Effect of proton pump inhibitor on microbial community, function, and kinetics in anaerobic digestion with ammonia stress

Leveraging machine learning for prediction of antibiotic resistance genes post thermal hydrolysis-anaerobic digestion in dairy waste

Anaerobic digestion holds promise as a method for removing antibiotic resistance genes (ARGs) from dairy waste. However, accurately predicting the efficiency of ARG removal remains a challenge. This study introduces a novel appproach utilizing machine learning to forecast changes in ARG abundances following thermal hydrolysis-anaerobic digestion (TH-AD) treatment. Through network analysis and redundancy analyses, key determinants of affect ARG fluctuations were identified, facilitating the development of machine learning models capable of accurately predicting ARG changes during TH-AD processes. The decision tree model demonstrated impressive predictive power, achieving an impessive R2 value of 87% against validation data. Feature analysis revealed that the genes intI2 and intI1 had a critical impact on the absolute abundance of ARGs. The predictive model developed in this study offers valuable insights for improving operational and managerial practices in dairy waste treatment facilities, with the ultimate goal of mitigating the spread of antibiotic resistance.

Microbiome-functionality in anaerobic digesters: A critical review

Microbially driven anaerobic digestion (AD) processes are of immense interest due to their role in the biovalorization of biowastes into renewable energy resources. The function-versatile microbiome, interspecies syntrophic interactions, and trophic-level metabolic pathways are important microbial components of AD. However, the lack of a comprehensive understanding of the process hampers efforts to improve AD efficiency. This study presents a holistic review of research on the microbial and metabolic "black box" of AD processes. Recent research on microbiology, functional traits, and metabolic pathways in AD, as well as the responses of functional microbiota and metabolic capabilities to optimization strategies are reviewed. The diverse ecophysiological traits and cooperation/competition interactions of the functional guilds and the biomanipulation of microbial ecology to generate valuable products other than methane during AD are outlined. The results show that AD communities prioritize cooperation to improve functional redundancy, and the dominance of specific microbes can be explained by thermodynamics, resource allocation models, and metabolic division of labor during cross-feeding. In addition, the multi-omics approaches used to decipher the ecological principles of AD consortia are summarized in detail. Lastly, future microbial research and engineering applications of AD are proposed. This review presents an in-depth understanding of microbiome-functionality mechanisms of AD and provides critical guidance for the directional and efficient bioconversion of biowastes into methane and other valuable products.

Assessment of small intestinal bacterial overgrowth and methane production in patients on chronic proton-pump inhibitor treatment: prevalence and role of rifaximin in its management in primary care

BACKGROUND

Although proton pump inhibitor (PPI) drugs have considered able to induce small intestinal bacterial overgrowth (SIBO), no data are so far available from primary care (PC). We assessed the prevalence of SIBO and methane (CH4) production consequent to chronic PPI therapy using Lactulose Breath Test (LBT). Secondary aim was to explore the possible role of rifaximin in treating PPI-induced SIBO patients.

METHODS

One hundred twenty-five gastroesophageal reflux disease patients, constantly treated with PPI for at least 6 months and undergoing to LBT, were retrospectively assessed. An age-matched control population (control) of 100 patients, which had not used PPI in the last 6 months, was also enrolled. In the PPI group, SIBO positive patients and CH4 producers were treated with rifaximin 1200 mg/daily for 14 days and re-checked with LBT one month after the end of treatment. The area under the curve (AUC) before and after treatment was also calculated for both SIBO positive patients and CH4 producers.

RESULTS

In the PPI group, SIBO prevalence was significantly higher vs. controls (38/125 [30.4%] vs. 27/100 [27%], P<0.05). 77/125 (61.6%) PPI patients were found to be CH4 producers vs. 21/100 (21%) controls (P<0.05). Among SIBO patients in the PPI group, 34 (89.4%) were also CH4 producers vs. 17/27 (63%) controls (P<0.05). After treatment, LBT resulted negative in 15/22 SIBO patients (68.1%) (P<0.05) and in 18/34 CH4 producers (52.9%) (P<0.05). At the AUC analysis, an overall reduction of 54.2% for H2 in SIBO patients and of 47.7% for CH4 was assessed after rifaximin treatment (P<0.05).

CONCLUSIONS

Our data showed that chronic use of PPI could be able to increase the prevalence of SIBO and to shift the intestinal microbial composition towards a CH4-producing flora. rifaximin could represent a useful therapeutical option for PPI-induced SIBO and for modulating CH4-producing flora.

Enhancement of anaerobic digestion of high salinity food waste by magnetite and potassium ions: Digestor performance, microbial and metabolomic analyses

The study investigated the effectiveness of magnetite and potassium ions (K+) in enhancing anaerobic digestion of high salinity food waste. Results indicated that both magnetite and K+ improved anaerobic digestion in high-salt environments, and their combination yielded even better results. The combination of magnetite and K+ promoted microorganism activity, and resulted in increased abundance of DMER64, Halobacteria and Methanosaeta. Metabolomic analysis revealed that magnetite mainly influenced quorum sensing, while K+ mainly stimulated the synthesis of compatible solutes, aiding in maintaining osmotic balance. The combined additives regulated pathways such as ATP binding cassette transport, methane metabolism, and inhibitory substance metabolism, enabling cells to resist environmental stress and maintain normal metabolic activity. Overall, this study demonstrated the potential of magnetite and K+ to enhance food waste anaerobic digestion in high salt conditions and provided valuable insights into the molecular mechanism.

Untangling the effect of solids content on thermal-alkali pre-treatment and anaerobic digestion of sludge

Total solids (TS) content is critical for thermal hydrolysis and anaerobic digestion (AD) performance, but its role in thermal-alkaline pre-treatment (TAP) is unclear. Therefore, this study aimed to reveal the key role of TS content in TAP and AD of waste activated sludge. The results showed that the optimum TS content of TAP (at 90 °C for 1 h, pH = 10) was 8 %. Sludge disintegration and methane production increased from 19.7 ± 2.2 % to 34.3 ± 2.9 % and from 167.4 ± 4.2 to 246.0 ± 6.2 mL/g volatile solids, respectively, when TS content were increased from 2 % to 8 %. A high TS content will likely promote sludge disintegration since it will reduce heat loss and improve heating efficiency. Additionally, increasing TS content from 2 % to 10 % minimized the production of intracellular reactive oxygen species by 30.4 ± 0.7 % and increased cell viability by 11.5 ± 2.6 %. In contrast, excessive TS content (i.e., ≥10 %) deteriorated the fluidity of sludge, which prevents it from disintegration. Once TS reached 10 %, the accumulation of ammonia nitrogen and volatile fatty acids reached 812.7 ± 27.4 and 1932.0 ± 5.3 mg/L, respectively, which reduced the activity of acidulase and coenzyme F420 and shifted the archaeal community from acetylotrophic to hydrogenotrophic methanogens. This article provides new insights into the TS content in TAP and AD technology.

Effect of water regime on the dynamics of free ammonia during high solid anaerobic digestion of pig manure

Free ammonia (FAN) inhibition is commonly encountered during high solid anaerobic digestion (HSAD) of pig manure. The performance of HSAD is highly related to its operational water regime; however, little information is available regarding the dynamics of free ammonia with varied water regimes. In this work, four treatments were set with equal amount of water supply but varied addition frequencies, i.e. add once but at different times in treatments T1 and T2, add twice in T3 while it was three times in treatment T4. Results showed that the whole methanogenic process ran smoothly with the average methane gas production rate maintaining at 191.1 LCH₄/kgVS_added. Although a higher methane gas production rate of 217.4 LCH₄/kgVS_added was achieved in T1, one time water addition triggered a higher ammonia inhibition potential. Cumulative FAN release was 6.03 mgFAN/kgVS_added in T1 while the balance between FAN and ammonia tended to the fraction of FAN. In T4, cumulative FAN of 5.07 mgFAN/kgVS_added was evolved, which was lower than that in T1 but similar to the situation in T2. The lowest FAN was observed in T3, indicating that a moderate frequency of dilution might be conducive to alleviate free ammonia inhibition.

Biochar addition augmented the microbial community and aided the digestion of high-loading slaughterhouse waste: Active enzymes of bacteria and archaea

The biogas production (BP), volatile fatty acids (VFAs), microbial communities, and microbes' active enzymes were studied upon the addition of biochar (0-1.5%) at 6% and 8% slaughterhouse waste (SHW) loadings. The 0.5% biochar enhanced BP by 1.5- and 1.6-folds in 6% and 8% SHW-loaded reactors, respectively. Increasing the biochar up to 1.5% caused a reduction in BP at 6% SHW. However, the BP from 8% of SHW was enhanced by 1.4-folds at 1.5% biochar. The VFAs production in all 0.5% biochar amended reactors was highly significant compared to control (p-value < 0.05). The biochar addition increased the bacterial and archaeal diversity at both 6% and 8% SHW loadings. The highest number of OTUs at 0.5% biochar were 567 and 525 in 6% and 8% SHW, respectively. Biochar prompted the Clostridium abundance and increased the lyases and transaminases involved in the degradation of lipids and protein, respectively. Biochar addition improved the Methanosaeta and Methanosphaera abundance in which the major enzymes were reductase and hydrogenase. The archaeal enzymes showed mixed acetoclastic and hydrogenotrophic methanogenesis.

Melon/cowpea intercropping pattern influenced the N and C soil cycling and the abundance of soil rare bacterial taxa

The high use of pesticides, herbicides, and unsustainable farming practices resulted in losses of soil quality. Sustainable farming practices such as intercropping could be a good alternative to traditional monocrop, especially using legumes such as cowpea (Vigna unguiculata L. Walp). In this study, different melon and cowpea intercropping patterns (melon mixed with cowpea in the same row (MC1); alternating one melon row and one cowpea row (MC2); alternating two melon rows and one cowpea row (MC3)) were assayed to study the intercropping effect on soil bacterial community through 16S rRNA region in a 3-year experiment. The results indicated that intercropping showed high content of total organic carbon, total nitrogen and ammonium, melon yield, and bacterial diversity as well as higher levels of beneficial soil microorganisms such a Pseudomonas, Aeromicrobium, Niastella, or Sphingomonas which can promote plant growth and plant defense against pathogens. Furthermore, intercropping showed a higher rare taxa diversity in two (MC1 and MC2) out of the three intercropping systems. In addition, N-cycling genes such as nirB, nosZ, and amoA were more abundant in MC1 and MC2 whereas the narG predicted gene was far more abundant in the intercropping systems than in the monocrop at the end of the 3-year experiment. This research fills a gap in knowledge about the importance of soil bacteria in an intercropping melon/cowpea pattern, showing the benefits to yield and soil quality with a decrease in N fertilization.

Elucidating the role of solids content in low-temperature thermal hydrolysis and anaerobic digestion of sewage sludge

The role of total solids content in low-temperature thermal hydrolysis and anaerobic digestion of sewage sludge was investigated. Increasing total solids from 2% to 6% improved thermal hydrolysis and anaerobic digestion performance, while increasing it further to 12% decreased methane production. Maximum sludge solubility (22.9% ± 0.6%) and methane production (320 ± 7 mL/g volatile solids) were achieved at 6% solids. The increase in solids content from 2% to 6% improved heating efficiency and volatile fraction content, which facilitated sludge solubilization and enrichment of methanogens. However, further increases in solids content resulted in a stable floc structure with excess ammonia nitrogen and volatile fatty acids, which limited the release of substrates and reduced the abundance of acidifying bacteria and methanogens, ultimately leading to reduced methane production. An in-depth understanding of the role of solids content opens up new avenues for improved low-temperature thermal hydrolysis of sludge.

Effects of pretreatment methods on biomethane production kinetics and microbial community by solid state anaerobic digestion of sugarcane trash

Solid state anaerobic digestion (SS-AD) of lignocellulose is effective in improving biomethane productivity but is limited by low biomass digestibility and lack of substrate-specific working microorganisms. In this study, the effects of different pretreatment methods on biomethane production by SS-AD of sugarcane trash were studied. The biomethane production, fitted to a modified Gompertz's model, predicted a maximum methane yield of 214.2 L/kg volatile solids (VS) and productivity of 6.9 L/kg VS/day from KOH-pretreated trash, respectively. Microbial community analysis showed that bacterial community was significantly associated with volatile acids and pretreatment types while archaeal community was significantly associated with methane yield. Microbial community dynamics was revealed in SS-AD. Main genera related to pretreatment method were identified and discussed. This study generated important information on SS-AD of lignocellulosic biomass pretreated by different methods, which is useful for developing bioaugmentation strategies to improve biomethane production by SS-AD.

Application of machine learning in anaerobic digestion: Perspectives and challenges

Anaerobic digestion (AD) is widely adopted for remediating diverse organic wastes with simultaneous production of renewable energy and nutrient-rich digestate. AD process, however, suffers from instability, thereby adversely affecting biogas production. There have been significant efforts in developing strategies to control the AD process to maintain process stability and predict AD performance. Among these strategies, machine learning (ML) has gained significant interest in recent years in AD process optimization, prediction of uncertain parameters, detection of perturbations, and real-time monitoring. ML uses inductive inference to generalize correlations between input and output data, subsequently used to make informed decisions in new circumstances. This review aims to critically examine ML as applied to the AD process and provides an in-depth assessment of important algorithms (ANN, ANFIS, SVM, RF, GA, and PSO) and their applications in AD modeling. The review also outlines some challenges and perspectives of ML, and highlights future research directions.

Delivery and effects of proton pump inhibitor on anaerobic digestion of food and kitchen waste under ammonia stress

Ammonia stress changes microbial metabolism of anaerobic digestion and decreases methane yield, where proton pump overactivated by free ammonia suggested to be the centre of the metabolism changes in anaerobic digestion under ammonia stress. The work demonstrated that proton pump inhibitor (PPI) could alleviate the overactivated proton pump and mitigate ammonia inhibition. Its impacts on iron transporter, substrates uptake, and energy conservation were investigated in anaerobic digestion treating food and kitchen waste. The PPI formed a stimuli-responsive drug delivery system driven by pH for the more inhibited microbe (p < 0.01), confirmed by FE-SEM/EDS and high throughput sequencing, implying the PPI was activated at inhibited microbe more than mixed liquor. Consistent microbial population increase observed in syntrophs and methanogens, who utilized the substrates for high yielding pathway and facilitated the energy sharing by direct interspecies electron transfer. These results demonstrated PPI could recovery methane production and could mitigate fatty-acid accumulation under high ammonia stress by delivery and activation in acetoclastic methanogen.

Protein biomethanation: insight into the microbial nexus

Biomethanation of carbohydrates (e.g., lignocellulosic biomass) and lipids (e.g., waste oils) has been well studied. However, investigations on the biomethanation of protein-rich biowastes (PRBs) and associated microbial communities have not been reported. This review summarizes the challenges in the metabolic process of anaerobic digestion of PRBs and the microbial instability associated with it. We discuss the diversity of bacterial and archaeal communities via metagenomics under PRB mono- and codigestion. A stable community structure with enhanced metabolic activity is a core factor in PRB biomethanation. The application of strategies such as codigestion of PRBs with carbon-rich biomass and microbial stimulation/augmentation would make PRB biomethanation more feasible.

Anaerobic co-digestion of chicken manure and cardboard waste: Focusing on methane production, microbial community analysis and energy evaluation

This study aimed to investigate the synergistic effect and microbial community changes between chicken manure (CM) and cardboard (CB) during anaerobic co-digestion. Meanwhile, the energy balance of biogas engineering was extrapolated based on the batch tests. In batch tests, co-digestion system achieved the highest improvement (14.2%) and produced 319.62 mL CH₄/gVS with a 65:35 ratio of CB: CM. More extracellular polymeric substance secretion promoted the electron transfer for acidogenesis and more hydrolase was provided with 31.6% improvement. The microbial analysis illustrated that higher acetoclastic Methanosaeta abundance was achieved, leading to 211% enhancement of acetoclastic pathway. Moreover, associated network illustrated that the higher methane production was mainly achieved through matching of hydrolytic bacteria and acidogenesis bacteria. As for energy balance, the synergistic effect increased the energy output by 38% and energy recovery to 46.4%.