obtained by generating a clone library and a high abundance of OTUs was correlated with ammonium, pH, NO₂^-, and NO₃^-. Comammox and Comammox Nitrospira were identified by phylogenetic tree analysis, indicating that mangrove sediments harbor newly discovered nitrifiers. Additionally, many AOA and NOB were mainly distributed in the surface layer of the rhizosphere, whereas AOB and Comammox Nitrospira were in the subsurface of non-rhizosphere, as determined by qPCR analysis. Collectively, our findings highlight the limitations of some primers for the identification of specific nitrifying bacteria. Therefore, primers must be carefully selected to gain accurate insights into the ecological distribution of nitrifiers in mangroves. KEY POINTS: • Several sets of PCR primers perform well for the detection of nitrifiers in mangroves. • Mangroves are an important source of newly discovered nitrifiers. • Ammonium, pH, NO₂^-, and NO₃^- are important shapers of nitrifier communities in mangroves.

The Effect of the Conversion from Natural Broadleaved Forests into Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) Plantations on Soil Microbial Communities and Nitrogen Functional Genes

The conversion of forests could change soil characteristics and, in turn, impact the microbial community. However, the long-term effect of forest transformation on bacterial and archaeal composition and diversity, especially on nitrogen functional communities, is poorly understood. This study aimed to explore the response of soil bacterial and archaeal communities, as well as nitrogen functional groups, to the conversion from natural broadleaved forests to Chinese fir (Cunninghamia lanceolate (Lamb.) Hook.) plantations in subtropical China by 16S rRNA amplicon sequencing. Except for soil bulk density (BD) and ammonium nitrogen (NH4+–N) content, other soil properties all decreased with the conversion from natural forests to plantations. Alpha diversity of bacteria and archaea declined with the transformation from natural forests to plantations. The composition of bacteria and archaea was significantly different between natural forests and plantations, which could be mainly attributed to the change in the content of soil organic carbon (SOC), total nitrogen (TN), nitrate nitrogen (NO3−–N), and available phosphorus (AP). The conversion of natural forests to plantations decreased the gene copies of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nifH (nitrogen fixation function) but increased denitrification gene copies (i.e., nirS, nirK, and nosZ). In summary, our study emphasizes the long-term negative effect of the conversion from natural broadleaved forests into Chinese fir plantations on the diversity and richness of soil microbial communities, thereby deeply impacting the cycling of soil nitrogen.

Dissimilatory nitrate reduction and functional genes in two subtropical rivers, China

Dissimilatory nitrate reduction processes, including denitrification, anaerobic ammonium oxidation (anammox), and dissimilatory nitrate reduction to ammonium (DNRA), are important pathways of nitrate transformation in the aquatic environments. In this study, we investigated potential rates of denitrification, anammox, and DNRA in the sediments of two subtropical rivers, Jinshui River and Qi River, with different intensities of human activities in their respective catchment, China. Our objectives were to assess the seasonality of dissimilatory nitrate reduction rates, quantify their respective contributions to nitrate reduction, and reveal the relationship between dissimilatory nitrate reduction rates, functional gene abundances, and physicochemicals in the river ecosystems. Our results showed higher rates of denitrification and anammox in the intensively disturbed areas in autumn and spring, and higher potential DNRA in the slightly disturbed areas in summer. Generally, denitrification, anammox, and DNRA were higher in summer, autumn, and spring, respectively. Relative contributions of nitrate reduction from denitrification, anammox, and DNRA were quite different in different seasons. Dissimilatory nitrate reduction rates and gene abundances correlated significantly with water temperature, dissolved organic carbon (DOC), sediment total organic carbon (SOC), NO₃^-, NH₄⁺, DOC/NO₃^-, iron ions, and sulfide. Understanding dissimilatory nitrate reduction is essential for restoring nitrate reduction capacity and improving and sustaining ecohealth of the river ecosystems.

Diversity, abundance, and distribution of anammox bacteria in shipping channel sediment of Hong Kong by analysis of DNA and RNA

Anammox bacteria have been detected in various ecosystems, but their occurrence and community composition along the shipping channels have not been reported. In this study, anammox bacteria were recovered by PCR-amplified biomarker hzsB gene from the genomic DNA of the sediment samples. Phylogenetic tree revealed that Candidatus Scalindua and Ca. Brocadia dominated the anammox community of the Hong Kong channels; Ca. Scalindua spp. was present abundantly at the sites farther from the shore, whereas Ca. Jettenia and Ca. Kuenenia were detected as the minor members in the estuarine sediments near the shipping terminals. The highest values of Shannon-Wiener index and Chao1 were identified in the sediments along the Urmston road (UR), suggesting the highest α-diversity and species richness of anammox bacteria. PCoA analysis indicated that anammox bacterial communities along UR and Tai Hong (TH) channel were site-specific because these samples were grouped and clearly separated from the other samples. The maximum diversity of anammox bacteria was detected in UR samples, ranging from 6.28 × 10⁵ to 1.28 × 10⁶ gene copies per gram of dry sediment. A similar pattern of their transcriptional activities was also observed among these channels. Pearson's moment correlation and redundancy analysis indicated that NH₄⁺-N was a strong factor shaping the community structure, which showed significant positive correlation with the anammox bacterial abundance and anammox transcriptional activities (p < 0.01, r > 0.8). Also, NH₄⁺-N, (NO₃^- + NO₂^-)-N, and NH₄⁺/NO_X were additional key environmental factors that influenced the anammox community diversity and distribution. This study yields a better understanding of the ecological distribution of anammox bacteria and the dominant genera in selective niche.

High-rate nitrogen removal in a continuous biofilter anammox reactor for treating low-concentration nitrogen wastewater at moderate temperature

The high-rate nitrogen removal in a continuous biofilter anammox reactor (CBAR) was investigated to treat low-concentration nitrogen wastewater. Shortening hydraulic retention time (HRT) gradually could restart CBAR and accumulate anammox bacteria effectively in the reactor, where the carmine anammox granular sludge and biofilm were coexisted well. It spent 21 days to restart CBAR completely after it had been idle for 116 days. Meanwhile, the total nitrogen removal rate remained stable at 86.42% accompanied with a total biomass concentration of 26.02 g-SS/L in 0 ~ 20 cm zone under nitrogen loading rate of 4.25 ± 0.10 kg-N/(m³·day), HRT of 20 min and 25 ℃. In addition, the specific anammox activity of biomass exceeded 0.28 g-N/(g-VSS·day) in 0 ~ 20 cm zone, which was related with a high relative abundance of Candidatus Brocadia (>30%) in the same zone. Thus, it is a feasible approach to adopt CBAR to treat low-concentration nitrogen wastewater efficiently.

Distribution of ammonia-oxidizing archaea and bacteria along an engineered coastal ecosystem in subtropical China

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are the crucial players in nitrogen cycle. Both AOA and AOB were examined along a gradient of human activity in a coastal ecosystem from intertidal zone, grassland, and Casuarina equisetifolia forest to farmland. Results showed that the farmland soils had noticeably higher nitrate-N, available P than soils in the other three sites. Generally, AOA and AOB community structures varied across sites. The farmland mainly had Nitrosotalea-like AOA, intertidal zone was dominated by Nitrosopumilus AOA, while grassland and C. equisetifolia forest primarily harbored Nitrososphaera-like AOA. The farmland and C. equisetifolia forest owned Nitrosospira-like AOB, intertidal zone possessed Nitrosomonas-like AOB, and no AOB was detected in the grassland. AOA abundance was significantly greater than AOB in this coastal ecosystem (p < 0.05, n = 8). AOB diversity and abundance in the farmland were significantly higher than those in the other three sites (p < 0.05, n = 2). The biodiversity and abundance of AOA were not significantly correlated with any soil property (p < 0.05, n = 8). However, the diversity of AOB was significantly correlated with pH, available P and total P (p < 0.05, n = 6). The abundance of AOB was significantly correlated with pH, nitrite, available N, available P and total P (p < 0.05, n = 6). This study suggested that the community structures of AOA and AOB vary in the different parts in the bio-engineered coastal ecosystem and agricultural activity appears to influence these nitrifiers.

Spatial variability pattern of the anaerobic ammonia-oxidizing bacterial community across a salinity gradient from river to ocean

In natural habitats, the diversity of anaerobic ammonia-oxidizing (anammox) bacteria could be affected by multiple environmental variables. In this study, we investigated the distribution of the anammox bacterial community in surface sediment from the Dongjiang River (riverine sediment, DJ) to the Pearl River Estuary (estuarine sediment, PRE) and then to the South China Sea (coastal sediment, SCS). The results revealed evident differences in the structural diversity of anammox bacteria in three different habitats. Candidatus Brocadia accounted for approximately 90% of the total anammox bacteria in DJ, conversely, Ca. Scalindua dominated in the SCS. Nevertheless, Ca. Scalindua, Ca. Brocadia and Ca. Kuenenia coexisted in the PRE. The qPCR results indicated that anammox bacterial 16S rRNA gene abundance ranged from 2.23 × 10⁵ to 1.19 × 10⁷ copies g^-1 of wet weight, but no significant correlation was found between the abundances and environmental variables (p > 0.05). The relative abundances of Ca. Brocadia gradually decreased with increasing salinity, and Ca. Scalindua showed the opposite trend, suggesting that salinity was a crucial factor in sculpturing the community composition of anammox bacteria in natural environments. Ca. Brocadia should be able to live in freshwater ecosystems, but it can also tolerate a certain level of salinity. Ca. Scalindua was halophilic anammox bacterium and exists only in saline environments. Ca. Kuenenia could adapt to a wide range of salinity and preferred to live in high DIN level conditions according to our search. The distribution pattern of anammox bacteria may be the result of microbial migration and long-term adaptation to salinity.

Saline and alkaline stresses alter soil properties and composition and structure of gene-based nitrifier and denitrifier communities in a calcareous desert soil

BACKGROUND

Saline and alkaline stresses damages the health of soil systems. Meanwhile, little is known about how saline or alkaline stress affects soil nitrifier and denitrifier communities. Therefore, we compared the responses of gene-based nitrifier and denitrifier communities to chloride (CS), sulfate (SS), and alkaline (AS) stresses with those in a no-stress control (CK) in pots with a calcareous desert soil.

RESULTS

Compared with CK, saline and alkaline stress decreased potential nitrification rate (PNR) and NO₃-N; increased pH, salinity, water content, and NH₄-N; and decreased copy numbers of amoA-AOA and amoA-AOB genes but increased those of denitrifier nirS and nosZ genes. Copies of nirK increased in SS and AS but decreased in CS. There were more copies of amoA-AOB than of amoA-AOA and of nirS than of nirK or nosZ. Compared with CK, SS and AS decreased operational taxonomic units (OTUs) of amoA-AOB but increased those of nirS and nosZ, whereas CS decreased nirK OTUs but increased those of nosZ. The numbers of OTUs and amoA-AOB genes were greater than those of amoA-AOA. There were positive linear relations between PNR and amoA-AOA and amoA-AOB copies. Compared with CK, the Chao 1 index of amoA-AOA and amoA-AOB decreased in AS, that of nirK increased in CS and SS, but that of nirS and nosZ increased in all treatments. The Shannon index of amoA-AOB decreased but that of nirS increased in CS and SS, whereas the index of nirK decreased in all treatments. Saline and alkaline stress greatly affected the structure of nitrifier and denitrifier communities and decreased potential biomarkers of nirS-type; however, AS increased those of nirK- and nosZ-type, and SS decreased those of nosZ-type. Soil water content, pH, and salinity were important in shaping amoA-AOA and denitrifier communities, whereas soil water and pH were important to amoA-AOB communities.

CONCLUSION

These results indicate that the nitrifier and denitrifier communities respond to saline and alkaline stresses conditions. Communities of amoA-AOA and amoA-AOB contribute to nitrification in alluvial gray desert soil, and those of nirS are more important in denitrification than those of nirK or nosZ.

Marine aquaculture regulates dissimilatory nitrate reduction processes in a typical semi-enclosed bay of southeastern China

Marine aquaculture in semi-enclosed bays can significantly influence nutrient cycling in coastal ecosystems. However, the impact of marine aquaculture on the dynamics of dissimilatory nitrate reduction processes (DNRPs) and the fate of reactive nitrogen remain poorly understood. In this study, the rates of DNRPs and the abundances of related functional genes were investigated in aquaculture and non-aquaculture areas. The results showed that marine aquaculture significantly increased the denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) rates and decreased the rate of anaerobic ammonium oxidation (ANA), as compared with non-aquaculture sites. DNF was the dominant pathway contributing to the total nitrate reduction, and its contribution to the total nitrate reduction significantly increased from 66.72% at non-aquaculture sites to 78.50% at aquaculture sites. Marine aquaculture can significantly affect the physicochemical characteristics of sediment and the abundances of related functional genes, leading to variations in the nitrate reduction rates. Although nitrate removal rates increased in the marine aquaculture area, ammonification rates and the nitrogen retention index in the aquaculture areas were 2.19 and 1.24 times, respectively, higher than those at non-aquaculture sites. Net reactive nitrogen retention exceeded nitrogen removal in the aquaculture area, and the retained reactive nitrogen could diffuse with the tidal current to the entire bay, thereby aggravating N pollution in the entire study area. These results show that marine aquaculture is the dominant source of nitrogen pollution in semi-enclosed bays. This study can provide insights into nitrogen pollution control in semi-enclosed bays with well-developed marine aquaculture.

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.

Effect of hydraulic retention time on effluent pH in anammox bioreactors: Characteristics of effluent pH and pH as an indicator of reactor performance

In order to assess the performance of anaerobic ammonium oxidation (anammox) bioreactors, it is necessary to study the stoichiometry of the anammox reaction and pH. This study focused on the effect of the hydraulic retention time (HRT) on the effluent pH in anammox-upflow anaerobic sludge blanket (UASB) bioreactors. Anammox-UASB bioreactors with and without a recirculation system were used to investigate the effluent pH and bioreactor performance. It was concluded that under varying HRT conditions, the decrease in effluent pH did not indicate the deterioration of nitrogen removal, but did indicate that the nitrogen removal efficiency was reduced owing to a sudden increase in the nitrogen loading rate resulting from the decrease in HRT. Moreover, the results showed that the HRT directly affected the concentration of OH^-, which affected the increase/decrease in effluent pH. This study demonstrated that effluent pH is a more powerful tool than previous techniques used to assess bioreactor performance. We suggest that the effluent pH could be used for preliminary assessment.

Robust Nitritation of Anaerobic Digester Centrate Using Dual Stressors and Timed Alkali Additions

Nitrogen is commonly removed from wastewater by nitrification to nitrate followed by nitrate reduction to N₂. Shortcut N removal saves energy by limiting ammonia oxidation to nitrite, but nitrite accumulation can be unstable. We hypothesized that repeated short-term exposures of ammonia-oxidizing communities to free ammonia (FA) and free nitrous acid (FNA) would stabilize nitritation by selecting against nitrite-oxidizing bacteria (NOB). Accordingly, we evaluated ammonium oxidation of anaerobic digester centrate in two bench-scale sequencing batch reactors (SBRs), seeded with the same inoculum and operated identically but with differing pH-control strategies. A single stressor SBR (SS/SBR) using pH set-point control produced HNO₃, while a dual stressor SBR (DS/SBR) using timed alkalinity addition (TAA) produced HNO₂ (ammonium removal efficiency of 97 ± 2%; nitrite accumulation ratio of 98 ± 1%). The TAA protocol was developed during an adaptation period with continuous pH monitoring. After adaptation, automated TAA enabled stable nitritation without set-point control. In the SS/SBR, repeatedly exposing the community to FA (8-10 h/exposure, one exposure/cycle) selected for FA-tolerant ammonia-oxidizing bacteria (Nitrosomonas sp. NM107) and NOB (Nitrobacter sp.). In the DS/SBR, repeatedly exposing the community to FA (2-4 h/exposure, three exposures/cycle) and FNA (4-6 h/exposure, two exposures/cycle) selected for FA- and FNA-resistant AOB (Nitrosomonas IWT514) and against NOB, stabilizing nitritation.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community’s diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92–2.09%) followed by NOB (0.99–2%), and then AOB (0.2–0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4–9.5%), followed by AOA (0.27–0.51%) and AOB (0.01–0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Response and Adaptation of Microbial Community in a CANON Reactor Exposed to an Extreme Alkaline Shock

Responses of a microbial community in the completely autotrophic nitrogen removal over nitrite (CANON) process, which was shocked by a pH of 11.0 for 12 h, were investigated. During the recovery phase, the performance, anaerobic ammonia oxidation (anammox) activity, microbial community, and correlation of bacteria as well as the influencing factors were evaluated synchronously. The performance of the CANON process deteriorated rapidly with a nitrogen removal rate (NRR) of 0.13 kg·m^-3·d^-1, and Firmicutes, spore-forming bacteria, were the dominant phyla after alkaline shock. However, it could self-restore within 107 days after undergoing four stages, at which Planctomycetes became dominant with a relative abundance of 64.62%. Network analysis showed that anammox bacteria (Candidatus Jettenia, Kuenenia, and Brocadia) were positively related to some functional bacteria such as Nitrosomonas, SM1A02, and Calorithrix. Canonical correspondence analysis presented a strong correlation between the microbial community and influencing factors during the recovery phase. With the increase of nitrogen loading rate, the decrease of free nitrous acid and the synergistic effects, heme c content, specific anammox activity (SAA), NRR, and the abundance of dominant genus increased correspondingly. The increase of heme c content regulates the quorum sensing system, promotes the secretion of extracellular polymeric substances, and further improves SAA, NRR, and the relative abundance of the dominant genus. This study highlights some implications for the recovery of the CANON reactor after being exposed to an alkaline shock.

Responses of AOA and AOB activity and DNA/cDNA community structure to allylthiourea exposure in the water level fluctuation zone soil

Ammonia oxidation is mainly performed by ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Allylthiourea (ATU) has been found to specifically inhibit ammonia oxidation. However, the effect of ATU on AOA and AOB transcription has been infrequently studied. In the present study, we examined the responses of AOA and AOB activity and DNA/cDNA community structure to ATU exposure. The ammonia oxidation activity in the 100-mg/L ATU group was 4.3% of that in the control group after 7 days. When exposed to ATU, the gene abundance of AOA was favored compared with that of AOB, and there were no statistically significant differences in the abundance of AOB amoA in DNA and cDNA between the two groups. Compared with the control group, the gene abundance of AOA significantly increased by 5.23 times, while the transcription of AOA significantly decreased by 0.70 times. Moreover, the transcriptional ratio of AOA in the ATU group was only 0.05 times as high as that in the control group. ATU selectively affected AOB and completely inhibited Nitrosomonas europaea and Bacterium amoA.22.HaldeII.kultur at the genetic level. Under ATU exposure, all AOA clusters were transcribed, but three AOB clusters were not transcribed. Our results indicated that the ammonia oxidation potential of the soil of water level fluctuation areas, based on ATU inhibition, was associated mainly with AOA amoA gene abundance and AOB community shifts in DNA and cDNA.

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.

The dominance of non-halophilic archaea in autotrophic ammonia oxidation of activated sludge under salt stress: A DNA-based stable isotope probing study

Dynamics of nitrification activity, ammonia-oxidizing archaea (AOA) and bacteria (AOB) abundance and active ammonia oxidizers of activated sludge were explored under different salinities. Results showed that specific ammonium oxidation rates were significantly negative with increasing salinity. The responses of AOA and AOB populations to salt stress were distinct. AOA abundance decreased at moderate salinities (2.5, 5 and 7 g L^-1) and increased at high salinities (10, 15, 20 and 30 g L^-1), while AOB abundance showed opposite tendency. DNA-based stable isotope probing assays indicated AOA exclusively dominated active ammonia oxidation of test samples under different salinities. The active AOA communities retrieved were all non-halophilic and regulated by salinities. Candidatus Nitrosocosmicus exaquare and Ca. Nitrosocosmicus franklandus were the predominantly active AOA in both salt-free and salt-containing microcosms, while ¹³C-labeled Nitrososphaera viennensis and Ca. Nitrososphaera gargensis were only retrieved from the microcosms amended with 0 and 30 g L^-1 salinity, respectively.

Response and recovery of aerobic granular sludge to pH shock for simultaneous removal of aniline and nitrogen

Considering the pH fluctuation in industrial wastewater, the response and resilience to pH shock should be investigated during aerobic granular sludge (AGS) system operation. In this work, three AGS reactors, namely R1, R2, and R3 for simultaneous removal of aniline and nitrogen were exposed to neutral, acidic, and alkaline conditions, respectively. The removal efficiency of aniline and chemical oxygen demand with pH variation was over 99.9% and 91.0%, respectively after stable in the three reactors. The aniline removal rate modestly decreased in R2 and R3 after pH varied and denitrification was slightly improved in acidic environment with average removal efficiency of 61.2%. The mature AGS could maintain settleability in R1 and R2 with 30 min sludge volume index below 35 mL g^-1 but was unstable under alkaline condition. Correspondingly, the secretion of extracellular polymeric substances especially protein decreased notably in R3. The bacterial groups varied with pH shock, but some could recover after adjustment to original pH value. Proteobacteria was the predominant phylum in the three reactors and Bacteroidetes was enriched in alkaline conditions. In addition, the main functional genera such as Achromobacter, Defluviimonas, Enterobacter, Pseudomonas, and Pseudoxanthomonas, were detected in the system and were found to be responsible for reduction of aniline and nitrogen.

Nitrogen release and its influence on anammox bacteria during the decay of Potamogeton crispus with different values of initial debris biomass

Aquatic macrophytes play a significant role in the nutrient cycle of freshwater ecosystems. However, nutrients from plant debris release into both sediments and overlying water if not timely harvested. To date, minimal information is available regarding nutrient release and its subsequent influences on bacterial communities with decaying debris. In this study, Potamogeton crispus was used as a model plant. Debris biomass levels of 0 g (control, J-CK), 10 g dry weight (DW) (100 g DW/m², J-10 g), 40 g DW (400 g DW/m2, J-40 g) and 80 g DW (800 g DW/m², J-80 g) were used to simulate the different biomass densities of P. crispus in field. The physicochemical parameters of overlying water and sediment samples were analysed. The community composition of anammox bacteria in the sediment was also analysed using 16S rRNA genes as markers. The results showed that dissolved oxygen and pH dramatically decreased, whereas total nitrogen (TN) and NH₄⁺-N concentrations increased in the overlying water in the initial stage of P. crispus decomposition. However, NO₃^--N concentration changes in the overlying water were more complicated. The concentrations of organic matter, TN and NH₄⁺-N in the sediment all increased, but the rate of increase varied among the groups with different initial biomass levels, indicating that these physicochemical properties in sediment are significantly affected by debris biomass level and decay time. In addition, the order of anammox bacteria abundance was J-40 g > J-CK > J-80 g > J-10 g. Moreover, the community structure of anammox bacteria were simpler compared to that of J-CK as debris biomass level increased. The results demonstrate that P. crispus debris decomposition could affect the ecological distribution of anammox bacteria. Such influence clearly varies with varying amounts of P. crispus biomass debris. This information could be useful for the management of aquatic macrophytes in freshwater ecosystems.

Shifts in the anammox bacterial community structure and abundance in sediments from the Changjiang Estuary and its adjacent area

Anaerobic ammonium oxidation (anammox) is an important process in marine nitrogen cycle. In this study, diverse anammox bacteria were identified in the sediments of the Changjiang (Yangtze) Estuary and its adjacent area. Specifically, the community characters of anammox bacteria in the studied area were studied by quantitative polymerase chain reaction (qPCR), as well as 16S rRNA gene- and functional gene (hzo)-based Roche 454 sequencing. The abundance of denitrifying bacteria detected by the nirS gene was greater than that of anammox bacteria. 16S rRNA and hzo gene fragments affiliating with known anammox bacterial lineages were recovered, and the two major phylotypes belonged to the Candidatus Scalindua (Ca. Scalindua) genus, with >90% sequence similarity. A phylogenetic analysis detected the Scalindua and Brocadia genera together with some anammox-like bacterial clusters, which suggested a higher diversity in the studied ecosystem than in open ocean environment, where only Scalindua genus was detected. A redundancy analysis (RDA) showed that total organic carbon (TOC) and total nitrogen (TN) content in sediments significantly influenced anammox bacterial abundance of. Spearman correlation analyses confirmed that the spatial variation in anammox bacterial abundance was highly correlated with TOC (P<0.01) and TN (P<0.01) contents in sediments.

Anaerobic ammonium oxidation in agricultural soils-synthesis and prospective

Denitrification is considered as the dominant nitrogen (N) removing pathway, however, anaerobic oxidation of ammonium (anammox) also plays a significant part in N loss in agricultural ecosystems. Large N inputs into agricultural soils may stimulate the growth of anammox bacteria, resulting in high activity and diversity of anammox bacteria and subsequent more N loss. In some specific niches, like oxic-anoxic interface, three processes, nitrification, anammox and denitrification couple with each other, and significant anammox reaction could be observed. Soil parameters like pH, dissolved oxygen, salinity, oxidation-reduction potential (ORP), and substrate concentrations impact the anammox process. Here we summarize the current knowledge on anammox activity and contribution to N loss, abundance and diversity of anammox bacteria, factors affecting anammox, and the relationship between anammox and other N loss pathways in agricultural soils. We propose that more investigations are required for (1) the role of anammox to N loss with different agricultural management strategies; (2) microscale research on the coupling of nitrification-anammox-denitrification, that might be a very complex process but ideal model for further studies responsible for N cycling in terrestrial ecosystems; and (3) new methods to estimate differential contributions of anammox, codenitrification and denitrification in total N loss in agricultural ecosystems. New research will provide much needed information to quantify the contribution of anammox in N loss from soils at landscape, ecosystem and global scales.

Abundance and Diversity of Aerobic/Anaerobic Ammonia/Ammonium-Oxidizing Microorganisms in an Ammonium-Rich Aquitard in the Pearl River Delta of South China

Natural occurring groundwater with abnormally high ammonium concentrations was discovered in the aquifer-aquitard system in the Pearl River Delta, South China. The community composition and abundance of aerobic/anaerobic ammonia/ammonium-oxidizing microorganisms (AOM) in the aquitard were investigated in this study. The alpha subunit of ammonia monooxygenase gene (amoA) was used as the biomarker for the detection of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), and also partial 16S rRNA gene for Plantomycetes and anaerobic ammonium-oxidizing (anammox) bacteria. Phylogenetic analysis showed that AOA in this aquitard were affiliated with those from water columns and wastewater treatment plants; and AOB were dominated by sequences among the Nitrosomonas marina/Nitrosomonas oligotropha lineage, which were affiliated with environmental sequences from coastal eutrophic bay and subtropical estuary. The richness and diversity of both AOA and AOB communities had very little variations with the depth. Candidatus Scalindua-related sequences dominated the anammox bacterial community. AOB amoA gene abundances were always higher than those of AOA at different depths in this aquitard. The Pearson moment correlation analysis showed that AOA amoA gene abundance positively correlated with pH and ammonium concentration, whereas AOB amoA gene abundance negatively correlated with C/N ratio. This is the first report that highlights the presence with low diversity of AOM communities in natural aquitard of rich ammonium.

Numerical Relationships Between Archaeal and Bacterial amoA Genes Vary by Icelandic Andosol Classes

Bacterial amoA genes had not been detectable by qPCR in freshly sampled Icelandic Andosols thus far. Hence, a new primer set yielding shorter gene fragments has been designed to verify the absence of ammonia-oxidizing bacteria in different Icelandic Andosol classes. At the same time, a new primer set was also constructed for archaeal amoA genes that should improve the quality of PCR products. Although a large part of the soil samples were found to be amoA-negative, bacterial amoA genes were detectable with new as well as old primer sets. The same results were obtained for the archaeal amoA genes. The relative distribution of archaeal and bacterial amoA genes varied between Andosol classes. Archaeal amoA genes were significantly more abundant in Brown than in Histic Andosols, while the opposite was observed for bacterial amoA genes. The numbers of archaeal and bacterial amoA genes in Gleyic Andosols were not significantly different from those in Histic and Brown Andosols. The numbers of bacterial amoA genes, but not the numbers of archaeal amoA genes, correlated significantly and positively with potential ammonia oxidation activities. The presence of the bacterial nitrification inhibitor allylthiourea inhibited the potential ammonia oxidation activities during the first 12 h of incubation. Hence, it was concluded that ammonia-oxidizing bacteria profited most from the conditions during the measurements of potential ammonia oxidation activities.

Influence of temperature and pH on the anammox process: A review and meta-analysis

The anammox (anaerobic ammonium oxidation) process was considered a very efficient and economic wastewater treatment technology immediately after its discovery in 1995, thus research in this field was intensified. The anammox process is characterised by a high temperature optimum and is very sensitive to both temperature and pH fluctuations. The process can also be inhibited by many factors, including by its substrates, i.e. nitrite and ammonium (or its unionised forms: free ammonia and free nitrous acid). This paper presents a comprehensive study of the most important and recent findings on the influence of two parameters that are crucial in wastewater treatment, i.e. temperature and pH. Because both parameters may influence the anammox process simultaneously, a meta-analysis was conducted of the data from the literature. Although meta-analysis is commonly used in medical research, mathematical analysis of the literature data has become an interesting and important step in the environmental sciences. This paper presents information on the influence of both temperature and pH on process efficiency and microbial composition. Additionally, the responses of different operating systems on both temperature and pH changes are described. Moreover, the role of both adaptation to changed conditions and of pH control as well as indicated areas of process operation are discussed.

Faunal Burrows Alter the Diversity, Abundance, and Structure of AOA, AOB, Anammox and n-Damo Communities in Coastal Mangrove Sediments

In the present work, the diversity, community structures, and abundances of aerobic ammonia-oxidizing archaea (AOA) and bacteria (AOB), anaerobic ammonium-oxidizing (anammox) bacteria, and denitrifying anaerobic methane oxidization (n-damo) bacteria were unraveled in the bioturbated areas of the coastal Mai Po mangrove sediments. Results indicated that the bioturbation by burrowing in mangrove sediments was associated with higher concentration of NH₄⁺ but lower concentrations of both NO₂^- and NO₃^-, and increase in diversity and richness of both AOA and AOB, but relatively lower diversity and richness of n-damo bacteria. The phylotypes of anammox bacterial community were significantly increased while their phylogenetic lineages observed in the less bioturbated areas were also maintained. Infauna also showed a great impact on the composition of n-damo bacterial phylotypes and burrowing activity altered the n-damo community structure profoundly in the sampled areas. The communities of n-damo bacteria in the surrounding bulk sediments showed similar structures to marine n-damo communities, but those on the burrow wall and in the ambient surface layer had a freshwater pattern, which was different from previous findings in Mai Po wetland. On the other hand, the abundances of AOA, AOB, and n-damo bacteria were greatly stimulated on burrow walls while the abundance of anammox bacteria remained unchanged. Infaunal burrows and mangrove roots affected the relative abundance of AOA and AOB. The benthic infauna stimulated the abundances of AOA, AOB, anammox, and n-damo bacteria. Furthermore, NH₄⁺ and NO₂^- were important environmental factors changing the structure of each group. The communities of anammox and n-damo bacteria in bioturbated areas showed a competitive relationship.

The role of Plant Growth Promoting Bacteria in improving nitrogen use efficiency for sustainable crop production: a focus on wheat

Due to the increase in both human population growth and environmental pressure, it is necessary to raise agricultural productivity without enhancing environmental footprint. Within this context, soil inoculation with PGPB (Plant Growth Promoting Bacteria) may be considered a promising tool of integrated management systems. In particular, PGPB may improve plant growth either directly, by facilitating resource use or modulating plant hormone levels, or indirectly by decreasing the inhibitory effects of various pathogenic agents. PGPB comprise different functional and taxonomic groups of bacteria like Pseudomonas, Bacillus, Rhizobium and others. Their ability to either mobilize mineral or organic bound nutrients from the pedosphere or to fix atmospheric N2 and make it available to the plants, is a crucial feature in their application. In literature some data are available on the use of commercial PGPB, while less efforts have been made on the study of the effect of autochthonous PGPB isolated from soils on sustainability of cropping systems; thus a literature survey on these aspects was carried out with special focus on wheat, a staple food for a large part of world population. In particular, the main topic of this review is the potential of PGPB to enhance use efficiency of agro-environmental resources focusing on the interaction PGPB-wheat for improving nitrogen use efficiency.

Individual and combined inhibition of phenol and thiocyanate on microbial activity of partial nitritation

This study evaluated the individual and interactive effect of phenol and thiocyanate (SCN^-) on partial nitritation (PN) activity using batch test and response surface methodology. The IC₅₀ of phenol and SCN^- on PN sludge were 5.6 and 351 mg L^-1, respectively. The PN sludge was insensitive to phenol and SCN^- at levels lower than 1.77 and 43.3 mg L^-1, respectively. A regression model equation was developed and validated to predict the relative specific respiration rate (RSRR) of PN sludge exposed to different phenol and SCN^- concentrations. In the range of independent variables, the most severe inhibition was observed with a valley value (17%) for RSRR, when the phenol and SCN^- concentrations were 4.08 and 198 mg L^-1, respectively. An isobole plot was used to judge the combined toxicity of phenol and SCN^-, and the joint inhibitory effect was variable depending on the composition and concentration of the toxic components. Furthermore, the toxic compounds showed independent effects, which is the most common type of combined toxicity.

Screening and optimizing of inhibitors for ammonia-oxidizing bacteria in sediments of malodorous river

The proper use of selective ammonia-oxidizing archaea (AOA) and/or ammonia-oxidizing bacteria (AOB) inhibitors is critical to distinguish AOA and AOB contribution. In this research, three inhibitors including ampicillin, dicyandiamide (DCD), and allylthiourea (ATU) were examined mainly focusing on inhibiting dosage, adaptability, and effects. The results showed that the optimized inhibitory dosage of ampicillin, DCD, and ATU was separately 1.5 g L^-1, 1 mM, and 25 μM. Among the three inhibitors, ATU exhibited the strongest and persistent inhibition effects and resulted in up to 90% inhibition in the AOB-enriched culture. The seemingly weakening inhibiting effects of ATU in the simulated river systems can be attributed to the involved role of AOA, the uneven spatial distribution of ATU, and protection by sediment structure in complex malodorous rivers. The high-throughput pyrosequencing analysis showed the AOB-related genus Nitrosomonas and Nitrosococcus were mostly affected by ATU in the enrichments and the river systems, respectively. The inhibition of ATU was realized mainly by reducing the abundance and activity of AOB. The decrease of the ratio of AOB/AOA amoA gene copy numbers after addition of ATU further confirmed the inhibiting effectiveness of ATU in complex microbial community of malodorous rivers.

Chemical treatment of contaminated sediment for phosphorus control and subsequent effects on ammonia-oxidizing and ammonia-denitrifying microorganisms and on submerged macrophyte revegetation

In this work, sediments were treated with calcium nitrate, aluminum sulfate, ferric sulfate, and Phoslock®, respectively. The impact of treatments on internal phosphorus release, the abundance of nitrogen cycle-related functional genes, and the growth of submerged macrophytes were investigated. All treatments reduced total phosphorus (TP) and soluble reactive phosphorus (SRP) in interstitial water, and aluminum sulfate was most efficient. Aluminum sulfate also decreased TP and SRP in overlying water. Treatments significantly changed P speciations in the sediment. Phoslock® transformed other P species into calcium-bound P. Calcium nitrate, ferric sulfate, and Phoslock® had negative influence on ammonia oxidizers, while four chemicals had positive influence on denitrifies, indicating that chemical treatment could inhibit nitrification but enhance denitrification. Aluminum sulfate had decreased chlorophyll content of the leaves of submerged macrophytes, while ferric sulfate and Phoslock® treatment would inhibit the growth of the root. Based on the results that we obtained, we emphasized that before application of chemical treatment, the effects on submerged macrophyte revegetation should be taken into consideration.

Nitrogen removal properties in a continuous marine anammox bacteria reactor under rapid and extensive salinity changes

Salinity tolerance is one of the most important factors for the application of bioreactors to high-salinity wastewater. Although marine anammox bacteria (MAB) might be expected to tolerate higher salinities than freshwater anammox bacteria, there is little information on the effects of salinity on MAB activity. This study aimed to reveal the nitrogen removal properties in a continuous MAB reactor under conditions of rapid and extensive salinity changes. The reactor demonstrated stable nitrogen removal performance with a removal efficiency of over 85% under salinity conditions ranging from 0 to 50 g/L NaCl. The reactor performance was also well maintained, even though the salinity was rapidly changed from 30 to 50 g/L and from 30 to 0 g/L. Other evidence suggested that the seawater medium used contained components essential for effective MAB performance. Bacterial community analysis using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) showed that planctomycete UKU-1, the dominant MAB species in the inoculum, was the main contributor to anammox activity under all conditions. The PCR-DGGE using a universal bacterial primer set showed different DNA band patterns between the reactor biomass sample collected under conditions of 75 g/L NaCl and all other conditions (0, 30, 50 and freshwater-medium). All DNA sequences determined were very similar to those of bacterial species from marine environments, anaerobic environments, or wastewater-treatment facilities.

Physiological characterization of anaerobic ammonium oxidizing bacterium 'Candidatus Jettenia caeni'

To date, six candidate genera of anaerobic ammonium-oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus 'Candidatus Jettenia'. Planctomycete KSU-1 was found to be a mesophilic (20-42.5°C) and neutrophilic (pH 6.5-8.5) bacterium with a maximum growth rate of 0.0020 h(-1) . Planctomycete KSU-1 cells showed typical physiological and structural features of anammox bacteria; i.e. (29) N2 gas production by coupling of (15) NH4 (+) and (14) NO2 (-) , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone-7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl-CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU-1 cells. On the basis of these experimental results, we proposed the name 'Ca. Jettenia caeni' sp. nov. for the bacterial clade of the planctomycete KSU-1.

Distribution patterns of ammonia-oxidizing bacteria and anammox bacteria in the freshwater marsh of Honghe wetland in Northeast China

Community characteristics of aerobic ammonia-oxidizing bacteria (AOB) and anaerobic ammonium-oxidizing (anammox) bacteria in Honghe freshwater marsh, a Ramsar-designated wetland in Northeast China, were analyzed in this study. Samples were collected from surface and low layers of sediments in the Experimental, Buffer, and Core Zones in the reserve. Community structures of AOB were investigated using both 16S rRNA and amoA (encoding for the α-subunit of the ammonia monooxygenase) genes. Majority of both 16S rRNA and amoA gene-PCR amplified sequences obtained from the samples in the three zones affiliated with Nitrosospira, which agreed with other wetland studies. A relatively high richness of β-AOB amoA gene detected in the freshwater marsh might suggest minimal external pressure was experienced, providing a suitable habitat for β-AOB communities. Anammox bacteria communities were assessed using both 16S rRNA and hzo (encoding for hydrazine oxidoreductase) genes. However, PCR amplification of the hzo gene in all samples failed, suggesting that the utilization of hzo biomarker for detecting anammox bacteria in freshwater marsh might have serious limitations. Results with 16S rRNA gene showed that Candidatus Kuenenia was detected in only the Experimental Zone, whereas Ca. Scalindua including different lineages was observed in both the Buffer and Experimental Zones but not the Core Zone. These results indicated that both AOB and anammox bacteria have specific distribution patterns in the ecosystem corresponding to the extent of anthropogenic impact.

Niche specificity of ammonia-oxidizing archaeal and bacterial communities in a freshwater wetland receiving municipal wastewater in Daqing, Northeast China

Ecophysiological differences between ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) enable them to adapt to different niches in complex freshwater wetland ecosystems. The community characters of AOA and AOB in the different niches in a freshwater wetland receiving municipal wastewater, as well as the physicochemical parameters of sediment/soil samples, were investigated in this study. AOA community structures varied and separated from each other among four different niches. Wetland vegetation including aquatic macrophytes and terrestrial plants affected the AOA community composition but less for AOB, whereas sediment depths might contribute to the AOB community shift. The diversity of AOA communities was higher than that of AOB across all four niches. Archaeal and bacterial amoA genes (encoding for the alpha-subunit of ammonia monooxygenases) were most diverse in the dry-land niche, indicating O2 availability might favor ammonia oxidation. The majority of AOA amoA sequences belonged to the Soil/sediment Cluster B in the freshwater wetland ecosystems, while the dominant AOB amoA sequences were affiliated with Nitrosospira-like cluster. In the Nitrosospira-like cluster, AOB amoA gene sequences affiliated with the uncultured ammonia-oxidizing beta-proteobacteria constituted the largest portion (99%). Moreover, independent methods for phylogenetic tree analysis supported high parsimony bootstrap values. As a consequence, it is proposed that Nitrosospira-like amoA gene sequences recovered in this study represent a potentially novel cluster, grouping with the sequences from Gulf of Mexico deposited in the public databases.