Microbial nitrate respiration – Genes, enzymes and environmental distribution

Pseudomonas Stutzeri may alter the environmental fate of polystyrene nanoplastics by trapping them with increasing extracellular polymers

Pseudomonas Stutzeri (P. stutzeri) is a denitrifying bacterium that is essential in biological nitrogen removal. To study the interaction between P. stutzeri and polystyrene nanoplastics (PS-NPs), the effects of PS-NPs posed on P. stutzeri were evaluated in terms of bacterial growth, physiology, denitrification function and extracellular polymers (EPS) secretion. Results of confocal laser scanning microscopy (LCSM), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and flow cytometry confirmed that PS-NPs were trapped by P. stutzeri. Exposure to PS-NPs inhibited bacterial growth and expression of denitrification-related genes, but unaffected the denitrifying enzyme activities. The enhanced secretion of EPS caused PS-NPs and bacterial aggregation. And the enzyme activity of SOD in P. stutzeri was increased while that of CAT was decreased. The results of flow cytometry showed that high concentrations of PS-NPs increased the complexity of P. stutzeri cells. These results reveal that P. stutzeri may be affected after trapping PS-NPs and alter their environmental fate as well. SYNOPSIS: This study contributes to the understanding of the possible effect of P. stutzeri on the distribution of PS-NPs and illustrates the potential impact of PS-NPs on P. stutzeri.

Linking morphology, genome, and metabolic activity of uncultured magnetotactic Nitrospirota at the single-cell level

BACKGROUND

Magnetotactic bacteria (MTB) are a unique group of microorganisms that sense and navigate through the geomagnetic field by biomineralizing magnetic nanoparticles. MTB from the phylum Nitrospirota (previously known as Nitrospirae) thrive in diverse aquatic ecosystems. They are of great interest due to their production of hundreds of magnetite (Fe3O4) magnetosome nanoparticles per cell, which far exceeds that of other MTB. The morphological, phylogenetic, and genomic diversity of Nitrospirota MTB have been extensively studied. However, the metabolism and ecophysiology of Nitrospirota MTB are largely unknown due to the lack of cultivation techniques.

METHODS

Here, we established a method to link the morphological, genomic, and metabolic investigations of an uncultured Nitrospirota MTB population (named LHC-1) at the single-cell level using nanoscale secondary-ion mass spectrometry (NanoSIMS) in combination with rRNA-based in situ hybridization and target-specific mini-metagenomics.

RESULTS

We magnetically separated LHC-1 from a freshwater lake and reconstructed the draft genome of LHC-1 using genome-resolved mini-metagenomics. We found that 10 LHC-1 cells were sufficient as a template to obtain a high-quality draft genome. Genomic analysis revealed that LHC-1 has the potential for CO2 fixation and NO3- reduction, which was further characterized at the single-cell level by combining stable-isotope incubations and NanoSIMS analyses over time. Additionally, the NanoSIMS results revealed specific element distributions in LHC-1, and that the heterogeneity of CO2 and NO3- metabolisms among different LHC-1 cells increased with incubation time.

CONCLUSIONS

To our knowledge, this study provides the first metabolic measurements of individual Nitrospirota MTB cells to decipher their ecophysiological traits. The procedure constructed in this study provides a promising strategy to simultaneously investigate the morphology, genome, and ecophysiology of uncultured microbes in natural environments. Video Abstract.

Molecular insight into the allocation of organic carbon to heterotrophic bacteria: Carbon metabolism and the involvement in nitrogen and phosphorus removal

Carbon metabolism and nutrient removal are crucial for biological wastewater treatment. This study focuses on analyzing carbon allocation and utilization by heterotrophic bacteria in response to increasing COD concentration in the influent. The study also assesses the effect of denitrification and biological phosphorus removal, particularly in combination with anaerobic ammonia oxidation (anammox). The experiment was conducted in a SBR operating under anaerobic/anoxic/oxic conditions. As COD concentration in the influent increased from 100 to 275 mg/L, intracellular COD accounted for 95.72 % of the COD removed. By regulating the NO3- concentration in the anoxic stage from 10 to 30 mg/L, the nitrite accumulation rate reached 69.46 %, which could serve as an electron acceptor for anammox. Most genes related to the tricarboxylic acid (TCA) cycle declined, while the genes involved in the glyoxylate cycle, gluconeogenesis, PHA synthesis increased. This suggests that glycogen accumulation and carbon storage, rather than direct carbon oxidation, was the dominant pathway for carbon metabolism. However, the genes responsible for the reduction of NO2--N (nirK) and NO (nosB) decreased, contributing to NO2- accumulation. The study also employed metagenomic analysis to reveal microbial interactions. The enrichment of specific bacterial species, including Dechloromonas sp. (D2.bin.10), Ca. Competibacteraceae bacterium (D9.bin.8), Ca. Desulfobacillus denitrificans (D6.bin.17), and Ignavibacteriae bacterium (D3.bin.9), played a collaborative role in facilitating nutrient removal and promoting the combination with anammox.

Recent mechanistic developments for cytochrome c nitrite reductase, the key enzyme in the dissimilatory nitrate reduction to ammonium pathway

Cytochrome c nitrite reductase, NrfA, is a soluble, periplasmic pentaheme cytochrome responsible for the reduction of nitrite to ammonium in the Dissimilatory Nitrate Reduction to Ammonium (DNRA) pathway, a vital reaction in the global nitrogen cycle. NrfA catalyzes this six-electron and eight-proton reduction of nitrite at a single active site with the help of its quinol oxidase partners. In this review, we summarize the latest progress in elucidating the reaction mechanism of ammonia production, including new findings about the active site architecture of NrfA, as well as recent results that elucidate electron transfer and storage in the pentaheme scaffold of this enzyme.

Synergies of chemodenitrification and denitrification in a saline inland lake

The interconnection between biotic and abiotic pathways involving the nitrogen and iron biogeochemical cycles has recently gained interest. While lacustrine ecosystems are considered prone to the biotic nitrate reduction (denitrification), their potential for promoting the abiotic nitrite reduction (chemodenitrification) remains unclear. In the present study, batch incubations were performed to assess the potential for chemodenitrification and denitrification in the saline inland lake Gallocanta. Sulfidic conditions are found in top sediments of the system while below (5-9 cm), it presents low organic carbon and high sulfate and ferrous iron availability. Anoxic incubations of sediment (5-9 cm) and water from the lake with nitrite revealed potential for chemodenitrification, especially when external ferrous iron was added. The obtained isotopic fractionation values for nitrite (ɛ15NNO2) were -6.8 and -12.3 ‰ and therefore, fell in the range of those previously reported for the nitrite reduction. The more pronounced ɛ15NNO2 (-12.3 ‰) measured in the experiment containing additional ferrous iron was attributed to a higher contribution of the chemodenitrification over biotic denitrification. Incubations containing nitrate also confirmed the potential for denitrification under autotrophic conditions (low organic carbon, high ferrous iron). Higher reaction rate constants were found in the experiment containing 100 μM compared to 400 μM nitrate. The obtained ɛ15NNO3 values (-8.5 and -15.1 ‰) during nitrate consumption fell in the range of those expected for the denitrification. A more pronounced ɛ15NNO3 (-15.1 ‰) was determined in the experiment presenting a lower reaction rate constant (400 μM nitrate). Therefore, in Gallocanta lake, nitrite generated during nitrate reduction can be further reduced by both the abiotic and biotic pathways. These findings establish the significance of chemodenitrification in lacustrine systems and support further exploration in aquatic environments with different levels of C, N, S, and Fe. This might be especially useful in predicting nitrous oxide emissions in natural ecosystems.

Nitrate reduction to ammonium: a phylogenetic, physiological, and genetic aspects in Prokaryotes and eukaryotes

The microbe-mediated conversion of nitrate (NO3-) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3- reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3- -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3--reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3- assimilation genes in response to NO3- availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.

Novel Alphaproteobacteria transcribe genes for nitric oxide transformation at high levels in a marine oxygen-deficient zone

Marine oxygen-deficient zones (ODZs) are portions of the ocean where intense nitrogen loss occurs primarily via denitrification and anammox. Despite many decades of study, the identity of the microbes that catalyze nitrogen loss in ODZs is still being elucidated. Intriguingly, high transcription of genes in the same family as the nitric oxide dismutase (nod) gene from Methylomirabilota has been reported in the anoxic core of ODZs. Here, we show that the most abundantly transcribed nod genes in the Eastern Tropical North Pacific ODZ belong to a new order (UBA11136) of Alphaproteobacteria, rather than Methylomirabilota as previously assumed. Gammaproteobacteria and Planctomycetia also transcribe nod, but at lower relative abundance than UBA11136 in the upper ODZ. The nod-transcribing Alphaproteobacteria likely use formaldehyde and formate as a source of electrons for aerobic respiration, with additional electrons possibly from sulfide oxidation. They also transcribe multiheme cytochrome (here named ptd) genes for a putative porin-cytochrome protein complex of unknown function, potentially involved in extracellular electron transfer. Molecular oxygen for aerobic respiration may originate from nitric oxide dismutation via cryptic oxygen cycling. Our results implicate Alphaproteobacteria order UBA11136 as a significant player in marine nitrogen loss and highlight their potential in one-carbon, nitrogen, and sulfur metabolism in ODZs.IMPORTANCEIn marine oxygen-deficient zones (ODZs), microbes transform bioavailable nitrogen to gaseous nitrogen, with nitric oxide as a key intermediate. The Eastern Tropical North Pacific contains the world's largest ODZ, but the identity of the microbes transforming nitric oxide remains unknown. Here, we show that highly transcribed nitric oxide dismutase (nod) genes belong to Alphaproteobacteria of the novel order UBA11136, which lacks cultivated isolates. These Alphaproteobacteria show evidence for aerobic respiration, using oxygen potentially sourced from nitric oxide dismutase, and possess a novel porin-cytochrome protein complex with unknown function. Gammaproteobacteria and Planctomycetia transcribe nod at lower levels. Our results pinpoint the microbes mediating a key step in marine nitrogen loss and reveal an unexpected predicted metabolism for marine Alphaproteobacteria.

Do oral and gut microbiota communicate through redox pathways? A novel asset of the nitrate-nitrite-NO pathway

Nitrate may act as a regulator of •NO bioavailability via sequential reduction along the nitrate-nitrite-NO pathway with widespread health benefits, including a eubiotic effect on the oral and gut microbiota. Here, we discuss the molecular mechanisms of microbiota-host communication through redox pathways, via the production of •NO and oxidants by the family of NADPH oxidases, namely hydrogen peroxide (via Duox2), superoxide radical (via Nox1 and Nox2) and peroxynitrite, which leads to downstream activation of stress responses (Nrf2 and NFkB pathways) in the host mucosa. The activation of Nox2 by microbial metabolites is also discussed. Finally, we propose a new perspective in which both oral and gut microbiota communicate through redox pathways, with nitrate as the pivot linking both ecosystems.

Grazing exclusion alters denitrification N2O/(N2O + N2) ratio in alpine meadow of Qinghai-Tibet Plateau

Grazing exclusion has been implemented worldwide as a nature-based solution for restoring degraded grassland ecosystems that arise from overgrazing. However, the effect of grazing exclusion on soil nitrogen cycle processes, subsequent greenhouse gas emissions and underlying mechanisms remain unclear. Here, we investigated the effect of four-year grazing exclusion on plant communities, soil properties, and soil nitrogen cycle-related functional gene abundance in an alpine meadow on the Qinghai-Tibet Plateau. Using an automated continuous-flow incubation system, we performed an incubation experiment and measured soil-borne N2O, N2, and CO2 fluxes to three successive "hot moment" events (precipitation, N deposition, and oxic-to-anoxic transition) between grazing-excluded and grazing soil. Higher soil N contents (total nitrogen, NH4+, NO3-) and extracellular enzyme activities (β-1,4-glucosidase, β-1,4-N-acetyl-glucosaminidase, cellobiohydrolase) are observed under grazing exclusion. The aboveground and litter biomass of plant community was significantly increased by grazing exclusion, but grazing exclusion decreased the average number of plant species and microbial diversity. The N2O + N2 fluxes observed under grazing exclusion were higher than those observed under free grazing. The N2 emissions and N2O/(N2O + N2) ratios observed under grazing exclusion were higher than those observed under free grazing in oxic conditions. Instead, higher N2O fluxes and lower denitrification functional gene abundances (nirS, nirK, nosZ, and nirK + nirS) under anoxia were found under grazing exclusion than under free grazing. The N2O site-preference value indicates that under grazing exclusion, bacterial denitrification contributes more to higher N2O production compared with under free grazing (81.6 % vs. 59.9 %). We conclude that grazing exclusion could improve soil fertility and plant biomass, nevertheless it may lower plant and microbial diversity and increase potential N2O emission risk via the alteration of the denitrification end-product ratio. This indicates that not all grassland management options result in a mutually beneficial situation among wider environmental goals such as greenhouse gas mitigation, biodiversity, and social welfare.

Mechanism of denitrification in subsurface-dammed Ryukyu limestone aquifer, southern Okinawa Island, Japan

Denitrification crucially regulates the attenuation of groundwater nitrate and is unlikely to occur in a fast-flowing aquifer such as the Ryukyu limestone aquifer in southern Okinawa Island, Japan. However, evidences of denitrification have been observed in several wells within this region. This study analyzed environmental isotopes (δ15NNO3 and ẟ18ONO3) to derive the rationale for denitrification at this site. Additionally, the presence of two subsurface dams in the study area may influence the processes involved in nitrate attenuation. Herein, we analyzed 150 groundwater samples collected spatially and seasonally to characterize the variations in the groundwater chemistry and stable isotopes during denitrification. The values of δ15NNO3 and δ18ONO3 displayed a progressive trend up to +59.7 ‰ and + 21 ‰, respectively, whereas the concentrations of NO3--N decreased to 0.1 mg L-1. In several wells, the enrichment factors of δ15NNO3 ranged from -6.6 to -2.1, indicating rapid denitrification, and the δ15NNO3 to δ18ONO3 ratios varied from 1.3:1 to 2:1, confirming the occurrence of denitrification. Denitrification intensively proceeds under conditions of depleted dissolved oxygen concentrations (<2 mg L-1), sluggish groundwater flow with longer residence times, high concentrations of dissolved organic carbon (>1.2 mg L-1), and low groundwater levels during the dry season with precipitation rates of <100 mm per month (Jun-Sep). SF6 analysis indicated the exclusive occurrence of denitrification in specific wells with groundwater residence times exceeding 30 years. These wells are located in close proximity to the major NE-SW fault system in the Komesu area, where the hydraulic gradient was below 0.005. Detailed geological and lithological investigations based on borehole data revealed that subsurface dams did not cause denitrification while the major NE-SW fault system uplifted the impermeable basement rock of the Shimajiri Group, creating a lithological gap at an equivalent depth that ultimately formed a sluggish groundwater area, promoting denitrification.

Unveiling the crucial role of soil microorganisms in carbon cycling: A review

Soil microorganisms, by actively participating in the decomposition and transformation of organic matter through diverse metabolic pathways, play a pivotal role in carbon cycling within soil systems and contribute to the stabilization of organic carbon, thereby influencing soil carbon storage and turnover. Investigating the processes, mechanisms, and driving factors of soil microbial carbon cycling is crucial for understanding the functionality of terrestrial carbon sinks and effectively addressing climate change. This review comprehensively discusses the role of soil microorganisms in soil carbon cycling from three perspectives: metabolic pathways, microbial communities, and environmental influences. It elucidates the roles of different microbial species in carbon cycling and highlights the impact of microbial interactions and environmental factors on carbon cycling. Through the synthesis of 2171 relevant papers in the Web of Science Core database, we elucidated the ecological community structure, activity, and assembly mechanisms of soil microorganisms crucial to the soil carbon cycle that have been widely analyzed. The integration of soil microbial carbon cycle and its driving factors are vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change. Such integration is vital for accurately predicting and modeling biogeochemical cycles and effectively addressing the challenges posed by global climate change.

Metabolically-versatile Ca. Thiodiazotropha symbionts of the deep-sea lucinid clam Lucinoma kazani have the genetic potential to fix nitrogen

Lucinid clams are one of the most diverse and widespread symbiont-bearing animal groups in both shallow and deep-sea chemosynthetic habitats. Lucinids harbor Ca. Thiodiazotropha symbionts that can oxidize inorganic and organic substrates such as hydrogen sulfide and formate to gain energy. The interplay between these key metabolic functions, nutrient uptake and biotic interactions in Ca. Thiodiazotropha is not fully understood. We collected Lucinoma kazani individuals from next to a deep-sea brine pool in the eastern Mediterranean Sea, at a depth of 1150 m and used Oxford Nanopore and Illumina sequencing to obtain high-quality genomes of their Ca. Thiodiazotropha gloverae symbiont. The genomes served as the basis for transcriptomic and proteomic analyses to characterize the in situ gene expression, metabolism and physiology of the symbionts. We found genes needed for N2 fixation in the deep-sea symbiont's genome, which, to date, were only found in shallow-water Ca. Thiodiazotropha. However, we did not detect the expression of these genes and thus the potential role of nitrogen fixation in this symbiosis remains to be determined. We also found the high expression of carbon fixation and sulfur oxidation genes, which indicate chemolithoautotrophy as the key physiology of Ca. Thiodiazotropha. However, we also detected the expression of pathways for using methanol and formate as energy sources. Our findings highlight the key traits these microbes maintain to support the nutrition of their hosts and interact with them.

Discovery of New Fusobacterium nucleatum Inhibitors to Attenuate Migratory Capability of Colon Cancer Cells by the Drug Repositioning Strategy

Recent studies revealed that intestinal microbiota played important roles in colorectal cancer (CRC) carcinogenesis. Particularly, Fusobacterium nucleatum was confirmed to promote the proliferation and metastasis of CRC. Therefore, targeting F. nucleatum may be a potential preventive and therapeutic approach for CRC. Herein, 2,272 off-patent drugs were screened inhibitory activity against F. nucleatum. Among the hits, nitisinone was identified as a promising anti-F. nucleatum lead compound. Further optimization of nitisinone led to the discovery of more potent derivatives. Particularly, compounds 19q and 22c showed potent anti-F. nucleatum activity (MIC50 = 1 and 2 μg/mL, respectively) with low cytotoxicity. Among them, compound 19q effectively attenuated the migratory ability of MC-38 cells induced by F. nucleatum. Preliminary mechanism studies suggested that nitisinone and its derivatives might act by downregulating nitroreductase and tryptophanase. Thus, the development of small molecule F. nucleatum inhibitors represents an effective strategy to treat CRC.

Simultaneous denitrification and organics removal by denitrifying bacteria inoculum in a multistage biofilm process for treating desulfuration and denitration wastewater

This study aimed to treat real wastewater from the desulfuration and denitration process in a petrochemical plant with high-strength nitrogen (TN≈200 mg/L, > 90% nitrate), sulfate (2.7%) and extremely low-strength organics (CODCr < 30 mg/L). Heterotrophic denitrification of multistage anoxic and oxic biofilm (MAOB) process in three tanks using facultative denitrifying bacteria inoculum was developed to simultaneously achieve desirable effluent nitrogen and organics at different hydraulic retention time (HRT) and carbon to nitrogen (C/N) mass ratios. The optimum condition was recommended as a C/N ratio of 1.5 and a HRT of A (24 h)/O (12-24 h) to achieve > 90% of nitrogen and organics removal as well as no significant variation of sulfate. The denitrifying biofilm in various tanks was dominant by Hyphomicrobium (8.9%-25.7%), Methylophaga (18.6%-25.8%) and Azoarcus (3.3%-19.6%), etc., containing > 20% aerobic denitrifiers. This explained that oxic zone in MAOB process also exhibited simultaneous nitrogen and organics removal.

Inhibition of nitrous oxide reduction in forest soil microcosms by different forms of methanobactin

Copper plays a critical role in controlling greenhouse gas emissions as it is a key component of the particulate methane monooxygenase and nitrous oxide reductase. Some methanotrophs excrete methanobactin (MB) that has an extremely high copper affinity. As a result, MB may limit the ability of other microbes to gather copper, thereby decreasing their activity as well as impacting microbial community composition. Here, we show using forest soil microcosms that multiple forms of MB; MB from Methylosinus trichosporium OB3b (MB-OB3b) and MB from Methylocystis sp. strain SB2 (MB-SB2) increased nitrous oxide (N2 O) production as well caused significant shifts in microbial community composition. Such effects, however, were mediated by the amount of copper in the soils, with low-copper soil microcosms showing the strongest response to MB. Furthermore, MB-SB2 had a stronger effect, likely due to its higher affinity for copper. The presence of either form of MB also inhibited nitrite reduction and generally increased the presence of genes encoding for the iron-containing nitrite reductase (nirS) over the copper-dependent nitrite reductase (nirK). These data indicate the methanotrophic-mediated production of MB can significantly impact multiple steps of denitrification, as well as have broad effects on microbial community composition of forest soils.

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland

Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.

Trichlorobacter ammonificans, a dedicated acetate-dependent ammonifier with a novel module for dissimilatory nitrate reduction to ammonia

Dissimilatory nitrate reduction to ammonia (DNRA) is a common biochemical process in the nitrogen cycle in natural and man-made habitats, but its significance in wastewater treatment plants is not well understood. Several ammonifying Trichlorobacter strains (former Geobacter) were previously enriched from activated sludge in nitrate-limited chemostats with acetate as electron (e) donor, demonstrating their presence in these systems. Here, we isolated and characterized the new species Trichlorobacter ammonificans strain G1 using a combination of low redox potential and copper-depleted conditions. This allowed purification of this DNRA organism from competing denitrifiers. T. ammonificans is an extremely specialized ammonifier, actively growing only with acetate as e-donor and carbon source and nitrate as e-acceptor, but H2 can be used as an additional e-donor. The genome of G1 does not encode the classical ammonifying modules NrfAH/NrfABCD. Instead, we identified a locus encoding a periplasmic nitrate reductase immediately followed by an octaheme cytochrome c that is conserved in many Geobacteraceae species. We purified this octaheme cytochrome c protein (TaNiR), which is a highly active dissimilatory ammonifying nitrite reductase loosely associated with the cytoplasmic membrane. It presumably interacts with two ferredoxin subunits (NapGH) that donate electrons from the menaquinol pool to the periplasmic nitrate reductase (NapAB) and TaNiR. Thus, the Nap-TaNiR complex represents a novel type of highly functional DNRA module. Our results indicate that DNRA catalyzed by octaheme nitrite reductases is a metabolic feature of many Geobacteraceae, representing important community members in various anaerobic systems, such as rice paddy soil and wastewater treatment facilities.

Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses

Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3- into NO2- and Type-II DARPs having potential to reduce NO3- to NH4+. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.

Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios

Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4+:NO2-, where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4+:NO2- ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4+:NO2- ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4+:NO2- ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.

Rational design of an acidic erythritol (ACER) medium for the enhanced isolation of the environmental pathogen Burkholderia pseudomallei from soil samples

The soil bacterium Burkholderia pseudomallei causes melioidosis, a potentially fatal and greatly underdiagnosed tropical disease. Detection of B. pseudomallei in the environment is important to trace the source of infections, define risk areas for melioidosis and increase the clinical awareness. Although B. pseudomallei polymerase chain reaction (PCR)-based environmental detection provides important information, the culture of the pathogen remains essential but is still a methodological challenge. B. pseudomallei can catabolize erythritol, a metabolic pathway, which is otherwise rarely encountered among bacteria. We recently demonstrated that replacing threonine with erythritol as a single carbon source in the pH-neutral threonine-basal salt solution (TBSS-C50) historically used improved the isolation of B. pseudomallei from rice paddy soils. However, further culture medium parameters for an optimized recovery of B. pseudomallei strains from soils are still ill-defined. We, therefore, aimed to design a new erythritol-based medium by systematically optimizing parameters such as pH, buffer capacity, salt and nutrient composition. A key finding of our study is the enhanced erythritol-based growth of B. pseudomallei under acidic medium conditions. Our experiments with B. pseudomallei strains from different geographical origin led to the development of a phosphate-buffered acidic erythritol (ACER) medium with a pH of 6.3, higher erythritol concentration of 1.2%, supplemented vitamins and nitrate. This highly selective medium composition shortened the lag phase of B. pseudomallei cultures and greatly increased growth densities compared to TBSS-C50 and TBSS-C50-based erythritol medium. The ACER medium led to the highest enrichments of B. pseudomallei as determined from culture supernatants by quantitative PCR in a comparative validation with soil samples from the central part of Vietnam. Consequently, the median recovery of B. pseudomallei colony forming units on Ashdown's agar from ACER subcultures was 5.4 times higher compared to TBSS-C50-based erythritol medium (p = 0.005) and 30.7 times higher than TBSS-C50 (p < 0.001). In conclusion, our newly developed ACER medium significantly improves the isolation of viable B. pseudomallei from soils and, thereby, has the potential to reduce the rate of false-negative environmental cultures in melioidosis risk areas.

Magnetite enhancing sludge anaerobic fermentation to improve wastewater biological nitrogen removal: Pilot-scale verification

Alkaline anaerobic fermentation for acids production has been considered as an effective method to recover resources from waste activated sludge, and magnetite could improve the quality of fermentation liquid. Here we have constructed a pilot-scale sludge alkaline anaerobic fermentation process enhanced by magnetite to produce short chain fatty acids (SCFAs), and used them as external carbon sources to improve the biological nitrogen removal of municipal sewage. Results showed that the addition of magnetite could significantly increase the production of SCFAs. The average concentration of SCFAs in fermentation liquid reached 3718.6 ± 101.5 mg COD/L and the average concentration of acetic acid reached 2368.8 ± 132.1 mg COD/L. The fermentation liquid enhanced by magnetite were used in the mainstream A²O process, and the TN removal efficiency increased from 48.0% ± 5.4%-62.2% ± 6.6%. The main reason is that the fermentation liquid is conducive to the succession of microbial community in the denitrification process, increasing the abundance of denitrification functional bacteria and realizing the enhancement of denitrification process. Besides, magnetite can promote the activity of enzyme to enhance biological nitrogen removal. Finally, the economic analysis showed that magnetite enhancing sludge anaerobic fermentation was economically and technically feasible to promote biological nitrogen removal of municipal sewage.

Insights into solid phase denitrification in wastewater tertiary treatment: the role of solid carbon source in carbon biodegradation and heterotrophic denitrification

The practical application of solid phase denitrification (SPD) was hindered by either poor water quality from natural plant-like materials or high cost of pure synthetic biodegradable polymers. In this study, by combining polycaprolactone (PCL) with new natural materials (peanut shell, sugarcane bagasse), two novel economical solid carbon sources (SCSs) named as PCL/PS and PCL/SB were developed. Pure PCL and PCL/TPS (PCL with thermal plastic starch) were supplied as controls. During the 162-day operation, especially in the shortest HRT (2 h), higher NO₃^--N removal was achieved by PCL/PS (87.60%±0.06%) and PCL/SB (87.93%±0.05%) compared to PCL (83.28%±0.07%) and PCL/TPS (81.83%±0.05%). The predicted abundance of functional enzymes revealed the potential metabolism pathways of major components of SCSs. The natural components entered the glycolytic cycle by enzymatical generation of intermediates, while biopolymers being converted into small molecule products under specific enzyme activities (i.e., carboxylesterase, aldehyde dehydrogenase), together providing electrons and energy for denitrification.

Study of NIT domain-containing chemoreceptors from two global phytopathogens and identification of NIT domains in eukaryotes

Bacterial signal transduction systems are typically activated by the binding of signal molecules to receptor ligand binding domains (LBDs), such as the NIT LBD. We report here the identification of the NIT domain in more than 15,000 receptors that were present in 30 bacterial phyla, but also in 19 eukaryotic phyla, expanding its known phylogenetic distribution. The NIT domain formed part of seven receptor families that either control transcription, mediate chemotaxis or regulate second messenger levels. We have produced the NIT domains from chemoreceptors of the bacterial phytopathogens Pectobacterium atrosepticum (PacN) and Pseudomonas savastanoi (PscN) as individual purified proteins. High-throughput ligand screening using compound libraries revealed a specificity for nitrate and nitrite binding. Isothermal titration calorimetry experiments showed that PacN-LBD bound preferentially nitrate ( K _D  = 1.9 μM), whereas the affinity of PscN-LBD for nitrite ( K _D  = 2.1 μM) was 22 times higher than that for nitrate. Analytical ultracentrifugation experiments indicated that PscN-LBD is monomeric in the presence and absence of ligands. The R182A mutant of PscN did not bind nitrate or nitrite. This residue is not conserved in the NIT domain of the Pseudomonas aeruginosa chemoreceptor PA4520, which may be related to its failure to bind nitrate/nitrite. The magnitude of P. atrosepticum chemotaxis towards nitrate was significantly greater than that of nitrite and pacN deletion almost abolished responses to both compounds. This study highlights the important role of nitrate and nitrite as signal molecules in life and advances our knowledge on the NIT domain as universal nitrate/nitrite sensor module.

Evaluation of sludge anaerobic fermentation driving partial denitrification capability: In view of kinetics and metagenomic mechanisms

Partial denitrification (PD) provides a promising approach of efficient and stable nitrite (NO₂^--N) generation for annamox. In this study, the feasibility of short-term sludge anaerobic fermentation driving PD was evaluated. It was found that a higher NO₂^--N accumulation in nitrate (NO₃^--N) reduction was obtained with the 5-days fermented sludge compared to 8 and 15-days fermentation. Moreover, compared to acetate as carbon source, sludge fermentation products (SFPs) induced the higher NO₂^--N production with nitrate-to-nitrite transformation ratio (NTR) nearly 100 %. Denitrification activity of fermented sludge were obviously improved with SFPs as electron donor. Metagenomic analysis revealed that Thauera was the dominant bacteria, which was assumed to be the key contributor to PD performance by harboring the highest narGHI and napAB but much lower nirS and nirK. Under the conditions of SFPs and fermented sludge, Thauera was speculated to have higher resistance than other denitrifiers attributed to versatile carbon metabolic capabilities utilizing SFPs with the significantly improved genes for metabolism of complex organic carbon via glycolysis after anaerobic fermentation. A novel integration of sludge fermentation driving PD and anammox for mainstream wastewater treatment and sidestream polishing was proposed to offer a promising application with reduced commercial carbon source consumption and waste sludge reduction.

Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring

The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.

Causal Relationship between Physiological and Pathological Processes in the Brain and in the Gastrointestinal Tract: The Brain-Intestine Axis

The brain and gastrointestinal tract are the most important organs responsible for detecting, transmitting, integrating, and responding to signals coming from the internal and external environment. A bidirectional system of neurohumoral communication (the "intestine-brain" axis) combines the activity of the intestine and brain (or brain and intestine) of a person. It affects human development and behavior. This paper analyzes the literature data on the existence of a relationship between the central and enteral nervous systems. Based on data on the number of neurons in the enteral nervous system (approximately 250 million nerve cells), the concept of a "second brain" in the intestine has been proposed in foreign literature, which, by its influence on the brain, can have a more powerful influence than the spinal cord (approximately 10 million neurons) with its autonomic nervous system. However, it turned out that Russian scientists, academicians of the Academy of Sciences of the Soviet Union I.P. Pavlov, K.M. Bykov, and A.M. Ugolev, analyzed cortical-visceral relationships in the 20th century and wrote about the existence of a connection between the central and enteral nervous systems. One of the urgent problems of modern physiology, pathophysiology, biophysics, biochemistry, and medicine is to clarify the causal relationship between the central and enteral nervous systems, as well as between neurological, mental, and gastrointestinal diseases in order to combine the efforts of specialists of various medical and biological profiles to solve urgent medical problems.

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.

Functional Prediction of Microbial Communities in Sediment Microbial Fuel Cells

Sediment microbial fuel cells (MFCs) were developed in which the complex substrates present in the sediment could be oxidized by microbes for electron production. In this study, the functional prediction of microbial communities of anode-associated soils in sediment MFCs was investigated based on 16S rRNA genes. Four computational approaches, including BugBase, Functional Annotation of Prokaryotic Taxa (FAPROTAX), the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2), and Tax4Fun2, were applied. A total of 67, 9, 37, and 38 functional features were statistically significant. Among these functional groups, the function related to the generation of precursor metabolites and energy was the only one included in all four computational methods, and the sum total of the proportion was 93.54%. The metabolism of cofactor, carrier, and vitamin biosynthesis was included in the three methods, and the sum total of the proportion was 29.94%. The results suggested that the microbial communities usually contribute to energy metabolism, or the metabolism of cofactor, carrier, and vitamin biosynthesis might reveal the functional status in the anode of sediment MFCs.

Chitosan-graphene quantum dot based active film as smart wound dressing

Graphene quantum dots (GQDs), are biocompatible materials, with mechanical strength and stability. Chitosan, has antibacterial and anti-inflammatory properties, and biocompatibility. Wound healing is a challenging process especially in chronic diseases and infection. In this study, films consisting of chitosan and graphene quantum dots were developed for application in infected wounds. The chitosan-graphene films were prepared in the acidic solution followed by slow solvent evaporation and drying. The chitosan-graphene films were characterized by the scanning electron microscopy, x-ray diffraction, atomic force microscopy, Raman spectroscopy and thermogravimetric analysis. The films' was evaluated by the wound healing assays, hemolytic potential, and nitrite production, cytokine production and swelling potential. The obtained films were flexible and well-structured, promoting cell migration, greater antibacterial activity, lower hemolytic activity, and maintaining wound moisture. Our data suggested that the use of graphene quantum dot-containing chitosan films would be an efficient and promising way in combating wounds.

Effects of Bellamya purificata Cultivation at Different Stocking Densities on the Dynamics and Assembly of Bacterial Communities in Sediment

To optimize the integrated multi-trophic aquaculture (IMTA) model, improve the efficiency of resource utilization, and reduce environmental pollution, Bellamya purificata, as a potential bioremediation species, was studied to investigate the effect of B. purificata culture on the dynamics and assembly of bacterial communities in sediment. Four experimental groups were established at four different densities: 0, 234.38, 468.75, and 937.5 g/m² (represented as CON, LD, MD, and HD, respectively). Each group was with three replicates. The 16S ribosomal RNA (rRNA) high-throughput sequencing was used to evaluate the composition, function, and assembly of bacterial communities in sediment. B. purificata cultivation significantly altered the composition and function of the bacterial communities in sediment; at high stocking density, it significantly decreased anaerobic and increased aerobic organic matter decomposition, whereas at low stocking density, it decreased the number of bacteria involved in sulfate reduction and inhibited the denitrification process. B. purificata decreased direct competition and promoted collaboration or niche sharing in bacterial communities, especially at the high stocking density. Moreover, B. purificata cultivation resulted in greater changes in the environmental factors. Variations in dissolved oxygen, pH, total nitrogen, nitrate, and nitrite levels were closely related to the altered composition and function of the bacterial communities. Stochastic processes dominated the bacterial community assembly in the sediment and B. purificata cultivation had limited impacts on the bacterial community assembly. The study provided a reference for the dynamics and assembly of bacterial communities in sediment with different densities of B. purificata cultivation and we hope that the findings will provide a theoretical reference for the optimization of IMTA and improve management strategies for B. purificata polyculture.

Complete genome analysis of Pseudomonas furukawaii ZS1 isolated from grass carp (Ctenopharyngodon idellus) culture water

Pseudomonas furukawaii ZS1, isolated from grass carp (Ctenopharyngodon idellus) culture water, exhibits efficient aerobic nitrate reduction without nitrite accumulation; however, the molecular pathway underlying this aerobic nitrate reduction remains unclear. In this study, we constructed a complete genome map of P. furukawaii ZS1 and performed a comparative genomic analysis with a reference strain. The results showed that P. furukawaii ZS1 genome was 6 026 050 bp in size and contained 5427 predicted protein-coding sequences. The genome contained all the necessary genes for the dissimilatory nitrate reduction to ammonia pathway but lacked those for the assimilatory nitrate reduction pathway; additionally, genes that convert ammonia to organic nitrogen were also identified. The presence of putative genes associated with the nitrogen and oxidative phosphorylation pathways implied that ZS1 can perform respiration and nitrate reduction simultaneously under aerobic conditions, so that nitrite is rapidly consumed for detoxication by denitrification. The aim of this study is to indicate the great potential of strain ZS1 for future full-scale applications in aquaculture. This work provided insights at the molecular level on the nitrogen metabolic pathways in Pseudomonas species. The understanding of nitrogen metabolic pathways also provides significant molecular information for further Pseudomonas species modification and development.

Dynamic changes of gut bacterial communities present in larvae of Anoplophora glabripennies collected at different developmental stages

The Asian long-horned beetle, Anoplophora glabripennies (Motschulsky), is a destructive wood-boring pest that is capable of killing healthy trees. Gut bacteria in the larvae of the wood-boring pest is essential for the fitness of hosts. However, little is known about the structure of the intestinal microbiome of A. glabripennies during larval development. Here, we used Illumina MiSeq high-throughput sequencing technology to analyze the larval intestinal bacterial communities of A. glabripennies at the stages of newly hatched larvae, 1st instar larvae and 4th instar larvae. Significant differences were found in larval gut microbial community structure at different larvae developmental stages. Different dominant genus was detected during larval development. Acinetobacter were dominant in the newly hatched larvae, Enterobacter and Raoultella in the 1st instar larvae, and Enterococcus and Gibbsiella in the 4th instar larvae. The microbial richness in the newly hatched larvae was higher than those in the 1st and 4th instar larvae. Many important functions of the intestinal microbiome were predicted, for example, fermentation and chemoheterotrophy functions that may play an important role in insect growth and development was detected in the bacteria at all tested stages. However, some specific functions are found to be associated with different development stages. Our study provides a theoretical basis for investigating the function of the intestinal symbiosis bacteria of A. glabripennies.

Interaction mechanism between nitrogen conversion and the microbial community in the hydrodynamic heterogeneous interaction zone

To study the inorganic nitrogen in the process of interaction of river and groundwater and the changes in the microbial community, a vertical simulation device was used to simulate groundwater recharge to river water (upwelling) and river water recharge to groundwater (downwelling). The inorganic nitrogen concentrations in the soil and water solution as well as the characteristics of the microbial community were assessed to determine the inorganic nitrogen transformation and microbial community response in the heterogeneous interaction zone under hydrodynamic action, and the interaction mechanism between nitrogen transformation and the microbial community in the interaction zone was revealed. The removal rates of NO₃^--N in the simulated solution reached 99.1% and 99.3% under the two fluid-groundwater conversion modes, and the prolonged hydraulic retention time (HRT) of the oxidization-reduction layer in the fine clay area and the high organic matter content made the inorganic nitrogen transformation process dominated by microorganisms more complete. The denitrification during upwelling, dominated by denitrifying bacteria in Sphingomonas, Pseudomonas, Bacillus, and Arthrobacter, was stronger than that during downwelling. Dissimilatory nitrate reduction to ammonium (DNRA), controlled by some aerobic bacteria in Pseudomonas, Bacillus, and Desulfovibrio, was more intense in downflow mode than upflow mode.

The molybdate-binding protein ModA is required for Proteus mirabilis-induced UTI

Background

Proteus mirabilis is one of the pathogens commonly causing urinary tract infections (UTIs). The molybdate-binding protein ModA encoded by modA binds molybdate with high affinity and transports it. Increasing evidence shows that ModA promotes the survival of bacteria in anaerobic environments and participates in bacterial virulence by obtaining molybdenum. However, the role of ModA in the pathogenesis of P. mirabilis remains unknown.

Results

In this study, a series of phenotypic assays and transcriptomic analyses were used to study the role of ModA in the UTIs induced by P. mirabilis. Our data showed that ModA absorbed molybdate with high affinity and incorporated it into molybdopterin, thus affecting the anaerobic growth of P. mirabilis. Loss of ModA enhanced bacterial swarming and swimming and up-regulated the expression of multiple genes in flagellar assembly pathway. The loss of ModA also resulted in decreased biofilm formation under anaerobic growth conditions. The modA mutant significantly inhibited bacterial adhesion and invasion to urinary tract epithelial cells and down-regulated the expression of multiple genes associated with pilus assembly. Those alterations were not due to anaerobic growth defects. In addition, the decreased bacteria in the bladder tissue, the weakened inflammatory damage, the low level of IL-6, and minor weight change was observed in the UTI mouse model infected with modA mutant.

Conclusion

Here, we reported that in P. mirabilis, ModA mediated the transport of molybdate, thereby affecting the activity of nitrate reductase and thus affecting the growth of bacteria under anaerobic conditions. Overall, this study clarified the indirect role of ModA in the anaerobic growth, motility, biofilm formation, and pathogenicity of P. mirabilis and its possible pathway, and emphasized the importance of the molybdate-binding protein ModA to P. mirabilis in mediating molybdate uptake, allowing the bacterium to adapt to complex environmental conditions and cause UTIs. Our results provided valuable information on the pathogenesis of ModA-induced P. mirabilis UTIs and may facilitate the development of new treatment strategies.

An Important Role of the Type VI Secretion System of Pseudomonas aeruginosa Regulated by Dnr in Response to Anaerobic Environments

The type VI secretion system (T6SS) is capable of secreting a variety of metal-binding proteins involved in metal ion uptake, and it mediates an active metal ion transport system that contributes to competition between bacteria. Pseudomonas aeruginosa H2-T6SS can increase molybdenum ion acquisition and enhance bacterial survival advantage by promoting the secretion of the molybdate-binding protein ModA, in which the expression of H2-T6SS core genes hcp2, hsiA2, and clpV2 is activated by anaerobic conditions and are all regulated by the global regulator Anr. Here, we report the regulation of T6SS by Dnr, a dedicated dissimilatory nitrate respiration regulator in P. aeruginosa. Of the three distinct T6SS loci carried by P. aeruginosa, only the anaerobic expression of H2-T6SS was activated by Dnr; H1-T6SS or H3-T6SS did not respond to anaerobically induced activation. We also demonstrated that Dnr promotes the anaerobic secretion of ModA, which acts as a potential substrate for H2-T6SS, providing an advantage not only for the anaerobic growth of bacteria but also for functional competition. Overall, this study elucidates the important role played by Dnr in mediating the anaerobic expression of T6SS in P. aeruginosa, indicating that the functional advantage of H2-T6SS in response to anaerobic induction may be a conditional environmental adaptation. It also extends our understanding of the function of Dnr as a specific regulator of dissimilatory nitrate respiration. IMPORTANCE The type VI secretion system (T6SS) plays an important role in bacterial competition by mediating the transport of active metal ions. Pseudomonas aeruginosa carries three distinct T6SS loci (H1-, H2-, and H3-T6SS). The H2-T6SS promotes the secretion of the molybdate-binding protein ModA for the acquisition of molybdenum ions to adapt to anaerobic survival. Here, we report that the specialized dissimilatory nitrate respiration regulator Dnr in P. aeruginosa controls the anaerobic expression of H2-T6SS and that this regulation is essential for ModA protein secretion, anaerobic growth, and bacterial competition. This study elucidates the regulatory mechanism of Dnr on H2-T6SS in P. aeruginosa, revealing an important role played by H2-T6SS in adapting to an anaerobic environment.

Effects of modified biochars on the shifts of short-chain fatty acid profile, iron reduction, and bacterial community in paddy soil

Biochar is well known as an effective means for soil amendment, and modification on biochar with different methods could improve the benefits for environmental remediation. In this study, two modified biochars were generated with nitric acid (NBC) and hydrogen peroxide (OBC) pretreatment, and a control biochar was produced after washing with deionized water (WBC). The dynamics of short-chain fatty acids (SCFAs), iron concentration and bacterial community in rice paddy soil amended with different biochars or without adding biochar (CK) were studied during 70 days of anaerobic incubation. Compared to CK treatment, the accumulation of SCFAs was largely inhibited by the amendment of biochars. Besides, OBC and WBC increased the accumulation of Fe(II) at the initial stage of incubation. Via 16S rRNA gene sequencing, modified biochars caused significant response of bacterial community in comparison to WBC at Day 0-1, and three biochars favored bacterial α-diversity in the paddy soil at the end of the incubation. Interestingly, positive and negative correlations between NBC and several bacteria taxa (e.g. Geobacter, Fonticella and Clostridium) were observed. The study revealed that modified biochars had significant effects on the shifts of SCFAs, Fe(III) reduction and bacterial diversity, which provides fundamental information for future application of modified biochars in rice cropping ecosystem.

Soil characteristics and redox properties of infiltrating water are determinants of microbial communities at managed aquifer recharge sites

In this study, we conducted a meta-analysis of soil microbial communities at three, pilot-scale field sites simulating shallow infiltration for managed aquifer recharge (MAR). We evaluated shifts in microbial communities after infiltration across site location, through different soils, with and without carbon-rich amendments added to test plots. Our meta-analysis aims to enable more effective MAR basin design by identifying potentially important interactions between soil physical-geochemical parameters and microbial communities across several geographically separate MAR basins. We hypothesized infiltration and carbon amendments would lead to common changes in subsurface microbial communities at multiple field sites but instead found distinct differences. Sites with coarser (mainly sandy) soil had large changes in diversity and taxa abundance, while sites with finer soils had fewer significant changes in genera, despite having the greatest increase in nitrogen cycling. Below test plots amended with a carbon-rich permeable reactive barrier, we observed more nitrate removal and a decrease in genera capable of nitrification. Multivariate statistics determined that the soil texture (a proxy for numerous soil characteristics) was the main determinant of whether the microbial community composition changed because of infiltration. These results suggest that microbial communities in sandy soil with carbon-rich amendments are most impacted by infiltration. Soil composition is a critical parameter that links between microbial communities and nutrient cycling during infiltration and could influence the citing and operation of MAR to benefit water quality and supply.

The effect of modified biochar on methane emission and succession of methanogenic archaeal community in paddy soil

Modified biochars have been widely applied in ameliorating environmental problems. However, the effect of modified biochar on suppressing CH₄ emission in rice paddy soil is not fully understood. In order to further study CH₄ regulation in paddy soil via the modification of biochar and explore its influence on key archaeal communities, two modified biochars were generated with the pre-treatment of nitric acid (NBC) and hydrogen peroxide (OBC), respectively, and a control group was setup with water-washed biochar (WBC). Results showed that NBC significantly suppressed CH₄ emission, followed by OBC and WBC, while NBC promoted the CO₂ emission. Besides, the addition of biochars inhibited the accumulation of acetate and H₂ in rice paddy soil, especially in the NBC treatment. 16S rRNA gene sequencing revealed that biochars amendment increased α-diversity of archaeal community and the modified biochars could mitigate the loss of α-diversity in the early stage of anaerobic incubation. Additionally, NBC amendment largely declined the relative abundance of methanogens (especially Methanosarcina) in archaeal community, while OBC and NBC promoted the relative abundance of Candidatus_Methanoperedens. Via Spearman's correlation coefficient analysis, NBC had positive correlations with Methanosaeta, and OBC showed a negative correlation with Methanocella. Overall, this study provided a practical way to regulate the CH₄ emission and associated methanogenic archaea via the amendment of different modified biochars in rice paddy soil.

Economic, technical, and environmental evaluation of retrofitting scenarios in a full-scale industrial wastewater treatment system

The use of mathematical models is a well-established procedure in the field of (waste) water engineering to "virtually" evaluate the feasibility of novel process modifications. In this way, only options with the highest chance of success are further developed to be implemented at full-scale, while less interesting proposals can be disregarded at an early stage. Nevertheless, there is still lack of studies, where different plant-wide model predictions (effluent quality, process economics, and technical aspects) are comprehensibly verified in the field with full-scale data. In this work, a set of analysis/evaluation tools are used to assess alternative retrofitting options in the largest industrial wastewater treatment plant in Northern Europe. A mechanistic mathematical model is simulated to reproduce process behavior (deviation < 11%). Multiple criteria are defined and verified with plant data (deviation < 5%). The feasibility of three types of scenarios is tested: (1) stream refluxing, (2) change of operational conditions and (3) the implementation of new technologies. Experimental measurements and computer simulations show that the current plant´s main revenues are obtained from the electricity produced by the biogas engine (54%) and sales of the inactivated bio-solids for off-site biogas production (33%). The main expenditures are the discharge fee (39%), and transportation and handling of bio-solids (30%). Selective treatment of bio-solid streams strongly modifies the fate of COD and N compounds within the plant. In addition, it increases revenues (+3%), reduces cost (-9%) and liberates capacity in both activated sludge (+25%) and inactivation reactors (+50%). Better management of the buffer tank promotes heterotrophic denitrification instead of dissimilatory nitrate conversion to ammonia. In this way, 11% of the incoming nitrogen is removed within the anaerobic water line and does not overload the activated sludge reactors. Only a marginal increase in process performance is achieved when the anaerobic granular sludge reactor operates at full capacity. The latter reveals that influent biodegradability is the main limiting factor rather than volume. Usage of either NaOH or heat (instead of CaO) as inactivation agents allows anaerobic treatment of the reject water, which substantially benefits revenues derived from higher electricity recovery (+44%). However, there is a high toll paid on chemicals (+73%) or heat recovery (-19%) depending on the inactivation technology. In addition, partial nitration/Anammox and a better poly-aluminum chloride (PAC) dosage strategy is necessary to achieve acceptable (< 2%) N and P levels in the effluent. The scenarios are evaluated from a sustainability angle by using life cycle impact assessment (LCIA) in form of damage stressors grouped into three categories: human health, ecosystems quality, and resource scarcity. The presented decision support tool has been used by the biotech company involved in the study to support decision-making on how to handle future expansions.

Fe3O4-Fused Magnetic Air Stone Prepared From Wasted Iron Slag Enhances Denitrification in a Biofilm Reactor by Increasing Electron Transfer Flow

nFe₃O₄ was prepared from waste iron slag and loaded onto air stone (named magnetic air stone or MAS in the following text). The main component of air stone is carborundum. To study the magnetic effects of MAS on denitrification, a biofilm reactor was built, and its microbial community structure and electron transfer in denitrification were analyzed. The results showed that MAS improved the performance of the reactor in both carbon and nitrogen removal compared with air stone (AS) control, and the average removal efficiencies of COD, TN, and NH₄⁺-N increased by 17.15, 16.1, and 11.58%, respectively. High-throughput sequencing revealed that magnetism of MAS had a significant effect on the diversity and richness of microorganisms in the biofilm. The MAS also reduced the inhibition of rotenone, mipalene dihydrochloride (QDH), and sodium azide on the respiratory chain in denitrification and enhanced the accumulation of nitrite, in order to provide sufficient substrate for the following denitrification process. Therefore, the denitrification process is accelerated by the MAS. The results allowed us to deduce the acceleration sites of MAS in the denitrification electron transport chain.

The existence of MAS provides a new rapid method for the denitrifying electron transport process. Even in the presence of respiratory inhibitors of denitrifying enzymes, the electron transfer acceleration provided by MAS still exists objectively. This is the mechanism through which MAS can restore the denitrification process inhibited by respiratory inhibitors to a certain extent.

Inspired by Nature-Functional Analogues of Molybdenum and Tungsten-Dependent Oxidoreductases

Throughout the previous ten years many scientists took inspiration from natural molybdenum and tungsten-dependent oxidoreductases to build functional active site analogues. These studies not only led to an ever more detailed mechanistic understanding of the biological template, but also paved the way to atypical selectivity and activity, such as catalytic hydrogen evolution. This review is aimed at representing the last decade’s progress in the research of and with molybdenum and tungsten functional model compounds. The portrayed systems, organized according to their ability to facilitate typical and artificial enzyme reactions, comprise complexes with non-innocent dithiolene ligands, resembling molybdopterin, as well as entirely non-natural nitrogen, oxygen, and/or sulfur bearing chelating donor ligands. All model compounds receive individual attention, highlighting the specific novelty that each provides for our understanding of the enzymatic mechanisms, such as oxygen atom transfer and proton-coupled electron transfer, or that each presents for exploiting new and useful catalytic capability. Overall, a shift in the application of these model compounds towards uncommon reactions is noted, the latter are comprehensively discussed.

Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer

Nitrate pollution is a major threat to groundwater quality in agricultural areas. Natural attenuation of nitrate in contaminated aquifers is mediated by denitrifying microbial populations in anoxic environments. Vertical distribution of denitrifying microbial communities in aquifers is greatly influenced by groundwater redox conditions, local hydrogeological parameters, and seasonal variability in groundwater flow and recharge. In this study, we investigated groundwater geochemistry and the composition of bacterial and archaeal communities with increasing depth in a shallow nitrate-contaminated aquifer in British Columbia, Canada. High-resolution passive diffusion sampling was conducted to collect groundwater at 10-cm intervals from 4 to 20 m below ground surface (mbgs) in the aquifer. Geochemical analyses of major ions indicated a general shift in the groundwater chemistry below 16 mbgs including decreasing chloride concentrations that suggest two-end member mixing of shallow and deep groundwater with different chemistries. A redoxcline was further observed within a 2 m transition zone at 18-20 mbgs characterized by sharp declines in nitrate concentrations and increases in sulfate and total inorganic carbon. Excursions in δ¹⁵N-NO₃^- and δ¹⁸O-NO₃^- in the same depth interval are consistent with denitrification, and a concomitant decrease in δ³⁴S-SO₄^2- suggested that denitrification was coupled to sulfide or sulfur oxidation. Microbial communities within this depth interval were significantly dissimilar to those above and below, featuring putative lithotrophic denitrifying bacteria belonging to the genera Sulfurifustis, Sulfuritalea and Sulfuricella. These lineages were detected in greatest abundance at 19 mbgs while the abundances of putative heterotrophic sulfate-reducing bacteria belonging to the genus Desulfosporosinus were greatest at 20 mbgs. In addition to help distinguish denitrification from mixing-induced changes in groundwater chemistry, the above observed vertical stratification of the microbial key players connects nitrate removal to the locations of the aquifer sampled.

Salinity Impact on Composition and Activity of Nitrate-Reducing Fe(II)-Oxidizing Microorganisms in Saline Lakes

Nitrate-reducing Fe(II)-oxidizing (NRFeOx) microorganisms contribute to nitrogen, carbon, and iron cycling in freshwater and marine ecosystems. However, NRFeOx microorganisms have not been investigated in hypersaline lakes, and their identity, as well as their activity in response to salinity, is unknown. In this study, we combined cultivation-based most probable number (MPN) counts with Illumina MiSeq sequencing to analyze the abundance and community compositions of NRFeOx microorganisms enriched from five lake sediments with different salinities (ranging from 0.67 g/L to 346 g/L). MPN results showed that the abundance of NRFeOx microorganisms significantly (P < 0.05) decreased with increasing lake salinity, from 7.55 × 10³ to 8.09 cells/g dry sediment. The community composition of the NRFeOx enrichment cultures obtained from the MPNs differed distinctly among the five lakes and clustered with lake salinity. Two stable enrichment cultures, named FeN-EHL and FeN-CKL, were obtained from microcosm incubations of sediment from freshwater Lake Erhai and hypersaline Lake Chaka. The culture FeN-EHL was dominated by genus Gallionella (68.4%), while the culture FeN-CKL was dominated by genus Marinobacter (71.2%), with the former growing autotrophically and the latter requiring an additional organic substrate (acetate) and Fe(II) oxidation, caused to a large extent by chemodenitrification [reaction of nitrite with Fe(II)]. Short-range ordered Fe(III) (oxyhydr)oxides were the product of Fe(II) oxidation, and the cells were partially attached to or encrusted by the formed iron minerals in both cultures. In summary, different types of interactions between Fe(II) and nitrate-reducing bacteria may exist in freshwater and hypersaline lakes, i.e., autotrophic NRFeOx and chemodenitrification in freshwater and hypersaline environments, respectively. IMPORTANCE NRFeOx microorganisms are globally distributed in various types of environments and play a vital role in iron transformation and nitrate and heavy metal removal. However, most known NRFeOx microorganisms were isolated from freshwater and marine environments, while their identity and activity under hypersaline conditions remain unknown. Here, we demonstrated that salinity may affect the abundance, identity, and nutrition modes of NRFeOx microorganisms. Autotrophy was only detectable in a freshwater lake but not in the saline lake investigated. We enriched a mixotrophic culture capable of nitrate-reducing Fe(II) oxidation from hypersaline lake sediments. However, Fe(II) oxidation was probably caused by abiotic nitrite reduction (chemodenitrification) rather than by a biologically mediated process. Consequently, our study suggests that in hypersaline environments, Fe(II) oxidation is largely caused by chemodentrification initiated by nitrite formation by chemoheterotrophic bacteria, and additional experiments are needed to demonstrate whether or to what extent Fe(II) is enzymatically oxidized.

Reforming Nitrate Metabolism for Enhancing L-Arginine Production in Corynebacterium crenatum Under Oxygen Limitation

Various amino acids are widely manufactured using engineered bacteria. It is crucial to keep the dissolved oxygen at a certain level during fermentation, but accompanied by many disadvantages, such as high energy consumption, reactive oxygen species, and risk of phage infections. Thus, anaerobic production of amino acids is worth attempting. Nitrate respiration systems use nitrate as an electron acceptor under anoxic conditions, which is different from the metabolism of fermentation and can produce energy efficiently. Herein, we engineered Corynebacterium crenatum to enhance L-arginine production under anaerobic conditions through strengthening nitrate respiration and reforming nitrogen flux. The construction of mutant strain produced up to 3.84 g/L L-arginine under oxygen limitation with nitrate, and this value was 131.33% higher than that produced by the control strain under limited concentrations of oxygen without nitrate. Results could provide fundamental information for improving L-arginine production by metabolic engineering of C. crenatum under oxygen limitation.

Effect of Copper on Expression of Functional Genes and Proteins Associated with Bradyrhizobium diazoefficiens Denitrification

Nitrous oxide (N₂O) is a powerful greenhouse gas that contributes to climate change. Denitrification is one of the largest sources of N₂O in soils. The soybean endosymbiont Bradyrhizobium diazoefficiens is a model for rhizobial denitrification studies since, in addition to fixing N₂, it has the ability to grow anaerobically under free-living conditions by reducing nitrate from the medium through the complete denitrification pathway. This bacterium contains a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a Cu-dependent nitrous oxide reductase (Nos) encoded by the napEDABC, nirK, norCBQD and nosRZDFYLX genes, respectively. In this work, an integrated study of the role of Cu in B. diazoefficiens denitrification has been performed. A notable reduction in nirK, nor, and nos gene expression observed under Cu limitation was correlated with a significant decrease in NirK, NorC and NosZ protein levels and activities. Meanwhile, nap expression was not affected by Cu, but a remarkable depletion in Nap activity was found, presumably due to an inhibitory effect of nitrite accumulated under Cu-limiting conditions. Interestingly, a post-transcriptional regulation by increasing Nap and NirK activities, as well as NorC and NosZ protein levels, was observed in response to high Cu. Our results demonstrate, for the first time, the role of Cu in transcriptional and post-transcriptional control of B. diazoefficiens denitrification. Thus, this study will contribute by proposing useful strategies for reducing N₂O emissions from agricultural soils.

Assessment of Ammonia as a Biosignature Gas in Exoplanet Atmospheres

Ammonia (NH₃) in a terrestrial planet atmosphere is generally a good biosignature gas, primarily because terrestrial planets have no significant known abiotic NH₃ source. The conditions required for NH₃ to accumulate in the atmosphere are, however, stringent. NH₃'s high water solubility and high biousability likely prevent NH₃ from accumulating in the atmosphere to detectable levels unless life is a net source of NH₃ and produces enough NH₃ to saturate the surface sinks. Only then can NH₃ accumulate in the atmosphere with a reasonable surface production flux. For the highly favorable planetary scenario of terrestrial planets with hydrogen (H₂)-dominated atmospheres orbiting M dwarf stars (M5V), we find that a minimum of about 5 ppm column-averaged mixing ratio is needed for NH₃ to be detectable with JWST, considering a 10 ppm JWST systematic noise floor. When the surface is saturated with NH₃ (i.e., there are no NH₃-removal reactions on the surface), the required biological surface flux to reach 5 ppm is on the order of 10¹⁰ molecules/(cm²·s), comparable with the terrestrial biological production of methane (CH₄). However, when the surface is unsaturated with NH₃, due to additional sinks present on the surface, life would have to produce NH₃ at surface flux levels on the order of 10¹⁵ molecules/(cm²·s) (∼4.5 × 10⁶ Tg/year). This value is roughly 20,000 times greater than the biological production of NH₃ on the Earth and about 10,000 times greater than Earth's CH₄ biological production. Volatile amines have similar solubilities and reactivities to NH₃ and hence share NH₃'s weaknesses and strengths as a biosignature. Finally, to establish NH₃ as a biosignature gas, we must rule out mini-Neptunes with deep atmospheres, where temperatures and pressures are high enough for NH₃'s atmospheric production.

Heterotrophic nitrification and aerobic denitrification process: Promising but a long way to go in the wastewater treatment

The traditional biological nitrogen removal (BNR) follows the conventional scheme of sequential nitrification and denitrification. In recent years, novel processes such as anaerobic ammonia oxidation (anammox), complete oxidation of ammonia to nitrate in one organism (comammox), heterotrophic nitrification and aerobic denitrification (HN-AD), and dissimilatory nitrate reduction to ammonium (DNRA) are gaining tremendous attention after the discovery of metabolically versatile bacteria. Among them, HN-AD offers several advantages because individual bacteria could achieve one-stage nitrogen removal under aerobic conditions in the presence of organic carbon. In this review, besides classical BNR processes, we summarized the existing literature on HN-AD bacteria which have been isolated from diverse habitats. A particular focus was given on the diversity and physiology of HN-AD bacteria, influences of physiological and biochemical factors on their growth, nitrogen removal performances, as well as limitations and strategies in unraveling HN-AD metabolic pathways. We also presented case studies of HN-AD application in wastewater treatment facilities, pointed out forthcoming challenges of HN-AD in these systems, and presented modulation strategies for HN-AD application in engineering. This review may help improve the existing design of wastewater treatment plants by harnessing HN-AD bacteria for effective nitrogen removal.

Enzymatic cometabolic biotransformation of organic micropollutants in wastewater treatment plants: A review

Biotransformation of trace-level organic micropollutants (OMPs) by complex microbial communities in wastewater treatment facilities is a key process for their detoxification and environmental impact reduction. Therefore, understanding the metabolic activities and mechanisms that contribute to their biotransformation is essential when developing approaches aiming to minimize their discharge. This review addresses the relevance of cometabolic processes and discusses the main enzymatic activities currently known to take part in OMPs removal under different redox environments in the compartments of wastewater treatment plants. Furthermore, the most common methodologies to decipher such enzymes are discussed, including the use of in vitro enzyme assays, enzymatic inhibitors, the analysis of transformation products and the application of several -omic techniques. Finally, perspectives on major challenges and future research requirements to improve OMPs biotransformation are proposed.