Soil and sediment bacteria capable of aerobic nitrate respiration

A novel strategy of artificially regulating plant rhizosphere microbial community to promote plant tolerance to cold stress

Artificial regulation of plant rhizosphere microbial communities through the synthesis of microbial communities is one of the effective ways to improve plant stress resistance. However, the process of synthesizing stress resistant microbial communities with excellent performance is complex, time-consuming, and costly. To address this issue, we proposed a novel strategy for preparing functional microbial communities. We isolated a cultivable cold tolerant bacterial community (PRCBC) from the rhizosphere of peas, and studied its effectiveness in assisting rice to resist stress. The results indicate that PRCBC can not only improve the ability of rice to resist cold stress, but also promote the increase of rice yield after cold stress relieved. This is partly because PRCBC increases the nitrogen content in the rhizosphere soil, and promotes rice's absorption of nitrogen elements, thereby promoting rice growth and enhancing its ability to resist osmotic stress. More importantly, the application of PRCBC drives the succession of rice rhizosphere microbial communities, and promotes the succession of rice rhizosphere microbial communities towards stress resistance. Surprisingly, PRCBC drives the succession of rice rhizosphere microbial communities towards a composition similar to PRCBC. This provides a feasible novel method for artificially and directionally driving microbial succession. In summary, we not only proposed a novel and efficient strategy for preparing stress resistant microbial communities to promote plant stress resistance, but also unexpectedly discovered a possible directionally driving method for soil microbial community succession.

Effect of Fe2+-activated persulfate combined with biodegradation in removing gasoline BTX from karst groundwater: A box-column experimental study

In-situ chemical oxidation with persulfate (PS-ISCO) is a preferred approach for the remediation of fuel-contaminated groundwater. Persulfate (PS) can be activated by various methods to produce stronger sulfate radicals for more efficient ISCO. Despite karst aquifers being widespread, there are few reports on PS-ISCO combined with Fe2+-activated PS. To better understand the effects of Fe2+-activated PS for the remediation of gasoline-contaminated aquifers in karst areas, a box-column experiment was conducted under flow conditions, using karst groundwater and limestone particles to simulate an aquifer. Gasoline was used as the source of hydrocarbon contaminants. Dissolved oxygen and nitrate were added to enhance bioremediation (EBR) and ferrous sulfate was used to activate PS. The effect of Fe2+-activated PS combined with biodegradation was compared during the periods of EBR + ISCO and ISCO alone, using the mass flow method for data analysis. The results showed that the initial dissolution of benzene, toluene, and xylene (BTX) from gasoline injection was rapid and variable, with a decaying trend at an average pseudo-first-order degradation rate constant of 0.032 d-1. Enhanced aerobic biodegradation and denitrification played a significant role in limestone-filled environments, with dissolved oxygen and nitrate utilization ratios of 59 ~ 72% and 12-70%, respectively. The efficiency of EBR + ISCO was the best method for BTX removal, compared with EBR or ISCO alone. The pseudo-first-order degradation rate constants of BTX reached 0.022-0.039, 0.034-0.070, and 0.027-0.036 d-1, during the periods of EBR alone, EBR + ISCO, and ISCO alone, respectively. The EBR + ISCO had a higher BTX removal ratio range of 71.0 ~ 84.3% than the ISCO alone with 30.1 ~ 45.1%. The presence of Fe2+-activated PS could increase the degradation rate of BTX with a range of 0.060 ~ 0.070 d-1, otherwise, with a range of 0.034-0.052 d-1. However, Fe2+-activated PS also consumed about 3 times the mass of PS, caused a further decrease in pH with a range of 6.8-7.6, increased 3-4 times the Ca2+ and 1.6-1.8 times the HCO3- levels, and decreased the BTX removal ratio of ISCO + EBR, compared to the case without Fe2+ activation. In addition, the accumulation of ferric hydroxides within a short distance indicated that the range of PS activated by Fe2+ may be limited. Based on this study, it is suggested that the effect of Fe2+-activated PS should be evaluated in the remediation of non-carbonate rock aquifers.

Aerobic denitrification as an N2O source from microbial communities

Nitrous oxide (N2O) is a potent greenhouse gas of primarily microbial origin. Oxic and anoxic emissions are commonly ascribed to autotrophic nitrification and heterotrophic denitrification, respectively. Beyond this established dichotomy, we quantitatively show that heterotrophic denitrification can significantly contribute to aerobic nitrogen turnover and N2O emissions in complex microbiomes exposed to frequent oxic/anoxic transitions. Two planktonic, nitrification-inhibited enrichment cultures were established under continuous organic carbon and nitrate feeding, and cyclic oxygen availability. Over a third of the influent organic substrate was respired with nitrate as electron acceptor at high oxygen concentrations (>6.5 mg/L). N2O accounted for up to one-quarter of the nitrate reduced under oxic conditions. The enriched microorganisms maintained a constitutive abundance of denitrifying enzymes due to the oxic/anoxic frequencies exceeding their protein turnover-a common scenario in natural and engineered ecosystems. The aerobic denitrification rates are ascribed primarily to the residual activity of anaerobically synthesised enzymes. From an ecological perspective, the selection of organisms capable of sustaining significant denitrifying activity during aeration shows their competitive advantage over other heterotrophs under varying oxygen availabilities. Ultimately, we propose that the contribution of heterotrophic denitrification to aerobic nitrogen turnover and N2O emissions is currently underestimated in dynamic environments.

Hongsoonwoonella zoysiae gen. nov., sp. nov., a new member of the family Stappiaceae isolated from a tidal mudflat

A Gram stain-negative bacterial strain, designated SY4-7^T, was isolated from rhizosphere mudflat of a halophyte (Zoysia sinica) collected around Seonyu Island, Republic of Korea. Cells of the organism were strictly aerobic, non-sporulating, non-motile rods and grew at 20-42 °C, pH 6-8 and 1-6% (w/v) NaCl. The 16S rRNA gene-based phylogenetic analyses revealed that strain SY4-7^T formed an independent cluster separated from the recognized genera of the family Stappiaceae, which was also supported by phylogenomic analysis-based 92-core gene sequences. The type stains of the phylogenetically closest relatives were Stappia indica (95.6% sequence similarity), Stappia stellulata (95.1%) and Roseibium hamelinense (95.1%). The isoprenoid quinone was Q-10. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminophospholipids, an unidentified phosphoglycolipid, an unidentified aminolipid, two unidentified phospholipids and an unidentified lipid. The major cellular fatty acids are C_18:1ω7c and C_19:1 cyclo ω8c. The G + C content of the genomic DNA is 60.7%. Discrimination of the organism from all the recognized genera of the family Stappiaceae was apparent by the chemotaxonomic and phylogenetic features. Based on the results presented here, strain SY4-7^T (= KCTC 72226^T = NBRC 113902^T) represents a novel species of a new genus in the family Stappiaceae, for which the name Hongsoonwoonella zoysiae sp. nov. is proposed.

New application of rutin: Repair the toxicity of emerging perfluoroalkyl substance to Pseudomonas stutzeri

Per- and polyfluoroalkyl substances (PFASs) are toxic to microorganisms, thereby affecting microbial communities in sludge and soil, but how to repair the toxicity of microorganisms remains unclear. In this study, rutin, an antioxidant, was added into a culture medium with an aerobic denitrification bacteria, Pseudomonas stutzeri, under the exposure of sodium perfluorononyloxy-benzenesulfonate (OBS) to evaluate the repair mechanisms of rutin to the toxicity of OBS to the bacteria. The results showed that rutin could repair the damage of OBS to cell structures, and reduce the death rates of the bacteria under OBS exposure. The dosage of rutin reduced the effect on the inhibition of denitrification ability of P. stutzeri under OBS exposure. Compared with the bacteria exposed to single OBS, the dosage of rutin resulted in that the death rates recovered from 96.2% to 66.4%, the growth inhibition rate decreased from 46.5% to 15.8%, the total nitrogen removal rate recovered from 66.9% to 100%, and the NO₂^- content recovered from 34.5 mg/L to 0.22 mg/L. The expressions of key denitrification genes (napA, nirS, norB, nosZ) were recovered after adding rutin under OBS exposure. Rutin changed the positive rate of reactive oxygen species, the relative superoxide dismutase and catalase activities in the bacteria which exposed to OBS. The mechanism by which rutin repaired the toxicity of OBS to P. stutzeri related to inhibiting the activities of antioxidant and denitrification enzymes rather than affecting the expressions of genes involved in these enzymes. This study sheds light on the repair method of micro-organics and reveals the repair mechanisms under PFASs exposure.

Salt tolerance of nitrate reductase in Halomonas sp. B01

A systematic study on the lack of dissimilatory nitrate reductase (NAR) properties in Halomonas strains had been reported so far. The effects of different factors on Halomonas sp. B01 NAR activity were investigated. The salt tolerance of NAR was characterized. The denitrification process under high salt conditions was reported. Halomonas sp. B01 expressed membrane-bound NAR under induced culture by nitrate. The optimum pH of the enzyme reaction system was 8, and the optimum temperature was 30 °C. The mRNA expression abundance of narH in NAR encoding gene was highest in the 60 g/L NaCl inducing matrix. The NaCl concentration of optimum growth and induction of NAR were both 60 g/L. The ectoine added to the NAR vitro enzyme reaction system could maintain NAR activity under high NaCl concentration. In the range of 0-60 g/L NaCl, the NAR activity was stable at 17.7 (± 0.3) U/mg. The denitrification was performed by Halomonas sp. B01 at 60 g/L NaCl, and the denitrification rate reached 97.1% at 24 h. This study reveals for the first time the NAR properties of Halomonas strains, which provides a theoretical and technical basis for the nitrogen removal of high-salt nitrogenous wastewater using this strain.

Taxonomic and functional diversity of the microbiome in a jet fuel contaminated site as revealed by combined application of in situ microcosms with metagenomic analysis

Natural attenuation represents all processes that govern contaminant mass removal, which mainly occurs via microbial degradation in the environment. Although this process is intrinsic its rate and efficiency depend on multiple factors. This study aimed to characterize the microbial taxonomic and functional diversity in different aquifer sediments collected in the saturated zone and in situ microcosms (BACTRAP®s) amended with hydrocarbons (¹³C-labeled and non-labeled benzene, toluene and naphthalene) using 16S rRNA gene and "shotgun" Illumina high throughput sequencing at a jet-fuel contaminated site. The BACTRAP®s were installed to assess hydrocarbon metabolism by native bacteria. Results indicated that Proteobacteria, Actinobacteria and Firmicutes were the most dominant phyla (~98%) in the aquifer sediment samples. Meanwhile, in the benzene- and toluene-amended BACTRAP®s the phyla Firmicutes and Proteobacteria accounted for about 90% of total community. In the naphthalene-amended BACTRAP®, members of the SR-FBR-L83 family (Order Ignavibacteriales) accounted for almost 80% of bacterial community. Functional annotation of metagenomes showed that only the sediment sample located at the source zone border and with the lowest BTEX concentration, has metabolic potential to degrade hydrocarbons aerobically. On the other hand, in situ BACTRAP®s allowed enrichment of hydrocarbon-degrading bacteria. Metagenomic data suggest that fumarate addition is the main mechanism for hydrocarbon activation of toluene. Also, indications for methylation, hydroxylation and carboxylation as activation mechanisms for benzene anaerobic conversion were found. After 120 days of exposure in the contaminated groundwater, the isotopic analysis of fatty acids extracted from BACTRAP®s demonstrated the assimilation of isotopic labeled compounds in the cells of microbes expressed by strong isotopic enrichment. We propose that the microbiota in this jet-fuel contaminated site has metabolic potential to degrade benzene and toluene by a syntrophic process, between members of the families Geobacteraceae and Peptococcaceae (genus Pelotomaculum), coupled to nitrate, iron and/or sulfate reduction.

Enhancement of facultative anaerobic denitrifying communities by oxygen release from roots of the macrophyte in constructed wetlands

The radial oxygen loss (ROL) of wetland plants is a crucial factor that can influence the efficiency required for nitrogen (N) removal and microbial activities responsible for N removal in constructed wetlands (CWs). However, the shift of microbial community in different niches in response to ROL has been rarely studied. This study aims to unravel the link between the ROL and microbial response in sediment, water and rhizoplane by a surface flow CW planted with Myriophyllum aquaticum for treating high-strength swine wastewater. Ti³⁺-citrate colorimetric method demonstrated that M. aquaticum was a wetland species with a ROL of 0.019 mg/h/plant. Using quantitative polymerase chain reactions (qPCR) and high-throughput sequencing of microbial 16S rRNA gene, we demonstrated that the abundance of facultative anaerobic denitrifiers in the rhizoplane was the most of the three niches, that in the water (5-10 cm) was the less and that in the sediment was the least. Acinetobacter was enriched and dominated amongst denitrifiers in the water. Denitrifiers in the rhizoplane were mainly dominated by enriched Pseudomonas, Aeromonas, and Acinetobacter. The theoretical calculation of oxygen sources and consumptions indicated that water reaeration should support the oxygen demands for nitrification in the aerobic layer (0-5 cm), and the ROL could stimulate the growth of facultative anaerobic denitrifiers in the rhizoplane and water (5-10 cm) to achieve denitrification within CW systems.

The effect of cations (Na+, Mg2+, and Ca2+) on the activity and structure of nitrifying and denitrifying bacterial communities

Wastewaters generated in regions with water scarcity usually have high alkalinity, hardness, and elevated osmotic pressure (OP). Those characteristics should be considered when using biological systems for wastewater treatment along with the salinity heterogeneity. The interaction of different salts in mixed electrolyte solutions may cause inhibition, antagonism, synergism, and stimulation effects on microbial communities. Little is known about those effects on microbial activity and community structure of nitrifying and denitrifying bacteria. In this work, factorial design was used to evaluate the effects of NaCl, MgCl₂ and CaCl₂ on nitrifying and denitrifying communities. Antagonistic relationships between all salts were observed and they had greater magnitude on the nitrifying community. Stimulus and synernism were more evident on the nitrifying and denitrifying experiments, respectively. For this reason, the highest nitrification and denitrification specific rates were 1.1 × 10^-1 mgN-NH₄⁺ gSSV^-1 min^-1 for condition 01 and 6.5 × 10^-2 mgN-NO₃^- gSSV^-1 min^-1 for control condition, respectively. The toxicity of the salts followed the order of NaCl > MgCl₂ > CaCl₂ and the antagonism between MgCl₂ and NaCl was the most significant. PCR/DGGE analyses showed that Mg²⁺ may be the element that expresses the least influence in the differentiation of microbial structure even though it significantly affects the activity of the autotrophic microorganisms. The same behavior was observed for Ca²⁺ on denitrifying microorganism. In addition, microbial diversity and richness was not negatively affected by different salinities. Genetic sequencing suggested that the genus Aeromonas, Alishewanella, Azospirillum, Pseudoalteromonas, and Thioalkalivibrio were outstanding on ammonium and nitrate removal under saline conditions. The specific toxicity of each salt and the interactions among them are the major effects on microbial activity in biological wastewater treatments rather than the osmotic pressure caused by the final salinity.

In Situ Water Quality Improvement Mechanism (Nitrogen Removal) by Water-Lifting Aerators in a Drinking Water Reservoir

A field scale experiment was performed to explore the nitrogen removal performance of the water and surface sediment in a deep canyon-shaped drinking water reservoir by operating WLAs (water-lifting aerators). Nitrogen removal performance was achieved by increasing the densities and N-removal genes (nirK and nirS) of indigenous aerobic denitrifiers. After the operation of WLAs, the total nitrogen removal rate reached 29.1 ± 0.8% in the enhanced area. Ammonia and nitrate concentrations were reduced by 72.5 ± 2.5% and 40.5 ± 2.1%, respectively. No nitrite accumulation was observed. Biolog results showed improvement of carbon metabolism and carbon source utilization of microbes in the enhanced area. Miseq high-throughput sequencing indicated that the denitrifying bacteria percentage was also higher in the enhanced area than that in the control area. Microbial communities had changed between the enhanced and control areas. Thus, nitrogen removal through enhanced indigenous aerobic denitrifiers by the operation of WLAs was feasible and successful at the field scale.

Perchlorate contamination in Chile: Legacy, challenges, and potential solutions

This paper reviews the unique situation of perchlorate contamination in Chile, including its sources, presence in environmental media and in the human population, and possible steps to mitigate its health impacts. Perchlorate is a ubiquitous water contaminant that inhibits thyroid function. Standards for drinking water range from 2 to 18 µg L^-1 in United States and Europe. A major natural source of perchlorate contamination is Chile saltpeter, found in the Atacama Desert. High concentrations of perchlorate have presumably existed in this region, in soils, sediments, surface waters and groundwaters, for millions of years. As a result of this presence, and the use of Chile saltpeter as a nitrogen fertilizer, perchlorate in Chile has been found at concentrations as high as 1480 µg L^-1 in drinking water, 140 µg/kg^-1 in fruits, and 30 µg L^-1 in wine. Health studies in Chile have shown concentrations of 100 µg L^-1 in breast milk and 20 µg L^-1 in neonatal serum. It is important to acknowledge perchlorate as a potential health concern in Chile, and assess mitigation strategies. A more thorough survey of perchlorate in Chilean soils, sediments, surface waters, groundwaters, and food products can help better assess the risks and potentially develop standards. Also, perchlorate treatment technologies should be more closely assessed for relevance to Chile. The Atacama Desert is a unique biogeochemical environment, with millions of years of perchlorate exposure, which can be mined for novel perchlorate-reducing microorganisms, potentially leading to new biological treatment processes for perchlorate-containing waters, brines, and fertilizers.

Microbial population dynamics in response to bioaugmentation in a constructed wetland system under 10°C

Compound microbial inocula were enriched and applied to a pilot-scale constructed wetland system to investigate their bioaugmentation effect on nitrogen removal under cold temperature (10°C). The results showed a 10% higher removal efficiency of ammonia and total nitrogen compared to a control (unbioaugmented) group. The microbial community structures before and after the bioaugmentation were analyzed through high throughput sequencing using Miseq Illumina platform. A variation of species richness and community equitability was observed in both systems. It is demonstrated that, based on the response of both the performance and microbial community, bioaugmentation using compound microbial inocula can fine tune the bacterial population and enhance the nitrogen removal efficiency of a constructed wetland system.

Efficient production and secretion of pyruvate from Halomonas sp. KM-1 under aerobic conditions

The alkaliphilic, halophilic bacterium Halomonas sp. KM-1 can utilize both hexose and pentose sugars for the intracellular storage of bioplastic poly-(R)-3-hydroxybutyric acid (PHB) under aerobic conditions. In this study, we investigated the effects of the sodium nitrate concentration on PHB accumulation in the KM-1 strain. Unexpectedly, we observed the secretion of pyruvate, a central intermediate in carbon- and energy-metabolism processes in all organisms; therefore, pyruvate is widely used as a starting material in the industrial biosynthesis of pharmaceuticals and is employed for the production of crop-protection agents, polymers, cosmetics, and food additives. We then further analyzed pyruvate productivity following changes in culture temperature and the buffer concentration. In 48-h batch-cultivation experiments, we found that wild-type Halomonas sp. KM-1 secreted 63.3 g/L pyruvate at a rate of 1.32 g/(L·h), comparable to the results of former studies using mutant and recombinant microorganisms. Thus, these data provided important insights into the production of pyruvate using this novel strain.

Nitrogen removal characteristics of enhanced in situ indigenous aerobic denitrification bacteria for micro-polluted reservoir source water

Indigenous oligotrophic aerobic denitrifiers nitrogen removal characteristics, community metabolic activity and functional genes were analyzed in a micro-polluted reservoir. The results showed that the nitrate in the enhanced system decreased from 1.71±0.01 to 0.80±0.06mg/L, while the control system did little to remove and there was no nitrite accumulation. The total nitrogen (TN) removal rate of the enhanced system reached 38.33±1.50% and the TN removal rate of surface sediment in the enhanced system reached 23.85±2.52%. TN removal in the control system experienced an 85.48±2.37% increase. The densities of aerobic denitrifiers in the enhanced system ranged from 2.24×10(5) to 8.13×10(7)cfu/mL. The abundance of nirS and nirK genes in the enhanced system were higher than those of in the control system. These results suggest that the enhanced in situ indigenous aerobic denitrifiers have potential applications for the bioremediation of micro-polluted reservoir system.

Simulation of nitrous oxide emissions at field scale using the SPACSYS model

Nitrous oxide emitted to the atmosphere via the soil processes of nitrification and denitrification plays an important role in the greenhouse gas balance of the atmosphere and is involved in the destruction of stratospheric ozone. These processes are controlled by biological, physical and chemical factors such as growth and activity of microbes, nitrogen availability, soil temperature and water availability. A comprehensive understanding of these processes embodied in an appropriate model can help develop agricultural mitigation strategies to reduce greenhouse gas emissions, and help with estimating emissions at landscape and regional scales. A detailed module to describe the denitrification and nitrification processes and nitrogenous gas emissions was incorporated into the SPACSYS model to replace an earlier module that used a simplified first-order equation to estimate denitrification and was unable to distinguish the emissions of individual nitrogenous gases. A dataset derived from a Scottish grassland experiment in silage production was used to validate soil moisture in the top 10 cm soil, cut biomass, nitrogen offtake and N2O emissions. The comparison between the simulated and observed data suggested that the new module can provide a good representation of these processes and improve prediction of N2O emissions. The model provides an opportunity to estimate gaseous N emissions under a wide range of management scenarios in agriculture, and synthesises our understanding of the interaction and regulation of the processes.

Nitrogen Removal Characteristics of a Newly Isolated Indigenous Aerobic Denitrifier from Oligotrophic Drinking Water Reservoir, Zoogloea sp. N299

Nitrogen is considered to be one of the most widespread pollutants leading to eutrophication of freshwater ecosystems, especially in drinking water reservoirs. In this study, an oligotrophic aerobic denitrifier was isolated from drinking water reservoir sediment. Nitrogen removal performance was explored. The strain was identified by 16S rRNA gene sequence analysis as Zoogloea sp. N299. This species exhibits a periplasmic nitrate reductase gene (napA). Its specific growth rate was 0.22 h-1. Obvious denitrification and perfect nitrogen removal performances occurred when cultured in nitrate and nitrite mediums, at rates of 75.53%±1.69% and 58.65%±0.61%, respectively. The ammonia removal rate reached 44.12%±1.61% in ammonia medium. Zoogloea sp. N299 was inoculated into sterilized and unsterilized reservoir source waters with a dissolved oxygen level of 5-9 mg/L, pH 8-9, and C/N 1.14:1. The total nitrogen removal rate reached 46.41%±3.17% (sterilized) and 44.88%±4.31% (unsterilized). The cell optical density suggested the strain could survive in oligotrophic drinking water reservoir water conditions and perform nitrogen removal. Sodium acetate was the most favorable carbon source for nitrogen removal by strain N299 (p<0.05). High C/N was beneficial for nitrate reduction (p<0.05). The nitrate removal efficiencies showed no significant differences among the tested inoculums dosage (p>0.05). Furthermore, strain N299 could efficiently remove nitrate at neutral and slightly alkaline and low temperature conditions. These results, therefore, demonstrate that Zoogloea sp. N299 has high removal characteristics, and can be used as a nitrogen removal microbial inoculum with simultaneous aerobic nitrification and denitrification in a micro-polluted reservoir water ecosystem.

Nitrogen removal from micro-polluted reservoir water by indigenous aerobic denitrifiers

Treatment of micro-polluted source water is receiving increasing attention because of environmental awareness on a global level. We isolated and identified aerobic denitrifying bacteria Zoogloea sp. N299, Acinetobacter sp. G107, and Acinetobacter sp. 81Y and used these to remediate samples of their native source water. We first domesticated the isolated strains in the source water, and the 48-h nitrate removal rates of strains N299, G107, and 81Y reached 33.69%, 28.28%, and 22.86%, respectively, with no nitrite accumulation. We then conducted a source-water remediation experiment and cultured the domesticated strains (each at a dry cell weight concentration of 0.4 ppm) together in a sample of source water at 20–26 °C and a dissolved oxygen concentration of 3–7 mg/L for 60 days. The nitrate concentration of the system decreased from 1.57 ± 0.02 to 0.42 ± 0.01 mg/L and that of a control system decreased from 1.63 ± 0.02 to 1.30 ± 0.01 mg/L, each with no nitrite accumulation. Total nitrogen of the bacterial system changed from 2.31 ± 0.12 to 1.09 ± 0.01 mg/L, while that of the control system changed from 2.51 ± 0.13 to 1.72 ± 0.06 mg/L. The densities of aerobic denitrification bacteria in the experimental and control systems ranged from 2.8 × 10⁴ to 2 × 10⁷ cfu/mL and from 7.75 × 10³ to 5.5 × 10⁵ cfu/mL, respectively. The permanganate index in the experimental and control systems decreased from 5.94 ± 0.12 to 3.10 ± 0.08 mg/L and from 6.02 ± 0.13 to 3.61 ± 0.11 mg/L, respectively, over the course of the experiment. Next, we supplemented samples of the experimental and control systems with additional bacteria or additional source water and cultivated the systems for another 35 days. The additional bacteria did little to improve the water quality. The additional source water provided supplemental carbon and brought the nitrate removal rate in the experimental system to 16.97%, while that in the control system reached only 3.01%, with no nitrite accumulation in either system. Our results show that aerobic denitrifying bacteria remain highly active after domestication and demonstrate the applicability of such organisms in the bioremediation of oligotrophic ecosystems.

Acidophilic denitrifiers dominate the N2O production in a 100-year-old tea orchard soil

Aerobic denitrification is the main process for high N2O production in acid tea field soil. However, the biological mechanisms for the high emission are not fully understood. In this study, we examined N2O emission and denitrifier communities in 100-year-old tea soils with four pH levels (3.71, 5.11, 6.19, and 7.41) and four nitrate concentration (0, 50, 200, and 1000 mg kg(-1) of NO3 (-)-N) addition. Results showed the highest N2O emission (10.1 mg kg(-1) over 21 days) from the soil at pH 3.71 with 1000 mg kg(-1) NO3 (-) addition. The N2O reduction and denitrification enzyme activity in the acid soils (pH <7.0) were significantly higher than that of soils at pH 7.41. Moreover, TRF 78 of nirS and TRF 187 of nosZ dominated in soils of pH 3.71, suggesting an important role of acidophilic denitrifiers in N2O production and reduction. CCA analysis also showed a negative correlation between the dominant denitrifier ecotypes (nirS TRF 78, nosZ TRF 187) and soil pH. The representative sequences were identical to those of cultivated denitrifiers from acidic soils via phylogenetic tree analysis. Our results showed that the acidophilic denitrifier adaptation to the acid environment results in high N2O emission in this highly acidic tea soil.

Soil moisture and pH control relative contributions of fungi and bacteria to N2O production

Fungal N(2)O production has been progressively recognized, but its controlling factors remain unclear. This study examined the impacts of soil moisture and pH on fungal and bacterial N(2)O production in two ecosystems, conventional farming and plantation forestry. Four treatments, antibiotic-free soil and soil amended with streptomycin, cycloheximide, or both were used to determine N(2)O production of fungi versus bacteria. Soil moisture and pH effects were assessed under 65-90 % water-filled pore space (WFPS) and pH 4.0-9.0, respectively. Irrespective of antibiotic treatments, soil N(2)O fluxes peaked at 85-90 % WFPS and pH 7.0 or 8.0, indicating that both fungi and bacteria preferred more anoxic and neutral or slightly alkaline conditions in producing N(2)O. However, compared with bacteria, fungi contributed more to N(2)O production under sub-anoxic and acidic conditions. Real-time polymerase chain reaction of 16S, ITS rDNA, and denitrifying genes for quantifications of bacteria, fungi, and denitrifying bacteria, respectively, showed that fungi were more abundant at acidic pH, whereas total and denitrifying bacteria favored neutral conditions. Such variations in the abundance appeared to be related to the pH effects on the relative fungal and bacterial contribution to N(2)O production.

Oxygen-dependent control of respiratory nitrate reduction in mycelium of Streptomyces coelicolor A3(2)

Several members of the obligately aerobic genus Streptomyces are able to reduce nitrate, catalyzed by Nar-type respiratory nitrate reductases. A unique feature of Streptomyces coelicolor A3(2) compared with other streptomycetes is that it synthesizes three nonredundant Nar enzymes. In this study, we show that Nar2 is the main Nar enzyme active in mycelium and could characterize the conditions governing its synthesis. Nar2 was present at low levels in aerobically cultivated mycelium, but synthesis was induced when cultures were grown under oxygen limitation. Growth in the presence of high oxygen concentrations prevented the induction of Nar2 synthesis. Equally, an abrupt shift from aerobiosis to anaerobiosis did not result in the immediate induction of Nar2 synthesis. This suggests that the synthesis of Nar2 is induced during a hypoxic downshift, probably to allow maintenance of a proton gradient during the transition to anaerobiosis. Although no Nar2 could be detected in freshly harvested mature spores, synthesis of the enzyme could be induced after long-term (several days) incubation of these resting spores under anaerobic conditions. Induction of Nar2 synthesis in spores was linked to transcriptional control. Nar2 activity in whole mycelium was strictly dependent on the presence of a putative nitrate transporter, NarK2. The oxygen-dependent inhibition of nitrate reduction by Nar2 was mediated by NarK2-dependent nitrate:nitrite antiport. This antiport mechanism likely prevents the accumulation of toxic nitrite in the cytoplasm. A deletion of the narK2 gene had no effect on Nar1-dependent nitrate reduction in resting spores. Together, our results indicate redox-dependent transcriptional and posttranslational control of nitrate reduction by Nar2.

Mustard catch crop enhances denitrification in shallow groundwater beneath a spring barley field

Over-winter green cover crops have been reported to increase dissolved organic carbon (DOC) concentrations in groundwater, which can be used as an energy source for denitrifiers. This study investigates the impact of a mustard catch crop on in situ denitrification and nitrous oxide (N2O) emissions from an aquifer overlain by arable land. Denitrification rates and N2O-N/(N2O-N+N2-N) mole fractions were measured in situ with a push-pull method in shallow groundwater under a spring barley system in experimental plots with and without a mustard cover crop. The results suggest that a mustard cover crop could substantially enhance reduction of groundwater nitrate NO3--N via denitrification without significantly increasing N2O emissions. Mean total denitrification (TDN) rates below mustard cover crop and no cover crop were 7.61 and 0.002 μg kg(-1) d(-1), respectively. Estimated N2O-N/(N2O-N+N2-N) ratios, being 0.001 and 1.0 below mustard cover crop and no cover crop respectively, indicate that denitrification below mustard cover crop reduces N2O to N2, unlike the plot with no cover crop. The observed enhanced denitrification under the mustard cover crop may result from the higher groundwater DOC under mustard cover crop (1.53 mg L(-1)) than no cover crop (0.90 mg L(-1)) being added by the root exudates and root masses of mustard. This study gives insights into the missing piece in agricultural nitrogen (N) balance and groundwater derived N2O emissions under arable land and thus helps minimise the uncertainty in agricultural N and N2O-N balances.

Increasing polyhydroxyalkanoate (PHA) yields from Cupriavidus necator by using filtered digestate liquors

The production of polyhydroxyalkanoates (PHAs) using digestate liquor as culture media is a novel application to extend the existing uses of digestates. In this study, two micro-filtered digestates (0.22 μm) were evaluated as a source of complex culture media for the production of PHA by Cupriavidus necator as compared to a conventional media. Culture media using a mixture of micro-filtered liquors from food waste and from wheat feed digesters showed a maximum PHA accumulation of 12.29 g/l PHA, with 90% cell dry weight and a yield of 0.48 g PHA/g VFA consumed, the highest reported to date for C. necator studies. From the analysis of the starting and residual media, it was concluded that ammonia, potassium, magnesium, sulfate and phosphate provided in the digestate liquors were vital for the initial growth of C. necator whereas copper, iron and nickel may have played a significant role in PHA accumulation.

Transport and degradation of propylene glycol in the vadose zone: model development and sensitivity analysis

Transport and degradation of de-icing chemical (containing propylene glycol, PG) in the vadose zone were studied with a lysimeter experiment and a model, in which transient water flow, kinetic degradation of PG and soil chemistry were combined. The lysimeter experiment indicated that aerobic as well as anaerobic degradation occurs in the vadose zone. Therefore, the model included both types of degradation, which was made possible by assuming advection-controlled (mobile) and diffusion-controlled (immobile) zones. In the mobile zone, oxygen can be transported by diffusion in the gas phase. The immobile zone is always water-saturated, and oxygen only diffuses slowly in the water phase. Therefore, the model is designed in a way that the redox potential can decrease when PG is degraded, and thus, anaerobic degradation can occur. In our model, manganese oxide (MnO2, which is present in the soil) and NO3- (applied to enhance biodegradation) can be used as electron acceptors for anaerobic degradation. The application of NO3- does not result in a lower leaching of PG nor in a slower depletion of MnO2. The thickness of the snowcover influences the leached fraction of PG, as with a high infiltration rate, transport is fast, there is less time for degradation and thus more PG will leach. The model showed that, in this soil, the effect of the water flow dominates over the effect of the degradation parameters on the leaching at a 1-m depth.

Denitrification and indirect N₂O emissions in groundwater: hydrologic and biogeochemical influences

Identification of specific landscape areas with high and low groundwater denitrification potential is critical for improved management of agricultural nitrogen (N) export to ground and surface waters and indirect nitrous oxide (N₂O) emissions. Denitrification products together with concurrent hydrogeochemical properties were analysed over two years at three depths at two low (L) and two high (H) permeability agricultural sites in Ireland. Mean N₂O-N at H sites were significantly higher than L sites, and decreased with depth. Conversely, excess N₂-N were significantly higher at L sites than H sites and did not vary with depth. Denitrification was a significant pathway of nitrate (NO₃⁻-N) reduction at L sites but not at H sites, reducing 46-77% and 4-8% of delivered N with resulting mean NO₃⁻-N concentrations of 1-4 and 12-15 mg N L⁻¹ at L and H sites, respectively. Mean N₂O-N emission factors (EF₅g) were higher than the most recent Intergovernmental Panel on Climate Change (IPCC, 2006) default value and more similar to the older IPCC (1997) values. Recharge during winter increased N₂O but decreased excess dinitrogen (excess N₂-N) at both sites, probably due to increased dissolved oxygen (DO) coupled with low groundwater temperatures. Denitrifier functional genes were similar at all sites and depths. Data showed that highly favourable conditions prevailed for denitrification to occur--multiple electron donors, low redox potential (Eh<100 mV), low DO (<2 mg L⁻¹), low permeability (k(s)<0.005 m·d⁻¹) and a shallow unsaturated zone (<2 m). Quantification of excess N₂-N in groundwater helps to close N balances at the local, regional and global scales.

Effects of multiple electron acceptors on microbial interactions in a hydrogen-based biofilm

To investigate interactions among multiple electron acceptors in a H2-fed biofilm, we operated a membrane biofilm reactor with H2-delivery capacity sufficient to reduce all acceptors. ClO4(-) and O2 were input electron acceptors in all stages at surface loadings of 0.08 ± 0.006 g/m(2)-d (1.0 ± 0.7 e(-) meq/m(2)-d) for ClO4(-) and 0.51 g/m(2)-d (76 e(-) meq/m(2)-d) for O2. SO4(2-) was added in Stage 2 at 3.77 ± 0.39 g/m(2)-d (331 ± 34 e(-) meq/m(2)-d), and NO3(-) was further added in Stage 3 at 0.72 ± 0.03 g N/m(2)-d (312 ± 13 e(-) meq/m(2)-d). At steady state for each stage, ClO4(-), O2, and NO3(-) (when present in the influent) were completely reduced; measured SO4(2-) reduction decreased from 78 ± 4% in Stage 2 to 59 ± 4% in Stage 3, when NO3(-) was present. While perchlorate-reducing bacteria (PRB), assayed by qPCR targeting the pcrA gene, remained stable throughout, sulfate-reducing bacteria (SRB), assayed by the dsrA gene, increased almost 3 orders of magnitude when significant SO4(2-) reduction occurred in stage 2. The abundance of denitrifying bacteria (DB), assayed by the nirK and nirS genes, increased in Stage 3, while SRB remained at high numbers, but did not increase. Based on pyrosequencing analyses, β-Proteobacteria dominated in Stage 1, but ε-Proteobacteria became more important in Stages 2 and 3, when the input of multiple electron acceptors favored genera with broader electron-accepting capabilities. Sulfuricurvum (a sulfur oxidizer and NO3(-) reducer) and Desulfovibrio (a SO4(2-) reducer) become dominant in Stage 3, suggesting redox cycling of sulfur in the biofilm.

Removal of dissolved organic carbon and nitrogen during simulated soil aquifer treatment

Soil aquifer treatment was simulated in 1 m laboratory soil columns containing silica sand under saturated and unsaturated soil conditions to examine the effect of travel length through the unsaturated zone on the removal of wastewater organic matter, the effect of soil type on dissolved organic carbon removal and also the type of microorganisms involved in the removal process. Dissolved organic carbon removal and nitrification did enhance when the wastewater travelled a longer length through the unsaturated zone. A similar consortium of microorganisms was found to exist in both saturated and unsaturated columns. Microbial concentrations however were lowest in the soil column containing silt and clay in addition to silica sand. The presence of silt and clay was detrimental to DOC removal efficiency under saturated soil conditions due to their negative effect on the hydraulic performance of the soil column and microbial growth.

Denitrification and aerobic respiration, hybrid electron transport chains and co-evolution

This paper explores the bioenergetics and potential co-evolution of denitrification and aerobic respiration. The advantages and disadvantages of combining these two pathways in a single, hybrid respiratory chain are discussed and the experimental evidence for the co-respiration of nitrate and oxygen is critically reviewed. A scenario for the co-evolution of the two pathways is presented. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems.

Characteristics of an aerobic denitrifier that utilizes ammonium and nitrate simultaneously under the oligotrophic niche

INTRODUCTION

An aerobic denitrifier was isolated from the Hua-Jia-Chi pond in China and identified as Pseudomonas mendocina 3-7 (Genbank No. HQ285879). This isolated strain could express periplasmic nitrate reductase which is essential for aerobic denitrification occurred when the dissolved oxygen (DO) level maintains at 3-10 mg L(-1).

METHODS

To determine whether the ability of isolated strain is exhibited in the bioremediation of polluted drinking source water, the heterotrophic nitrification and aerobic denitrification characteristics of P. mendocina 3-7 under different cultural conditions such as oxygen level, nitrate and organic concentrations were studied from the nitrogenous balance in the paper.

RESULTS AND CONCLUSIONS

By measuring the nitrogen balance in all experiments under different culture conditions, the removal of total organic carbon and ammonium was positively correlated with total nitrogen removal, especially under high substrate level. With substrate concentration decreasing, ammonium and nitrate removal occurred separately, and ammonium was completely utilized first under low substrate concentration. Compared to that under high substrate level, the specific growth rate of P. mendocina 3-7 was not low under the low substrate level and the pollutant removal efficiencies remained high, which implies the stronger nitrogen removal and acclimatization capacities of the strain in oligotrophic niches.

Bacterial adaptation of respiration from oxic to microoxic and anoxic conditions: redox control

Under a shortage of oxygen, bacterial growth can be faced mainly by two ATP-generating mechanisms: (i) by synthesis of specific high-affinity terminal oxidases that allow bacteria to use traces of oxygen or (ii) by utilizing other substrates as final electron acceptors such as nitrate, which can be reduced to dinitrogen gas through denitrification or to ammonium. This bacterial respiratory shift from oxic to microoxic and anoxic conditions requires a regulatory strategy which ensures that cells can sense and respond to changes in oxygen tension and to the availability of other electron acceptors. Bacteria can sense oxygen by direct interaction of this molecule with a membrane protein receptor (e.g., FixL) or by interaction with a cytoplasmic transcriptional factor (e.g., Fnr). A third type of oxygen perception is based on sensing changes in redox state of molecules within the cell. Redox-responsive regulatory systems (e.g., ArcBA, RegBA/PrrBA, RoxSR, RegSR, ActSR, ResDE, and Rex) integrate the response to multiple signals (e.g., ubiquinone, menaquinone, redox active cysteine, electron transport to terminal oxidases, and NAD/NADH) and activate or repress target genes to coordinate the adaptation of bacterial respiration from oxic to anoxic conditions. Here, we provide a compilation of the current knowledge about proteins and regulatory networks involved in the redox control of the respiratory adaptation of different bacterial species to microxic and anoxic environments.

Isolation of aerobic denitrifiers and characterization for their potential application in the bioremediation of oligotrophic ecosystem

In recent years, nitrogen pollution has been increasingly serious in environmental waters in China, especially in drinking source. Seven predominant aerobic denitrifiers were isolated and characterized from the oligotrophic ecosystems. Based on their phenotypic and phylogenetic characteristics, the isolates were identified as the genera of Pseudomonas, Achromobacter and Acinetobacter, and all isolates could express periplasmic nitrate reductase which was essential for the aerobic denitrification. The growth rates of the isolates were at 0.30-0.83 h(-1), and obvious denitrification occurred when the dissolved oxygen (DO) level maintained at 3-10 mg L(-1). The isolates were able to conduct heterotrophic nitrification for realizing completely nitrogen removal in aerobic oligotrophic niche. Furthermore, three strains especially Pseudomonas sp.3-7 showed outstanding capacities of extracellular polymeric substances (EPS) secretion and aggregation. Results demonstrated that the isolation of aerobic denitrifiers favored the bioremediation of oligotrophic ecosystems.

Genetic potential for N2O emissions from the sediment of a free water surface constructed wetland

Removal of nitrogen is a key aspect in the functioning of constructed wetlands. However, incomplete denitrification may result in the net emission of the greenhouse gas nitrous oxide (N(2)O) resulting in an undesired effect of a system supposed to provide an ecosystem service. In this work we evaluated the genetic potential for N(2)O emissions in relation to the presence or absence of Phragmites and Typha in a free water surface constructed wetland (FWS-CW), since vegetation, through the increase in organic matter due to litter degradation, may significantly affect the denitrification capacity in planted areas. Quantitative real-time PCR analyses of genes in the denitrification pathway indicating capacity to produce or reduce N(2)O were conducted at periods of different water discharge. Genetic potential for N(2)O emissions was estimated from the relative abundances of all denitrification genes and nitrous oxide reductase encoding genes (nosZ). nosZ abundance was invariably lower than the other denitrifying genes (down to 100 fold), and differences increased significantly during periods of high nitrate loads in the CW suggesting a higher genetic potential for N(2)O emissions. This situation coincided with lower nitrogen removal efficiencies in the treatment cell. The presence and the type of vegetation, mainly due to changes in the sediment carbon and nitrogen content, correlated negatively to the ratio between nitrate and nitrite reducers and positively to the ratio between nitrite and nitrous oxide reducers. These results suggest that the potential for nitrous oxide emissions is higher in vegetated sediments.

Soil aquifer treatment of artificial wastewater under saturated conditions

A 2000 mm long saturated laboratory soil column was used to simulate soil aquifer treatment under saturated conditions to assess the removal of chemical and biochemical oxygen demand (COD and BOD), dissolved organic carbon (DOC), nitrogen and phosphate, using high strength artificial wastewater. The removal rates were determined under a combination of constant hydraulic loading rates (HLR) and variable COD concentrations as well as variable HLR under a constant COD. Within the range of COD concentrations considered (42 mg L⁻¹-135 mg L⁻¹) it was found that at fixed hydraulic loading rate, a decrease in the influent concentrations of dissolved organic carbon (DOC), biochemical oxygen demand (BOD), total nitrogen and phosphate improved their removal efficiencies. At the high COD concentrations applied residence times influenced the redox conditions in the soil column. Long residence times were detrimental to the removal process for COD, BOD and DOC as anoxic processes and sulphate reduction played an important role as electron acceptors. It was found that total COD mass loading within the range of 911 mg d⁻¹-1780 mg d⁻¹ applied as low COD wastewater infiltrated coupled with short residence times would provide better effluent quality than the same mass applied as a COD with higher concentration at long residence times. The opposite was true for organic nitrogen where relatively high concentrations coupled with long residence time gave better removal efficiency.

Four PCR primers necessary for the detection of periplasmic nitrate reductase genes in all groups of Proteobacteria and in environmental DNA

Generic primers are available for detecting bacterial genes required for almost every reaction of the biological nitrogen cycle, the one notable exception being napA (gene for the molybdoprotein of the periplasmic nitrate reductase) encoding periplasmic nitrate reductases. Using an iterative approach, we report the first successful design of three forward oligonucleotide primers and one reverse primer that, in three separate PCRs, can amplify napA DNA from all five groups of Proteobacteria. All 140 napA sequences currently listed in the NCBI (National Center for Biotechnology Information) database are predicted to be amplified by one or more of these primer pairs. We demonstrate that two pairs of these primers also amplify PCR products of the predicted sizes from DNA isolated from human faeces, confirming their ability to direct the amplification of napA fragments from mixed populations. Analysis of the resulting amplicons by high-throughput sequencing will enable a good estimate to be made of both the range and relative abundance of nitrate-reducing bacteria in any community, subject only to any unavoidable bias inherent in a PCR approach to molecular characterization of a highly diverse target.

Aerobic denitrification in permeable Wadden Sea sediments

Permeable or sandy sediments cover the majority of the seafloor on continental shelves worldwide, but little is known about their role in the coastal nitrogen cycle. We investigated the rates and controls of nitrogen loss at a sand flat (Janssand) in the central German Wadden Sea using multiple experimental approaches, including the nitrogen isotope pairing technique in intact core incubations, slurry incubations, a flow-through stirred retention reactor and microsensor measurements. Results indicate that permeable Janssand sediments are characterized by some of the highest potential denitrification rates (> or =0.19 mmol N m(-2) h(-1)) in the marine environment. Moreover, several lines of evidence showed that denitrification occurred under oxic conditions. In intact cores, microsensor measurements showed that the zones of nitrate/nitrite and O(2) consumption overlapped. In slurry incubations conducted with (15)NO(3)(-) enrichment in gas-impermeable bags, denitrification assays revealed that N(2) production occurred at initial O(2) concentrations of up to approximately 90 microM. Initial denitrification rates were not substantially affected by O(2) in surficial (0-4 cm) sediments, whereas rates increased by twofold with O(2) depletion in the at 4-6 cm depth interval. In a well mixed, flow-through stirred retention reactor (FTSRR), (29)N(2) and (30)N(2) were produced and O(2) was consumed simultaneously, as measured online using membrane inlet mass spectrometry. We hypothesize that the observed high denitrification rates in the presence of O(2) may result from the adaptation of denitrifying bacteria to recurrent tidally induced redox oscillations in permeable sediments at Janssand.

Four novel Arthrobacter species isolated from filtration substrate

Four Gram-positive, non-motile, non-spore-forming bacterial strains, LC4(T), LC6(T), LC10(T) and LC13(T), were isolated from a filtration substrate made from trass, a volcanic rock, and their taxonomic positions were investigated by a polyphasic taxonomic approach. The novel strains grew over a temperature range of 5-40 degrees C, at pH values of 6-11 and in the presence of 3-7 % (w/v) NaCl. A phylogenetic tree based on 16S rRNA gene sequences showed the novel strains formed a distinct evolutionary lineage within the genus Arthrobacter. Chemotaxonomic analyses demonstrated that the major menaquinone was MK-9(H(2)), a menaquinone typical of the Arthrobacter globiformis group. The major fatty acid was anteiso-C(15 : 0) and the major amino acid present in the cell-wall peptidoglycan was l-lysine. These observations supported the affiliation of the novel strains to the genus Arthrobacter. On the basis of their morphological, physiological and genotypic characteristics, the new isolates are considered to represent four novel species of the genus Arthrobacter, for which the names Arthrobacter niigatensis sp. nov. (type strain LC4(T)=IAM 15382(T)=CCTCC AB 206012(T)), Arthrobacter alkaliphilus sp. nov. (type strain LC6(T)=IAM 15383(T)=CCTCC AB 206013(T)), Arthrobacter echigonensis sp. nov. (type strain LC10(T)=IAM 15385(T)=CCTCC AB 206017(T)) and Arthrobacter albidus sp. nov. (type strain LC13(T)=IAM 15386(T)=CCTCC AB 206018(T)) are proposed.

Nitrate attenuation in groundwater: a review of biogeochemical controlling processes

Biogeochemical processes controlling nitrate attenuation in aquifers are critically reviewed. An understanding of the fate of nitrate in groundwater is vital for managing risks associated with nitrate pollution, and to safeguard groundwater supplies and groundwater-dependent surface waters. Denitrification is focused upon as the dominant nitrate attenuation process in groundwater. As denitrifying bacteria are essentially ubiquitous in the subsurface, the critical limiting factors are oxygen and electron donor concentration and availability. Variability in other environmental conditions such as nitrate concentration, nutrient availability, pH, temperature, presence of toxins and microbial acclimation appears to be less important, exerting only secondary influences on denitrification rates. Other nitrate depletion mechanisms such as dissimilatory nitrate reduction to ammonium and assimilation of nitrate into microbial biomass are unlikely to be important in most subsurface settings relative to denitrification. Further research is recommended to improve current understanding on the influence of organic carbon, sulphur and iron electron donors, physical restrictions on microbial activity in dual porosity aquifers, influences of environmental condition (e.g. pH in poorly buffered environments and salinity in coastal or salinized soil settings), co-contaminant influences (particularly the contrasting inhibitory and electron donor influences of pesticides) and improved quantification of denitrification rates in the laboratory and field.

Aerobic TMAO respiration in Escherichia coli

In the absence of oxygen, Escherichia coli can use alternative exogenous electron acceptors, including trimethylamine oxide (TMAO), to generate energy. In this study, we showed that in contrast to the other anaerobic respiratory systems, the TMAO reductase (Tor) system was expressed during both aerobiosis and anaerobiosis. By using a torA-lacZ fusion and quantitative reverse transcription polymerase chain reaction, we established that the torCAD operon encoding the Tor system was induced in the presence of TMAO mainly during exponential phase, and that optimal induction required a certain level of DNA supercoiling. We also showed that the presence of oxygen prevented neither the biogenesis of the Tor system nor the reduction of TMAO. The physiological role of TMAO reduction during aerobiosis has not been yet established, but our experiments suggest that alkaline TMA production could enhance the growth conditions by increasing the pH of the culture.

Two-stage removal of nitrate from groundwater using biological and chemical treatments

In this study, we attempted to treat groundwater contaminated with nitrate using a two-stage removal system: one is biological treatment using the nitrate-degrading bacteria Pseudomonas sp. RS-7 and the other is chemical treatment using a coagulant. For the biological system, the effect of carbon sources on nitrate removal was first investigated using mineral salt medium (MSM) containing 500 mg l(-1) nitrate to select the most effective carbon source. Among three carbon sources, namely, glucose, starch and cellulose, starch at 1% was found to be the most effective. Thus, starch was used as a representative carbon source for the remaining part of the biological treatment where nitrate removal was carried out for MSM solution and groundwater samples containing 500 mg l(-1) and 460 mg l(-1) nitrate, respectively. About 86% and 89% of nitrate were removed from the MSM solution and groundwater samples, respectively at 72 h. Chemical coagulants such as alum, lime and poly aluminium chloride were tested for the removal of nitrate remaining in the samples. Among the coagulants, lime at 150 mg l(-1) exhibited the highest nitrate removal efficiency with complete disappearance for the MSM solutions. Thus, a combined system of biological and chemical treatments was found to be more effective for the complete removal of nitrate from groundwater.

Relative abundances of proteobacterial membrane-bound and periplasmic nitrate reductases in selected environments

Dissimilatory nitrate reduction is catalyzed by a membrane-bound and a periplasmic nitrate reductase. We set up a real-time PCR assay to quantify these two enzymes, using the narG and napA genes, encoding the catalytic subunits of the two types of nitrate reductases, as molecular markers. The narG and napA gene copy numbers in DNA extracted from 18 different environments showed high variations, with most numbers ranging from 2 x 10(2) to 6.8 x 10(4) copies per ng of DNA. This study provides evidence that, in soil samples, the number of proteobacteria carrying the napA gene is often as high as that of proteobacteria carrying the narG gene. The high correlation observed between narG and napA gene copy numbers in soils suggests that the ecological roles of the corresponding enzymes might be linked.

Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments

Estuarine systems are the major conduits for the transfer of nitrate from agricultural and other terrestrial-anthropogenic sources into marine ecosystems. Within estuarine sediments some microbially driven processes (denitrification and anammox) result in the net removal of nitrogen from the environment, while others (dissimilatory nitrate reduction to ammonium) do not. In this study, molecular approaches have been used to investigate the diversity, abundance, and activity of the nitrate-reducing communities in sediments from the hypernutrified Colne estuary, United Kingdom, via analysis of nitrate and nitrite reductase genes and transcripts. Sequence analysis of cloned PCR-amplified narG, napA, and nrfA gene sequences showed the indigenous nitrate-reducing communities to be both phylogenetically diverse and also divergent from previously characterized nitrate reduction sequences in soils and offshore marine sediments and from cultured nitrate reducers. In both the narG and nrfA libraries, the majority of clones (48% and 50%, respectively) were related to corresponding sequences from delta-proteobacteria. A suite of quantitative PCR primers and TaqMan probes was then developed to quantify phylotype-specific nitrate (narG and napA) and nitrite reductase (nirS and nrfA) gene and transcript numbers in sediments from three sites along the estuarine nitrate gradient. In general, both nitrate and nitrite reductase gene copy numbers were found to decline significantly (P < 0.05) from the estuary head towards the estuary mouth. The development and application, for the first time, of quantitative reverse transcription-PCR assays to quantify mRNA sequences in sediments revealed that transcript numbers for three of the five phylotypes quantified were greatest at the estuary head.

Concurrent nitrite oxidation and aerobic denitrification in activated sludge exposed to volatile fatty acids

The goal of this research was to investigate the simultaneous occurrence of nitrification and denitrification by activated sludge exposed to volatile fatty acids (VFAs) during aerobic wastewater treatment using a single-stage reactor. A mixture of VFAs was spiked directly into a continuous-stirred tank reactor (CSTR) to assess subsequent impacts on nitrite removal, nitrate formation, CO(2) fixation, total bacterial density, and dominant nitrite oxidizing bacteria (NOB) concentration (i.e., Nitrospira). The activity of the periplasmic nitrate reductase (NAP) enzyme and the presence of nap gene were also measured. A rapid decrease in the nitrate formation rate (>70% reduction) was measured for activated sludge exposed to VFAs; however, the nitrite removal rate was not reduced. The total bacterial density and Nitrospira concentration remained essentially constant; therefore, the reduction in nitrate formation rate was likely not due to heterotrophic uptake of nitrogen or to a decrease in the dominant NOB population. Additionally, VFA exposure did not impact microbial CO(2) fixation efficiency. The activity of NAP enzyme increased in the presence of VFAs suggesting that nitrate produced as a consequence of nitrite oxidation was likely further reduced to gaseous denitrification products via catalysis by NAP. Little, if any, nitrogen was discharged in the aqueous effluent of the CSTR after exposure to VFAs demonstrating that activated sludge treatment yielded compounds other than those typically produced solely by nitrification.

A membrane-bound nitrate reductase encoded by the narGHJI operon is responsible for anaerobic respiration in Halomonas maura

The halophilic bacterium Halomonas maura is capable of anaerobic respiration on nitrates. By insertional mutagenesis with the minitransposon Tn-5 we obtained the mutant Tc62, which was incapable of anaerobic respiration on nitrates. An analysis of the regions adjacent to the transposon allowed us to characterize the membrane-bound anaerobic-respiratory nitrate reductase narGHJI gene cluster in H. maura. We identified consensus sequences for fumarate and nitrate reductase regulator (FNR)-like protein-binding sites in the promoter regions of the nar genes and consensus sequences corresponding to the NarL binding sites upstream of the nar genes. RT-PCR analysis showed that the narGHJI operon was expressed in response to anaerobic conditions when nitrate was available as electron acceptor. This membrane-bound nitrate reductase is the only enzyme responsible for anaerobic respiration on nitrate in H. maura. In this article we discuss the possible relationship between this enzyme and a dissimilatory nitrate-reduction-to-ammonia process (DNRA) in H. maura and its role in the colonization of the rhizosphere.

Finding the missing link between diversity and activity using denitrifying bacteria as a model functional community

The recent development and application of numerous methods mainly based on 16S rDNA analyses have brought insights into the questions of which and how many bacterial populations can be found in a given ecosystem. A new and challenging question for microbial ecologists has emerged from the exploration of this diversity: what is its significance for ecosystem functioning? We propose the denitrifying bacteria as a model microbial community for understanding the relationship between community structure and activity, and have summarized the recent progress in studies of this functional community.

Nitrate reduction in the presence of wüstite

Recent strategies to reduce elevated nitrate concentrations employ metallic Fe0 as a reductant. Secondary products of Fe0 corrosion include magnetite (Fe3O4), green rust [Fe6(OH)12SO4], and wüstite [FeO(s)]. To our knowledge, no studies have been reported on the reactivity of NO3- with FeO(s). This project was initiated to evaluate the reactivity of FeO(s) with NO3- under abiotic conditions. Stirred batch reactions were performed in an anaerobic chamber over a range of pH values (5.45, 6.45, and 7.45), initial FeO(s) concentrations (1, 5, and 10 g L(-1)), initial NO3- concentrations (1, 10, and 15 mM), and temperatures (3, 21, 31, and 41 degrees C) for kinetic and thermodynamic determinations. Suspensions were periodically removed and filtered to measure dissolved nitrogen and iron species. Solid phases were characterized using X-ray diffraction (XRD) and scanning electron microscopy (SEM). Nitrate reduction by FeO was rapid and characterized by nearly stoichiometric conversion of NO3- to NH4+. Transient NO2- formation also occurred. The XRD and SEM results indicated the formation of Fe3O4 as a reaction product of the heterogeneous redox reaction. Kinetics of NO3- reduction suggested a rate equation of the type: -d[NO3-]/dt = k[FeO]0.57[H]0.22[NO3-]1.12 where k = 3.46 x 10(-3) +/- 0.38 x 10(-3) M(-1) s(-1), at 25 degrees C. Arrhenius and Eyring plots indicate that the reaction is surface chemical-controlled and proceeds by an associative mechanism involving a step where both NO3- and FeO(s) bind together in an intermediate complex.