Ammonia stress decreased biomarker genes of acetoclastic methanogenesis and second peak of production rates during anaerobic digestion of swine manure

Ammonia-stressed anaerobic digestion: Sensitivity dynamics of key syntrophic interactions and methanogenic pathways-A review

The problematic anaerobic digestion (AD) of protein-rich substrates owing to their high ammonia content continues to hinder optimum methanation despite their high potential for offsetting greenhouse gas (GHG) emissions. This review focuses on the analyses of the sensitivity dynamics of key AD processes as well as the microbial interactions and exchanges that occur with them. Aside from the apparent increased risk associated with thermophilic ammonia-rich substrate AD, the marginally higher energy generation compared to mesophilic systems is not commensurate to the energy requirement. Moreover, while comparable FAN thresholds have been confirmed, TAN thresholds are susceptible to physical chemistry and so vary greatly. Profiling of the metabolic capability of front-end AD microbiome revealed Bacteroidetes, Firmicutes, and Synergistetes as some of the ammonia-resilient bacteria groups while Proteobacteria and Actinobacteria were the most fragile taxa. Besides the predominance of incomplete propionate oxidizing bacteria under ammonia stress conditions, syntrophic propionate oxidation (SPO) is usually shifted from the methylmalonyl CoA to the dismutation pathway. Furthermore, besides their different recoverability potentials, distinct methanogenic groups are differentially impacted by different ammonia species. Prevailing literature evidence suggests that conductive material assisted bioaugmentation with SAO-HM consortia, and in-situ H2 supplementation are the most effective for expediting electron transfer and relieving ammonia stress. These valuable insights should inform the design of targeted ammonia inhibition mitigation strategies.

Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome

BACKGROUND

Mangroves are complex and dynamic coastal ecosystems under frequent fluctuations in physicochemical conditions related to the tidal regime. The frequent variation in organic matter concentration, nutrients, and oxygen availability, among other factors, drives the microbial community composition, favoring syntrophic populations harboring a rich and diverse, stress-driven metabolism. Mangroves are known for their carbon sequestration capability, and their complex and integrated metabolic activity is essential to global biogeochemical cycling. Here, we present a metabolic reconstruction based on the genomic functional capability and flux profile between sympatric MAGs co-assembled from a tropical restored mangrove.

RESULTS

Eleven MAGs were assigned to six Bacteria phyla, all distantly related to the available reference genomes. The metabolic reconstruction showed several potential coupling points and shortcuts between complementary routes and predicted syntrophic interactions. Two metabolic scenarios were drawn: a heterotrophic scenario with plenty of carbon sources and an autotrophic scenario with limited carbon sources or under inhibitory conditions. The sulfur cycle was dominant over methane and the major pathways identified were acetate oxidation coupled to sulfate reduction, heterotrophic acetogenesis coupled to carbohydrate catabolism, ethanol production and carbon fixation. Interestingly, several gene sets and metabolic routes similar to those described for wastewater and organic effluent treatment processes were identified.

CONCLUSION

The mangrove microbial community metabolic reconstruction reflected the flexibility required to survive in fluctuating environments as the microhabitats created by the tidal regime in mangrove sediments. The metabolic components related to wastewater and organic effluent treatment processes identified strongly suggest that mangrove microbial communities could represent a resourceful microbial model for biotechnological applications that occur naturally in the environment.

Multivariate comparison of taxonomic, chemical and operational data from 80 different full-scale anaerobic digester-related systems

BACKGROUND

The holistic characterization of different microbiomes in anaerobic digestion (AD) systems can contribute to a better understanding of these systems and provide starting points for bioengineering. The present study investigates the microbiome of 80 European full-scale AD systems. Operational, chemical and taxonomic data were thoroughly collected, analysed and correlated to identify the main drivers of AD processes.

RESULTS

The present study describes chemical and operational parameters for a broad spectrum of different AD systems. With this data, Spearman correlation and differential abundance analyses were applied to narrow down the role of the individual microorganisms detected. The authors succeeded in further limiting the number of microorganisms in the core microbiome for a broad range of AD systems. Based on 16S rRNA gene amplicon sequencing, MBA03, Proteiniphilum, a member of the family Dethiobacteraceae, the genus Caldicoprobacter and the methanogen Methanosarcina were the most prevalent and abundant organisms identified in all digesters analysed. High ratios for Methanoculleus are often described for agricultural co-digesters. Therefore, it is remarkable that Methanosarcina was surprisingly high in several digesters reaching ratios up to 47.2%. The various statistical analyses revealed that the microorganisms grouped according to different patterns. A purely taxonomic correlation enabled a distinction between an acetoclastic cluster and a hydrogenotrophic one. However, in the multivariate analysis with chemical parameters, the main clusters corresponded to hydrolytic and acidogenic microorganisms, with SAOB bacteria being particularly important in the second group. Including operational parameters resulted in digester-type specific grouping of microbes. Those with separate acidification stood out among the many reactor types due to their unexpected behaviour. Despite maximizing the organic loading rate in the hydrolytic pretreatments, these stages turned into extremely robust methane production units.

CONCLUSIONS

From 80 different AD systems, one of the most holistic data sets is provided. A very distinct formation of microbial clusters was discovered, depending on whether taxonomic, chemical or operational parameters were combined. The microorganisms in the individual clusters were strongly dependent on the respective reference parameters.

Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics

The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4+/LR and 5 g NH4+/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.

Bioaugmentation with marine sediment-derived microbial consortia in mesophilic anaerobic digestion for enhancing methane production under ammonium or salinity stress

Ammonium (NH₄⁺) and salinity (NaCl) inhibit CH₄ production in anaerobic digestion. However, whether bioaugmentation using marine sediment-derived microbial consortia can relieve the inhibitory effects of NH₄⁺ and NaCl stresses on CH₄ production remains unclear. Thus, this study evaluated the effectiveness of bioaugmentation using marine sediment-derived microbial consortia in alleviating the inhibition of CH₄ production under NH₄⁺ or NaCl stress and elucidated the underlying mechanisms. Batch anaerobic digestion experiments under 5 gNH₄-N/L or 30 g/L NaCl were performed with or without augmentation using two marine sediment-derived microbial consortia pre-acclimated to high NH₄⁺ and NaCl. Compared with non-bioaugmentation, bioaugmentation reinforced CH₄ production. Network analysis revealed the joint effects of microbial connections by Methanoculleus, which promoted the efficient consumption of propionate accumulated under NH₄⁺ and NaCl stresses. In conclusion, bioaugmentation with pre-acclimated marine sediment-derived microbial consortia can mitigate the inhibition under NH₄⁺ or NaCl stress and enhance CH₄ production in anaerobic digestion.

Thermodynamic restrictions determine ammonia tolerance of methanogenic pathways in Methanosarcina barkeri

Ammonia is a ubiquitous potential inhibitor of anaerobic digestion processes, mainly exhibiting inhibition towards methanogenic activity. However, knowledge as to how ammonia affects the methanogens is still limited. In this study, we cultured a multitrophic methanogen, Methanosarcina barkeri DSM 800, with acetate, H₂/CO₂, and methanol to evaluate the influence of ammonia on different methanogenic pathways. Aceticlastic methanogenesis was more sensitive to increased ammonia concentrations than hydrogenotrophic and methylotrophic methanogenesis. Theoretical maximum NH₃ tolerances of M. barkeri fed with acetate, H₂/CO₂, and methanol were calculated to be 39.1 ± 9.0, 104.3 ± 7.4, and 85.7 ± 1.0 mg/L, respectively. The order of the ΔG range of M. barkeri under three methanogenic pathways reflected the order of ammonia tolerance of M. barkeri. Our results provide insights into the role of the thermodynamic potential of methanogenesis on the tolerance of ammonia stress; and shed light on the mechanism of ammonia inhibition on anaerobic digestion.

Evaluation of digestate-derived biochar to alleviate ammonia inhibition during long-term anaerobic digestion of food waste

The feasibility of using food waste anaerobic digestate-derived biochar (FWDB) to mitigate ammonia toxicity in an anaerobic digester was evaluated. The optimal conditions for preparing and adding the activated FWDB were explored using response surface experiments, and the long-term effects of adding activated FWDB on digester performance under optimum conditions were verified in semi-continuous experiments. The results showed that the optimal preparation and addition conditions for activated FWDB were pyrolysis temperature of 565 °C, particle size of 0-0.30 mm, and dosage of 15.52 g·L-1. During the long-term operation of the digesters, when the total ammonia nitrogen (TAN) concentration was higher than 2000 mg·L-1, the control and experimental digesters showed deteriorated reactor performance. Volatile fatty acids in the control digester accumulated to 20,306 mg·L-1 after the TAN concentration increased to 3391 mg·L-1, the methane yield decreased to 31 mL·g VS-1, and the digester experienced process failure. In contrast, the experimental digester with added activated FWDB only suffered a slight short-term accumulation of acetate and a slight decline in methane yield. This may be attributed to the adsorption of NH4+/NH3 by activated FWDB, which reduced the TAN concentration in the anaerobic digestion (AD) system and mitigated ammonia toxicity. Microbial analysis and metagenome predictions demonstrated that the community richness, diversity, and evenness, as well as the abundance of acetogens and related key genes (ACSM1, paaF, and acdA) were higher in the experimental digester than in the control digester. This study provides a closed-loop AD enhancement strategy by pyrolysis of digestate and in-situ supplementation into the digester.

Zero-valent iron is not always effective in enhancing anaerobic digestion performance

Liquid nitrogen was employed as a low-temperature medium to activate zero-valent iron (ZVI) powder in an attempt to strengthen its enhancement effect on anaerobic digestion (AD) of swine manure (SM). Surprisingly, it was found that both pristine ZVI and liquid nitrogen-pretreated ZVI (LZVI) did not significantly improve the AD performance or change the archaeal community structure. It was hypothesized that ZVI might not be effective at stress-free environment like in these digesters. To confirm this, an additional set of AD experiments were performed at high ammonia stress (about 4000 mg/L), results showed that ZVI and LZVI greatly alleviated ammonia inhibition and increased the CH₄ yield by 11.6% and 28.2%, respectively. Apparently, ZVI mainly affected AD systems by changing the metabolism pathways and enhancing the microbial activity to overcome process inhibition, and pretreatment of liquid nitrogen could significantly accelerate the dissolution of ZVI and improve its utilization efficiency, contributing to a greater extend of process recovery and improvement.

Role of interspecies electron transfer stimulation in enhancing anaerobic digestion under ammonia stress: Mechanisms, advances, and perspectives

Ammonia stress is a commonly encountered issue in anaerobic digestion (AD) process when treating proteinaceous substrates. The enhanced relationship between syntrophic bacteria and methanogens triggered by interspecies electron transfer (IET) stimulation is one of the potential mechanisms for an improved methane yield from the AD plant under ammonia-stressed condition. There is, however, lack of synthesized information on the mechanistic understanding of IET facilitation in the ammonia-stressed AD processes. This review critically discusses recovery of AD system from ammonia-stressed condition, focusing on H₂ transfer, redox compound-mediated IET, and conductive material-induced direct IET. The effects and the associated mechanisms of IET stimulation on mitigating ammonia stress and promoting methanogenesis were elucidated. Finally, prospects and challenges of IET stimulation were critically discussed. This review highlights, for the first time, the critical role of IET stimulation in enhancing AD process under ammonia-stressed condition.

Elucidating the kinetics of ammonia inhibition to anaerobic digestion through extended batch experiments and stimulation-inhibition modeling

Ammonia can be accumulated to a level inhibitory to methanogenesis. There are large discrepancies in the reported inhibition thresholds. Through extended batch digestion experiments (up to 110 d) at 6 ammonia concentrations (0.70-13 g N/L), this study discovered sequential occurrence of adaptable and unadaptable inhibition that reveals the discrepancies. Lag phase length representing adaptable inhibition increased exponentially with ammonia concentration. The kinetics of specific biogas yield that reveals unadaptable inhibition was best simulated with the Han & Levenspiel model. The 50% unadaptable inhibition thresholds were 10.7 g N/L with active inoculum and 6.8 g/L with stressed inoculum. The digesters with stressed inoculum had faster adaptation to adaptable inhibition though less resistance to unadaptable inhibition. The inhibition sequence was evidenced by microbial population shifts and confirmed by earlier studies employing short (2-65 d) and long (80-198 d) batch experiments. Distinguishing adaptable from unadaptable inhibition provides precise guidance for mitigating ammonia inhibition.

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.

Synergistic digestion of banana pseudo-stems with chicken manure to improve methane production: Semi-continuous manipulation and microbial community analysis

This study aimed to investigate the interactions between banana pseudo-stems (BPS) and chicken manure (CM) during anaerobic co-digestion (AcoD) in batch and semi-continuous experiments. The batch experiments results showed that the methane yield was the highest (193.7 mL/g VS) in AcoD with BPS: CM ratio of 4:1, which was increased by 57.2% and 66.1%, respectively. Semi-continuous experiments revealed that AcoD resulted in higher methane production. Monitoring of the system parameters indicated that AcoD could better adapt to the increasing organic loading rate, with better system stability and methane production efficiency. The microbial analysis illustrated that AcoD increased the relative abundance of hydrolytic bacteria such as Firmicutes, Patescibacteria, and Bacteroidetes. With regard to archaea, AcoD improved the abundance of Methanosaeta, the major acetoclastic methanogens. These changes in the microbial flora allowed AcoD to remain stable while efficiently producing methane and improved the BPS and CM processing efficiency.