Exploring the Functions of Efficient Canonical Denitrifying Bacteria as N2O Sinks: Implications from 15N Tracer and Transcriptome Analyses

Actively N2O-Reducing Oxygen-Tolerant Microbial Consortium Attained by Using a High-Dilution-Rate Chemostat Fed with Methanol

Nitrous oxide-reducing bacteria (N2ORB) are generally considered the only biological sink for the potent greenhouse gas N2O. Although N2O consumption activities by diverse heterotrophic N2ORB have been detected, knowledge gaps remain about the phylogenies, physiologies, and activities of N2ORB. Here, we successfully enriched a methylotrophic N2ORB consortium under intermittent oxygen and N2O supplies. 15N tracer analysis showed that the N2O consumption activity of the enriched consortium was higher than its N2O production activity in the presence of either a single or multiple electron acceptors (i.e., nitrogen oxides). The observed maximum N2O consumption was 80.7 μmol·g-biomass-1·h-1. Quantitative PCR results showed that clade I nosZ bacteria overwhelmed clade II nosZ bacteria at high (0.41 mmol·min-1) and low (0.08 mmol·min-1) N2O loading rates. The dilution rate and N2O loading rate affected the microbial community composition and activity. A higher N2O loading rate stimulated active and oxygen-tolerant N2ORB that boosted N2O consumption by approximately 50% in the presence of oxygen. Metagenomic analysis unraveled the predominance of a novel methylotrophic N2ORB, possessing entire denitrifying genes and high-affinity terminal oxidase genes, from the reactor with a high N2O loading rate. The unique physiological traits of the consortium enriched by methanol shed light on a novel function─aerobic N2O consumption by N2ORB─and pave the way for innovative N2O mitigation strategies applying powerful N2O sinks in engineered systems.

Microbial biomass stoichiometry and proportion of Fe organic complexes separately shape the heterogeneity of mixotrophic denitrification and net N2O sinks in iron-carbon amended ecological ditch

Coupling of iron-carbon can form a mixotrophic denitrification and is regarded as a promising solution for purifying nitrate-rich agricultural runoff. However, its prevalence and efficacy of the synergistic augmentation of nitrogen elimination and net N2O sinks remain crucial knowledge gaps in ecological ditches (eco-ditches). Here, we investigated the underlying variability mechanisms by implementing sponge iron (sFe)-coupled Iris hexagonus (IH)- or Myriophyllum aquaticum (MA)-derived biochar produced via microwave-assisted (MW) pyrolysis and conventional pyrolysis. Surprisingly, unamened eco-ditch became net N2O sink while exhibiting a significant increase in total nitrogen (TN) removal rate of 319 % (P < 0.001) compared to soil ditch. The integration of MW pyrolyzed IH-derived biochar with sFe to amend eco-ditch achieved synchronous enhancement in net N2O sinks (P < 0.01) and TN removal rate (P < 0.001), whereas the remaining amended eco-ditches that significantly intensified TN removal performance, were N2O emitters. Such heterogeneity primarily depends on Fe organic complexes (Fep) / the total reactive Fe oxides (Fed) ratio, rather than the prevailing nosZ gene, underscoring that low density metastable reactive iron plays a more important role than biological reactions during the mixotrophic denitrification process. As such, iron oxides are not necessarily a bottleneck for denitrification and contribute to N2O sinks. Conversely, microbial biomass C:(C + N), together with nirK and nosZ genes, mainly explain the TN removal heterogeneity of sFe-biochar eco-ditch. This study revisits the discrepant resilience of iron-carbon coupling to N abatement and N2O sink-induced cooling and has significant practical implications for better understanding the cascading effects of mixotrophic denitrification driven by iron-carbon interactions.

Tire Wear Particles Exposure Enhances Denitrification in Soil by Enriching Labile DOM and Shaping the Microbial Community

Tire wear particles (TWP) are emerging contaminants in the soil environment due to their widespread occurrence and potential threat to soil health. However, their impacts on soil biogeochemical processes remain unclear. Here, we investigated the effects of TWP at various doses and their leachate on soil respiration and denitrification using a robotized continuous-flow incubation system in upland soil. Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing were employed to elucidate the mechanisms underpinning the TWP effects. We show that TWP increased soil CO2, N2, and N2O emissions, which were attributed to the changes in content and composition of soil dissolved organic matter (DOM) induced by TWP and their leachate. Specifically, the labile DOM components (H/C ≥ 1.5 and transformation >10), which were crucial in shaping the denitrifying community, were significantly enriched by TWP exposure. Furthermore, the abundances of denitrification genes (nirK/S and nosZ-I) and the specific denitrifying genera Pseudomonas were increased following TWP exposure. Our findings provide new insights into impacts of TWP on carbon and nitrogen cycling in soil, highlighting that TWP exposure may exacerbate greenhouse gas emissions and fertilizer N loss, posing adverse effects on soil fertility in peri-urban areas and climate change mitigation.

Reduction of methane and nitrous oxide emissions from stormwater bioretention cells through microbial electrolytic cells

This study investigated the reduction of methane (CH4) and nitrous oxide (N2O) emissions from stormwater bioretention cells through microbial electrolytic cell (MEC), showing the largest reduction of 32.21 % (CH4) at 9.2 μA/m2 of current density and 56.16 % (N2O) at 3.5 μA/m2 of current density, compared with the corresponding in the control (0 μA/m2 of current density). Kinetic of CH4 and N2O emissions could be well fitted by Logistic model with high correlation coefficient (R2 > 0.9500) and model efficiency (ME > 0.95) but low relative root mean square error (RRMSE < 7.88). The increase of pmoA and polysaccharide (PS) were responsible for CH4 reduction, while N2O reduction was attributed to the decrease of nirS and the increase for nosZ and protein (PN), which could explain the lowest GWPd (10.67 mgCO2-eq/m2/h) at 3.5 μA/m2 of current density, suggesting that MEC could be promising for the reduction of CH4 and N2O emissions from bioretention cells.

Assessing the aerobic/anoxic enrichment efficiency at different C/N ratios: polyhydroxyalkanoate production from waste activated sludge

Polyhydroxyalkanoates (PHA) can be produced using fermentation products of an excess sewage sludge fermentation process. An efficient method to enrich a PHA-producing community is an aerobic-feast/anoxic-famine enrichment strategy. The effect of different carbon to nitrogen (C/N) feed ratios of 1, 2 and 3.5 g COD/g N on the process performance was studied. The study was executed on a pilot plant scale using fermented waste activated sludge as the organic carbon source. The system's performance was monitored in terms of removing contaminants, producing PHA, and reducing N2O emissions. The results indicated that a lower C/N ratio results in lower PHA production, with PHA content in the sludge of 20, 24 and 36 % w/w for C/N ratios of 1, 2 and 3.5 g COD/g N, respectively. At the lowest C/N ratio, the highest nitrite accumulation rate (77 %), nitrification efficiency (89 %) and denitrification efficiency (89 %) were observed, but the N2O production was also the highest (0.77 mg N2O-N/L). The long-term comprehensive monitoring carried out in this study revealed high carbon and ammonia removal efficiencies (never below 80 %) despite the C/N shifts and high COD and ammonia concentrations. At the same time, the system showed relatively low PHA production and high environmental impact in terms of high gaseous N2O emission. These findings question the sustainability of the aerobic-feast/anoxic-famine enrichment strategy for PHA production in full-scale plants.

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Benthic clade II-type nitrous oxide reducers suppress nitrous oxide emissions in shallow lakes

Shallow lakes, recognized as hotspots for nitrogen cycling, contribute to the emission of the potent greenhouse gas nitrous oxide (N2O), but the current emission estimates for this gas have a high degree of uncertainty. However, the role of N2O-reducing bacteria (N2ORB) as N2O sinks and their contribution to N2O reduction in aquatic ecosystems in response to N2O dynamics have not been determined. Here, we investigated the N2O dynamics and microbial processes in the nitrogen cycle, which included both N2O production and consumption, in five shallow lakes spanning approximately 500 km. The investigated sites exhibited N2O oversaturation, with excess dissolved N2O concentrations (ΔN2O) ranging from 0.55 ± 0.61 to 53.17 ± 15.75 nM. Sediment-bound N2O (sN2O) was significantly positively correlated with the nitrate concentration in the overlying water (p < 0.05), suggesting that nitrate accumulation contributes to benthic N2O generation. High N2O consumption activity (RN2O) corresponded to low ΔN2O. In addition, a significant negative correlation was found between RN2O and nir/nosZ, showing that bacteria encoding nosZ contributed to N2O consumption in the benthic sediments. Redundancy analysis indicated that benthic functional genes effectively reflected the variations in RN2O and ∆N2O. qPCR analysis revealed that the clade II nosZ gene was more sensitive to ΔN2O than the clade I nosZ gene. Furthermore, four novel genera of potential nondenitrifying N2ORB were identified based on metagenome-assembled genome analysis. These genera, which are affiliated with clade II, lack genes responsible for N2O production. Collectively, benthic N2ORB, especially for clade II-type N2ORB, harnesses N2O consumption activity leading to low N2O emissions from shallow lakes. This study advances our knowledge of the role of benthic clade II-type N2ORB in regulating N2O emissions in shallow lakes.

Complete genome sequence of Afipia carboxidovorans strain SH125, a non-denitrifying nitrous oxide-reducing bacterium isolated from anammox biomass

Here, we report a genome sequence of Afipia carboxidovorans strain SH125 isolated from an anammox reactor. This facultative anaerobic strain possesses the clade I-type nitrous oxide (N2O) reductase gene, devoid of nitrite- and nitric oxide reductase genes. Deciphering the genome will help explore N2O reducers instrumental in N2O mitigation.

Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide

N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria‍ ‍and an‍ ‍exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A 15N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.

Composition and Diversity of the Endobacteria and Ectobacteria of the Invasive Bark Beetle Hylurgus ligniperda (Fabricius) (Curculionidae: Scolytinae) in Newly Colonized Areas

Hylurgus ligniperda (Fabricius) (Curculionidae: Scolytinae) is a new invasive pest beetle in China, which colonized the Shandong province, causing devastating damage. Originating in Europe, it has spread to Oceania, Asia, North and South America. Bacterial associates have been frequently reported to play a vital role in strengthening the ecological adaptations of bark and ambrosia beetles. The environmental adaptability of H. ligniperda may be supported by their associated bacteria. Bacterial communities colonizing different body parts of insects may have different functions. However, little is known about the bacteria associated with H. ligniperda and their potential involvement in facilitating the adaptation and invasion of the beetles into new environments. In this study, we employed high-throughput sequencing technology to analyze the bacterial communities associated with male and female adults of H. ligniperda by comparing those colonizing the elytra, prothorax, and gut. Results showed that the bacterial communities of male and female adults were similar, and the elytra samples had the highest bacterial diversity and richness, followed by the gut, while the prothorax had the lowest. The dominant phyla were Proteobacteria, Firmicutes, and Actinobacteriota, while the dominant genera were Serratia, Lactococcus, Rhodococcus, unclassified Enterobacteriaceae, and Gordonia. Among these, Rhodococcus and Gordonia were the specific genera of endobacteria and ectobacteria, respectively. Differences in the distribution of associated bacteria may suggest that they have different ecological functions for H. ligniperda. The results of functional prediction showed that bacteria were enriched in terpenoid backbone biosynthesis, degradation of aromatic compounds, limonene and pinene degradation, neomycin, kanamycin and gentamicin biosynthesis, indicating that they may assist their beetles in synthesizing pheromones, degrading toxic secondary metabolites of host trees, and antagonizing pathogenic fungi. These results help us understand the interaction between H. ligniperda and bacteria and highlight possible contributions to the invasion process.

Synthetic phylogenetically diverse communities promote denitrification and stability

Denitrification is an important process of the global nitrogen cycle as some of its intermediates are environmentally important or related to global warming. However, how the phylogenetic diversity of denitrifying communities affects their denitrification rates and temporal stability remains unclear. Here we selected denitrifiers based on their phylogenetic distance to construct two groups of synthetic denitrifying communities: one closely related (CR) group with all strains from the genus Shewanella and the other distantly related (DR) group with all constituents from different genera. All synthetic denitrifying communities (SDCs) were experimentally evolved for 200 generations. The results showed that high phylogenetic diversity followed by experimental evolution promoted the function and stability of synthetic denitrifying communities. Specifically, the productivity and denitrification rates were significantly (P < 0.05) higher with Paracocus denitrificans as the dominant species (since the 50th generation) in the DR community than those in the CR community. The DR community also showed significantly (t = 7.119, df = 10, P < 0.001) higher stability through overyielding and asynchrony of species fluctuations, and showed more complementarity than the CR group during the experimental evolution. This study has important implications for applying synthetic communities to remediate environmental problems and mitigate greenhouse gas emissions.