Detection methods for the expression of the dissimilatory copper-containing nitrite reductase gene (DnirK) in environmental samples

Anaerobic Ammonium Oxidation in Acidic Red Soils

Anaerobic ammonium oxidation (anammox) has been proven to be an important nitrogen removal process in terrestrial ecosystems, particularly paddy soils. However, the contribution of anammox in acidic red soils to nitrogen loss has not been well-documented to date. Here, we investigated the activity, abundance, and distribution of anammox bacteria in red soils collected from nine provinces of Southern China. High-throughput sequencing analysis showed that Candidatus Brocadia dominates the anammox bacterial community (93.03% of sequence reads). Quantification of the hydrazine synthase gene (hzsB) and anammox 16S rRNA gene indicated that the abundance of anammox bacteria ranged from 6.20 × 10⁶ to 1.81 × 10⁹ and 4.81 × 10⁶ to 4.54 × 10⁸ copies per gram of dry weight, respectively. Contributions to nitrogen removal by anammox were measured by a ¹⁵N isotope-pairing assay. Anammox rates in red soil ranged from 0.01 to 0.59 nmol N g⁻¹ h⁻¹, contributing 16.67–53.27% to N₂ production in the studied area, and the total amount of removed nitrogen by anammox was estimated at 2.33 Tg N per year in the natural red soils of southern China. Pearson correlation analyses revealed that the distribution of anammox bacteria significantly correlated with the concentration of nitrate and pH, whereas the abundance and activity of anammox bacteria were significantly influenced by the nitrate and total nitrogen concentrations. Our findings demonstrate that Candidatus Brocadia dominates anammox bacterial communities in acidic red soils and plays an important role in nitrogen loss of the red soil in Southern China.

Targeted quantification of functional enzyme dynamics in environmental samples for microbially mediated biogeochemical processes

Microbial enzymes catalytically drive biogeochemical processes in environments. The dynamic linkage between functional enzymes and biogeochemical species transformation has, however, rarely been investigated for decades because of the challenges to directly quantify enzymes in environmental samples. The diversity of microorganisms, the low amount of available biomass and the complexity of chemical composition in environmental samples represent the main challenges. To address the diversity challenge, we first identify several signature peptides that are conserved in the targeted enzymes with the same functionality across many phylogenetically diverse microorganisms using metagenome-based protein sequence data. Quantification of the signature peptides then allows estimation of the targeted enzyme abundance. To achieve analyses of the requisite sensitivity for complex environmental samples with low available biomass, we adapted a recently developed ultrasensitive targeted quantification technology, termed high-pressure high-resolution separations with intelligent selection and multiplexing (PRISM) by improving peptide separation efficiency and method detection sensitivity. Nitrate reduction dynamics catalyzed by dissimilatory and assimilatory enzymes in a hyporheic zone sediment was used as an example to demonstrate the application of the enzyme quantification approach. Together with the measurements of biogeochemical species, the approach enables investigating the dynamic linkage between functional enzymes and biogeochemical processes.

Simulation of the Denitrification Process of Waste Water with a Biochemical Systems Model: A Non-Conventional Approach

Matching experimental and theoretical approaches have often been fruitful in the investigation of complex biological processes. Here we develop a novel non-conventional model for the denitrification of waste water. Earlier models of the denitrification process were compiled by the International Association on Water Quality group. The Activated Sludge Models 1–3, which are the most frequently used all over the world, are presently not adapted towards the integration of both nitrous and nitric oxide emissions during the denitrification process. In the present work, a Generalized Mass Action model, based on Biochemical Systems Theory, was designed to simulate the nitrate reduction observed in specific experimental conditions. The model was implemented and analysed with the software package PLAS. Data from a representative experiment were chosen (T=10°C, pH=7, C/N=3, with acetate as carbon source) to simulate greenhouse NO and N2O gas emissions, in order to test hypotheses about the corresponding bacterial metabolic pathways. The results show that the reduction of nitrate and nitrite is kinetically limiting and that nitrate reduction is limited by diffusion and support that distinct microbial subpopulations are involved in the denitrification pathway, which has consequences for NO emissions.

Denitrification and N2O:N2 production in temperate grasslands: processes, measurements, modelling and mitigating negative impacts

In this review we explore the biotic transformations of nitrogenous compounds that occur during denitrification, and the factors that influence denitrifier populations and enzyme activities, and hence, affect the production of nitrous oxide (N2O) and dinitrogen (N2) in soils. Characteristics of the genes related to denitrification are also presented. Denitrification is discussed with particular emphasis on nitrogen (N) inputs and dynamics within grasslands, and their impacts on the key soil variables and processes regulating denitrification and related gaseous N2O and N2 emissions. Factors affecting denitrification include soil N, carbon (C), pH, temperature, oxygen supply and water content. We understand that the N2O:N2 production ratio responds to the changes in these factors. Increased soil N supply, decreased soil pH, C availability and water content generally increase N2O:N2 ratio. The review also covers approaches to identify and quantify denitrification, including acetylene inhibition, (15)N tracer and direct N2 quantification techniques. We also outline the importance of emerging molecular techniques to assess gene diversity and reveal enzymes that consume N2O during denitrification and the factors affecting their activities and consider a process-based approach that can be used to quantify the N2O:N2 product ratio and N2O emissions with known levels of uncertainty in soils. Finally, we explore strategies to reduce the N2O:N2 product ratio during denitrification to mitigate N2O emissions. Future research needs to focus on evaluating the N2O-reducing ability of the denitrifiers to accelerate the conversion of N2O to N2 and the reduction of N2O:N2 ratio during denitrification.

Novel denitrifying bacterium Ochrobactrum anthropi YD50.2 tolerates high levels of reactive nitrogen oxides

Most studies of bacterial denitrification have used nitrate (NO3-) as the first electron acceptor, whereas relatively less is understood about nitrite (NO2-) denitrification. We isolated novel bacteria that proliferated in the presence of high levels of NO2- (72 mM). Strain YD50.2, among several isolates, was taxonomically positioned within the alpha subclass of Proteobacteria and identified as Ochrobactrum anthropi YD50.2. This strain denitrified NO2-, as well as NO3-. The gene clusters for denitrification (nar, nir, nor, and nos) were cloned from O. anthropi YD50.2, in which the nir and nor operons were linked. We confirmed that nirK in the nir-nor operon produced a functional NO2- reductase containing copper that was involved in bacterial NO2- reduction. The strain denitrified up to 40 mM NO2- to dinitrogen under anaerobic conditions in which other denitrifiers or NO3- reducers such as Pseudomonas aeruginosa and Ralstonia eutropha and nitrate-respiring Escherichia coli neither proliferated nor reduced NO2-. Under nondenitrifying aerobic conditions, O. anthropi YD50.2 and its type strain ATCC 49188(T) proliferated even in the presence of higher levels of NO2- (100 mM), and both were considerably more resistant to acidic NO2- than were the other strains noted above. These results indicated that O. anthropi YD50.2 is a novel denitrifier that has evolved reactive nitrogen oxide tolerance mechanisms.

Nitrogen transformations in stratified aquatic microbial ecosystems

New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a microm-mm scale. A large and ever-expanding knowledge base about nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.

The effects of salinity and other factors on nitrite reduction by Ochrobactrum anthropi 49187

The nitrite reductase (NIR) gene was cloned from Ochrobactrum anthropi 49187 and found to contain an open reading frame of 1131 nucleotides, encoding a polypeptide of 376 amino acids. The O. anthropi NIR gene encodes a copper-type dissimilatory reductase based on sequence homology with other genes. The polypeptide product is predicted to form a trimeric holoenzyme of 37 kDa subunits based on molecular weight estimates of extracts in activity gels. Expression of the enzyme is up-regulated by nitrate, presumably through the intermediate nitrite, and its activity is influenced by inhibitors. Salinity enhances the activity of existing NIR enzyme, but appears to decrease the expression of new enzyme.

Microbial gene expression in soil: methods, applications and challenges

About 99% of soil microorganisms are unculturable. However, advances in molecular biology techniques allow for the analysis of living microorganisms. With the advent of new technologies and the optimization of previous methods, various approaches to studying gene expression are expanding the field of microbiology and molecular biology. Methods used for RNA extraction, DNA microarrays, real-time PCR, competitive RT-PCR, stable isotope probing and the use of reporter genes provide methods for detecting and quantifying gene expression. Through the use of these methods, researchers can study the influence of soil environmental factors such as nutrients, oxygen status, pH, pollutants, agro-chemicals, moisture and temperature on gene expression and some of the mechanisms involved in the responses of cells to their environment. This review will also address information gaps in bacterial gene expression in soil and possible future research to develop an understanding of microbial activities in soil environments.

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

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

Complete conversion of nitrate into dinitrogen gas in co-cultures of denitrifying bacteria

In the past 10 years many molecular aspects of microbial nitrate reduction have been elucidated, but the ecophysiology of this process is hardly understood. In this contribution, our efforts to study the complex microbial communities and interactions involved in the reduction of nitrate to dinitrogen gas are summarized. The initial work concentrated on emission of the greenhouse gas nitrous oxide during incomplete denitrification by Alcaligenes faecalis. As more research methods became available, the fitness of A. faecalis could be tested in mixed cultures with other denitrifying bacteria, most notably with the nitrate-reducing bacterium Pseudomonas G9. Finally, the advancement of molecular diagnostic tools made it possible to survey complex microbial communities using specific primer sets for/and antibodies raised against the various NO(x) reductases. Given the enormous complexity of substrates and environmental conditions, it is evident that mixed cultures rather than single species are responsible for denitrification in man-made and natural ecosystems. However, it is surprising that even for the breakdown of a single compound, such as acetate, mixed cultures are responsible, and that the consecutive denitrification steps are commonly performed by mutualistic co-operating species. Our observations also indicate that we seldom know the identity of the major key players in the nitrogen cycle of these ecosystems.

Propionate oxidation by and methanol inhibition of anaerobic ammonium-oxidizing bacteria

Anaerobic ammonium oxidation (anammox) is a recently discovered microbial pathway and a cost-effective way to remove ammonium from wastewater. Anammox bacteria have been described as obligate chemolithoautotrophs. However, many chemolithoautotrophs (i.e., nitrifiers) can use organic compounds as a supplementary carbon source. In this study, the effect of organic compounds on anammox bacteria was investigated. It was shown that alcohols inhibited anammox bacteria, while organic acids were converted by them. Methanol was the most potent inhibitor, leading to complete and irreversible loss of activity at concentrations as low as 0.5 mM. Of the organic acids acetate and propionate, propionate was consumed at a higher rate (0.8 nmol min(-1) mg of protein(-1)) by Percoll-purified anammox cells. Glucose, formate, and alanine had no effect on the anammox process. It was shown that propionate was oxidized mainly to CO(2), with nitrate and/or nitrite as the electron acceptor. The anammox bacteria carried out propionate oxidation simultaneously with anaerobic ammonium oxidation. In an anammox enrichment culture fed with propionate for 150 days, the relative amounts of anammox cells and denitrifiers did not change significantly over time, indicating that anammox bacteria could compete successfully with heterotrophic denitrifiers for propionate. In conclusion, this study shows that anammox bacteria have a more versatile metabolism than previously assumed.