Effect of trace elements on the development of co-cultured nitrite-dependent anaerobic methane oxidation and methanogenic bacteria consortium

The Effects of Model Insoluble Copper Compounds in a Sedimentary Environment on Denitrifying Anaerobic Methane Oxidation (DAMO) Enrichment

The contribution of denitrifying anaerobic methane oxidation (DAMO) as a methane sink across different habitats, especially those affected by anthropogenic activities, remains unclear. Mining and industrial and domestic use of metals/metal-containing compounds can all cause metal contamination in freshwater ecosystems. Precipitation of metal ions often limits their toxicity to local microorganisms, yet microbial activity may also cause the redissolution of various precipitates. In contrast to most other studies that apply soluble metal compounds, this study investigated the responses of enriched DAMO culture to model insoluble copper compounds, malachite and covellite, in simulated sedimentary environments. Copper ≤ 0.22 µm from covellite appeared to cause immediate inhibition in 10 h. Long-term tests (54 days) showed that apparent methane consumption was less impacted by various levels of malachite and covellite than soluble copper. However, the medium-/high-level malachite and covellite caused a 46.6-77.4% decline in denitrification and also induced significant death of the representative DAMO microorganisms. Some enriched species, such as Methylobacter tundripaludum, may have conducted DAMO or they may have oxidized methane aerobically using oxygen released by DAMO bacteria. Quantitative polymerase chain reaction analysis suggests that Candidatus Methanoperedens spp. were less affected by covellite as compared to malachite while Candidatus Methylomirabilis spp. responded similarly to the two compounds. Under the stress induced by copper, DAMO archaea, Planctomycetes spp. or Phenylobacterium spp. synthesized PHA/PHB-like compounds, rendering incomplete methane oxidation. Overall, the findings suggest that while DAMO activity may persist in ecosystems previously exposed to copper pollution, long-term methane abatement capability may be impaired due to a shift of the microbial community or the inhibition of representative DAMO microorganisms.

Biochar modulates intracellular electron transfer for nitrate reduction in denitrifying anaerobic methane oxidizing archaea

Denitrifying anaerobic methane oxidizing (DAMO) archaea plays a significant role in simultaneously nitrogen removal and methane mitigation, yet its limited metabolic activity hinders engineering applications. This study employed biochar to explore its potential for enhancing the metabolic activity and nitrate reduction capacity of DAMO microorganisms. Sawdust biochar (7 g/L) was found to increase the nitrate reduction rate by 2.85 times, although it did not affect the nitrite reduction rate individually. Scanning electron microscopy (SEM) and fluorescence excitation-emission matrix (EEM) analyses revealed that biochar promoted microbial aggregation, and stimulated the secretion of extracellular polymeric substances (EPS). Moreover, biochar bolstered the redox capacity and conductivity of the biofilm, notably enhancing the activity of the electron transfer system by 1.65 times. Key genes involved in intracellular electron transport (Hdr, MHC, Rnf) and membrane transport proteins (BBP, ABC, NDH) of archaea were significantly up-regulated. These findings suggest that biochar regulates electrons generated by reverse methanogenesis to the membrane for nitrate reduction.

The mechanism of microbial sulfate reduction in high concentration sulfate wastewater enhanced by maifanite

Excessive sulfate levels in water bodies pose a dual threat to the ecological environment and human health. The microbial removal of sulfate encounters challenges, particularly in environments with high sulfate concentrations, where the gradual accumulation of sulfide hampers microbial activity. This study focuses on elucidating the mechanisms underlying the enhancement of microbial sulfate reduction in high-concentration sulfate wastewater through a comparative analysis of maifanite and zeolite biostimulants. The investigation reveals that zeolite primarily facilitates microbial growth by providing attachment sites, while maifanite augments sulfate-reducing bacteria (SRB) activity through the release of active substances such as Mo, Ca, and Cu. The addition of maifanite proves instrumental in enhancing microbial activity, manifesting as increased microbial load and protein production, augmented extracellular polymer generation, accelerated electron transfer, and facilitated microbial growth and biofilm formation. Noteworthy is the observation that the combined application of maifanite and zeolite exhibited a synergistic effect, resulting in a 167 % and 68 % increase in sulfate reduction rate compared to the utilization of maifanite (0.12 d-1) or zeolite (0.19 d-1) in isolation. Within this synergistic context, the relative abundance of Desulfobacteraceae reaches a peak of 15.4 %. The outcomes of this study corroborate the distinct promotion mechanisms of maifanite and zeolite in microbial sulfate reduction, offering novel insights into the application of maifanite in the context of high-concentration sulfate removal.

Iron-mediated DAMO-anammox process: Revealing the mechanism of electron transfer

The nitrate denitrifying anaerobic methane oxidation-anaerobic ammonia oxidation (DAMO-anammox) can accomplish nitrogen removal and methane (CH4) reduction. This process greatly contributes to carbon emission mitigation and carbon neutrality. In this study, we investigated the electron transfer process of functional microorganisms in the iron-mediated DAMO-anammox system. Fe3+ could be bound to several functional groups (-CH3, COO-, -CH) in extracellular polymeric substance (EPS), and the functional groups bound were different at different iron concentration. Fe3+ underwent reduction reactions to produce Fe2+. Most Fe3+ and Fe2+ react with microorganisms and formed chelates with EPS. Three-dimensional fluorescence spectra showed that Fe3+ affected the secretion of tyrosine and tryptophan, which were essential for cytochrome synthesis. The presence of Fe3+ accelerated c-type cytochrome-mediated extracellular electron transfer (EET), and when more Fe3+ existed, the more cytochrome C expressed. DAMO archaea (M. nitroreducens) in the system exhibited a high positive correlation with the functional genes (resa and ccda) for cytochrome c synthesis. Some denitrifying microorganisms showed positive correlations with the abundance of riboflavin. This finding showed that riboflavin secreted by functional microorganisms acted as an electron shuttle. In addition, DAMO archaea were positively correlated with the hair synthesis gene pily1, which indicated that direct interspecies electron transfer (DIET) may exist in the iron-mediated DAMO-anammox system.

Effects of Antibiotics on the DAMO Process and Microbes in Cattle Manure

Denitrifying anaerobic methane oxidation (DAMO) can mitigate methane emissions; however, this process has not been studied in cattle manure, an important source of methane emissions in animal agriculture. The objective of this study was to investigate the occurrence of DAMO microbes in cattle manure and examine the impacts of veterinary antibiotics on the DAMO process in cattle manure. Results show that DAMO archaea and bacteria consistently occur at high concentrations in beef cattle manure. During the long-term operation of a sequencing batch reactor seeded with beef cattle manure, the DAMO activities intensified, and DAMO microbial biomass increased. Exposure to chlortetracycline at initial concentrations up to 5000 μg L-1 did not inhibit DAMO activities or affect the concentrations of the 16S rRNA gene and functional genes of DAMO microbes. In contrast, exposure to tylosin at initial concentrations of 50 and 500 μg L-1 increased the activities of the DAMO microbes. An initial concentration of 5000 μg L-1 TYL almost entirely halted DAMO activities and reduced the concentrations of DAMO microbes. These results show the occurrence of DAMO microbes in cattle manure and reveal that elevated concentrations of dissolved antibiotics could inhibit the DAMO process, potentially affecting net methane emissions from cattle manure.

Enhancement of nitrogen removal in coupling Anammox and DAMO via Fe-modified granular activated carbon

Anaerobic ammonium oxidation (Anammox) coupled with Denitrifying anaerobic methane oxidation (DAMO) is an attractive technology to simultaneously remove nitrogen and mitigate methane emissions from wastewater. However, its nitrogen removal rate is usually limited due to the low methane mass transfer efficiency, low metabolic activity and slow growth rate of functional microorganisms. In this study, GAC and Fe-modified GAC (Fe-GAC) were added into Anammox-DAMO process to investigate their effects on nitrogen removal rates and then reveal the mechanism. The results showed that after 80-day experiments, the total nitrogen removal rate was slightly improved in the presence of GAC (3.94 mg L^-1·d^-1), while it reached high as 16.66 mg L^-1·d^-1 in the presence of Fe-GAC, which was ca.17 times that of non-amended control group (0.96 mg L^-1·d^-1). The addition of Fe-GAC stimulated the secretion of extracellular polymeric substance (EPS), improved the electron transfer capability and promoted the production of Cytochrome C. Besides, the key functional enzyme activities (HZS, HDH and NAR) were highest in the Fe-GAC group, which were approximately 1.06-1.56 times higher than those of GAC-amended and blank control groups. Microbial community analysis showed that the abundance of the DAMO archaea (Candidatus Methanoperedens) and Anammox bacteria (Candidatus Brocadia) were remarkably increased with the addition of Fe-GAC. Functional genes associated with nitrogen removal and methane oxidation in Fe-GAC system were up-regulated. This study provides a promising strategy for achieving high rate of nitrogen removal upon Anammox-DAMO process.

Metalloenzymes play major roles to achieve high-rate nitrogen removal in N-damo communities: Lessons from metaproteomics

Nitrite-driven anaerobic methane oxidation (N-damo) is a promising biological process to achieve carbon-neutral wastewater treatment solutions, aligned with the sustainable development goals. Here, the enzymatic activities in a membrane bioreactor highly enriched in N-damo bacteria operated at high nitrogen removal rates were investigated. Metaproteomic analyses, with a special focus on metalloenzymes, revealed the complete enzymatic route of N-damo including their unique nitric oxide dismutases. The relative protein abundance evidenced that "Ca. Methylomirabilis lanthanidiphila" was the predominant N-damo species, attributed to the induction of its lanthanide-binding methanol dehydrogenase in the presence of cerium. Metaproteomics also disclosed the activity of the accompanying taxa in denitrification, methylotrophy and methanotrophy. The most abundant functional metalloenzymes from this community require copper, iron, and cerium as cofactors which was correlated with the metal consumptions in the bioreactor. This study highlights the usefulness of metaproteomics for evaluating the enzymatic activities in engineering systems to optimize microbial management.

A comprehensive review on food waste anaerobic co-digestion: Research progress and tendencies

Food waste (FW) anaerobic digestion systems are prone to imbalance during long-term operation, and the imbalance mechanism is complex. Anaerobic co-digestion (AcoD) of FW and other substrates can overcome the performance limitations of single digestion, allowing for the mutual use of multiple wastes and resource recovery. Research on the AcoD of FW has been widely conducted and successfully applied to a practical engineering scale. Therefore, this review describes the research progress of AcoD of FW with other substrates. By analyzing the problems and challenges faced by AcoD of FW, the synergistic effects and influencing factors of different biomass wastes are discussed, and improvement strategies to improve the performance of AcoD of FW are summarized from different reaction stages of anaerobic digestion. By combing the research progress of AcoD of FW, it provides a reference for the optimization and improvement of the performance of the co-digestion system.

Enhancement of nitrate-dependent anaerobic methane oxidation via granular activated carbon

Denitrifying anaerobic methane oxidation (DAMO) is a bioprocess utilizing methane as the electron source to remove nitrate or nitrite, but denitrification rate especially for nitrate-dependent DAMO is usually limited due to the low methane mass transfer efficiency. In this research, granular active carbon (GAC) was added to enhance the nitrate-dependent DAMO process. The results showed that the maximum nitrate removal rate of GAC assisted DAMO system reached as high as 61.17 mg L^-1 d^-1, 8 times higher than that of non-amended control SBR. The porous structure of GAC can not only adsorb methane, but also keep the internal DAMO archaea from being washed out, and thus benefits for DAMO archaea enrichment. The relative abundance of DAMO archaea accounted for 96.3% in GAC-SBR, which was significantly higher than that of non-amended control SBR system (29.9%). Furthermore, GAC amendment up-regulated metabolic status of denitrification and methane oxidation based on gene sequence composition. The absolute abundances of function genes (NC10 pmoA and ANME mcrA) in GAC-SBR were almost 20 times higher than that of non-amended control SBR. This study provides a novel technique to stimulate the nitrate-dependent DAMO process.

Heavy metal impact on lipid production from oleaginous microorganism cultivated with wastewater sludge

Using municipal wastewater sludge to produce microbial lipid is an effective way of resource recycling. Sludge contains heavy metals and may lead to negative impact on lipid production. However, relative study has not been reported. In this study, metal impact on Lipomyces starkeyi lipid accumulation was conducted. Results showed that Cd²⁺ had great impact on lipid accumulation, but other metals had no much impact. The maximum lipid content of L. starkeyi cultivated in 0.55 mg/L of Cd²⁺ was only 41% w/w, which was lower than the control (51% w/w). The inhibition on acetyl-CoA formation was observed when Cd²⁺ was in the medium. After removing metals from sludge, the lipid accumulation was only around half of the one without metal removal. It would be due to that not only the toxic metals in the sludge were removed as well as the metals such as Zn²⁺ which can enhance lipid accumulation.

Denitrifying anaerobic methane oxidation (DAMO) cultures: Factors affecting their enrichment, performance and integration with anammox bacteria

The recently discovered process, denitrifying anaerobic methane oxidation (DAMO), links the carbon and nitrogen biogeochemical cycles via coupling the anaerobic oxidation of methane to denitrification. The DAMO process, in this respect, has the potential to mitigate the greenhouse effect through the assimilation of dissolved methane. Denitrification via methane oxidation rather than organic matter, provides a new perspective to performing this once thought to be well established process. The two main species responsible for this process are "Candidatus Methylomirabilis oxyfera (M. oxyfera), and "Candidatus Methanoperedens nitroreducens" (M. nitroreducens). M. oxyfera is responsible of reducing nitrite while M. nitroreducens reduces nitrate to nitrite. These two microorganisms, despite their different pathways, were found to exist together in nature through a syntrophic relationship. Their co-existence with anaerobic ammonium oxidation (Anammox) bacteria was also revealed in the last decade. Anammox bacteria are chemolithoautotrophs, converting ammonium and nitrite to N₂ and nitrate. They are responsible for the release of more than 50% of oceanic N₂, hence play an important role in the global nitrogen cycle. Factors leading to the enrichment of DAMO cultures and their cultivation with Anammox cultures are of significance for improved nitrogen removal systems with decreased greenhouse effect, and even for further full-scale applications. This study, therefore, aims to present an updated review of the DAMO process, by focusing on the factors that might have a significant role in enrichment of DAMO microorganisms and their co-existence with Anammox bacteria. Factors such as temperature, pH, inoculum and feed type, trace metals and reactor configuration are among the ones discussed in detail. Factors, which have not been investigated, are also elucidated to provide a better understanding of the process and set research goals that will aid in the development of DAMO-centered wastewater treatment alternatives.

Bacterioferritin: a key iron storage modulator that affects strain growth and butenyl-spinosyn biosynthesis in Saccharopolyspora pogona

Background

Butenyl-spinosyn, produced by Saccharopolyspora pogona, is a promising biopesticide due to excellent insecticidal activity and broad pesticidal spectrum. Bacterioferritin (Bfr, encoded by bfr) regulates the storage and utilization of iron, which is essential for the growth and metabolism of microorganisms. However, the effect of Bfr on the growth and butenyl-spinosyn biosynthesis in S. pogona has not been explored.

Results

Here, we found that the storage of intracellular iron influenced butenyl-spinosyn biosynthesis and the stress resistance of S. pogona, which was regulated by Bfr. The overexpression of bfr increased the production of butenyl-spinosyn by 3.14-fold and enhanced the tolerance of S. pogona to iron toxicity and oxidative damage, while the knockout of bfr had the opposite effects. Based on the quantitative proteomics analysis and experimental verification, the inner mechanism of these phenomena was explored. Overexpression of bfr enhanced the iron storage capacity of the strain, which activated polyketide synthase genes and enhanced the supply of acyl-CoA precursors to improve butenyl-spinosyn biosynthesis. In addition, it induced the oxidative stress response to improve the stress resistance of S. pogona.

Conclusion

Our work reveals the role of Bfr in increasing the yield of butenyl-spinosyn and enhancing the stress resistance of S. pogona, and provides insights into its enhancement on secondary metabolism, which provides a reference for optimizing the production of secondary metabolites in actinomycetes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12934-021-01651-x.

Fundamentals and potential environmental significance of denitrifying anaerobic methane oxidizing archaea

Many properties of denitrifying anaerobic methane oxidation (DAMO) bacteria have been explored since their first discovery, while DAMO archaea have attracted less attention. Since nitrate is more abundant than nitrite not only in wastewater but also in the natural environment, in depth investigations of the nitrate-DAMO process should be conducted to determine its environmental significance in the global carbon and nitrogen cycles. This review summarizes the status of research on DAMO archaea and the catalyzed nitrate-dependent anaerobic methane oxidation, including such aspects as laboratory enrichment, environmental distribution, and metabolic mechanism. It is shown that appropriate inocula and enrichment parameters are important for the culture enrichment and thus the subsequent DAMO activity, but there are still relatively few studies on the environmental distribution and physiological metabolism of DAMO archaea. Finally, some hypotheses and directions for future research on DAMO archaea, anaerobic methanotrophic archaea, and even anaerobically metabolizing archaea are also discussed.

Nitric oxide reduction by microbial fuel cell with carbon based gas diffusion cathode for power generation and gas purification

Nitric oxide (NO) from anthropogenic emission is one of the main air contaminants and induces many environmental problems. Microbial fuel cells (MFCs) with gas diffusion cathode provide an alternative technology for NO reduction. In this work, pure NO as the sole electron acceptor of MFCs with gas diffusion cathode (NO-MFCs) was verified. The NO-MFCs obtained a maximum power density of 489 ± 50 mW/m². Compared with MFCs using O₂ in air as electron acceptor (Air-MFCs), the columbic efficiency increased from 23.2% ± 4.3% (Air-MFCs) to 55.7% ± 4.6% (NO-MFCs). The NO removal rate was 12.33 ± 0.14 mg/L/h and N₂ was the main reduction product. Cathode reduction was the dominant pathway of NO conversion in NO-MFCs, including abiotic electrochemical reduction and microbial denitrification process. The predominant genera in anodic microbial community changed from exoelectrogenic bacteria in Air-MFCs to denitrifying bacteria in NO-MFCs and effected the power generation.

Granular activated carbon assisted nitrate-dependent anaerobic methane oxidation-membrane bioreactor: Strengthening effect and mechanisms

Eutrophication and global warming are two main urgent environmental problems around the world. Nitrate-dependent Anaerobic Methane Oxidation (NdAMO) is a bioprocess coupling nitrate reduction with anaerobic methane oxidation, which could mitigate of these two environmental issues simultaneously. In this study, a newly granular active carbon-NdAMO-membrane bioreactor (GAC-NdAMO-MBR) system was established to evaluate its nitrogen removal efficiency, membrane fouling property and the probable strengthening mechanism was also uncovered. Results indicated that the nitrate removal rate in GAC-NdAMO-MBR reached 31.85 ± 3.19 mgN·L^-1·d^-1 while it was only 10.35 ± 2.02 mgN·L^-1·d^-1 in NdAMO-MBR system (lack of GAC), which was multiplied three-fold. The membrane flux decay rate of GAC- NdAMO -MBR was 0.15 L/m²·h·d while it was 0.49 L/m²·h·d without GAC, and the addition of GAC could extend membrane fouling time for 2.5 times. Notablely, the relative abundance of NdAMO bacteria sharply increased from 27.15% to 56.91% after GAC addition while the NdAMO archaea showed similar variation trend. The physicochemical property of GAC mainly contributed the strengthening effect. The porous structure of GAC absorbed methane and adhered by microorganism, which enhance microorganism amount and metabolic activity. The mechanical strength of GAC scoured membrane surface to mitigate external fouling and pores absorbed EPS to reduce internal fouling. The combined effects could improve NdAMO microorganism growth and metabolism activity and finally improved nitrogen removal performance and controlled membrane fouling. These findings could deep the knowledge of NdAMO process and help extend its application potential in environment science and engineering.

New perspectives on microbial communities and biological nitrogen removal processes in wastewater treatment systems

Biological nitrogen removal (BNR) is a critical process in wastewater treatment. Recently, there have new microbial communities been discovered to be capable of performing BNR with novel metabolic pathways. This review presents the up-to-date status on these microorganisms, including ammonia oxidizing archaea (AOA), complete ammonia oxidation (COMAMMOX) bacteria, anaerobic ammonium oxidation coupled to iron reduction (FEAMMOX) bacteria, anaerobic ammonium oxidation (ANAMMOX) bacteria and denitrifying anaerobic methane oxidation (DAMO) microorganism. Their metabolic pathways and enzymatic reactions in nitrogen cycle are demonstrated. Generally, these novel microbial communities have advantages over canonical nitrifiers or denitrifiers, such as higher substrate affinities, better physicochemical tolerances and/or less greenhouse gas emission. Also, their recent development and/or implementation in BNR is discussed and outlook. Finally, the key implications of coupling these microbial communities for BNR are identified. Overall, this review illustrates novel microbial communities that could provide new possibilities for high-performance and energy-saving nitrogen removal from wastewater.

Anaerobic digestion

Worldwide waste generation has become a topic of interest since the accumulation of this waste has prompted environmental hazards. Among which, anaerobic digestion provides green and efficient alternate solution for removal of toxic waste and energy production. Therefore, this review emphasizes on the recent data published in 2018 on topics related to anaerobic process, enhancement of biogas production, and fermentation efficiency. Furthermore, more focus was made on the factors influencing anaerobic digestion and the effect of trace elements as ionic salts as well as nanoparticles on overall biogas production, respectively. PRACTITIONER POINTS: Anaerobic digestion provide green and efficient alternate solution to deal with. This review focused on the conditions related to anaerobic process to improve biogas production and fermentation efficiency. The trace elements were focused on how to influence biogas production during anaerobic digestion.

Heavy metals interact with the microbial community and affect biogas production in anaerobic digestion: A review

Heavy metals (HMs), which accumulate in digestion substrates, such as plant residues and livestock manure, can affect biogas yields during anaerobic digestion (AD). Low concentration of Cu²⁺ (0-100 mg/L), Fe²⁺ (50-4000 mg/L), Ni²⁺ (0.8-50 mg/L), Cd²⁺ (0.1-0.3 mg/L), and Zn²⁺ (0-5 mg/kg) promote biogas production, while high concentrations inhibit AD. Trace amounts of HMs are necessary for the activity of some enzymes. For example, Cu²⁺ and Cd²⁺ serve as cofactors in the catalytic center of cellulase and stimulate enzyme activity. High contents of Cd²⁺ and Cu²⁺ inhibit enzyme activity by disrupting protein structures. Trace amounts of HMs stimulate the growth and activity of methanogens, while high levels have toxic effects on methanogens. HMs affect the hydrolysis, acidification, and other biochemical reactions of organics in AD by changing the enzyme structure and they also impact methanogen growth. A better understanding of the impact of HMs on AD can provide valuable insights for improving the digestion of poultry manure and plant residues contaminated with HMs, as well as help mitigate HMs pollution. Although several studies have been conducted in this field, few comprehensive reviews have examined the effect of many common HMs on AD. This review summarizes the effects of HMs on the biogas production efficiency of AD and also discusses the effects of HMs on the activities of enzymes and microbial communities.