Nmol N2 Research Articles

Microbial nitrogen removal in reef-building corals: A light-sensitive process

Scleractinian corals are the main framework-building groups in tropical coral reefs. In the coral holobiont, nitrogen-cycling mediated by microbes is fundamental for sustaining the coral reef ecosystems. However, little direct evidence characterizing the activities of microbial nitrogen removal via complete denitrification and anaerobic ammonium oxidation (anammox) in stony corals has been presented. In this study, multiple incubation experiments using 15N-tracer were conducted to identify and characterize N2 production by denitrification and anammox in the stony coral Pocillopora damicornis. The rates of denitrification and anammox were recorded up to 0.765 ± 0.162 and 0.078 ± 0.009 nmol N2 cm−2 h−1 respectively. Denitrification contributed the majority (∼90%) of N2 production by microbial nitrogen removal in stony corals. The microbial nitrogen removal activities showed diel rhythms, which might correspond to photosynthetic oxygen production. The N2 production rates of anammox and denitrification increased with incubation time. To the authors' knowledge, this study is the first to confirm and characterize the activities of complete denitrification and anammox in stony corals via stable isotope techniques. This study extends the understanding on nitrogen-cycling in coral reefs and how it participates in corals’ resilience to environmental stressors.

Nitrogen loss processes in response to upwelling in a Peruvian coastal setting dominated by denitrification – a mesocosm approach

Abstract. Upwelling of nutrient-rich deep waters make eastern boundary upwelling systems (EBUSs), such as the Humboldt Current system, hot spots of marine productivity. Associated settling of organic matter to depth and consecutive aerobic decomposition results in large subsurface water volumes being oxygen depleted. Under these circumstances, organic matter remineralisation can continue via denitrification, which represents a major loss pathway for bioavailable nitrogen. Additionally, anaerobic ammonium oxidation can remove significant amounts of nitrogen in these areas. Here we assess the interplay of suboxic water upwelling and nitrogen cycling in a manipulative offshore mesocosm experiment. Measured denitrification rates in incubations with water from the oxygen-depleted bottom layer of the mesocosms (via 15N label incubations) mostly ranged between 5.5 and 20 nmol N2 L−1 h−1 (interquartile range), reaching up to 80 nmol N2 L−1 h−1. However, actual in situ rates in the mesocosms, estimated via Michaelis–Menten kinetic scaling, did most likely not exceed 0.2–4.2 nmol N2 L−1 h−1 (interquartile range) due to substrate limitation. In the surrounding Pacific, measured denitrification rates were similar, although indications of substrate limitation were detected only once. In contrast, anammox (anaerobic ammonium oxidation) made only a minor contribution to the overall nitrogen loss when encountered in both the mesocosms and the Pacific Ocean. This was potentially related to organic matter C / N stoichiometry and/or process-specific oxygen and hydrogen sulfide sensitivities. Over the first 38 d of the experiment, total nitrogen loss calculated from in situ rates of denitrification and anammox was comparable to estimates from a full nitrogen budget in the mesocosms and ranged between ∼ 1 and 5.5 µmol N L−1. This represents up to ∼ 20 % of the initially bioavailable inorganic and organic nitrogen standing stocks. Interestingly, this loss is comparable to the total amount of particulate organic nitrogen that was exported into the sediment traps at the bottom of the mesocosms at about 20 m depth. Altogether, this suggests that a significant portion, if not the majority of nitrogen that could be exported to depth, is already lost, i.e. converted to N2 in a relatively shallow layer of the surface ocean, provided that there are oxygen-deficient conditions like those during coastal upwelling in our study. Published data for primary productivity and nitrogen loss in all EBUSs reinforce such conclusion.

Dissimilatory nitrate reduction processes and corresponding nitrogen loss in tidal flow constructed wetlands

Nitrate reduction processes play significant roles in the retention and removal of nitrogen from water in anaerobic soils of constructed wetlands. The microbial mechanisms regulating nitrate reduction in artificial tidal wetlands remain poorly understood. The current study explored three microbial nitrate reduction processes in two tidal wetland mesocosms, PA (planted with Phragmites australis) and NP (unplanted) based on molecular and stable isotopic analyses. Potential rates of anaerobic ammonium oxidation (anammox), dissimilatory nitrate reduction to ammonium (DNRA) and denitrification ranged between 2.54 and 8.77, 0.12–0.93 and 40.11–387.94 nmol N2 g−1 ds (dry soil) d−1, with relatively higher values obtained in PA than NP. Denitrification contributed to 93.78–97.71% of total nitrate reduction, compared to 1.99–5.94% and 0.23–0.40% via anammox and DNRA, as 94.04–98.00% of nitrogen gas was produced through denitrification, with the rest via anammox. The absolute abundances of bacterial 16S rRNA and nitrogen functional genes were 3.22–9.11 × 109 and 0.8 × 104–1.1 × 108 copies g−1 ds, respectively. Proteobacteria, Chloroflexi, Acidobacteria, Nitrospirae, and Actinobacteria were the dominated phylum in artificial tidal wetlands, accounting for over 70%. The relative abundances of denitrification and anammox organisms varied from 0.97% to 3.60% and from 0.02% to 0.14%, respectively. Pearson correlation analyses indicate that nitrate played a vital role in the competition between DNRA and denitrification, while nitrite was the major factor regulating anammox. Collectively, these findings improve our understanding of nitrate removal mechanisms in tidal flow constructed wetlands, providing a sustainable solution to the nitrate pollution problem in the Yangtze River Estuary.

Nitrogen removal through collaborative microbial pathways in tidal flow constructed wetlands

Constructed wetlands are efficient in removing nitrogen from water; however, little is known about nitrogen-cycling pathways for nitrogen loss from tidal flow constructed wetlands. This study conducted molecular and stable isotopic analyses to investigate potential dissimilatory nitrate reduction to ammonium (DNRA), denitrification, nitrification, anaerobic ammonium oxidation (anammox), and their contributions to nitrogen removal by two tidal wetland mesocosms, PA (planted with Phragmites australis) and NP (unplanted), designated to treat Yangtze River Estuary water. Our results show the mesocosms removed ~22.6% of TN from nitrate-dominated river water (1.19 mg·L−1), with better performance obtained in PA than that in NP, which was consistent with the molecular and stable isotopic data. The potential activities of DNRA, anammox, denitrification and nitrification varied between 0.6 and 1.6, 4.6–37.3, 36.4–305.7, and 463.7–945.9 nmol N2 g−1 dry soil d−1, respectively, with higher values obtained in PA than NP. Nitrification accounted for 94.3–99.4% of NH4+ oxidation, with the rest through anammox. Denitrification contributed to 77.9–90.3% of NOx− reduction, compared to 9.2–21.6% and 0.5–1.5% via anammox and DNRA, respectively; 78.4–90.9% of N2 was produced through denitrification, with the rest via anammox. Pearson correlation analyses suggest NH4+ was the major factor regulating nitrification, while NO3− played an important role in the competition between denitrification and DNRA, and NO2− was a key restrictive factor for anammox. Overall, this study reveals the importance of nitrification, denitrification, anammox and DNRA in nitrogen removal, providing new insight into the nitrogen-cycling mechanisms in natural/artificial tidal wetlands.

Impact of functional microbes on nitrogen removal in artificial tidal wetlands in the Yangtze River estuary: Evidence from molecular and stable isotopic analyses

After decades of rapid development in the delta, the worsening water quality in the Yangtze River estuary has become a concern in China. To improve the situation, we explored the use of two tidal wetland mesocosms (PA and NP), by evaluating nitrogen removal performance, greenhouse gas emissions and underlying molecular mechanisms. Our results show the mesocosms removed ∼23.9% of TN from nitrate-dominated river water (1.20 mg L−1), with PA twice effective as NP, which is consistent with the molecular and stable isotopic data. The emissions of methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O) were low in the soil of both PA and NP, while integrated microbial analyses suggest nitrification was the major contributor of nitrite to anaerobic ammonium oxidation (anammox) and also the dominant ammonia removal pathway in the mesocosms, particularly PA. The simultaneous dissimilatory nitrate reduction to ammonium (DNRA), anammox, denitrification and nitrification had mainly contributed to the nitrogen removal and greenhouse gas emission reduction, with rates of 0.86–2.05, 11.94–24.38, 44.95–340.95, and 458.56–1046.91 nmol N2 g−1 dry soil d−1, respectively. This study would expand our understanding of the nitrogen-cycling in tidal wetlands, helping develop a sustainable solution to the water pollution problem in the Yangtze River estuary.

Removal Capacities and Environmental Constrains of Denitrification and Anammox Processes in Eutrophic Riverine Sediments

Excessive nitrogen (N) loading has had severe consequences in coastal zones around the world. Denitrification and anammox are major microbial pathways for removing N in aquatic environments before it is exported to the coast. To assess two processes in eutrophic riverine systems, the denitrification and anammox and their bacterial participants were investigated in sediments of the Xiaoqing (XQ) River and Jiaolai (JL) River in Northeast China. By combining the evidence from N15 isotope tracing experiment and functional gene-based analysis, it was found that denitrification and anammox are ubiquitous along the investigated riverine sediments. The denitrification varied from 39.38 to 1433.01 nmol N2 m−2 h−1. Moreover, the anammox rates were in the range of 15.91 to 1209.97 nmol N2 m−2 h−1. Quantitative PCR results revealed that the nirK and nirS genes were in the order of 104–106 copies g−1 and 103–105 copies g−1, respectively, in both river sediments, while the hzsA was in the order of 106–105 copies g−1 in XQ at approximately two orders of magnitude compared with JL. The phylogenetic analysis of functional genes revealed the high diversity of the denitrifier and low diversity of anammox bacteria. Variance partitioning analyses verified that the grain particle characteristics were the major factor group determined the N removal efficiency. The denitrification and anammox processes were estimated to have removed 16.1% of the inorganic nitrogen inputs before being exported to Laizhou Bay, which highlights that a more extensive understanding of the regularity of the N removal processes is important in the technical remediation of eutrophication problems.

Molecular and stable isotopic evidence for anaerobic ammonium-oxidizing bacteria in tidal flow constructed wetlands

The process of anaerobic ammonium oxidation (anammox) plays a significant part in global nitrogen cycling, yet its depth-specific distribution and importance in tidal flow constructed wetlands (TF CWs) remained unclear. Currently, the abundance, biodiversity, vertical distribution, rates and potential role of the anammox process in two TF CWs of the Yangtze Estuary, China, were explored. The results indicated that anammox bacteria were widely distributed in the TF CWs, and Candidatus Brocadia was the dominant group among the anammox genera. The widespread presence of the anammox bacteria was observed at different water depths of the soil cores, and the abundance of total bacterial 16S rRNA and hzsB genes was 4.47–20.08 × 109 and 0.81–5.91 × 105 copies per gram of dry soil (copies g−1 ds), respectively. The homogenized soils were incubated with stable nitrogen isotope to confirm the rates of anammox in the TF CWs, and the anammox activities were 2.38–6.72 nmol of N2 per gram of dry soil per day (nmol N2 g−1 dry soil d−1), with contributions of 2.7–7.5% nitrogen gas production and anammox that was more active in the deeper layer of the two TF CWs.

Nutrient stoichiometry (N:P) controls nitrogen fixation and distribution of diazotrophs in a tropical eutrophic estuary

Nitrogen fixation and its ecological regulation are poorly understood in the tropical estuaries, which are highly influenced by anthropogenic disturbances. In this study, we investigated the role of nutrient stoichiometry in the diversity, abundance and activity of N2-fixing bacterial community and their seasonal variations in the water column of a tropical eutrophic estuary (Cochin estuary). The N2 fixation rates in the estuary ranged from 0.1 to 2.0 nmol N2 l−1 h−1, with higher activity during post-monsoon and lower during monsoon. The rates are appeared to be primarily controlled by dissolved inorganic nitrogen and phosphorous (N:P) ratio. Clone library analysis of nitrogenase (nifH) gene revealed that the major N2 fixing phylotypes belong to Cluster I and Cluster III diazotrophs. The overall findings of this study suggest that monsoon induced seasonal changes in nutrient stoichiometry control the distribution and activity of diazotrophs in a tropical estuary.

Anammox microbial community and activity changes in response to water and dissolved oxygen managements in a paddy-wheat soil of Southern China

Anammox are unusual members of the microbial community contributing to N losses via anaerobic ammonium oxidation. Anammox use nitrite as a substrate and produce hydrazine as an intermediate product. Up to date, the effects of dissolved oxygen and moisture dynamics on anammox potential and microbial community in agricultural soils were poorly understood. In this study, we investigated the interaction of dissolved oxygen and moisture contents as factors affecting the soil anammox process. The experiment had four fertilization treatments i.e. Control (CK), Chemical fertilizer (CF), Pig composted manure plus chemical fertilizer (PMCF), and Straw returned to soil plus chemical fertilizer (SRCF) with different water contents, 70%-FC, Alternate wetting and drying (AWD), Flooding I (D.O 5.8 mg L−1), and Flooding II (D.O 2.6 mg L−1). 15N-isotopic tracer technique was used to evaluate the anammox and denitrification rates. The results showed that the anammox rate ranged from the lowest 0.56 nmol N2·g−1·h−1 in CF (with 70% FC water) to the highest rate of 1.47 nmol N2·g−1·h−1 in SRCF (with flooding II). In water treatments, the average lowest and highest anammox rates were in the 70% FC (0.61 nmol N2·g−1·h−1) and Flooding II (1.14 nmol N2·g−1·h−1), respectively. Moreover, under soil treatments, the minimum average anammox rate was found in the PMCF (0.76 nmol N2·g−1·h−1) and maximum in the SRCF (1.01 nmol N2·g−1·h−1). Interestingly, anammox genes copy numbers were highest in alternate wetting and drying conditions under all fertilizer treatments rather than in continuous flooding. The phylogenetic analysis showed that Ca. Brocadia was dominating while some of Ca. Jettenia was also present. In conclusion, alternate wetting and drying could increase the number of anammox bacteria and microbial diversity.

Role of organic components in regulating denitrification in the coastal water of Daya Bay, southern China.

Both dissolved and particulate organic materials have been proposed to be important factors in regulating heterotrophic denitrification in various aquatic environments. However, the specific pathways and mechanisms remain elusive. In this study, water column samples were collected from Daya Bay, southern China, to examine the relationships between potential denitrification and different organic components in the water column. Bulk dissolved organic carbon (DOC) was categorized into three major components including terrigenous fluorescent (tFDOC), autochthonous fluorescent (bFDOC) and non-fluorescent (nFDOC) fractions, while the bulk particulate organic carbon (POC) was divided into terrigenous (tPOC) and autochthonous (bPOC) fractions based on an isotope mixing model. Potential denitrification derived from in situ incubation experiments under anoxic conditions was evident (ranging from 6 to 107 nmol N2 perL per h) and varied markedly among stations. When normalized to nitrate concentration, the denitrification rate (NDR) followed a positive trend with either the concentration or proportion of tFDOC, and a negative trend with the proportion of nFDOC, suggesting tFDOC was potentially favorable while nFDOC was unfavorable for denitrifying degradation. In comparison, the NDR showed a significant positive correlation with the proportion of bPOC in the bulk POC (p = 0.01), with a predictive power of >70%, indicating that the composition of POC has a substantial impact on potential denitrification. Furthermore, if both bPOC and suspended particulate matter (SPM) were considered as variables concurrently, the variability of NDR can be better predicted with a predictive power as high as 80%. Therefore, denitrifiers may preferentially utilize fresher and labile autochthonous POC instead of DOC especially in coastal waters where particles/colloids are abundant. Our results thus provide new insights for a better understanding of denitrification mechanisms in water columns and the importance of both suspended particles and POC components in regulating denitrification, especially in turbid and productive coastal environments.

Seasonal variation of potential denitrification rate and enhanced denitrification performance via water-lifting aeration technology in a stratified reservoir—A case study of Zhoucun reservoir

Zhoucun reservoir is one of the major water resources in Zao Zhuang city, northern China. The seasonal distribution of surface sediment denitrification rate and enhanced performance of denitrification via water-lifting aeration technology were explored using the acetylene-inhibition technique. Surface sediment denitrification rates ranged from 2.57 ± 1.32 to 923.90 ± 86.81 nmol N2/(g dw·h), with the highest rates in November (ANOVA, p < 0.05) and significantly low rates in June, July, and August (ANOVA, p < 0.05), mainly because of the seasonal differences in nitrate concentration, water temperature, and sediment total nitrogen (STN). Meanwhile, the N2/(N2+N2O) ratio (83.44–91.70% for the highest sediment denitrification period) indicated that N2 accounted for a majority of denitrification. Correlation analysis between various environmental factors and denitrification was conducted, and nitrate concentration, STN, low molecular weight organic carbon, the number of aerobic denitrifying bacteria, and the environmental parameters of oxidation-reduction potential (ORP), pH, electrical conductivity (EC), and chlorophyll a (Chl-a) presented significant relationships during the entire study period. On the basis of the multiple regression model, nitrate and low molecular weight organic carbon concentration were the most influential factors on denitrification variability. Moreover, the denitrification rates of the surface sediment clearly increased, from 5.28 to 13.22 nmol N2/(g dw·h) to 1117.02–3129.47 nmol N2/(g dw·h), which were higher than those in the non-operating year. This suggests that the denitrification in the sediment system could be enhanced in situ by water-lifting and aeration technology in the reservoir ecosystem.

Cyanate distribution and uptake above and within the Eastern Tropical South Pacific oxygen deficient zone

AbstractCyanate is a simple reduced nitrogen (N) compound that can be a source of N and carbon (C) for marine organisms and may also be a substrate for dissimilatory N processes such as nitrification and anammox. We measured cyanate distributions and cyanate and urea uptake in the Eastern Tropical South Pacific, a region defined by coastal upwelling, high primary productivity, a shallow oxic layer, and rapid N loss from a large oxygen deficient zone (ODZ). Cyanate concentrations ranged from below the limit of detection (0.4 nM) to 45 nM in the oxic upper water column. Below the oxycline, cyanate concentrations were largely below detection except for small cyanate peaks (2–8.3 nM) within the core of the ODZ at some stations. The majority of N taken up in the shallow oxic layer was from ammonium and urea (78% ± 8%); cyanate uptake was &lt; 2% of these. Uptake of cyanate fluctuated diurnally with the highest rates of cyanate N uptake in the early afternoon. In the ODZ, rates of cyanate, urea, and ammonium uptake were similar to each other (0.1–14 nmol N L−1 d−1) and to previously reported rates of 29N2 production supported by cyanate and ammonium (3–14 nmol N2 L−1 d−1). This suggests a role for cyanate in the metabolism of anaerobic microbes and a potential role for cyanate in the anammox reaction (cyanammox). To our knowledge, these represent the first rates of N uptake in a marine anoxic water column.

Distribution and activity of anaerobic ammonium-oxidising bacteria in natural freshwater wetland soils.

Anaerobic ammonium oxidation (anammox) process plays a significant role in the marine nitrogen cycle. However, the quantitative importance of this process in nitrogen removal in wetland systems, particularly in natural freshwater wetlands, is still not determined. In the present study, we provided the evidence of the distribution and activity of anammox bacteria in a natural freshwater wetland, located in southeastern China, by using (15)N stable isotope measurements, quantitative PCR assays and 16S rRNA gene clone library analysis. The potential anammox rates measured in this wetland system ranged between 2.5 and 25.5 nmol N2 g(-1) soil day(-1), and up to 20% soil dinitrogen gas production could be attributed to the anammox process. Phylogenetic analysis of 16S rRNA genes showed that anammox bacteria related to Candidatus Brocadia, Candidatus Kuenenia, Candidatus Anammoxoglobus and two novel anammox clusters coexisted in the collected soil cores, with Candidatus Brocadia and Candidatus Kuenenia being the dominant anammox genera. Quantitative PCR of hydrazine synthase genes showed that the abundance of anammox bacteria varied from 2.3 × 10(5) to 2.2 × 10(6) copies g(-1) soil in the examined soil cores. Correlation analyses suggested that the soil ammonium concentration had significant influence on the activity of anammox bacteria. On the basis of (15)N tracing technology, it is estimated that a total loss of 31.1 g N m(-2) per year could be linked the anammox process in the examined wetland.

Comparison of methods to determine triple oxygen isotope composition of N2O

The oxygen isotope anomaly, Δ(17) O, of N2 O and nitrate is useful to elucidate nitrogen oxide dynamics. A comparison of different methods for Δ(17) O measurement was performed. For Δ(17) O measurements, N2 O was converted into O2 and N2 using microwave-induced plasma in a quartz or corundum tube reactor, respectively, or conversion was carried out in a gold wire oven. In each case, isotope ratios were measured by isotope ratio mass spectrometry. All the tested methods showed acceptable precision (coefficient of variation <2.4 % at 160 nmol N2 O) with high sample size but the sample size dependence was lowest when using microwave-induced plasma in a corundum tube reactor. The use of microwave-induced plasma in a corundum tube yields best results for Δ(17) O measurement on N2 O gas samples.

Nitrogen loss through anaerobic ammonium oxidation in agricultural drainage ditches

Agricultural drainage ditches are a key conduit of nitrogen from agricultural fields to surface water. Denitrification has been proven to be an important N removal pathway in agricultural drainage ditches; however, it is currently unknown about the role of anaerobic ammonium oxidation (anammox). Here, we investigated the N loss through anammox in six different agricultural drainage ditches, located in Nanjing City, Jiangsu Province (China). Stable isotope-labeling experiments confirmed the anammox activity in every examined ditch, and the potential anammox rates ranged from 4.4 to 23.8 nmol N2 g−1 sediment day−1. The anammox process contributed 2.1–18.8 % to sediment dinitrogen gas production, while the remainder would be due to denitrification. It is estimated that a total loss of 6.1–32.9 g N m-2 per year could be attributed to the anammox process in the examined ditches. Illumina-based 16S rRNA gene sequencing confirmed the presence of diverse anammox bacteria in the examined sediments, including Candidatus Brocadia, Candidatus Kuenenia, and Candidatus Anammoxoglobus. Quantitative PCR further confirmed the presence of anammox bacteria, varying between 1.9 × 104 and 1.2 × 105 copies g−1 sediment. The results of our study showed the evidence of anammox process in agricultural drainage ditches and demonstrated that the contribution of anammox to N removal from agricultural drainage ditches may not be negligible.

Evidence for anaerobic ammonium oxidation process in freshwater sediments of aquaculture ponds

The anaerobic ammonium oxidation (anammox) process, which can simultaneously remove ammonium and nitrite, both toxic to aquatic animals, can be very important to the aquaculture industry. Here, the presence and activity of anammox bacteria in the sediments of four different freshwater aquaculture ponds were investigated by using Illumina-based 16S rRNA gene sequencing, quantitative PCR assays and (15)N stable isotope measurements. Different genera of anammox bacteria were detected in the examined pond sediments, including Candidatus Brocadia, Candidatus Kuenenia and Candidatus Anammoxoglobus, with Candidatus Brocadia being the dominant anammox genus. Quantitative PCR of hydrazine synthase genes showed that the abundance of anammox bacteria ranged from 5.6 × 10(4) to 2.1 × 10(5) copies g(-1) sediment in the examined ponds. The potential anammox rates ranged between 3.7 and 19.4 nmol N2 g(-1) sediment day(-1), and the potential denitrification rates varied from 107.1 to 300.3 nmol N2 g(-1) sediment day(-1). The anammox process contributed 1.2-15.3% to sediment dinitrogen gas production, while the remainder would be due to denitrification. It is estimated that a total loss of 2.1-10.9 g N m(-2) per year could be attributed to the anammox process in the examined ponds, suggesting that this process could contribute to nitrogen removal in freshwater aquaculture ponds.

Occurrence and importance of anaerobic ammonium-oxidising bacteria in vegetable soils.

The quantitative importance of anaerobic ammonium oxidation (anammox) has been described in paddy fields, while the presence and importance of anammox in subsurface soil from vegetable fields have not been determined yet. Here, we investigated the occurrence and activity of anammox bacteria in five different types of vegetable fields located in Jiangsu Province, China. Stable isotope experiments confirmed the anammox activity in the examined soils, with the potential rates of 2.1 and 23.2 nmol N2 g(-1) dry soil day(-1), and the anammox accounted for 5.9-20.5% of total soil dinitrogen gas production. It is estimated that a total loss of 7.1-78.2 g N m(-2) year(-1) could be linked to the anammox process in the examined vegetable fields. Phylogenetic analyses showed that multiple co-occurring anammox genera were present in the examined soils, including Candidatus Brocadia, Candidatus Kuenenia, Candidatus Anammoxoglobus and Candidatus Jettenia, and Candidatus Brocadia appeared to be the most common anammox genus. Quantitative PCR further confirmed the presence of anammox bacteria in the examined soils, with the abundance varying from 2.8 × 10(5) to 3.0 × 10(6) copies g(-1) dry soil. Correlation analyses suggested that the soil ammonium concentration had significant influence on the activity and abundance of anammox bacteria in the examined soils. The results of our study showed the presence of diverse anammox bacteria and indicated that the anammox process could serve as an important nitrogen loss pathway in vegetable fields.

Nitrogen loss by anaerobic oxidation of ammonium in rice rhizosphere.

Anaerobic oxidation of ammonium (anammox) is recognized as an important process for nitrogen (N) cycling, yet its role in agricultural ecosystems, which are intensively fertilized, remains unclear. In this study, we investigated the presence, activity, functional gene abundance and role of anammox bacteria in rhizosphere and non-rhizosphere paddy soils using catalyzed reporter deposition–fluorescence in situ hybridization, isotope-tracing technique, quantitative PCR assay and 16S rRNA gene clone libraries. Results showed that rhizosphere anammox contributed to 31–41% N2 production with activities of 0.33–0.64 nmol N2 g−1 soil h−1, whereas the non-rhizosphere anammox bacteria contributed to only 2–3% N2 production with lower activities of 0.08–0.26 nmol N2 g−1 soil h−1. Higher anammox bacterial cells were observed (0.75–1.4 × 107 copies g−1 soil) in the rhizosphere, which were twofold higher compared with the non-rhizosphere soil (3.7–5.9 × 106 copies g−1 soil). Phylogenetic analysis of the anammox bacterial 16S rRNA genes indicated that two genera of ‘Candidatus Kuenenia' and ‘Candidatus Brocadia' and the family of Planctomycetaceae were identified. We suggest the rhizosphere provides a favorable niche for anammox bacteria, which are important to N cycling, but were previously largely overlooked.

Molecular and geochemical constraints on anaerobic ammonium oxidation (anammox) in a riparian zone of the Seine Estuary (France)

To expand the limited knowledge about the ecological significance of anaerobic ammonium oxidation (anammox) in continental aquatic and terrestrial ecosystems, we studied community structure, abundance, and activity of anammox bacteria in soils and sediments in the wetland of Trou Deshayes, a riparian zone in the Seine Estuary, France. Combining (i) molecular analyses of the genes coding for anammox bacterial 16S rRNA and the enzyme hydrazine oxidoreductase (hzo), (ii) quantification of unique anammox bacterial membrane lipids (i.e. ladderanes), and, (iii) 15N-isotope label incubation experiments with intertidal sediments and irregularly flooded soils nearby, we demonstrated that anammox bacteria were ubiquitous in the studied wetland ecosystem. In both soils and sediments, detected anammox bacteria were related to Candidatus ‘Brocadia’. 16S rRNA genes were generally lower in the more oxygenated soils, but on the same order of magnitude (107–108 copies g−1 d.w.) as found for other river estuaries, riparian zones and agricultural soils. While the C20-ladderane fatty acid with five cyclobutane moieties (C20-[5]-FA) was found in both sediments and soils, other ladderane species were detected only in the wetland sediments. The observed differential ladderane distribution suggests intra-genus differences in the community composition of anammox bacteria between the sediments and the floodplain soils. While the abundance of anammox bacteria was significantly lower in the soils versus the sediments, the potential anammox rates were similar (≤15 and ≤22 nmol N2 d−1 g−1 w.w. sediment and soil, respectively), suggesting lower cell-specific anammox rates in the sediments. The observed potential rates of anammox were rather low, leaving canonical denitrification as the main fixed N removal pathway in this riparian zone. The relative contribution of anammox to the total N2 production (between 3 and 8 %) was similar at all sites, highlighting the dependence of the anammox process on nitrite supply from denitrification across environmental boundaries. Due to this coupling, the dependence of organotrophic denitrification on the quality and stoichiometry of OM also seems to affect the anammox bacterial community. Our results suggest that N removal and mitigation of N supply from agriculture in wetlands by anammox is limited, and much less important than denitrification.

Temporal dynamics of nitrogen loss in the coastal upwelling ecosystem off central Chile: Evidence of autotrophic denitrification through sulfide oxidation

Coastal upwelling areas are highly productive marine systems in which the development of oxygen‐depleted conditions and the availability of diverse electron donors (e.g., organic matter, , H2S) favor the processes involved in nitrogen (N) loss. We characterize the temporal and vertical variability of anammox and denitrification over the continental shelf off central Chile (36.5°S), through 15N and 13C tracer experiments, including amendments with H2S and along with measurements of 15N2 and 15N2O production and oceanographic variables during a year (2009 to 2010). Restricted to the bottom waters, both anammox and denitrification contributed similarly (∼ 500 nmol N2 L−1 d−1) to N loss during spring, while a marked decrease in the activity of these processes occurred in summer (103 and 14 nmol N2 L−1 d−1 for anammox and denitrification, respectively). During fall, denitrification was the only contributor to the observed nitrogen deficit (894 nmol N2 L−1 d−1). Interestingly, a substantial increase in the rates of denitrification (∼ 1200 nmol N2 L−1 d−1) and dark 13C assimilation were observed after the addition of H2S, indicating an autotrophic contribution to denitrification, which could be fueled in situ by H2S emitted from sediments or produced in the water column. The observed patterns seem to be controlled (stimulated or inhibited) by the availability of oxygen, organic matter, and H2S. This study establishes the magnitude and co‐occurrence of the different processes responsible for N removal in the coastal upwelling system of central Chile. This linkage of the nitrogen, carbon, and sulfur cycles is relevant to a global climate change scenario.