narG Genes Research Articles

Denitrifying phosphorus removal from municipal wastewater and dynamics of “Candidatus Accumulibacter” and denitrifying bacteria based on genes of ppk1, narG, nirS and nirK

Relevance of clade-level population dynamics of “Candidatus Accumulibacter” to performance of denitrifying phosphorus (P) removal from municipal wastewater was investigated. Stable denitrifying P removal in anoxic zone of continuous-flow reactor was achieved, accounting for 90% of total P removal. Clades IIC and IIF affiliated with Accumulibacter lineage were the dominant clades during denitrifying P removal, reaching 90% of ppk1 clone library. NarG gene library indicated Gamma and Beta-proteobacteria played an important role in nitrate reduction. Diversity and abundance of nirS library was much more than nirK, and thus became the main functional gene to execute nitrite reduction. Based on abundance of nirS, nirK and ppk1, the ratio of Accumulibacter capable of denitrifying P removal to total Accumulibacter was 22%. No matter whether Accumulibacter had narG gene or not, high abundance of narG at a level of 109cells/(g dried-sludge) promoted nitrate reduced to nitrite, ensuring performance of denitrifying P removal.

Nitrate and ammonia as nitrogen sources for deep subsurface microorganisms.

We investigated the N-utilizing bacterial community in anoxic brackish groundwater of the low and intermediate level nuclear waste repository cave in Olkiluoto, Finland, at 100 m depth using 15N-based stable isotope probing (SIP) and enrichment with 14∕15N-ammonium or 14∕15N-nitrate complemented with methane. Twenty-eight days of incubation at 12°C increased the concentration of bacterial 16S rRNA and nitrate reductase (narG) gene copies in the substrate amended microcosms simultaneously with a radical drop in the overall bacterial diversity and OTU richness. Hydrogenophaga/Malikia were enriched in all substrate amended microcosms and Methylobacter in the ammonium and ammonium+methane supplemented microcosms. Sulfuricurvum was especially abundant in the nitrate+methane treatment and the unamended incubation control. Membrane-bound nitrate reductase genes (narG) from Polarimonas sp. were detected in the original groundwater, while Burkholderia, Methylibium, and Pseudomonas narG genes were enriched due to substrate supplements. Identified amoA genes belonged to Nitrosomonas sp. 15N-SIP revealed that Burkholderiales and Rhizobiales clades belonging to the minority groups in the original groundwater used 15N from ammonium and nitrate as N source indicating an important ecological function of these bacteria, despite their low number, in the groundwater N cycle in Olkiluoto bedrock system.

Enhanced long-term nitrogen removal and its quantitative molecular mechanism in tidal flow constructed wetlands.

Tidal flow constructed wetlands (TF CWs) have recently been studied as a sustainable technology to achieve enhanced nitrogen removal; however, the underlying mechanisms responsible for removing ammonium (NH4(+)) and nitrate (NO3(-)) have not been compared and quantified at the molecular level (genes) in controlled TF CWs. In this study, two TF CWs T1 (treating NH4(+) wastewater) and T2 (treating NO3(-) wastewater) achieved high removal efficiencies for chemical oxygen demand (COD, 92 ± 2.7% and 95 ± 2.4%, respectively), NH4(+)/NO3(-) (76 ± 3.9% and 97 ± 2.2%, respectively), and total nitrogen (TN, 81 ± 3.5% and 93 ± 2.3%, respectively). Combined analyses revealed that the presence of simultaneous nitrification, anammox, and denitrification processes and the coupling of dissimilatory nitrate reduction to ammonium, ammonia oxidation, and anammox were the primary reason accounted for the robust treatment performance in T1 and T2, respectively. Results from stepwise regression analysis suggested that the NH4(+) removal rate in T1 was collectively controlled by amoA, nxrA, and anammox, while the NO3(-) removal rate in T2 was governed by nxrA and narG gene.

Functional-Structural Analysis of Nitrogen-Cycle Bacteria in a Hypersaline Mat from the Omani Desert

Potential rates of ammonia oxidation, denitrification and anammox were measured in a hypersaline microbial mat. Ammonia oxidation and denitrification had potential rates of 0.8 ± 0.4 and 2.0 ± 1.0 nmol N g−1 h−1, respectively, anammox was not detectable. The rate of N2O production under anoxic conditions accounted for ca. 5% of total denitrification. Using qPCR, the ammonia-oxidation (amoA) genes of gammaproteobacteria had the highest copy number. The denitrification genes narG and nirS exhibited comparable estimates. Sequences of nirS gene were novel, whereas nirK sequences were related to sequences from the Rhizobiales group. Sequences of the nosZ gene were the most diverse and clustered with sequences from various genera. Our results demonstrate that the hypersaline mat from Oman harbors nitrifying and denitrifying bacteria with the potential to perform respective processes at detectable rates.

Response of Ammonium-Oxidizing (amoA) and Nitrate-Reducing (narG) Gene Abundances in Groundwater to Land Use Change

This study examines the effects of land use change on nitrate concentration and the abundances of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and narG-containing denitrifiers in shallow groundwater. The results reveal a general increase of nitrate in shallow groundwater following the change of land use from paddy fields to vegetable patches. Furthermore, a significant relationship between NO3−-N concentrations was observed both in groundwater and in soil at soil depths of 0–20, 20–40, 40–60, 60–80, and 80–100 cm. With regard to gene abundance in groundwater, the AOB amoA gene was most abundant and the AOA amoA gene copy numbers were lowest from the field with long-term paddy cultivation compared with the field under vegetable cultivation. The narG gene copy numbers were higher from the field under short-term vegetable cultivation compared with fields under long-term vegetable cultivation. The NO3−-N concentrations in groundwater correlated positively with AOA amoA gene copy numbers, negatively with the AOB amoA gene, but with no significant relationship with the narG gene. In conclusion, land use change from paddy fields to vegetable patches increases nitrate in groundwater, which is correlated significantly with nitrate in soil and the abundance of the amoA gene, but is not related to the narG gene in groundwater. This study also suggests that the removal of groundwater nitrate pollution is not feasible through biological denitrification without additional denitrifiers and that it might even become more aggravated because of the AOA.

Denitrifier Community in the Oxygen Minimum Zone of a Subtropical Deep Reservoir

Denitrification is an important pathway for nitrogen removal from aquatic systems and this could benefit water quality. However, little is known about the denitrifier community composition and key steps of denitrification in the freshwater environments, and whether different bacteria have a role in multiple processes of denitrification reduction. In this study, quantitative PCR, quantitative RT-PCR, clone library and 454 pyrosequencing were used together to investigate the bacterial and denitrifier community in a subtropical deep reservoir during the strongly stratified period. Our results indicated that the narG gene recorded the highest abundance among the denitrifying genes (2.76×109 copies L−1 for DNA and 4.19×108 copies L−1 for RNA), and the lowest value was nosZ gene (7.56×105 copies L−1 for DNA and undetected for RNA). The RNA: DNA ratios indicated that narG gene was the most active denitrifying gene in the oxygen minimum zone of Dongzhen Reservoir. Further, α-, β- and γ- Proteobacteria were the overwhelmingly dominant classes of denitrifier communities. Each functional gene had its own dominant groups which were different at the genus level: the narG gene was dominated by Albidiferax, while nirS gene was dominated by Dechloromonas. The main OTU of nirK gene was Rhodopseudomonas palustris, but for norB and nosZ genes, they were Bacillus and Bradyrhizobium, respectively. These results contribute to the understanding of linkages between denitrifier community, function and how they work together to complete the denitrification process. Studies on denitrifier community and activity may be useful in managing stratified reservoirs for the ecosystem services and aiding in constructing nitrogen budgets.

Effect of soil moisture status and a nitrification inhibitor, dicyandiamide, on ammonia oxidizer and denitrifier growth and nitrous oxide emissions in a grassland soil

Nitrous oxide (N2O) is a potent greenhouse gas and is produced in the soil by nitrification and denitrification processes. These processes are catalysed by a number of key enzymes from microbial communities in the soil. In grazed pasture soils, most of the N2O is emitted from nitrogen (N) returned in animal excreta deposited during outdoor grazing, particularly in the urine. The nitrification inhibitor, dicyandiamide (DCD), has been used to mitigate N2O emissions from grazed pasture soils. However, how the nitrifying and denitrifying communities and N2O emissions are affected by the urine and DCD applications under contrasting soil moisture conditions in grazed pasture soils is poorly understood. Here we report a laboratory incubation study to determine the impact of soil moisture status in combination with animal urine and DCD applications on the abundance of ammonia oxidizer (AO) and denitrifier functional genes, and N2O emissions from a grazed pasture soil. The soil used was a Horotiu silt loam (Typic Udivitrand) developed from volcanic ash. The treatments included three soil moisture contents: 60%, 100% and 130% field capacity (FC), each with Control, Urine and Urine + DCD treatments. The incubation temperature was 12 °C to simulate New Zealand autumn/winter soil temperatures (when DCD is used). Results showed that soil moisture significantly increased N2O emissions from the urine treated soil, with total N2O emissions at 100% and 130% FC being 9 and 400 times that at 60% FC, respectively. Soil moisture content also significantly affected the growth of ammonia oxidiser and denitrifier communities, with the functional genes increasing with increased soil moisture content. The application of urine significantly increased the abundance of AOB amoA, nirK and nosZ (clades I and II) genes, but decreased the abundance of AOA amoA and narG genes at 130% FC. DCD was highly effective in inhibiting the growth of AOB communities, and reducing N2O emissions at 100% and 130% FC. The abundance of nirK gene was also reduced by DCD at 130% FC, but this was, most likely, a reflection of changes in AOB populations, bearing the majority of the nirK gene detected in this study. DCD did not affect the other denitrifier genes studied. Total N2O emissions were significantly related to the abundance of AOB (R2 = 0.94, p < 0.001) and nirK genes (R2 = 0.57, p < 0.05), but not to the other genes studied. These results suggest that soil moisture has a major influence on ammonia oxidizing and denitrifying microbial communities in urine treated soils and that this affects the N2O emissions. Ammonia oxidizers are able to grow under very wet soil conditions, probably in part due to the growth of AOB communities that also carry the nirK gene.

Identification of Anaerobic Bacteria in patients with Rheumatoid Arthritis

Background & Objective: There is a report about the 2-5% prevalence for septic arthritis by anaerobic bacteria. The relevance between synovitis and intestinal microbial flora has been a hypothesis for ten years. The PCR with sensitivity and specificity 99% for microorganism detection in acute, chronic and relapse forms of septic arthritis is helpful. In this research we aimed to diagnose intestinal anaerobic bacteria which are able to occur in bacteremia or septicemia. Methods: The amplification of the 16srRNA and narG genes of anaerobic bacteria was carried out by three PCR reactions. Here we used universal primers for their detection. Results: From 100 patients with septic arthritis, 61% were bacterial arthritis and 18% were infected by anaerobic bacteria.

Effects of grazing on N2O production potential and abundance of nitrifying and denitrifying microbial communities in meadow-steppe grassland in northern China

PurposeThe aim of this study was to investigate the effects of cattle grazing on the nitrous oxide (N2O) production potential from meadow-steppe grassland soil in northern China, and the relationship between cattle grazing and the abundance of different functional microbial genes for potential of N2O emissions. Materials and methodsWe collected soil samples at a depth of 0–20 cm over six times during two plant growing seasons in 2011 and 2012 on a native Leymus chinensis grassland. At each of the six sampling occasions, soil samples were taken from three pairs of the cattle grazed vs. ungrazed plots. We then determined (1) the soil moisture, pH, total carbon and nitrogen, and mineral N (NH4+ and NO3−) content, (2) the potential rates of N2O production from nitrification (NN2O) and from denitrification (DN2O and DN2) using the acetylene inhibition method, and (3) the abundance of the amoA (ammonia monooxygenase) gene of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), the narG (nitrate reductase) gene and nosZ (nitrous oxide reductase) gene using quantitative real-time PCR (qPCR). The relationship among the changes in the N2O production potential rates, the abundance of microbial functional groups and the soil environment was analyzed using mix effects modeling and structural equation modeling. Results and discussionThe AOA, AOB, narG, nosZ genes and the potential N2O production rate all varied significantly with the season (P < 0.01). Grazing induced an overall reduction in soil moisture (P < 0.05) and soil total N in 2012 (P < 0.05), and a significant increase in the abundance of AOB genes (P < 0.05); but no significant difference between grazing treatments was found on the abundance of AOA, narG and nosZ genes, or on the NN2O and DN2O.Approximately 80% of the variation in NN2O could be explained by the abundance of AOA and AOB genes (P < 0.0001), which in turn was explained by soil NH4+ content and soil moisture; The abundance of narG gene, along with total C, NO3− content and soil moisture, explained 87% of variation in the DN2 (P < 0.0001). The abundance of narG gene was related to the production of N gases from denitrification (DN2O+N2), but not the DN2O. Soil moisture was the best predictor for DN2O. ConclusionsThe abundance of amoA and narG genes are good indicators for the potential nitrification and denitrification rates in the meadow steppe grassland. Soil moisture is the most important factor controlling the N2O emission potential in the meadow-steppe grassland. The grassland soils protected from animal grazing or that under a moderate grazing for five years did not show a significant difference in potential N2O emissions. Our results suggest that grazing induced grassland degradation may not necessarily be associated with a reduction in N2O emissions as reported in other semiarid grasslands in a more arid environment.

Chironomus plumosus larvae increase fluxes of denitrification products and diversity of nitrate-reducing bacteria in freshwater sediment

Benthic invertebrates affect microbial processes and communities in freshwater sediment by enhancing sediment-water solute fluxes and by grazing on bacteria. Using microcosms, the effects of larvae of the widespread midge Chironomus plumosus on the efflux of denitrification products (N2O and N2+N2O) and the diversity and abundance of nitrate- and nitrous-oxide-reducing bacteria were investigated. Additionally, the diversity of actively nitrate- and nitrous-oxide-reducing bacteria was analyzed in the larval gut. The presence of larvae increased the total effluxes of N2O and N2+N2O up to 8.6- and 4.2-fold, respectively, which was mostly due to stimulation of sedimentary denitrification; incomplete denitrification in the guts accounted for up to 20% of the N2O efflux. Phylotype richness of the nitrate reductase gene narG was significantly higher in sediment with than without larvae. In the gut, 47 narG phylotypes were found expressed, which may contribute to higher phylotype richness in colonized sediment. In contrast, phylotype richness of the nitrous oxide reductase gene nosZ was unaffected by the presence of larvae and very few nosZ phylotypes were expressed in the gut. Gene abundance of neither narG, nor nosZ was different in sediments with and without larvae. Hence, C. plumosus increases activity and diversity, but not overall abundance of nitrate-reducing bacteria, probably by providing additional ecological niches in its burrow and gut.

Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents

Over the past few years the relevance of nitrate respiration in microorganisms from deep-sea hydrothermal vents has become evident. In this study, we surveyed the membrane-bound nitrate reductase (Nar) encoding gene in three different deep-sea vent microbial communities from the East Pacific Rise and the Mid-Atlantic Ridge. Additionally, we tested pure cultures of vent strains for their ability to reduce nitrate and for the presence of the NarG-encoding gene in their genomes. By using the narG gene as a diagnostic marker for nitrate-reducing bacteria, we showed that nitrate reductases related to Gammaproteobacteria of the genus Marinobacter were numerically prevalent in the clone libraries derived from a black smoker and a diffuse flow vent. In contrast, NarG sequences retrieved from a community of filamentous bacteria located about 50 cm above a diffuse flow vent revealed the presence of a yet to be identified group of enzymes. 16S rRNA gene-inferred community compositions, in accordance with previous studies, showed a shift from Alpha- and Gammaproteobacteria to Epsilonproteobacteria as the vent fluids become warmer and more reducing. Based on these findings, we argue that Nar-catalyzed nitrate reduction is likely relevant in temperate and less reducing environments where Alpha- and Gammaproteobacteria are more abundant and where nitrate concentrations reflect that of background deep seawater.

Impacts of silver nanoparticles on cellular and transcriptional activity of nitrogen‐cycling bacteria

The widespread use of silver nanoparticles (AgNPs) raises the potential for environmental releases that could impact microbial ecosystem services. In the present study, the authors address how the AgNPs and Ag(+) that they release may impact nitrogen-cycling bacteria. The authors studied the cellular and transcriptional response of the denitrifier Pseudomonas stutzeri, the nitrogen fixer Azotobacter vinelandii, and the nitrifier Nitrosomonas europaea exposed to 35 nm (carbon-coated) AgNPs or to Ag(+) (added as AgNO3 ). Based on minimum inhibitory concentrations (MICs), Ag(+) was 20 times to 48 times more toxic to the tested strains than AgNPs (including Ag(+) released during exposure). Exposure to sublethal concentrations of AgNPs or Ag(+) (representing 10% of the respective MIC for AgNO3 ) resulted in no significant effect on the expression of the denitrifying genes narG, napB, nirH, and norB in P. stutzeri or the nitrogen-fixing genes nifD, nifH, vnfD, and anfD in A. vinelandii, whereas nitrifying genes (amoA1 and amoC2) in N. europaea were upregulated (2.1- to 3.3-fold). This stimulatory effect disappeared at higher silver concentrations (60% of the Ag(+) MIC), and toxicity was exerted at concentrations higher than 60% of the Ag(+) MIC. The MIC for N. europaea was 8 times to 24 times lower than for the other strains, indicating higher susceptibility to AgNPs. This was corroborated by the lower half-lethal concentration for N. europaea (87 µg/L) compared with P. stutzeri (124 µg/L) and A. vinelandii (>250 µg/L) when cells were exposed with Ag(+) for 24 h in 1 mM bicarbonate buffer. This suggests that ammonia oxidation would be the most vulnerable nitrogen-cycling process in wastewater treatment plants receiving AgNPs and in agricultural soils amended with biosolids that concentrate them.

Comparison of Gene Expression Profiles Between Pansensitive and Multidrug-Resistant Strains of Mycobacterium tuberculosis

Mycobacterium tuberculosis has developed resistance to anti-tuberculosis first-line drugs. Multidrug-resistant strains complicate the control of tuberculosis and have converted it into a worldwide public health problem. Mutational studies of target genes have tried to envisage the resistance in clinical isolates; however, detection of these mutations in some cases is not sufficient to identify drug resistance, suggesting that other mechanisms are involved. Therefore, the identification of new markers of susceptibility or resistance to first-line drugs could contribute (1) to specifically diagnose the type of M. tuberculosis strain and prescribe an appropriate therapy, and (2) to elucidate the mechanisms of resistance in multidrug-resistant strains. In order to identify specific genes related to resistance in M. tuberculosis, we compared the gene expression profiles between the pansensitive H37Rv strain and a clinical CIBIN:UMF:15:99 multidrug-resistant isolate using microarray analysis. Quantitative real-time PCR confirmed that in the clinical multidrug-resistant isolate, the esxG, esxH, rpsA, esxI, and rpmI genes were upregulated, while the lipF, groES, and narG genes were downregulated. The modified genes could be involved in the mechanisms of resistance to first-line drugs in M. tuberculosis and could contribute to increased efficiency in molecular diagnosis approaches of infections with drug-resistant strains.

New Primers for Denaturing Gradient Gel Electrophoresis Analysis of Nitrate-Reducing Bacterial Community in Soil

The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis. In this study, a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay. The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy. Specificity of the primers was determined by excision, amplification, and sequencing of bands resolved by DGGE. A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria. These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.

The spatial distribution of nitrogen removal functional genes in multimedia biofilters for sewage treatment

Real-time PCR was fist used to quantitatively study the spatial distribution of the absolute abundance, relative abundance, and relative richness of amoA, nxrA, narG, napA, nirK, qnorB, nosZ, nas, and nifH genes and anaerobic ammonium oxidation (anammox, or ANO) bacteria in four multimedia biofilters. The results showed that these multimedia biofilters could provide NH4+ and total nitrogen (TN) average removal efficiencies of 88%. Except for nifH, ANO and the other nitrogen removal functional genes all were dominantly enriched in different zones. In fact, ANO, napA, qnorB, nosZ, and nxrA were enriched by 5.6–330.1 times; and nirK, narG, amoA, and nas were enriched by 1.4–2.1 times. In addition, ANO, napA, qnorB, and nosZ showed partially or mutually beneficial cooperation. The nxrA and nirK genes showed protocooperation, and the amoA and narG genes showed partially beneficial cooperation.

Capacity for nitrate respiration as a new aspect of metabolism of the filamentous sulfur bacteria of the genus Thiothrix

Capacity of Thiothrix species (T. lacustris strains AS and BLT, T. caldifontis G1T, T. unzii A1T, and T. eikelboomii AR3T) for anaerobic respiration in the presence of nitrate was discovered. The dynamics of nitrate reduction to nitrite was studied and the coupling of this process to thiosulfate oxidation was shown. The investigated Thiothrix representatives performed anaerobic thiosulfate-dependent reduction of nitrate only to nitrite. The presence of the narG gene, encoding the α-subunit of respiratory nitrate reductase NarGHI, was revealed in the cells. The induction of this gene expression was shown for the T. lacustris strain AS under anaerobic conditions of growth. The activity of several enzymes involved in the conversion of reduced sulfur compounds was determined.

Higher nitrate-reducer diversity in macrophyte-colonized compared to unvegetated freshwater sediment

Freshwater macrophytes stimulate rhizosphere-associated coupled nitrification–denitrification and are therefore likely to influence the community composition and abundance of rhizosphere-associated denitrifiers and nitrate reducers. Using the narG gene, which encodes the catalytic subunit of the membrane-bound nitrate reductase, as a molecular marker, the community composition and relative abundance of nitrate-reducing bacteria were compared in the rhizosphere of the freshwater macrophyte species Littorella uniflora and Myriophyllum alterniflorum to nitrate-reducing communities in unvegetated sediment. Microsensor analysis indicated a higher availability of oxygen in the rhizosphere compared to unvegetated sediment, with a stronger release of oxygen from the roots of L. uniflora compared to M. alterniflorum. Comparison of narG clone libraries between samples revealed a higher diversity of narG phylotypes in association with the macrophyte rhizospheres compared to unvegetated sediment. Quantitative PCR targeting narG- and 16S rRNA-encoding genes pointed to a selective enrichment of narG gene copies in the rhizosphere. The results suggested that the microenvironment of macrophyte rhizospheres, characterized by the release of oxygen and labile organic carbon from the root system, had a stimulating effect on the diversity and relative abundance of rhizosphere-associated nitrate reducers.

Denitrifying communities differentially respond to flooding drying cycles in paddy soils

Paddy soils are an important source of nitrous oxide (N2O) emission, especially during frequent flooding and drying cycles. The N2O flux from paddy soils is mainly driven by denitrifying microorganisms, but the response of denitrifying communities to flooding drying cycles has been little studied. N2O emission was monitored under laboratory conditions in two paddy soils. Quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to determine the abundance and community composition of narG- and nosZ-genes in denitrifiers. The N2O emission was more significantly related to soil Eh than soil water content during the drying process. Significant increases in the copy number and obvious alterations in the community composition of both narG- and nosZ-containing denitrifiers were detected after only one day of drying. Among the two denitrifying communities, narG gene abundance was significantly correlated to both Eh and water content, whereas nosZ was only significantly correlated to water content during the flooding drying process, indicating that different responses among various denitrifiers occurred in flooding and drying cycles. Furthermore, narG copy number varied following the flooding drying cycles, where drying caused an obvious increase and flooding caused a decrease in numbers. However, despite the first drying phase resulting in a significant increase in nosZ copy number, further flooding and drying cycles did not cause any remarkable changes compared to the first drying. The narG-containing denitrifiers were much more closely correlated with the N2O flux than nosZ-containing communities in the flooding drying cycles in the paddy soils studied here.

Physiological response of Desulfurispirillum indicum S5 to arsenate and nitrate as terminal electron acceptors

The ability of anaerobic prokaryotes to employ different terminal electron acceptors for respiration enables these organisms to flourish in subsurface ecosystems. Desulfurispirillum indicum strain S5 is an obligate anaerobic bacterium that is able to grow by respiring a range of different electron acceptors, including arsenate and nitrate. Here, we examined the growth, electron acceptor utilization, and gene expression of D. indicum growing under arsenate and nitrate-reducing conditions. Consistent with thermodynamic predictions, the experimental results showed that the reduction of nitrate to ammonium yielded higher cell densities than the reduction of arsenate to arsenite. However, D. indicum grew considerably faster by respiration on arsenate compared with nitrate, with doubling times of 4.3 ± 0.2 h and 19.2 ± 2.0 h, respectively. Desulfurispirillum indicum growing on both electron acceptors exhibited the preferential utilization of arsenate before nitrate. The expression of the arsenate reductase gene arrA was up-regulated approximately 100-fold during arsenate reduction, as determined by qRT-PCR. Conversely, the nitrate reductase genes narG and napA were not differentially regulated under the conditions tested. The results of this study suggest that physiology, rather than thermodynamics, controls the growth rates and hierarchy of electron acceptor utilization in D. indicum.

Influence of depth and time on diversity of free-living microbial community in the variably saturated zone of a granitic aquifer

We investigated the temporal and vertical changes in the microbial communities related to hydrological variations an aquifer (Brittany, France). Five water samplings were carried out, spanning three hydrological cycles in the variably and the permanently saturated zones. Seasonal variations in the major anion concentrations (NO3 -, SO4 2- and Cl(-) ) indicated that different physical processes occurred during the recharge process in the two zones. The variably saturated zone is mainly dominated by diffusion and advection processes from the soil, whereas the permanently saturated zone is controlled by moderate advective transfer from the variably saturated zone. Bacterial diversity was investigated by flow cytometry, 16S rRNA and narG genes analyses. Part of this diversity was new in that 6 of the 27 16S rRNA gene sequence phylotypes were unknown even at the class or phylum level. The narG gene analysis did not reveal any clear variation in time or depth within the nitrate reducers' community. In contrast, 16S rRNA gene analyses showed modifications of community composition that could be related to the hydrologic and chemical contrast between the two zones. It was concluded that the physical processes of water transfer could influence bacterial diversity at the soil-aquifer interface.