Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Study of the key biotic and abiotic parameters influencing ammonium removal from wastewaters by Fe3+-mediated anaerobic ammonium oxidation (Feammox)

The release of ammonia (as NH4+) into water bodies causes serious environmental problems. Therefore, the removal of ammonia from wastewater effluents has become a worldwide concern. New autotrophic biological alternatives for ammonia removal could reduce the limitations of conventional organic carbon-dependent nitrification-denitrification methods. Here, the potential of anaerobic ammonium oxidation coupled to Fe3+ reduction (a process known as Feammox) is studied in wastewater treatment plants of the yeast and beer production industry, not related to ammonium or iron treatment. This process is presented as a viable option to improve the efficiency of ammonia removal from wastewater. The results of this study show that enrichments under Feammox conditions achieved removals of 28.19-32.25% of the total NH4+. The highest rates of ammonium removal and Fe3+ reduction were achieved using FeCl3 as iron source and pH = 7.0. Different environmental conditions for the enrichments were studied and it was found that the use of sodium acetate as a carbon source and an incubation temperature of 35 °C presented higher rates of iron reduction and higher increase in nitrate concentration, related to ammonium oxidative processes. Likewise, the presence of relevant species of the iron and nitrogen cycles as Ferrovum myxofaciens, Geobacter spp, Shewanella spp, Albidiferax ferrireducens and Anammox was verified, supporting the findings of this study. These results provide information that may be relevant to the potential applicability of Feammox to treat wastewater with high ammonia load and could help develop cost-effective and environmentally friendly methods for ammonium removal in wastewater treatment plants.

Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia

Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.

Diversity and Quantitative Detection of Clade I Type nosZ Denitrifiers in the Arabian Sea Oxygen Minimum Zone

A significant amount of nitrous oxide (N₂O) is effluxed into the atmosphere as a result of marine denitrification in the Arabian Sea (AS) oxygen minimum zone (OMZ). An assessment of temporal variations in the diversity and abundance of nosZ denitrifiers was performed to establish the relative importance of these bacteria in denitrification. Sampling was conducted at the Arabian Sea Time Series (ASTS) location and a quantitative PCR (qPCR) ana-lysis was performed. We detected a high abundance of the nosZ gene at core OMZ depths (250‍ ‍m and 500 m), indicating the occurrence of denitrification in the AS-OMZ. The maximum abundance of the nosZ gene was observed during the Spring Intermonsoon (SIM) at 250‍ ‍m (1.32×10⁶ copies L^-1) and 500‍ ‍m (1.50×10⁶ copies L^-1). Sequencing ana-lysis showed that nosZ denitrifiers belonged to the classes Alpha-, Beta-, and Gammaproteobacteria. Taxonomic ana-lysis revealed that most OTUs were affiliated with Pseudomonas, Rhodopseudomonas, and Bradyrhizobium. Diversity indices and richness estimators confirmed a higher diversity of nosZ denitrifiers at 250‍ ‍m than at 500‍ ‍m during all three seasons. The present results also indicated that dissolved oxygen (DO) and total organic carbon (TOC) are critical factors influencing the diversity and abundance of the nosZ-denitrifying bacterial community.

Denitrifier communities differ in mangrove wetlands across China

To explore the geographical variations in the nosZ-denitrifier community and the underlying influential factors, surface sediments were collected from six mangroves across China, including Yunxiao (YX), Futian (FT), Fangchenggang (FCG), Zhanjiang (ZJ), Dongzhaigang (DZG), and Dongfang (DF). The nosZ gene abundance in mangrove sediments were 1.60 × 10⁵-1.17 × 10⁶ copies g^-1 dry sediment, with a higher density in Avicennia marina forest than the mudflat. Denitrifier community richness and diversity increased with decreasing latitude based on the Chao1 richness and Shannon diversity index, with the highest diversity being observed in the DF mangrove. The denitrifier communities could be classified into three groups including south DF mangrove, middle FCG, ZJ and DZG mangroves, and north YX and FT mangroves based on HCA and PCoA analysis. The nosZ OTUs could be divided into seven distinct clusters with different proportionality characteristics among mangroves. Environmental factors (TN, TOC, and salinity) collectively shape denitrifier communities in mangrove sediments.

Simultaneous reduction of nitrate and Cr(VI) by Pseudomonas aeruginosa strain G12 in wastewater

The interference of toxic heavy metals in the process of microbial aerobic denitrification is a hot issue in industry wastewater treatment in recent years. In this study, a multifunctional aerobic denitrifying bacterium - Pseudomonas aeruginosa G12 isolated from sewage sludge was used to explore the simultaneous removal ability to NO₃^--N and Cr(VI) in wastewater by a series of batch experiments. The results showed that G12 could effectively remove NO₃^--N (500 mg L^-1) and Cr(VI) (10 mg L^-1) by 98% and 93%, respectively. Meanwhile, the study found that the strain G12 had the potential to adapt to the complex external environment, including different carbon resources, nitrogen sources, and the coexisting heavy metals (Mn²⁺ and Cu²⁺). The strain G12 also had the considerable tolerance to initial NO₃^--N (100-700 mg L^-1) and Cr(VI) (1-20 mg L^-1) concentrations. The instrument analysis methods-Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and X-ray diffraction (XRD), from the molecular level, further confirmed that the strain G12 could remove NO₃^--N by aerobic denitrification, and the reduced functional groups (amino group, amide group, hydroxyl group and carboxyl group) on the surface of bacteria could transform Cr(VI) to Cr(III) (mainly CrCl₃). This study will offer a promising new microbial resource for nitrogen and Cr(VI) removal in industry wastewater treatment.

Effects of combined biochar and organic fertilizer on nitrous oxide fluxes and the related nitrifier and denitrifier communities in a saline-alkali soil

This study intended to evaluate the combined effects of both biochar and organic fertilizer on nitrous oxide (N₂O) fluxes and composition of nitrifier and denitrifier of saline-alkali soil. Therefore, four different treatments such as CK (only chemical fertilizer), B (only biochar), M (only organic fertilizer), BM (B:M = 1:1) were used in this experiment. The results showed that N₂O emissions were decreased in B and BM treatments compare to the control. In contrast, N₂O emissions were highest before day 12 but lowest after day 19 in M treatment compare to the control. Application of biochar, organic fertilizer and biochar plus organic fertilizer decreased the nirS and nirK genes copies and enhanced the nosZ gene copies which resulting in the lower N₂O fluxes. The ammonia-oxidizing bacteria (AOB) amoA and nirK genes copies were significantly increased by organic fertilizer before day 12, leading to high N₂O emissions. The genera Nitrosospira (AOB) and Nitrososphaera (ammonia-oxidizing archaea, AOA) assumed absolute superiority. Additionally, Nitrosospira (AOB) was also appeared in nirK-type denitrifiers, illustrating denitrification was carried out by nitrifiers. The genera Azospirillum (nirS), Burkholderia (nosZ) and Polymorphum (nosZ) were dominant in CK. There was only one dominant genus, Mesorhizobium (nosZ) in the B treatment. The genera Mesorhizobium (nirK), Azoarcus (nirS), Kocuria (nirS) and Pseudomonas (nosZ) occupied the main status in the M treatment. The relative abundance of Rhodanobacter (nirS) and Azospirillum (nosZ) were higher in the BM treatment compared with other treatments. Soil water content (SWC), pH, NH₄⁺-N and NO₃^--N were the main factors affecting AOB and denitrifiers, which influencing N₂O emissions. Overall, combined application of biochar and organic fertilizer can reduce the N₂O emission where AOB and nirK-type denitrifier were the main contributors to the N₂O emission.

Quantitative responses of potential nitrification and denitrification rates to the size of microbial communities in rice paddy soils

Nitrification and denitrification are important to nitrogen balance in agricultural ecosystems. However, the molecular drivers and limiting steps for these microbial processes in rice paddy soils are not well understood. Here, we assessed soil properties and abundances of functional genes affiliated with nitrification (amoA and nxrA), denitrification (nirS, nirK and nosZ), nitrate reduction (narG and napA) processes, and measured potential nitrification and denitrification rates (PNRs and PDRs) at 15 sites in Xiamen, China. The soil properties imposed indirect impacts on the potential rates by mediating the relative abundances of microbial communities. No significant relationships between the size of microbial communities and the potential rates were observed. Instead, we found the variables that best explained the variations in the PNRs and PDRs were AOB/nirS and (nirK + nirS)/nosZ, respectively. The PNRs were mainly limited by the relative strength of two steps, namely bacterial ammonium oxidation and nitrite into nitric oxide reduction, whereas the PDRs were mainly limited by the relative strength of the second and last denitrification steps. These results indicated that the dynamics of microbial communities based on the relative gene abundances are valuable in integrating fluctuations in soil physicochemical properties and are indictive of potential rates in paddy soils. Results of this study contribute to our quantitative understanding of the relative importance of soil physicochemical and biological factors in driving microbial potential in paddy soils.

The effect of bio-irrigation by the polychaete Lanice conchilega on active denitrifiers: Distribution, diversity and composition of nosZ gene

The presence of large densities of the piston-pumping polychaete Lanice conchilega can have important consequences for the functioning of marine sediments. It is considered both an allogenic and an autogenic ecosystem engineer, affecting spatial and temporal biogeochemical gradients (oxygen concentrations, oxygen penetration depth and nutrient concentrations) and physical properties (grain size) of marine sediments, which could affect functional properties of sediment-inhabiting microbial communities. Here we investigated whether density-dependent effects of L. conchilega affected horizontal (m-scale) and vertical (cm-scale) patterns in the distribution, diversity and composition of the typical nosZ gene in the active denitrifying organisms. This gene plays a major role in N2O reduction in coastal ecosystems as the last step completing the denitrification pathway. We showed that both vertical and horizontal composition and richness of nosZ gene were indeed significantly affected when large densities of the bio-irrigator were present. This could be directly related to allogenic ecosystem engineering effects on the environment, reflected in increased oxygen penetration depth and oxygen concentrations in the upper cm of the sediment in high densities of L. conchilega. A higher diversity (Shannon diversity and inverse Simpson) of nosZ observed in patches with high L. conchilega densities (3,185-3,440 ind. m-2) at deeper sediment layers could suggest a downward transport of NO3- to deeper layers resulting from bio-irrigation as well. Hence, our results show the effect of L. conchilega bio-irrigation activity on denitrifying organisms in L. conchilega reefs.

Nitrogen Metabolism Genes from Temperate Marine Sediments

In this study, we analysed metagenomes along with biogeochemical profiles from Skagerrak (SK) and Bothnian Bay (BB) sediments, to trace the prevailing nitrogen pathways. NO₃^- was present in the top 5 cm below the sediment-water interface at both sites. NH₄⁺ increased with depth below 5 cm where it overlapped with the NO₃^- zone. Steady-state modelling of NO₃^- and NH₄⁺ porewater profiles indicates zones of net nitrogen species transformations. Bacterial protease and hydratase genes appeared to make up the bulk of total ammonification genes. Genes involved in ammonia oxidation (amo, hao), denitrification (nir, nor), dissimilatory NO₃^- reduction to NH₄⁺ (nfr and otr) and in both of the latter two pathways (nar, nap) were also present. Results show ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) are similarly abundant in both sediments. Also, denitrification genes appeared more abundant than DNRA genes. 16S rRNA gene analysis showed that the relative abundance of the nitrifying group Nitrosopumilales and other groups involved in nitrification and denitrification (Nitrobacter, Nitrosomonas, Nitrospira, Nitrosococcus and Nitrosomonas) appeared less abundant in SK sediments compared to BB sediments. Beggiatoa and Thiothrix 16S rRNA genes were also present, suggesting chemolithoautotrophic NO₃^- reduction to NO₂^- or NH₄⁺ as a possible pathway. Our results show the metabolic potential for ammonification, nitrification, DNRA and denitrification activities in North Sea and Baltic Sea sediments.

Impact of short-term storage temperature on determination of microbial community composition and abundance in aerated forest soil and anoxic pond sediment samples

Sampling strategy is important for unbiased analysis of the characteristics of microbial communities in the environment. During field work it is not always possible to analyze fresh samples immediately or store them frozen. Therefore, the effect of short-term storage temperature was investigated on the abundance and composition of bacterial, archaeal and denitrifying communities in environmental samples from two different sampling sites. Oxic forest soil and anoxic pond sediment were investigated by measuring microbial abundance (DNA) and transcriptional activity (RNA). Prior to investigating the effect of storage temperature, samples were immediately analyzed, in order to represent the original situation in the habitat. The effect of storage temperature was then determined after 11 days at different low temperatures (room temperature, 4 °C, −22 °C and −80 °C). Community profiling using terminal restriction fragment length polymorphism (T-RFLP) showed no significant differences between the immediately analyzed reference sample and the samples stored at different incubation temperatures, both for DNA and RNA extracts. The abundance of microbial communities was determined using quantitative PCR and it also revealed a stable community size at all temperatures tested. By contrast, incubation at an elevated temperature (37 °C) resulted in changed bacterial community composition. In conclusion, short-term storage, even at room temperature, did not affect microbial community composition, abundance and transcriptional activity in aerated forest soil and anoxic pond sediment.

Loss in microbial diversity affects nitrogen cycling in soil

Microbial communities have a central role in ecosystem processes by driving the Earth's biogeochemical cycles. However, the importance of microbial diversity for ecosystem functioning is still debated. Here, we experimentally manipulated the soil microbial community using a dilution approach to analyze the functional consequences of diversity loss. A trait-centered approach was embraced using the denitrifiers as model guild due to their role in nitrogen cycling, a major ecosystem service. How various diversity metrics related to richness, eveness and phylogenetic diversity of the soil denitrifier community were affected by the removal experiment was assessed by 454 sequencing. As expected, the diversity metrics indicated a decrease in diversity in the 1/10(3) and 1/10(5) dilution treatments compared with the undiluted one. However, the extent of dilution and the corresponding reduction in diversity were not commensurate, as a dilution of five orders of magnitude resulted in a 75% decrease in estimated richness. This reduction in denitrifier diversity resulted in a significantly lower potential denitrification activity in soil of up to 4-5 folds. Addition of wheat residues significantly increased differences in potential denitrification between diversity levels, indicating that the resource level can influence the shape of the microbial diversity-functioning relationship. This study shows that microbial diversity loss can alter terrestrial ecosystem processes, which suggests that the importance of functional redundancy in soil microbial communities has been overstated.

GeoChip-based analysis of the functional gene diversity and metabolic potential of soil microbial communities of mangroves

Mangroves are unique and highly productive ecosystems and harbor very special microbial communities. Although the phylogenetic diversity of sediment microbial communities of mangrove habitats has been examined extensively, little is known regarding their functional gene diversity and metabolic potential. In this study, a high-throughput functional gene array (GeoChip 4.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of microbial communities in mangrove habitats from mangrove national nature reserves in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 4.0 were detected in the mangrove microbial communities, including carbon (C) fixation, C degradation, methane generation, nitrogen (N) fixation, nitrification, denitrification, ammonification, N reduction, sulfur (S) metabolism, metal resistance, antibiotic resistance, and organic contaminant degradation. Detrended correspondence analysis (DCA) of all detected genes showed that Spartina alterniflora (HH), an invasive species, did not harbor significantly different microbial communities from Aegiceras corniculatum (THY), a native species, but did differ from other species, Kenaelia candel (QQ), Aricennia marina (BGR), and mangrove-free mud flat (GT). Canonical correspondence analysis (CCA) results indicated the microbial community structure was largely shaped by surrounding environmental variables, such as total nitrogen (TN), total carbon (TC), pH, C/N ratio, and especially salinity. This study presents a comprehensive survey of functional gene diversity of soil microbial communities from different mangrove habitats/species and provides new insights into our understanding of the functional potential of microbial communities in mangrove ecosystems.

Denitrification and environmental factors influencing nitrate removal in Guaymas Basin hydrothermally altered sediments

We measured potential nitrate removal and denitrification rates in hydrothermally altered sediments inhabited by Beggiatoa mats and adjacent brown oil stained sediments from the Guaymas Basin, Gulf of California. Sediments with Beggiatoa maintained slightly higher rates of potential denitrification than did brown sediments at 31.2 ± 12.1 versus 21.9 ± 1.4 µM N day⁻¹, respectively. In contrast, the nitrate removal rates in brown sediments were higher than those observed in mat-hosting sediments at 418 ± 145 versus 174 ± 74 µM N day⁻¹, respectively. Additional experiments were conducted to assess the responses of denitrifying communities to environmental factors [i.e., nitrate, sulfide, and dissolved organic carbon (DOC) concentration)]. The denitrifying community had a high affinity for nitrate (K_m = 137 ± 91 µM NO3−), in comparison to other environmental communities of denitrifiers, and was capable of high maximum rates of denitrification (V_max = 1164 ± 153 µM N day⁻¹). The presence of sulfide resulted in significantly lower denitrification rates. Microorganisms with the potential to perform denitrification were assessed in these sediments using the bacterial 16S rRNA gene and nitrous oxide reductase (nosZ) functional gene libraries. The bacterial 16S rRNA gene clone library was dominated by Epsilonproteobacteria (38%), some of which (e.g., Sulfurimonas sp.) have a potential for sulfide-dependent denitrification. The nosZ clone library did not contain clones similar to pure culture denitrifiers; these clones were most closely associated with environmental clones.

Comparison of denitrifier communities in the biofilms of bioaugmented and non-augmented zeolite-biological aerated filters

The denitrifier communities of a bioaugmented and non-augmented zeolite-biological aerated filter (Z-BAFs) were investigated and compared because the bioaugmented Z-BAF provided better and more stable treatment efficiency for nitrate and nitrite removal. Terminal restriction fragment length polymorphism (T-RFLP) and reverse transcription T-RFLP (RT-T-RFLP) were applied to analyse the denitrifier community diversity in the biofilm collected from each Z-BAF. The results showed that the bioaugmentation technology favourably changed the indigenous denitrifier community and enhanced denitrification under nitrogen loading shocks. The cDNA clone libraries were developed to explore the active denitrifier community structures of both filters. The results showed that the active denitrifiers in both the bioaugmented and non-bioaugmented Z-BAF belonged to alpha-, beta- and gamma-proteobacteria. However, the sequence of the introduced denitrifier (Paracoccus sp. BW001) was not found in the clone library of the bioaugmented filter, which implied that the removal of nitrate and nitrite was attributed mainly to the indigenous denitrifiers in the adjusted bacterial community in the bioaugmented Z-BAF.

Bacterial communities in the sediments of Dianchi Lake, a partitioned eutrophic waterbody in China

Bacteria play an important role in the decomposition and cycling of a variety of compounds in freshwater aquatic environments, particularly nutrient-rich eutrophic lakes. A unique Chinese eutrophic lake--Dianchi--was selected for study because it has two separate and distinct basins, Caohai with higher organic carbon levels and Waihai with lower organic carbon levels. Sediment bacterial communities were studied in the two basins using samples collected in each season from June 2010 to March 2011. Barcoded pyrosequencing based on the 16 S rRNA gene found that certain common phyla, Proteobacteria, Bacteroidetes, Firmicutes and Chloroflexi, were dominant in the sediments from both basins. However, from the class to genus level, the dominant bacterial groups found in the sediments were distinct between the two basins. Correlation analysis revealed that, among the environmental parameters examined, total organic carbon (TOC) accounted for the greatest proportion of variability in bacterial community. Interestingly, study results suggest that increasing allochthonous organic carbon could enhance bacterial diversity and biomass in the sediment. In addition, analysis of function genes (amoA and nosZ) demonstrated that ammonia-oxidizing bacteria (AOB) were dominant in sediments, with 99% belonging to Nitrosomonas. Denitrifying bacteria were comparatively diverse and were associated with some cultivatable bacteria.

Functional diversity in the denitrifying biofilm of the methanol-fed marine denitrification system at the Montreal Biodome

Nitrate is a serious problem in closed-circuit public aquariums because its accumulation rapidly becomes toxic to many lifeforms. A moving bed biofilm denitrification reactor was installed at the Montreal Biodome to treat its 3,250-m(3) seawater system. Naturally occurring microorganisms from the seawater affluent colonized the reactor carriers to form a denitrifying biofilm. Here, we investigated the functional diversity of this biofilm by retrieving gene sequences related to narG, napA, nirK, nirS, cnorB, and nosZ. A total of 25 sequences related to these genes were retrieved from the biofilm. Among them, the corresponding napA1, nirK1, cnorB9, and nosZ3 sequences were identical to the corresponding genes found in Hyphomicrobium sp. NL23 while the narG1 and narG2 sequences were identical to the two corresponding narG genes found in Methylophaga sp. JAM1. These two bacterial strains were previously isolated from the denitrifying biofilm. To assess the abundance of denitrifiers and nitrate respirers in the biofilm, the gene copy number of all the narG, napA, nirS, and nirK sequences found in biofilm was determined by quantitative PCR. napA1, nirK1, narG1, and narG2, which were all associated with either Methylophaga sp. JAM1 or Hyphomicrobium sp. NL23, were the most abundant genes. The other genes were 10 to 10,000 times less abundant. nirK, cnorB, and nosZ but not napA transcripts from Hyphomicrobium sp. NL23 were detected in the biofilm, and only the narG1 transcripts from Methylophaga sp. JAM1 were detected in the biofilm. Among the 19 other genes, the transcripts of only two genes were detected in the biofilm. Our results show the predominance of Methylophaga sp. JAM1 and Hyphomicrobium sp. NL23 among the denitrifiers detected in the biofilm. The results suggest that Hyphomicrobium sp. NL23 could use the nitrite present in the biofilm generated by nitrate respirers such as Methylophaga sp. JAM1.

Denitrification prevails over anammox in tropical mangrove sediments (Goa, India)

Denitrification, anammox (Anx) and di-nitrogen fixation were examined in two mangrove ecosystems- the anthropogenically influenced Divar and the relatively pristine Tuvem. Stratified sampling at 2 cm increments from 0 to 10 cm depth revealed denitrification as the main process of N₂ production in mangrove sediments. At Divar, denitrification was ∼3 times higher than at Tuvem with maximum activity of 224.51 ± 6.63 nmol N₂ g⁻¹ h⁻¹ at 0-2 cm. Denitrifying genes (nosZ) numbered up to 2 × 10⁷ copies g⁻¹ sediment and belonged to uncultured microorganisms clustering within Proteobacteria. Anammox was more prominent at deeper depths (8-10 cm) mainly in Divar with highest activity of 101.15 ± 87.73 nmol N₂ g⁻¹ h⁻¹ which was 5 times higher than at Tuvem. Di-nitrogen fixation was detected only at Tuvem with a maximum of 12.47 ± 8.36 nmol N₂ g⁻¹ h⁻¹. Thus, in these estuarine habitats prone to high nutrient input, N₂-fixation is minimal and denitrification rather than Anx serves as an important mechanism for counteracting N loading.

Microbiology of nitrogen cycle in animal manure compost

Composting is the major technology in the treatment of animal manure and is a source of nitrous oxide, a greenhouse gas. Although the microbiological processes of both nitrification and denitrification are involved in composting, the key players in these pathways have not been well identified. Recent molecular microbiological methodologies have revealed the presence of dominant Bacillus species in the degradation of organic material or betaproteobacterial ammonia-oxidizing bacteria on nitrification on the surface, and have also revealed the mechanism of nitrous oxide emission in this complicated process to some extent. Some bacteria, archaea or fungi still would be considered potential key players, and the contribution of some pathways, such as nitrifier denitrification or heterotrophic nitrification, might be involved in composting. This review article discusses these potential microbial players in nitrification-denitrification within the composting pile and highlights the relevant unknowns through recent activities that focus on the nitrogen cycle within the animal manure composting process.

Biodegradation of carbazole by the seven Pseudomonas sp. strains and their denitrification potential

Carbazole, one representative of non-alkaline nitrogen heterocyclic compounds, is widespread in the natural environment and harmful to human health. In this research, the seven bacterial strains using carbazole as their sole carbon, nitrogen and energy source were isolated from activated sludge of a coking wastewater treatment plant. All strains efficiently degraded 500 mg/L of carbazole in the medium within 36 h. Based on the DNA sequence and phylogenetic tree analysis, the seven strains were identified as the genera Pseudomonas with different evolutionary pathways. PCR analysis revealed that the seven isolates carried the car gene. Moreover, all of these strains could utilize and transform ammonium and nitrate efficiently, and the six strains except BC043 strain coded the nitrite reductase gene (nirS) and the nitrous oxide reductase (nosZ), that indicated their denitrification ability. All these strains may be useful in the bioremediation of environments contaminated by carbazole.

Kangiella spongicola sp. nov., a halophilic marine bacterium isolated from the sponge Chondrilla nucula

A novel halophilic bacterium of the genus Kangiella was isolated from a marine sponge collected from the Florida Keys, USA. Strain A79T, an aerobic, Gram-negative, non-motile, rod-shaped bacterium, grew in 2–15 % (w/v) NaCl, at a temperature of 10–49 °C and at pH 4.5–10. Phylogenetic analysis placed strain A79T in the family Alcanivoraceae in the class Gammaproteobacteria. Strain A79T showed 98.5 % 16S rRNA gene sequence similarity to Kangiella japonica KMM 3899T, 96.6 % similarity to Kangiella koreensis DSM 16069T and 95.6 % similarity to Kangiella aquimarina DSM 16071T. The major cellular fatty acids were iso-C11 : 0, iso-C11 : 0 3-OH, iso-C15 : 0, iso-C17 : 0 and iso-C17 : 1ω9c and the G+C content of the genomic DNA was 44.9 mol%. On the basis of physiological, chemotaxonomic and phylogenetic comparisons, strain A79T represents a novel species in the genus Kangiella, for which the name Kangiella spongicola sp. nov. is proposed. The type strain is A79T ( = ATCC BAA-2076T = DSM 23219T).

Reassessing PCR primers targeting nirS, nirK and nosZ genes for community surveys of denitrifying bacteria with DGGE

We re-evaluated PCR primers targeting nirS, nirK and nosZ genes for denaturing gradient gel electrophoresis as a tool to survey denitrifying community composition in environmental samples. New primers for both nirS and nosZ were combined with existing primers, while for nirK the previously published F1aCu:R3Cu set was chosen for denaturing electrophoresis. All three sets yielded amplicons smaller than 500 bp and amplified the correct fragment in all environmental samples. The denaturing gradient gel electrophoresis worked satisfactorily for nirK and nosZ, but not for nirS. This was probably due to the multiple melting domains in this particular nirS fragment. From the excised and sequenced bands, only sequences related to the target genes were detected and tree analysis showed that the selected primers acted as broad range primers for each of the three genes. By use of the new nirS primers it was demonstrated that agricultural soil harbours a substantial diversity of nirS denitrifiers.

Denitrifying bacterial community composition changes associated with stages of denitrification in oxygen minimum zones

Denitrification in the ocean is a major sink for fixed nitrogen in the global N budget, but the process is geographically restricted to a few oceanic regions, including three oceanic oxygen minimum zones (OMZ) and hemipelagic sediments worldwide. Here, we describe the diversity and community composition of microbes responsible for denitrification in the OMZ using polymerase chain reaction, sequence and fragment analysis of clone libraries of the signature genes (nirK and nirS) that encode the enzyme nitrite reductase, responsible for key denitrification transformation steps. We show that denitrifying assemblages vary in space and time and exhibit striking changes in diversity associated with the progression of denitrification from initial anoxia through nitrate depletion. The initial denitrifying assemblage is highly diverse, but succession on the scale of 3-12 days leads to a much less diverse assemblage and dominance by one or a few phylotypes. This progression occurs in the natural environment as well as in enclosed incubations. The emergence of dominants from a vast reservoir of rare types has implications for the maintenance of diversity of the microbial population and suggests that a small number of microbial dominants may be responsible for the greatest rates of transformations involving nitrous oxide and global fixed nitrogen loss. Denitrifying blooms, driven by a few types responding to episodic environmental changes and distributed unevenly in time and space, are consistent with the sampling effect model of diversity-function relationships. Canonical denitrification thus appears to have important parallels with both primary production and nitrogen fixation, which are typically dominated by regionally and temporally restricted blooms that account for a disproportionate share of these processes worldwide.

Gut-associated denitrification and in vivo emission of nitrous oxide by the earthworm families megascolecidae and lumbricidae in new zealand

Previous studies have documented the capacity of European earthworms belonging to the family Lumbricidae to emit the greenhouse gas nitrous oxide (N(2)O), an activity attributed primarily to the activation of ingested soil denitrifiers. To extend the information base to earthworms in the Southern Hemisphere, four species of earthworms in New Zealand were examined for gut-associated denitrification. Lumbricus rubellus and Aporrectodea rosea (introduced species of Lumbricidae) emitted N(2)O, whereas emission of N(2)O by Octolasion cyaneum (an introduced species of Lumbricidae) and emission of N(2)O by Octochaetus multiporus (a native species of Megascolecidae) were variable and negligible, respectively. Exposing earthworms to nitrite or nitrate and acetylene significantly increased the amount of N(2)O emitted, implicating denitrification as the primary source of N(2)O and indicating that earthworms emitted dinitrogen (N(2)) in addition to N(2)O. The alimentary canal displayed a high capacity to produce N(2)O when it was supplemented with nitrite, and alimentary canal contents contained large amounts of carbohydrates and organic acids indicative of fermentation (e.g., succinate, acetate, and formate) that could serve as sources of reductant for denitrification. nosZ encodes a portion of the terminal oxidoreductase used in denitrification. The nosZ sequences detected in the alimentary canals of L. rubellus and O. multiporus were similar to those retrieved from soil and were distantly related to sequences of uncultured soil bacteria and genera common in soils (i.e., Bradyrhizobium, Azospirillum, Rhodopseudomonas, Rhodospirillum, Pseudomonas, Oligotropha, and Sinorhizobium). These findings (i) suggest that the capacity to emit N(2)O and N(2) is a general trait of earthworms and not geographically restricted, (ii) indicate that species belonging to different earthworm families (i.e., Megascolecidae and Lumbricidae) may not have equal capacities to emit N(2)O, and (iii) also corroborate previous findings that link this capacity to denitrification in the alimentary canal.

Comparision of nirS, cnorB, MCR genes against water quality parameters to monitor uncontrolled landfills

This study was conducted to investigate the possible relationship between a molecular biological investigation and water quality parameters in monitoring groundwater pollution at the immediate boundary of uncontrolled landfills and their downgradient aquifers, which may consequently facilitate unbiased monitoring for the sites. Two closed landfills, Jicksan and Taejang in Korea, were chosen for this study, where the diversity of the microbial community was characterized and three specific genes, i.e. nirS (nitrite reductase coding gene), cnorB (nitric oxide reductase coding gene) and MCR (methyl coenzyme M reductase coding gene), were quantified. The quantified genes were then compared with conventional water quality parameters. From the analyzed DNA sequences, Proteobacteria phylum was most dominantly observed. A quantitative analysis revealed that the copy numbers (gene abundance) of denitrification enzyme coding genes, i.e. nirS gene and cnorB gene in Jicksan (J) site, are seven and four times, respectively, higher than Taejang (T) site. This simply implied that denitrification was possibly higher in J site than T site. In addition, a methane production enzyme coding gene, i.e. MCR, in a J1 bore immediately bordering the sources in the J site showed the greatest concentration, but it was precipitously decreased in the downgradient direction toward the outer boundary of landfill. A comparative investigation between the copy numbers of three genes, i.e. nirS, cnorB, and MCR, and conventional monitoring parameters, i.e. Cl-, alkalinity, TOC, NH3-N, and NO2-N, showed that they had overall correlation as given by more than 0.99 of the squared correlation coefficient (R2) for almost all of the concerned bores. It was concluded that the comparison between the molecular biological investigation and the conventional groundwater monitoring parameters showed good relationship between them, so that both tools could be more efficiently used for assessing the levels of contamination and prediction of the fate of pollutants, rather than being applied separately.

Diversity surveys and evolutionary relationships of aoxB genes in aerobic arsenite-oxidizing bacteria

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.

Characterization of nitrifying, denitrifying, and overall bacterial communities in permeable marine sediments of the northeastern Gulf of Mexico

Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.

Dynamics of nitrous oxide reductase genes (nosZ) in intertidal rocky biofilms and sediments of the Douro River estuary (Portugal), and their relation to N-biogeochemistry

In this study, temporal variability of nosZ genotypes was evaluated in two intertidal rocky biofilms and two intertidal sediment sites of the Douro River estuary, Portugal. The results were compared to rates of key N-cycle processes and environmental variables to examine possible links between denitrifier community dynamics and N biogeochemistry. Genetic heterogeneity of the nosZ gene was evaluated by terminal restriction fragment length polymorphism analysis (T-RFLP) and by sequencing cloned nosZ gene fragments. Phylogenetic analysis showed that the majority of the nosZ genes detected were most similar to nosZ genes from isolates affiliated with alpha-subclass of the class Proteobacteria. Results revealed low nosZ genotype richness, and hierarchical cluster analysis showed significant differences in the composition of denitrifier communities that inhabit different intertidal environments of the Douro River estuary. Monthly surveys of nosZ genotypes from sandy sediments showed that, while the same T-RFLP peaks were present in all samples, shifts in the relative peak areas of the different nosZ genotypes occurred. Canonical correspondence analysis, based on data from the monthly survey, revealed a strong relationship between the relative peak areas of some T-RFLP operational taxonomic units (OTUs) with denitrification rate and NO3- availability. Results suggest that denitrifiers with specific nosZ genotypes (OTUs) have competitive advantage over others when NO3- fluctuates in the system; these fluctuations reflect, in turn, variability in denitrification rates.

Seasonal and diel distributions of denitrifying and bacterial communities in a hypersaline microbial mat (Camargue, France)

Changes in spatio-temporal distribution of bacterial and denitrifying communities were qualitatively studied in a microbial mat from Camargue (France). During a diel and a seasonal cycle, patterns of 16S rRNA and nitrite reductase genes (nirS and nirK) were compared by denaturing gradient gel electrophoresis (DGGE). Statistical analysis of DGGE profiles showed a significant seasonal shift in the community structure of the nirS-containing bacteria with a winter superficial population that extended in summer, whereas the nirK-containing bacteria seemed more affected by vertical gradients rather than by month-to month-changes. Denitrifying activities remained stable during these sampling times. The bacterial community at the surface of the mat also changed according to season, but appeared stable over a day. Finally, during a diel cycle nirK populations were localized in zones with large fluctuations of environmental parameters (oxygen, pH, and sulfur levels) while nirS populations seemed more restricted to the permanent anoxic layer of the microbial mat.

Analysis of nitrite reductase (nirK and nirS) genes and cultivation reveal depauperate community of denitrifying bacteria in the Black Sea suboxic zone

Chemical profiles of the Black Sea suboxic zone show a distribution of nitrogen species which is traditionally associated with denitrification, i.e. a secondary nitrite maximum associated with nitrate depletion and a N(2) gas peak. To better understand the distribution and diversity of the denitrifier community in the Black Sea suboxic zone, we combined a cultivation approach with cloning and sequencing of PCR-amplified nitrite reductase (nirS and nirK) genes. The Black Sea suboxic zone appears to harbour a homogeneous community of denitrifiers. For nirK, over 94% of the sequences fell into only three distinct phylogenetic clusters, and for nirS, a single closely related sequence type accounted for 91% of the sequences retrieved. Both nirS and nirK genes showed a dramatic shift in community composition at the bottom of the suboxic zone, but overall, nirK-based community composition showed much greater variation across depths compared with the highly uniform distribution of nirS sequences throughout the suboxic zone. The dominant nirK and nirS sequences differed at the amino acid level by at least 17% and 8%, respectively, from their nearest database matches. Denitrifying isolates recovered from the suboxic zone shared 97% 16S rRNA gene sequence similarity with Marinobacter maritimus. Analysis of the recently discovered nirS gene from the anammox bacterium Candidatus'Kuenenia stuttgartiensis' revealed that mismatches with commonly used primers may have prevented the previous detection of this divergent sequence.

Potential rates and pathways of microbial nitrate reduction in coastal sediments

Nitrate reduction plays a key role in the biogeochemical dynamics and microbial ecology of coastal sediments. Potential rates of nitrate reduction were measured on undisturbed sediment slices from two eutrophic coastal environments using flow-through reactors (FTR). Maximum potential nitrate reduction rates ranged over an order of magnitude, with values of up to 933 nmol cm(-3) h(-1), whereas affinity constants for NO(3) (-) fell mostly between 200 and 600 microM. Homogenized sediment slurries systematically yielded higher rates of nitrate reduction than the FTR experiments. Dentrification was the major nitrate removal pathway in the sediments, although excess ammonium production indicated a contribution of dissimilatory nitrate reduction to ammonium under nitrate-limiting conditions.

Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea

N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.

Microbial community diversity associated with carbon and nitrogen cycling in permeable shelf sediments

Though a large fraction of primary production and organic matter cycling in the oceans occurs on continental shelves dominated by sandy deposits, the microbial communities associated with permeable shelf sediments remain poorly characterized. Therefore, in this study, we provide the first detailed characterization of microbial diversity in marine sands of the South Atlantic Bight through parallel analyses of small-subunit (SSU) rRNA gene (Bacteria), nosZ (denitrifying bacteria), and amoA (ammonia-oxidizing bacteria) sequences. Communities were analyzed by parallel DNA extractions and clone library construction from both sediment core material and manipulated sediment within column experiments designed for geochemical rate determinations. Rapid organic-matter degradation and coupled nitrification-denitrification were observed in column experiments at flow rates resembling in situ conditions over a range of oxygen concentrations. Numerous SSU rRNA phylotypes were affiliated with the phyla Proteobacteria (classes Alpha-, Delta-, and Gammaproteobacteria), Planctomycetes, Cyanobacteria, Chloroflexi, and Bacteroidetes. Detectable sequence diversity of nosZ and SSU rRNA genes increased in stratified redox-stabilized columns compared to in situ sediments, with the Alphaproteobacteria comprising the most frequently detected group. Alternatively, nitrifier communities showed a relatively low and stable diversity that did not covary with the other gene targets. Our results elucidate predominant phylotypes that are likely to catalyze carbon and nitrogen cycling in marine sands. Although overall diversity increased in response to redox stabilization and stratification in column experiments, the major phylotypes remained the same in all of our libraries, indicating that the columns sufficiently mimic in situ conditions.

Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing

Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [(13)C]acetate or [(13)C]methanol as the main carbon source and nitrate as the electron acceptor. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from (13)C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from (13)C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. Rarefaction curves for clones retrieved from (13)C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria. Furthermore, we characterized nitrite reductase genes (nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. However, most of the nirS or nirK sequences retrieved from (13)C-DNA were clustered in some unidentified groups. On the basis of 16S rRNA gene clone libraries retrieved from (13)C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).

Biology of Pseudomonas stutzeri

Pseudomonas stutzeri is a nonfluorescent denitrifying bacterium widely distributed in the environment, and it has also been isolated as an opportunistic pathogen from humans. Over the past 15 years, much progress has been made in elucidating the taxonomy of this diverse taxonomical group, demonstrating the clonality of its populations. The species has received much attention because of its particular metabolic properties: it has been proposed as a model organism for denitrification studies; many strains have natural transformation properties, making it relevant for study of the transfer of genes in the environment; several strains are able to fix dinitrogen; and others participate in the degradation of pollutants or interact with toxic metals. This review considers the history of the discovery, nomenclatural changes, and early studies, together with the relevant biological and ecological properties, of P. stutzeri.

Characterization of Fe(III)-reducing enrichment cultures and isolation of Fe(III)-reducing bacteria from the Savannah River site, South Carolina

The Savannah River site, South Carolina (SRS), has been subjected to heavy metal and radionuclide contamination. Dissimilatory Fe(III)-reducing bacteria, by reducing insoluble Fe(III) to soluble Fe(II), may enhance contaminant mobility through subsurface environments. In order to investigate populations of the indigenous iron-reducing microbes from the SRS, duplicate enrichment cultures were initiated using a 10% inoculum of 7 sediment/soil samples, and serial dilutions were made into Wolfe's minimal salts media amended with 50 mM Fe(III) floc, 10 mM acetate and 0.01% yeast extract. Terminal restriction fragment length polymorphism (T-RFLP) analysis was used to generate fingerprints of the cultures and track changes in the microbial communities through the dilutions. Cluster analysis determined the relatedness of individual fingerprints. Initial enrichment cultures exhibited complex fingerprints consisting of many individual T-RF peaks, and demonstrated low similarity between sites. After four serial dilutions the fingerprints were less complex and clustered at higher similarities. Several individual T-RF peaks became dominant in a majority of the fingerprints. Cloning and sequence analysis revealed the presence of microbes closely related to Clostridium and Bacillus species and to known iron reducers such as Geobacter species and Pantoea agglomerans. Several Fe(III)-reducing isolates related to Aeromonas, Bacillus and Clostridium species were obtained.

Nitrous oxide reductase genes (nosZ) of denitrifying microbial populations in soil and the earthworm gut are phylogenetically similar

Earthworms emit nitrous oxide (N2O) and dinitrogen (N2). It has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (M. A. Horn, A. Schramm, and H. L. Drake, Appl. Environ. Microbiol. 69:1662-1669, 2003). This hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. To test this hypothesis, the denitrifier populations of gut and soil from three different sites were comparatively assessed by sequence analysis of nosZ, the gene for the terminal enzyme in denitrification, N2O reductase. A total of 182 and 180 nosZ sequences were retrieved from gut and soil, respectively; coverage of gene libraries was 79 to 100%. Many of the nosZ sequences were heretofore unknown, clustered with known soil-derived sequences, or were related to N2O reductases of the genera Bradyrhizobium, Brucella, Dechloromonas, Flavobacterium, Pseudomonas, Ralstonia, and Sinorhizobium. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived nosZ sequence did not group phylogenetically with any of the soil-derived nosZ sequences. Thus, the phylogenies of nosZ from gut and soil were not dissimilar, indicating that gut denitrifiers are soil derived.

TGGE analysis of the diversity of ammonia-oxidizing and denitrifying bacteria in submerged filter biofilms for the treatment of urban wastewater

The spatial and temporal diversity of the bacterial community-forming biofilms in a pilot-scale submerged biofilter used for the treatment of urban wastewater was analyzed by a temperature-gradient gel electrophoresis (TGGE) approach. TGGE profiles based on partial sequence of the 16S rRNA gene showed that the community composition of the biofilms remained fairly stable along the column system and during the whole time of operation of the biofilter (more than 1 year). Community-profiling based on the amplification and separation of partial ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ) genes demonstrated that ammonia-oxidizing and denitrifying bacteria coexisted in both the anoxic and the aerated parts of the system. Several amoA and nosZ bands separated by TGGE were reamplified and sequenced, in order to further analyze the composition of these microbial communities in the biofilm. Phylogeny inferred from amoA/AmoA revealed the prevalence of Nitrosomonas species with five sequences affiliated to Nitrosomonas oligotropha, six sequences affiliated to Nitrosomonas europaea, and three sequences that showed only 75.7-76.1% identity of the DNA sequence with the closest described species (Nitrosomonas nitrosa). According to literature, this low identity value is indicative of previously undiscovered species. Eighteen new partial nosZ sequences were obtained which were mostly related to nosZ of gamma-proteobacteria (Pseudomonas) or clustered in the periphery of previously known denitrifying alpha-proteobacteria (Bradyrhizobium and Azospirillum).

Communities of nirS-type denitrifiers in the water column of the oxygen minimum zone in the eastern South Pacific

The major sites of water column denitrification in the ocean are oxygen minimum zones (OMZ), such as one in the eastern South Pacific (ESP). To understand the structure of denitrifying communities in the OMZ off Chile, denitrifier communities at two sites in the Chilean OMZ (Antofagasta and Iquique) and at different water depths were explored by terminal restriction fragment length polymorphism analysis and cloning of polymerase chain reaction (PCR)-amplified nirS genes. NirS is a functional marker gene for denitrification encoding cytochrome cd1-containing nitrite reductase, which catalyses the reduction of nitrite to nitric oxide, the key step in denitrification. Major differences were found between communities from the two geographic locations. Shifts in community structure occurred along a biogeochemical gradient at Antofagasta. Canonical correspondence analysis indicated that O2, NO3-, NO2- and depth were important environmental factors governing these communities along the biogeochemical gradient in the water column. Phylogenetic analysis grouped the majority of clones from the ESP in distinct clusters of genes from presumably novel and yet uncultivated denitrifers. These nirS clusters were distantly related to those found in the water column of the Arabian Sea but the phylogenetic distance was even higher compared with environmental sequences from marine sediments or any other habitat. This finding suggests similar environmental conditions trigger the development of denitrifiers with related nirS genotypes despite large geographic distances.

Marine enzymes

Marine enzyme biotechnology can offer novel biocatalysts with properties like high salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and ease in large-scale cultivation. This review deals with the research and development work done on the occurrence, molecular biology, and bioprocessing of marine enzymes during the last decade. Exotic locations have been accessed for the search of novel enzymes. Scientists have isolated proteases and carbohydrases from deep sea hydrothermal vents. Cold active metabolic enzymes from psychrophilic marine microorganisms have received considerable research attention. Marine symbiont microorganisms growing in association with animals and plants were shown to produce enzymes of commercial interest. Microorganisms isolated from sediment and seawater have been the most widely studied, proteases, carbohydrases, and peroxidases being noteworthy. Enzymes from marine animals and plants were primarily studied for their metabolic roles, though proteases and peroxidases have found industrial applications. Novel techniques in molecular biology applied to assess the diversity of chitinases, nitrate, nitrite, ammonia-metabolizing, and pollutant-degrading enzymes are discussed. Genes encoding chitinases, proteases, and carbohydrases from microbial and animal sources have been cloned and characterized. Research on the bioprocessing of marine-derived enzymes, however, has been scanty, focusing mainly on the application of solid-state fermentation to the production of enzymes from microbial sources.