Influence of nitrate and nitrite concentration on N2 O production via dissimilatory nitrate/nitrite reduction to ammonium in Bacillus paralicheniformis LMG 6934

Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring

In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.

Review of the mechanisms involved in dissimilatory nitrate reduction to ammonium and the efficacies of these mechanisms in the environment

Dissimilatory nitrate reduction to ammonium (DNRA) is currently of great interest because it is an important method for recovering nitrogen from wastewater and offers many advantages, over other methods. A full understanding of DNRA requires the mechanisms, pathways, and functional microorganisms involved to be identified. The roles these pathways play and the effectiveness of DNRA in the environment are not well understood. The objectives of this review are to describe our current understanding of the molecular mechanisms and pathways involved in DNRA from the substrate transfer perspective and to summarize the effects of DNRA in the environment. First, the mechanisms and pathways involved in DNRA are described in detail. Second, our understanding of DNRA by actinomycetes is reviewed and gaps in our understanding are identified. Finally, the effects of DNRA in the environment are assessed. This review will help in the development of future research into DNRA to promote the use of DNRA to treat wastewater and recover nitrogen.

pH selects for distinct N2O-reducing microbiomes in tropical soil microcosms

Nitrous oxide (N2O), a greenhouse gas with ozone destruction potential, is mitigated by the microbial reduction to dinitrogen catalyzed by N2O reductase (NosZ). Bacteria with NosZ activity have been studied at circumneutral pH but the microbiology of low pH N2O reduction has remained elusive. Acidic (pH < 5) tropical forest soils were collected in the Luquillo Experimental Forest in Puerto Rico, and microcosms maintained with low (0.02 mM) and high (2 mM) N2O assessed N2O reduction at pH 4.5 and 7.3. All microcosms consumed N2O, with lag times of up to 7 months observed in microcosms with 2 mM N2O. Comparative metagenome analysis revealed that Rhodocyclaceae dominated in circumneutral microcosms under both N2O feeding regimes. At pH 4.5, Peptococcaceae dominated in high-N2O, and Hyphomicrobiaceae in low-N2O microcosms. Seventeen high-quality metagenome-assembled genomes (MAGs) recovered from the N2O-reducing microcosms harbored nos operons, with all eight MAGs derived from acidic microcosms carrying the Clade II type nosZ and lacking nitrite reductase genes (nirS/K). Five of the eight MAGs recovered from pH 4.5 microcosms represent novel taxa indicating an unexplored N2O-reducing diversity exists in acidic tropical soils. A survey of pH 3.5-5.7 soil metagenome datasets revealed that nosZ genes commonly occur, suggesting broad distribution of N2O reduction potential in acidic soils.

Isolation of a marine-derived yeast with potential applications in industrial nitrite utilizing

The nitrite efficient utilization microorganism Wickerhamomyces anomalus RZWP01 was identified. Using nitrite and ammonium as the sole nitrogen source, the nitrogen removal rate of W. anomalus RZWP01 was 97.4% and 87.1%, respectively. W. anomalus RZWP01 grew well in the nitrite medium with glucose or xylose as the only carbon source. However, the W. anomalus RZWP01 cannot live on the nitrite medium with lactose, citric acid, and methanol as the only carbon source. The maximal cell concentration occurred in the nitrite medium with glucose as the only carbon source at a C/N ratio of 20 for 48 h, reaching 8.92 × 108 cell mL-1. W. anomalus RZWP01 was the first reported yeast that can efficiently utilize nitrite. The isolation and identification of W. anomalus RZWP01 enriched the microbial resources of nitrite-degrading microorganisms and provided functional microorganisms for the water treatment of sustainable aquaculture.

Nitric oxide and nitrite removal by partial denitrifying hollow-fiber membrane biofilm reactor coupled with nitrous oxide generation as energy recovery

Nitrogen oxide (NOx) emissions cause significant impacts on the environment and must therefore be controlled even more stringently. This requires the development of cost-effective removal strategies which simultaneously create value-added by-products or energy from the waste. This study aims to treat gaseous nitric oxide (NO) by hollow-fibre membrane biofilm reactor (HFMBfR) in the presence of nitrite (NO2-) and evaluate nitrous oxide (N₂O) emissions formed as an intermediate product during the denitrification process. Accumulated N₂O can be utilised in methane oxidation as an oxidant to produce energy. In the first stage of the study, the HFMBfR was operated by feeding only gaseous NO as the nitrogen source. During this period, the best performance was achieved with 92% NO removal efficiency (RE). In the second stage, both NO gas and NO2- were supplied to the system, and 91% NO and 99% NO2- reduction were achieved simultaneously with the maximum N₂O generation of 386 ± 31 ppm. Lower influent carbon to nitrogen (C/N) ratios, such as 4.5 and 2.0, and higher NO2--N loading rate of 158 mg N day^-1 favoured N₂O generation. An improved NO removal rate and N₂O accumulation were seen with the increasing amount of PO43- in the medium. The 16S rDNA sequencing analysis revealed that Alicycliphilus denitrificans and Pseudomonas putida were the dominant species. The study shows that an HFMBfR can be successfully used to eliminate both NO2- and gaseous NO and simultaneously generate N₂O by adjusting the system parameters such as C/N ratio, NO2- and PO43- loading.

Biodegradation of polystyrene by deep-sea Bacillus paralicheniformis G1 and genome analysis

Polystyrene (PS) films were subjected to in vitro biodegradation by Bacillus paralicheniformis G1 (MN720578) isolated from 3538 m depth sediments of the Arabian Sea. The growth of the isolate was most favourable at pH 7.5, 30 °C and 4% salinity. A series of batch experiments were conducted to investigate the degradation of PS films up to 60 days. The results of this study indicated that the strain degraded 34% of PS film within 60 days of incubation. The complete genome sequence consists of 4,281,959 bp with 45.88% GC content and encodes 4213 protein coding genes. A high number of genes encoding monooxygenase, dioxygenase, peroxidase, esterase and hydrolase involved in the degradation of synthetic polymers were identified. Also genes associated with flagellum dependent motility, chemotaxis, biofilm formation and siderophores biosynthesis were identified in this deep-sea strain G1. This study suggests that B. paralicheniformis G1 could be a potential species for degradation of PS and its genome analysis provides insight into the molecular basis of biodegradation.

Involvement of NO3 - in Ecophysiological Regulation of Dissimilatory Nitrate/Nitrite Reduction to Ammonium (DNRA) Is Implied by Physiological Characterization of Soil DNRA Bacteria Isolated via a Colorimetric Screening Method

Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) has recently regained attention as a nitrogen retention pathway that may potentially be harnessed to alleviate nitrogen loss resulting from denitrification. Until recently, the ecophysiology of DNRA bacteria inhabiting agricultural soils has remained largely unexplored, due to the difficulty in targeted enrichment and isolation of DNRA microorganisms. In this study, >100 DNRA bacteria were isolated from NO₃ ^--reducing anoxic enrichment cultures established with rice paddy soils using a newly developed colorimetric screening method. Six of these isolates, each assigned to a different genus, were characterized to improve the understanding of DNRA physiology. All the isolates carried nrfA and/or nirB, and the Bacillus sp. strain possessed a clade II nosZ gene conferring the capacity for N₂O reduction. A common prominent physiological feature observed in the isolates was NO₂ ^- accumulation before NH₄ ⁺ production, which was further examined with Citrobacter sp. strain DNRA3 (possessing nrfA and nirB) and Enterobacter sp. strain DNRA5 (possessing only nirB). Both isolates showed inhibition of NO₂ ^--to-NH₄ ⁺ reduction at submillimolar NO₃ ^- concentrations and downregulation of nrfA or nirB transcription when NO₃ ^- was being reduced to NO₂ ^- In batch and chemostat experiments, both isolates produced NH₄ ⁺ from NO₃ ^- reduction when incubated with excess organic electron donors, while incubation with excess NO₃ ^- resulted in NO₂ ^- buildup but no substantial NH₄ ⁺ production, presumably due to inhibitory NO₃ ^- concentrations. This previously overlooked link between NO₃ ^- repression of NO₂ ^--to-NH₄ ⁺ reduction and the C-to-N ratio regulation of DNRA activity may be a key mechanism underpinning denitrification-versus-DNRA competition in soil.IMPORTANCE Dissimilatory nitrate/nitrite reduction to ammonium (DNRA) is an anaerobic microbial pathway that competes with denitrification for common substrates NO₃ ^- and NO₂ ^- Unlike denitrification, which leads to nitrogen loss and N₂O emission, DNRA reduces NO₃ ^- and NO₂ ^- to NH₄ ⁺, a reactive nitrogen compound with a higher tendency to be retained in the soil matrix. Therefore, stimulation of DNRA has often been proposed as a strategy to improve fertilizer efficiency and reduce greenhouse gas emissions. Such attempts have been hampered by lack of insights into soil DNRA bacterial ecophysiology. Here, we have developed a new screening method for isolating DNRA-catalyzing organisms from agricultural soils without apparent DNRA activity. Physiological characteristics of six DNRA isolates were closely examined, disclosing a previously overlooked link between NO₃ ^- repression of NO₂ ^--to-NH₄ ⁺ reduction and the C-to-N ratio regulation of DNRA activity, which may be a key to understanding why DNRA activity is rarely observed at substantial levels in nitrogen-rich agricultural soils.

Dominance of nitrous oxide production by nitrification and denitrification in the shallow Chaohu Lake, Eastern China: Insight from isotopic characteristics of dissolved nitrous oxide

In recent decades, most lakes in Eastern China have suffered unprecedented nitrogen pollution, making them potential "hotspots" for N₂O production and emission. Understanding the mechanisms of N₂O production and quantifying emissions in these lakes is essential for assessing regional and global N₂O budgets and for mitigating N₂O emissions. Here, we measure isotopic compositions (δ¹⁵N-N₂O and δ¹⁸O-N₂O) and site preference (SP) of dissolved N₂O in an attempt to differentiate the relative contribution of N₂O production processes in the shallow, eutrophic Chaohu Lake, Eastern China. Our results show that the bulk isotope ratios for δ¹⁵N-N₂O, δ¹⁸O-N₂O, and SP were 5.8 ± 3.9‰, 29.3 ± 13.4‰, and 18.6 ± 3.2‰, respectively. More than 76.8% of the dissolved N₂O was produced via microbial processes. Findings suggest that dissolved N₂O is primarily produced via nitrification (between 27.3% and 48.0%) and denitrification (between 31.9% and 49.5%). In addition, isotopic data exhibit significant N₂O consumption during denitrification. We estimate the average N₂O emission rate (27.5 ± 26.0 μg N m^-2 h^-1), which is higher than that from rivers in the Changjiang River network (CRN). We scaled-up the regional N₂O emission (from 1.98 Gg N yr^-1 to 4.58 Gg N yr^-1) using a N₂O emission factor (0.51 ± 0.63%) for shallow lakes in the middle and lower region of the CRN. We suggest that beneficial circumstances for promoting complete denitrification may be helpful for reducing N₂O production and emissions in fresh surface waters.

Influence of nitrate and nitrite concentration on N2 O production via dissimilatory nitrate/nitrite reduction to ammonium in Bacillus paralicheniformis LMG 6934

Until now, the exact mechanisms for N2 O production in dissimilatory nitrate/nitrite reduction to ammonium (DNRA) remain underexplored. Previously, we investigated this mechanism in Bacillus licheniformis and Bacillus paralicheniformis, ubiquitous gram-positive bacteria with many industrial applications, and observed significant strain dependency and media dependency in N2 O production which was thought to correlate with high residual NO2- . Here, we further studied the influence of several physicochemical factors on NO3- (or NO2- ) partitioning and N2 O production in DNRA to shed light on the possible mechanisms of N2 O production. The effects of NO3- concentrations under variable or fixed C/N-NO3- ratios, NO2- concentrations under variable or fixed C/N-NO2- ratios, and NH4+ concentrations under fixed C/N-NO3- ratios were tested during anaerobic incubation of soil bacterium B. paralicheniformis LMG 6934 (previously known as B. licheniformis), a strain with a high nitrite reduction capacity. Monitoring of growth, NO3- , NO2- , NH4+ concentration, and N2 O production in physiological tests revealed that NO3- as well as NO2- concentration showed a linear correlation with N2 O production. Increased NO3- concentration under fixed C/N-NO3- ratios, NO2- concentration, and NH4+ concentration had a significant positive effect on NO3- (or NO2- ) partitioning ([N-NH4+ ]/[N-N2 O]) toward N2 O, which may be a consequence of the (transient) accumulation and subsequent detoxification of NO2- . These findings extend the information on several physiological parameters affecting DNRA and provide a basis for further study on N2 O production during this process.