Certain Environmental Conditions Maximize Ammonium Accumulation and Minimize Nitrogen Loss During Nitrate Reduction Process by Pseudomonas putida Y-9

A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar

The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.

Deterministic factors modulating assembly of groundwater microbial community in a nitrogen-contaminated and hydraulically-connected river-lake-floodplain ecosystem

The river-lake-floodplain system (RLFS) undergoes intensive surface-groundwater mass and energy exchanges. Some freshwater lakes are groundwater flow-through systems, serving as sinks for nitrogen (N) entering the lake. Despite the threat of cross-nitrogen contamination, the assembly of the microbial communities in the RLFS was poorly understood. Herein, the distribution, co-occurrence, and assembly pattern of microbial community were investigated in a nitrogen-contaminated and hydraulically-connected RLFS. The results showed that nitrate was widely distributed with greater accumulation on the south than on the north side, and ammonia was accumulated in the groundwater discharge area (estuary and lakeshore). The heterotrophic nitrifying bacteria and aerobic denitrifying bacteria were distributed across the entire area. In estuary and lakeshore with low levels of oxidation-reduction potential (ORP) and high levels of total organic carbon (TOC) and ammonia, dissimilatory nitrate reduction to ammonium (DNRA) bacteria were enriched. The bacterial community had close cooperative relationships, and keystone taxa harbored nitrate reduction potentials. Combined with multivariable statistics and self-organizing map (SOM) results, ammonia, TOC, and ORP acted as drivers in the spatial evolution of the bacterial community, coincidence with the predominant deterministic processes and unique niche breadth for microbial assembly. This study provides novel insight into the traits and assembly of bacterial communities and potential nitrogen cycling capacities in RLFS groundwater.

Efficient Mn(II) removal mechanism by Serratia marcescens QZB-1 at high manganese concentration

Manganese (Mn(II)) pollution has recently increased and requires efficient remediation. In this study, Serratia marcescens QZB-1, isolated from acidic red soil, exhibited high tolerance against Mn(II) (up to 364 mM). Strain QZB-1 removed a total of 98.4% of 18 mM Mn(II), with an adsorption rate of 71.4% and oxidation rate of 28.6% after incubation for 48 h. The strain synthesized more protein (PN) to absorb Mn(II) when stimulated with Mn(II). The pH value of the cultural medium continuously increased during the Mn(II) removal process. The product crystal composition (mainly MnO₂ and MnCO₃), Mn-O functional group, and element-level fluctuations confirmed Mn oxidation. Overall, strain QZB-1 efficiently removed high concentration of Mn(II) mainly via adsorption and showed great potential for manganese wastewater removal.

Effects of carbon load on nitrate reduction during riverbank filtration: Field monitoring and batch experiment

Riverbank filtration (RBF) is a well-established technique worldwide, and is critical for the maintenance of groundwater quality and production of clean drinking water. Evaluation of the decay of exogenous nitrate (NO₃^-) in river water and the enrichment of ammonium (NH₄⁺) in groundwater during RBF is important; these two processes are mainly influenced by denitrification (DNF) and dissimilatory nitrate reduction to ammonium (DNRA) controlled by the groundwater carbon load. In this study, the effects of carbon load (organic carbon [OC]: NO₃^-) on the competing nitrate reduction (DNRA and DNF) were assessed during RBF using field monitoring and a laboratory batch experiment. Results show the groundwater OC: NO₃^- ratio did not directly affect the reaction rate of DNRA and DNF, however, it could control the competitive partitioning between the two. In the near-shore zone, the groundwater OC: NO₃^- ratio shows significant seasonal variations along the filtration path owing to the changing conditions of redox, OC-rich, and NO₃^--limited. A greater proportion of NO₃^- would be available for DNRA in the wet season with higher OC: NO₃^- ratio (> 10), resulting in a significantly NH₄⁺-N enrichment rate (from 1.43 × 10^-3 to 9.54 × 10^-4 mmol L^-1 d^-1) in the near-shore zone where the zone of Mn (IV) oxide reduction. However, the activity of DNRA was suppressed with lower OC: NO₃^- ratio (< 10) in the dry season, resulting in a stable NH₄⁺-N enrichment rate (from 3.12 × 10^-4 to 1.30 × 10^-4 mmol L^-1 d^-1). Benefiting from seasonal variation of OC-rich and NO₃^--limited conditions, DNRA bacteria outcompeted denitrifiers, which eventually led to seasonal differences in NO₃^- reduction in the near-shore zone. Overall, under the effect of DNRA induced by continuous high carbon load in RBF systems, nitrogen input is not permanently removed but rather retained in groundwater during RBF.

The nitrite reductase encoded by nirBDs in Pseudomonas putida Y-9 influences ammonium transformation

It is unknown whether nirBDs, which conventionally encode an NADH nitrite reductase, play other novel roles in nitrogen cycling. In this study, we explored the role of nirBDs in the nitrogen cycling of Pseudomonas putida Y-9. nirBDs had no effect on organic nitrogen transformation by strain Y-9. The △nirBD strain exhibited higher ammonium removal efficiency (90.7%) than the wild-type strain (76.1%; P < 0.05) and lower end gaseous nitrogen (N2O) production. Moreover, the expression of glnA (control of the ammonium assimilation) in the △nirBD strain was higher than that in the wild-type strain (P < 0.05) after being cultured in ammonium-containing medium. Furthermore, nitrite noticeably inhibited the ammonium elimination of the wild-type strain, with a corresponding removal rate decreasing to 44.8%. However, no similar impact on ammonium transformation was observed for the △nirBD strain, with removal efficiency reaching 97.5%. In conclusion, nirBDs in strain Y-9 decreased the ammonium assimilation and increased the ammonium oxidation to nitrous oxide.