Variation of volatile fatty acid oxidation and methane production during the bioaugmentation of anaerobic digestion system: Microbial community analysis revealing the influence of microbial interactions on metabolic pathways

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Comparative effect of acid and heat inoculum pretreatment on dark fermentative biohydrogen production

This study delves into the impact of various pretreatment methods on the inoculum in dark fermentation trials, specifically exploring thermal shock at different temperatures (60, 80, and 100 °C) and durations (15, 30, and 60 min), as well as acid shock at pH 5.5. Initial acidification of the substrate/inoculum mixture facilitates H2 generation, making acid shock an effective pretreatment option. However, it is also observed that combining thermal and acid pretreatments boosts H2 production synergistically. The synergy between thermal and acid pretreatments results in a significant improvement, increasing the overall hydrogen production efficiency by more than 9% compared to assays involving acidification alone. This highlights the considerable potential for optimizing pretreatment strategies. Furthermore, the study sheds light on the critical role of inoculum characteristics in the process, with diverse hydrogen-generating bacteria significantly influencing outcomes. The established equivalent performance of HCl and H2SO4 in inoculum pretreatment demonstrates the versatility of these acids in shaping the microbial community and influencing hydrogen production. The analysis of glucose conversion data highlights a prevalence of butyric acid in all trials, irrespective of the pretreatment method, emphasizing the dominance of the butyrate pathway in hydrogen generation. Additionally, an examination of the microbial community offers valuable insights into the intricate relationships between temperature, pH, and microbial diversity. Bacteroidota established its dominance among the bacterial populations, with a relative abundance exceeding 20-25% in the raw inoculum, and this dominance further increased following the treatment. Thermal and acid pretreatments result in significant shifts in dominant microbial communities, with some non-dominant phyla like Cloacimonadota and Spirochaetota becoming more prominent. These shifts in microbial diversity underscore the sensitivity of microbial communities to environmental conditions and pretreatment methods, further highlighting the importance of understanding their dynamics in dark fermentation processes.

Distinguishing anaerobic digestion from electrochemical anaerobic digestion: Metabolic pathways and the role of the microbial community

In this study, we explored why electrochemical anaerobic digestion (EAD) results in higher methane conversion and lower CO₂ emissions than anaerobic digestion (AD). Single-chamber AD and EAD reactors were used in this experiment, and the temperature was set as the disturbance factor. Current, pH, electrode potential, gas content, and microbial community were used as indicators for our analysis. Flux balance analysis (FBA) and high-pass next-generation sequencing (NGS) were used to explore the relationships between AD and EAD methane-producing metabolic fluxes and microorganisms. The results showed that the average methane fluxes were 22.27 (AD) and 29.65 (EAD). Compared with AD, EAD had improved hydrogen-dependent CO₂ reduction pathway. Trichloromonas was the dominant electricity-producing microorganism on the EAD anode film, which was closely related to the H₂ flux at the cathode. Oscillibacter and Syntrophomonas were the dominant bacteria in the fermentation broth, specific to EAD. The abundance of Oscillibacter was positively correlated with the H₂ flux, and the presence of Oscillibacter enhanced CO₂ reduction by hydrogen. Methanosaeta was the only dominant methanogenic bacterium in AD and EAD, and its abundance was higher in the experimental group with a greater methane flux.

Fast detection of volatile fatty acids in biogas slurry using NIR spectroscopy combined with feature wavelength selection

To analyze the state of anaerobic digestion (AD), fast detection models of volatile fatty acids (VFAs) were constructed using near-infrared transmission spectroscopy combined with partial least squares regression to measure concentrations of the acetic acid (AA), propionic acid (PA) and total acid (TA) in biogas slurry. CARS-SA-BPSO algorithm was proposed based on competitive adaptive reweighted sampling (CARS) and simulated annealing binary particle swarm optimization algorithm (SA-BPSO) for selecting feature wavelengths of the AA, PA and TA. Regression models were established with the determination coefficient of prediction (R_p²) of 0.989, root mean squared error of prediction (RMSEP) of 0.111 and residual predictive deviation (RPD) of 9.706 for AA; R_p² of 0.932, RMSEP of 0.116 and RPD of 3.799 for PA; R_p² of 0.895, RMSEP of 0.689 and RPD of 3.676 for TA. It is sufficient to meet the fast detection needs of the AA and PA concentrations in biogas slurry, and basically meet the measuring demand of the TA concentration. CARS-SA-BPSO effectively improves the performance of the calibration model using sensitive wavelength selections, which provides theoretical support for establishing the spectral quantitative regression model to meet the requirements of practical application.

A Review of Basic Bioinformatic Techniques for Microbial Community Analysis in an Anaerobic Digester

Biogas production involves various types of intricate microbial populations in an anaerobic digester (AD). To understand the anaerobic digestion system better, a broad-based study must be conducted on the microbial population. Deep understanding of the complete metagenomics including microbial structure, functional gene form, similarity/differences, and relationships between metabolic pathways and product formation, could aid in optimization and enhancement of AD processes. With advancements in technologies for metagenomic sequencing, for example, next generation sequencing and high-throughput sequencing, have revolutionized the study of microbial dynamics in anaerobic digestion. This review includes a brief introduction to the basic process of metagenomics research and includes a detailed summary of the various bioinformatics approaches, viz., total investigation of data obtained from microbial communities using bioinformatics methods to expose metagenomics characterization. This includes (1) methods of DNA isolation and sequencing, (2) investigation of anaerobic microbial communities using bioinformatics techniques, (3) application of the analysis of anaerobic microbial community and biogas production, and (4) restriction and prediction of bioinformatics analysis on microbial metagenomics. The review has been concluded, giving a summarized insight into bioinformatic tools and also promoting the future prospects of integrating humungous data with artificial intelligence and neural network software.

Burkholderia vietnamiensis G4 as a biological agent in bioremediation processes of polycyclic aromatic hydrocarbons in sludge farms

Polycyclic aromatic hydrocarbons (PAHs) are one of the main pollutants generated by the refining and use of oil. To search bioremediation alternatives for these compounds, mainly in situ, considering the biotic and abiotic variables that affect the contaminated sites is determinant for the success of bioremediation techniques. In this study, bioremediation strategies were evaluated in situ, including biostimulation and bioaugmentation for 16 priority PAHs present in activated sludge farms. B. vietnamiensis G4 was used as a biodegradation agent for bioaugmentation tests. The analyses occurred for 12 months, and temperature and humidity were measured to verify the effects of these factors on the biodegradation. We used the technique GC-MS to evaluate and quantify the degradation of PAHs over the time of the experiment. Of the four treatments applied, bioaugmentation with quarterly application proved to be the best strategy, showing the degradation of compounds of high (34.4% annual average) and low (21.9% annual average) molecular weight. A high degradation rate for high molecular weight compounds demonstrates that this technique can be successfully applied in bioremediation of areas with compounds considered toxic and stable in nature, contributing to the mitigation of impacts generated by PAHs.

Impact of magnesium ions on lysozyme-triggered disintegration and solubilization of waste activated sludge

Lysozyme can efficiently accelerate solubilization and hydrolysis of waste activated sludge (WAS) for anerobic digestion. However, the effect of lysozyme was easily to be inhibited by metal ions in WAS. The impact of magnesium ions (Mg²⁺) on lysozyme catalyze WAS disintegration was investigated in this study. The effect of lysozyme on WAS hydrolysis could be hindered by Mg²⁺. Relatively high concentrations (>50 mg/L) of Mg²⁺ in sludge significantly reduced the release of soluble polysaccharides and proteins from WAS, while sulfate ions or chloride ions caused no such effect. Proteins were difficult to be extracted from extracellular polymeric substances (EPS) of WAS in the presence of Mg²⁺ (>10 mg/L) due to the divalent cation bridging (DCB) behavior, while the extraction of polysaccharides was not significantly affected. The polysaccharides and proteins in the inner EPS layer were transferred to the outer layer during the lysozyme treatment, and total quantities of both components maintained constantly. At least 23.1% lysozymes were trapped in the liquid phase of 100 mg Mg²⁺/L in the first hour. Mg²⁺ could significantly affect the transfer of lysozyme from liquid phase to the inner layer of sludge. Mg²⁺ neutralized the negative surface charge of the sludge particles, which hindered the absorption of positively charged lysozyme molecules by sludge flocs from the liquid phase. The proteins of TB-EPS had higher ratios of α-helixes and tighter structures than those in LB-EPS, which could impede the lysozyme transfer to the cell wall.

Next-generation -omics approaches to drive carboxylate production by acidogenic fermentation of food waste: a review

Acidogenic fermentation of food waste using mixed microbial cultures can produce carboxylates [or volatile fatty acids (VFA)] as high-valued bioproducts via a complex interplay of microorganisms during different stages of this process. However, the present fermentation systems are incapable of reaching the industrially relevant VFA production yields of ≥50 g/L primarly due to the complex process operation, competitive metabolic pathways, and limited understanding of microbial interplays. Recent reports have demonstrated the significant roles played by microbial communities from different phyla, which work together to control the process kinetics of various stages underlying acidogenic fermentation. In order to fully delineate the abundance, structure, and functionality of these microbial communities, next-generation high-throughput meta-omics technologies are required. In this article, we review the potential of metagenomics and metatranscriptomics approaches to enable microbial community engineering. Specifically, a deeper analysis of taxonomic relationships, shifts in microbial communities, and differences in the genetic expression of key pathway enzymes under varying operational and environmental parameters of acidogenic fermentation could lead to the identification of species-level functionalities for both cultivable and non-cultivable microbial fractions. Furthermore, it could also be used for successful gene sequence-guided microbial isolation and consortium development for bioaugmentation to allow VFA production with high concentrations and purity. Such highly controlled and engineered microbial systems could pave the way for tailored and high-yielding VFA synthesis, thereby creating a petrochemically competitive waste-to-value chain and promoting the circular bioeconomy.Research HighlightsMixed microbial mediated acidogenic fermentation of food waste.Metagenomics and metatranscriptomics based microbial community analysis.Omics derived function-associated microbial isolation and consortium engineering.High-valued sustainable carboxylate bio-products, i.e. volatile fatty acids.

Bioaugmentation with syntrophic volatile fatty acids-oxidizing consortia to alleviate the ammonia inhibition in continuously anaerobic digestion of municipal sludge

Ammonia inhibition easily affects the performance of anaerobic digestion (AD) for municipal sludge and the oxidization of volatile fatty acids (VFAs) is the rate-limiting step of this process. Bioaugmentation is considered to be an effective method to alleviate ammonia inhibition of AD, but most study used the hydrogenotrophic methanogens as the bioaugmentation culture. In this study, bioaugmentation of mesophilic AD (MAD) and thermophilic AD (TAD) under ammonia inhibition with syntrophic acetate and propionate oxidizing consortia was investigated. The results showed that the bioaugmented reactors recovered earlier than control reactors with 20 (MAD) and 8 (TAD) days, respectively. The high-throughput 16S rRNA gene sequencing indicated that the relative abundance of carbohydrates fermenter (Lentimicrobium), syntrophic VFAs-oxidizing bacteria (Rikenellaceae_DMER64, Smithella and Syntrophobacter) and acetoclastic and hydrogenotrophic methanogens (Methanosaeta, Methanolinea and Methanospirillum) increased in MAD after bioaugmentation. However, part of the bioaugmentation culture could not adapt to the high free ammonia (FAN) concentration in MAD and the effect was weakened. In TAD, proteolytic bacteria (Keratinibaculum and Tepidimicrobium), syntrophic VFAs-oxidizing bacteria (Syntrophomonas) and hydrogenotrophic methanogen (Methanosarcina) were strengthened. The effect of bioaugmentation in TAD was durable even at higher organic loading rate (OLR), due to its positive influence on microbial community. These results suggested that the different bioaugmentation mechanism occurred in MAD and TAD, which are derived from the synergetic effects of ammonia tolerance and microbial interactions. Our study revealed the VFAs-oxidizing consortia as bioaugmented culture could be the potential strategy to alleviate the ammonia stress of AD.

Bioaugmentation of Bacillus amyloliquefaciens-Bacillus kochii co-cultivation to improve sensory quality of flue-cured tobacco

Flue-cured tobacco (FCT) with irritating and undesirable flavor must be aged. However, the spontaneous aging usually takes a very long time for the low efficiency. Bioaugmentation with functional strains is a promising method to reduce aging time and improve sensory quality. To eliminate the adverse effect of excessive starch or protein content on the FCT quality, we used the flow cytometry to sort Bacillus amyloliquefaciens LB with high alpha-amylase and Bacillus kochii SC with high neutral protease from the FCT microflora. The mono, co-culture of strains was performed the solid-state fermentation with FCT. Bacillus amyloliquefaciens monoculture for 2 days and Bacillus kochii monoculture for 2.5 days achieved the optimum quality. B. amyloliquefaciens-B. kochii co-culture at a ratio of 3:1 for 2 days of fermentation showed a more comprehensive quality enhancement and higher functional enzyme activity than mono-cultivation. Through OPLS-DA model (orthogonal partial least-squares-discriminant analyzes), there were 38 differential compounds between bioaugmentation samples. In co-cultivation, most of Maillard reaction products and terpenoid metabolites were at a higher level than other samples, which promoted an increase in aroma, softness and a decrease in irritation. This result validated the hypothesis of quality improvement via the co-culture. In our study, we presented a promising bioaugmentation technique for changing the sensory attributes of FCT in a short aging time.

Syntrophic butyrate-oxidizing methanogenesis promoted by anthraquinone-2-sulfonate and cysteine: Distinct tendencies towards the enrichment of methanogens and syntrophic fatty-acid oxidizing bacteria

Interspecies electron transfer (IET) between syntrophic fatty-acid oxidizing bacteria (SFOBs) and methanogens decided the performance of anaerobic digestion. Electron shuttles, as potential IET accelerators, were controversial concerning their influences on methanogenesis. In this study, concentration-dependent effects of anthraquinone-2-sulfonate (AQS) and cysteine on glucose digestion were firstly demonstrated: low dosage of AQS and cysteine (50 and 100 µM, respectively) had highest methane yield (133.5% and 148.6%, respectively). Using butyrate as substrate, distinct tendencies towards the enrichment of methanogenic community were further revealed. Cysteine just acted as a reductant which lowered ORP quickly and enriched most methanogens. It benefited methanogenesis right until methanogenic substrates accumulated. AQS, however, showed characteristic features of electron shuttles: it was firstly oxidized by SFOBs and then reduced by hydrogenotrophic methanogens, which accelerated methanogenic butyrate degradation. This study showed wide spectrum of SFOBs and methanogens benefited from the addition of electron shuttles, which laid foundation for future application.

Interactions of functional microorganisms and their contributions to methane bioconversion to short-chain fatty acids

Methane bioconversion to value-added liquid chemicals has been proposed as a promising solution to augment the petroleum-dominated chemical market. Recent investigations have reported that various electron acceptors (e.g., nitrite and nitrate) are available to drive methane bioconversion to short-chain fatty acids (SCFAs). However, little is known about effects of the rate electron acceptor supplied on liquid chemical production from methane. Herein, three independent membrane biofilm reactors (MBfRs) feeding with respective nitrate, nitrite, combined nitrate and nitrite were operated under high and low rate condition in succession, to study whether feeding rate of electron acceptors could impact the methane bioconversion to SCFAs and the associated microbiological features. Long-term operation showed that all tested electron acceptors with a high supply rate were favorable for methane bioconversion to SCFAs (990.9 mg L^-1d^-1, 1695.7 mg L^-1d^-1, and 2425.7 mg L^-1d^-1), while under a low electron acceptor feeding rate, the SCFA production rate decreased to 8.9 mg L^-1d^-1, 16.8 mg L^-1d^-1, and 260.1 mg L^-1d^-1, respectively. Microbial community characterization showed that the biofilm was predominated by Methanosarcina, Methanobacterium, Propionispora and Clostridium. On the basis of the known metabolism characteristics of these microorganisms, it was assumed that these methanogens and fermenters contributed jointly to methane bioconversion to SCFAs. The findings could be helpful to understand the role of electron acceptor rate in methane bioconversion to liquid chemicals.