Chemically Stressed Bacterial Communities in Anaerobic Digesters Exhibit Resilience and Ecological Flexibility

A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review

The increasing reliance on fossil fuels and the growing accumulation of organic waste necessitates the exploration of sustainable energy alternatives. Anaerobic digestion (AD) presents one such solution by utilizing secondary biomass to produce biogas while reducing greenhouse gas emissions. Given the crucial role of microbial activity in anaerobic digestion, a deeper understanding of the microbial community is essential for optimizing biogas production. While metagenomics has emerged as a valuable tool for unravelling microbial composition and providing insights into the functional potential in biodigestion, it falls short of interpreting the functional and metabolic interactions, limiting a comprehensive understanding of individual roles in the community. This emphasizes the significance of expanding the scope of metagenomics through innovative tools that highlight the often-overlooked, yet crucial, role of microbiota in biomass digestion. These tools can more accurately elucidate microbial ecological fitness, shared metabolic pathways, and interspecies interactions. By addressing current limitations and integrating metagenomics with other omics approaches, more accurate predictive techniques can be developed, facilitating informed decision-making to optimize AD processes and enhance biogas yields, thereby contributing to a more sustainable future.

Microwave-assisted organic acids and green hydrogen production during mixed culture fermentation

BACKGROUND

The integration of anaerobic digestion into bio-based industries can create synergies that help render anaerobic digestion self-sustaining. Two-stage digesters with separate acidification stages allow for the production of green hydrogen and short-chain fatty acids, which are promising industrial products. Heat shocks can be used to foster the production of these products, the practical applicability of this treatment is often not addressed sufficiently, and the presented work therefore aims to close this gap.

METHODS

Batch experiments were conducted in 5 L double-walled tank reactors incubated at 37 °C. Short microwave heat shocks of 25 min duration and exposure times of 5-10 min at 80 °C were performed and compared to oven heat shocks. Pairwise experimental group differences for gas production and chemical parameters were determined using ANOVA and post-hoc tests. High-throughput 16S rRNA gene amplicon sequencing was performed to analyse taxonomic profiles.

RESULTS

After heat-shocking the entire seed sludge, the highest hydrogen productivity was observed at a substrate load of 50 g/l with 1.09 mol H2/mol hexose. With 1.01 mol H2/mol hexose, microwave-assisted treatment was not significantly different from oven-based treatments. This study emphasised the better repeatability of heat shocks with microwave-assisted experiments, revealing low variation coefficients averaging 29%. The pre-treatment with microwaves results in a high predictability and a stronger microbial community shift to Clostridia compared to the treatment with the oven. The pre-treatment of heat shocks supported the formation of butyric acid up to 10.8 g/l on average, with a peak of 24.01 g/l at a butyric/acetic acid ratio of 2.0.

CONCLUSION

The results support the suitability of using heat shock for the entire seed sludge rather than just a small inoculum, making the process more relevant for industrial applications. The performed microwave-based treatment has proven to be a promising alternative to oven-based treatments, which ultimately may facilitate their implementation into industrial systems. This approach becomes economically sustainable with high-temperature heat pumps with a coefficient of performance (COP) of 4.3.

Biobased short chain fatty acid production - Exploring microbial community dynamics and metabolic networks through kinetic and microbial modeling approaches

In recent years, there has been growing interest in harnessing anaerobic digestion technology for resource recovery from waste streams. This approach has evolved beyond its traditional role in energy generation to encompass the production of valuable carboxylic acids, especially volatile fatty acids (VFAs) like acetic acid, propionic acid, and butyric acid. VFAs hold great potential for various industries and biobased applications due to their versatile properties. Despite increasing global demand, over 90% of VFAs are currently produced synthetically from petrochemicals. Realizing the potential of large-scale biobased VFA production from waste streams offers significant eco-friendly opportunities but comes with several key challenges. These include low VFA production yields, unstable acid compositions, complex and expensive purification methods, and post-processing needs. Among these, production yield and acid composition stand out as the most critical obstacles impacting economic viability and competitiveness. This paper seeks to offer a comprehensive view of combining complementary modeling approaches, including kinetic and microbial modeling, to understand the workings of microbial communities and metabolic pathways in VFA production, enhance production efficiency, and regulate acid profiles through the integration of omics and bioreactor data.

Process stability in expanded granular sludge bed bioreactors enhances resistance to organic load shocks

Environmental perturbations such as changes in organic loading rate (OLR) can have deleterious effects on the anaerobic digestion process, leading to VFA accumulation and process failure. However, the operational history of a reactor, such as prior exposure to VFA build up, can impact a reactor's resistance to shock loads. In the present study, the effects of long term (>100 days) bioreactor (un)stability on OLR shock resistance were assessed. Three 4 L EGSB bioreactors were subjected to varying levels of process stability. Operational conditions such as OLR, temperature and pH were maintained stable in R1; R2 was subjected to a series of minor OLR perturbations and R3 was subjected to a series of non-OLR perturbations, including ammonium, temperature, pH and sulfide. The effect of these different operational histories on each reactor's resistance to a sudden 8-fold increase in OLR were assessed by monitoring COD removal efficiency and biogas production. The microbial communities of each reactor were monitored using 16S rRNA gene sequencing to understand the relationship between microbial diversity and reactor stability. It was determined that the stable (un-perturbed) reactor performed best in terms of its resistance to a large OLR shock, despite its lower microbial community diversity.

Conductive Materials on Biocathodes Altered the Electron-Transfer Paths and Modulated γ-HCH Dechlorination and CH4 Production in Microbial Electrochemical Systems

Adding conductive materials to the cathode of a microbial electrochemical system (MES) can alter the route of interspecies electron transfer and the kinetics of reduction reactions. We tested reductive dechlorination of γ-hexachlorocyclohexane (γ-HCH), along with CH₄ production, in MES systems whose cathodes were coated with conductive magnetite nanoparticles (NaFe), biochar (BC), magnetic biochar (FeBC), or anti-conductive silica biochar (SiBC). Coating with NaFe enriched electroactive microorganisms, boosted electro-bioreduction, and accelerated γ-HCH dechlorination and CH₄ production. In contrast, BC only accelerated dechlorination, while FeBC only accelerated methanogenesis, because of their assemblies of functional taxa that selectively transferred electrons to those electron sinks. SiBC, which decreased electro-bioreduction, yielded the highest CH₄ production and increased methanogens and the mcrA gene. This study provides a strategy to selectively control the distribution of electrons between reductive dechlorination and methanogenesis by adding conductive or anti-conductive materials to the MES's cathode. If the goal is to maximize dechlorination and minimize methane generation, then BC is the optimal conductive material. If the goal is to accelerate electro-bioreduction, then the best addition is NaFe. If the goal is to increase the rate of methanogenesis, adding anti-conductive SiBC is the best.

Characterization of microbial communities in anaerobic acidification reactors fed with casein and/or lactose

Abstract

Protein-rich agro-industrial waste streams are high in organic load and represent a major environmental problem. Anaerobic digestion is an established technology to treat these streams; however, retardation of protein degradation is frequently observed when carbohydrates are present. This study investigated the mechanism of the retardation by manipulating the carbon source fed to a complex anaerobic microbiota and linking the reactor performance to the variation of the microbial community. Two anaerobic acidification reactors were first acclimated either to casein (CAS reactor) or lactose (LAC reactor), and then fed with mixtures of casein and lactose. Results showed that when lactose was present, the microbial community acclimated to casein shifted from mainly Chloroflexi to Proteobacteria and Firmicutes, the degree of deamination in the CAS reactor decreased from 77 to 15%, and the VFA production decreased from 75 to 34% of the effluent COD. A decrease of 75% in protease activity and 90% in deamination activity of the microbiota was also observed. The microorganisms that can ferment both proteins and carbohydrates were predominant in the microbial community, and from a thermodynamical point of view, they consumed carbohydrates prior to proteins. The frequently observed negative effect of carbohydrates on protein degradation can be mainly attributed to the substrate preference of these populations.

Keypoints

• The presence of lactose shifted the microbial community and retarded anaerobic protein degradation.

• Facultative genera were dominant in the presence and absence of lactose.

• Substrate-preference caused retardation of anaerobic protein degradation.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12132-5.

Biogas Production Enhancement through Chicken Manure Co-Digestion with Pig Fat

Chicken manure and pig fat are found abundantly around the globe, and there is a challenge to get rid of them. This waste has considerable energy potential to be recovered into fuel, but extracting this energy from some by-products, especially fat, isn’t an easy task. When anaerobic digestion technology stepped to the level of anaerobic co-digestion, the utilisation of hardly degradable waste became feasible. Our research was conducted on anaerobic co-digestion of chicken manure as the primary substrate with pig fat as a fat reach supplement in a semi-continuous mode at different organic load rates. The influence of fat waste on the process of biogas production from chicken manure and the composition of the obtained products was determined using an organic load rate of 3.0–4.5 kg VS·(m3·day)−1. A sturdy and continuously growing biogas production was observed at all organic load rates, implying the synergetic effect on chicken manure and pig fat co-digestion. The highest specific methane yield, 441.3 ± 7.6 L·kg VS−1, was observed at an organic load rate of 4.5 kg VS·(m3·day)−1. The research results showed that co-digestion of chicken manure with pig fat is an appropriate measure for fat utilisation and contributes to the increase in biogas yield, methane concentration, and overall methane yield at investigated organic load rates.

Evolution of sulfate reduction behavior in leachate saturated zones in landfills

The sulfate reduction behavior of the landfill leachate saturated zone under different temperatures was investigated. The results showed that temperature had significant effects on sulfate reduction behavior. The sulfate reduction efficiency was the highest at high temperatures (55 °C and 45 °C), followed by mesophilic temperature (35 °C). Normal temperature 25 °C was far less effective than 55 °C, 45 °C and 35 °C. High abundances of aprA and dsrA genes were distributed under high temperatures. Through indicator species analysis and functional comparison, some key taxa were identified as putative key genera for sulfate reduction. Under high temperature, Paenibacillus could effectively degrade dimethyl sulfide. DsrAB is present in the genome of Tissierella. Gordonia, Syntrophomonas, and Lysinibacillus under mesophilic temperature indicates the potential of these organisms to degrade heterogenous biomass, environmental pollutants or other natural polymers with slow biodegradation. This microbial function is similar to that of the putative key genera under normal (25 °C) temperature. Most of the putative key genera belong to Firmicutes, Proteobacteria and Myxococcota. This study provides theoretical support for the control of hydrogen sulfide release from landfills.

Comparative Metagenomics of Anaerobic Digester Communities Reveals Sulfidogenic and Methanogenic Microbial Subgroups in Conventional and Plug Flow Residential Septic Tank Systems

On-site wastewater treatment systems (OWTS) are primarily monitored using physiochemical factors, including chemical oxygen demand (COD) and residual total suspended solids (TSS), which are indirect measures of the microbial action during the anaerobic digestion process. Changes in anaerobic digester microbial communities can alter the digester performance, but this information cannot be directly obtained from traditional physicochemical indicators. The potential of metagenomic DNA sequencing as a tool for taxonomic and functional profiling of microbial communities was examined in both common conventional and plug flow-type anaerobic digesters (single-pass and recirculating). Compared to conventional digesters, plug flow-type digesters had higher relative levels of sulfate-reducing bacteria (Desulfovibrio spp.) and hydrogenotrophic methanogens (Methanospirillum spp.). In contrast, recirculating anaerobic digesters were enriched with denitrifier bacteria and hydrogenotrophic methanogens, and both were significantly correlated with physicochemical factors such as COD and TSS. Stratification of microbial communities was observed along the digester treatment process according to hydrolytic, acidogenic, acetogenic, and methanogenic subgroups. These results indicate that the high-throughput DNA sequencing may be useful as a monitoring tool to characterize the changes in bacterial communities and the functional profile due to differences in digester design in on-site systems.

Thermophilic anaerobic digestion of olive mill wastewater in an upflow packed bed reactor: Evaluation of 16S rRNA amplicon sequencing for microbial analysis

Olive mill wastewater, a by-product of olive oil production after the operation of three-phase decanters, was used in a thermophilic anaerobic digester targeting efficient bioconversion of its organic load into biogas. An active anaerobic inoculum originating from a mesophilic reactor, was acclimatized under thermophilic conditions and was filled into a high-rate upflow packed bed reactor. Its performance was tested towards the treatment efficacy of olive mill wastewater under thermophilic conditions reaching the minimum hydraulic retention time of 4.2 d with promising results. As analysis of the microbial communities is considered to be the key for the development of anaerobic digestion optimization techniques, the present work focused on characterizing the microbial community and its variation during the reactor's runs, via 16S rRNA amplicon sequencing. Identification of new microbial species and taxonomic groups determination is of paramount importance as these representatives determine the bioprocess outcome. The current study results may contribute to further olive mill wastewater exploitation as a potential source for efficient biogas production.

Bioaugmented Mixed Culture by Clostridium aceticum to Manipulate Volatile Fatty Acids Composition From the Fermentation of Cheese Production Wastewater

Production of targeted volatile fatty acid (VFA) composition by fermentation is a promising approach for upstream and post-stream VFA applications. In the current study, the bioaugmented mixed microbial culture by Clostridium aceticum was used to produce an acetic acid dominant VFA mixture. For this purpose, anaerobic sequencing batch reactors (bioaugmented and control) were operated under pH 10 and fed by cheese processing wastewater. The efficiency and stability of the bioaugmentation strategy were monitored using the production and composition of VFA, the quantity of C. aceticum (by qPCR), and bacterial community profile (16S rRNA Illumina Sequencing). The bioaugmented mixed culture significantly increased acetic acid concentration in the VFA mixture (from 1170 ± 18 to 122 ± 9 mgCOD/L) compared to the control reactor. Furthermore, the total VFA production (from 1254 ± 11 to 5493 ± 36 mgCOD/L) was also enhanced. Nevertheless, the bioaugmentation could not shift the propionic acid dominancy in the VFA mixture. The most significant effect of bioaugmentation on the bacterial community profile was seen in the relative abundance of the Thermoanaerobacterales Family III. Incertae sedis, its relative abundance increased simultaneously with the gene copy number of C. aceticum during bioaugmentation. These results suggest that there might be a syntropy between species of Thermoanaerobacterales Family III. Incertae sedis and C. aceticum. The cycle analysis showed that 6 h (instead of 24 h) was adequate retention time to achieve the same acetic acid and total VFA production efficiency. Biobased acetic acid production is widely applicable and economically competitive with petroleum-based production, and this study has the potential to enable a new approach as produced acetic acid dominant VFA can replace external carbon sources for different processes (such as denitrification) in WWTPs. In this way, the higher treatment efficiency for WWTPs can be obtained by recovered substrate from the waste streams that promote a circular economy approach.

A lab in the field: applications of real-time, in situ metagenomic sequencing

High-throughput metagenomic sequencing is considered one of the main technologies fostering the development of microbial ecology. Widely used second-generation sequencers have enabled the analysis of extremely diverse microbial communities, the discovery of novel gene functions, and the comprehension of the metabolic interconnections established among microbial consortia. However, the high cost of the sequencers and the complexity of library preparation and sequencing protocols still hamper the application of metagenomic sequencing in a vast range of real-life applications. In this context, the emergence of portable, third-generation sequencers is becoming a popular alternative for the rapid analysis of microbial communities in particular scenarios, due to their low cost, simplicity of operation, and rapid yield of results. This review discusses the main applications of real-time, in situ metagenomic sequencing developed to date, highlighting the relevance of this technology in current challenges (such as the management of global pathogen outbreaks) and in the next future of industry and clinical diagnosis.