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.

Effect of inoculum composition on the microbial community involved in the anaerobic digestion of sugarcane bagasse

In anaerobic digestion (AD), the choice of inoculum type seems to be relevant for methane production for complex substrates, such as lignocellulosic material. Previous work demonstrated that the addition of fresh manure and ruminal fluid to anaerobic sludge improved methane productivity and kinetics of AD of crude sugarcane bagasse (CSB). Considering that the improvement of methane production could be a result of a more adapted microbial community, the present study performed the Next Generation Sequencing analysis to identify changes in the microbiome of anaerobic sludge inoculum, resulting from fresh manure and ruminal fluid addition. In comparison with AD performed only with anaerobic sludge inoculum (50:50, U), accumulated methane production was 15% higher with anaerobic sludge plus ruminal fluid inoculum (50:50, UR) and even higher (68%) with anaerobic sludge with fresh bovine manure inoculum (50:50, UFM), reaching the value of 143 NmLCH4.gVS-1. Clostridium species were highly abundant in all inocula, playing an important role during the hydrolysis and fermentation of CSB, and detoxifying potential inhibitors. Microbial composition also revealed the occurrence of Pseudomonas and Anaerobaculum at UFM inoculum that seem to have contributed to the higher methane production rate, mainly due to their hydrolytic and fermentative ability on lignocellulosic substrates. On the other hand, the presence of Alcaligenes might have had a negative effect on methane production due to their ability to perform methane oxidation.

Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches

The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.

Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics

Ammonia release from proteinaceous feedstocks represents the main inhibitor of the anaerobic digestion (AD) process, which can result in a decreased biomethane yield or even complete failure of the process. The present study focused on the adaptation of mesophilic AD communities to a stepwise increase in the concentration of ammonium chloride in synthetic medium with casein used as the carbon source. An adaptation process occurring over more than 20 months allowed batch reactors to reach up to 20 g of NH4+ N/L without collapsing in acidification nor ceasing methane production. To decipher the microbial dynamics occurring during the adaptation and determine the genes mostly exposed to selective pressure, a combination of biochemical and metagenomics analyses was performed, reconstructing the strains of key species and tracking them over time. Subsequently, the adaptive metabolic mechanisms were delineated by following the single nucleotide variants (SNVs) characterizing the strains and prioritizing the associated genes according to their function. An in-depth exploration of the archaeon Methanoculleus bourgensis vb3066 and the putative syntrophic acetate-oxidizing bacteria Acetomicrobium sp. ma133 identified positively selected SNVs on genes involved in stress adaptation. The intraspecies diversity with multiple coexisting strains in a temporal succession pattern allows us to detect the presence of an additional level of diversity within the microbial community beyond the species level.

Chemical and microbiological characterization of pig manures and digestates

Livestock and poultry breeding modes, feed compositions and manure collection systems have regional characteristics, which can directly affect the composition of livestock and poultry breeding manure, energy production by anaerobic digestion and resource utilization of products. The chemical, heavy metal contents and microbiological characteristics of pig manures and digestates were characterized in five pig farms and biogas plants in Quzhou (Zhejiang Province) in this study. The results showed that hemicellulose and cellulose of pig manures could be partly degraded in anaerobic digestion, but lignin was difficultly degraded and accumulated in digestates. The content of Zn was highest in the pig manure and digestate samples, followed by Cu, Cr, As, Ni, Pb, Cd, T1 and Hg. The As content was 16.09-31.22 mg kg^-1 in the pig manure and digestate samples, which exceeded the standard limitation requirements in fertilizers in China (≤15 mg kg^-1). Bacteroidota, Firmicutes, Proteobacteria and Spirochaetota dominated in the pig manure and digestate samples, with a relative abundance of 73.6%-99.4%. The microbial community structure in the pig manure samples was quite different among the five farms. The pH, contents of lignin, T1 and As had a significant effect on the microbial community structure in the pig manure samples, while the contents of total phosphorus, NO₃^--N, cellulose and Pb could significantly influence the microbial community structure in the digestate samples. These findings can provide a theoretical basis for recycling manure and improving biogas engineering in large-scale pig farms.

Bacterial Communities Associated with Crude Oil Bioremediation through Composting Approaches with Indigenous Bacterial Isolate

In this study, we aim to investigate the efficiency of crude oil bioremediation through composting and culture-assisted composting. First, forty-eight bacteria were isolated from a crude oil-contaminated soil, and the isolate with the highest crude oil degradation activity, identified as Pseudomonas aeruginosa, was selected. The bioremediation was then investigated and compared between crude oil-contaminated soil (S), the contaminated soil composted with fruit-based waste (SW), and the contaminated soil composted with the same waste with the addition of the selected bacterium (SWB). Both compost-based methods showed high efficiencies of crude oil bioremediation (78.1% and 83.84% for SW and SWB, respectively). However, only a slight difference between the treatments without and with the addition of P. aeruginosa was observed. To make a clear understanding of this point, bacterial communities throughout the 4-week bioremediation period were analyzed. It was found that the community dynamics between both composted treatments were similar, which corresponds with their similar bioremediation efficiencies. Interestingly, Pseudomonas disappeared from the system after one week, which suggests that this genus was not the key degrader or only involved in the early stage of the process. Altogether, our results elaborate that fruit-based composting is an effective approach for crude oil bioremediation.

Prolonged acetogenic phase and biological succession during anaerobic digestion using swine manure

In recent years, global warming and the limitation of fossil fuels have been causing the governments of different countries to think about the search for more sustainable fuel sources. Biomethane (CH₄) has gained increasing attention in recent years as an alternative option for a sustainable source of energy. Biogas is generated during the anaerobic digestion of organic materials by the metabolism of complex microbial communities in the substrates that make up this digestion. The microbial community evaluation using 16S rDNA metabarcoding in a bench covered pond bioreactor using swine effluent revealed the dominant bacteria belonging to Firmicutes, Proteobacteria, and Bacteroidetes phyla. The methanogenic group was represented by the Euryarchaeota phylum. It was possible to observe that the relative frequency of the methanogenic archaea community decreased with the anaerobic digestion, indicating a biological succession stage. On the other hand, there was a predominant acetogenic diversity in this final stage. These data showed stabilization of biomethane production, although the microbial community of methanogens has drastically reduced in the late process.

Effects of Pig Manure and Its Organic Fertilizer Application on Archaea and Methane Emission in Paddy Fields

Paddy fields account for 10% of global CH4 emissions, and the application of manure may increase CH4 emissions. In this study, high-throughput sequencing technology was used to investigate the effects of manure application on CH4 emissions and methanogens in paddy soil. Three treatments were studied: a controlled treatment (CK), pig manure (PM), and organic fertilizer (OF). The results showed that the contents of Zn, Cr and Ni in paddy soil increased with the application of manure, but the contents of heavy metals gradually decreased with the growth of rice. The Shannon index and Ace index showed that the application of pig manure and organic fertilizer less affected the diversity and richness of soil Archaea. The results of community composition analysis showed that Methanobacterium, Methanobrevibacter, Methanosphaera, Methanosarcina and Rice_Cluster_I were the main methanogens in paddy soil after manure and organic fertilizer application. Soil environmental factors were changed after applied manure, among which total potassium (TK) and total nitrogen (TN) were the main environmental factors affecting methanogens in paddy soil. The changes of soil environmental factors affected the community composition of methanogens, and the increase of the relative abundance of methanogens maybe the main reason for the increase of CH4 emission flux. The relative abundance of methanogens and CH4 emission flux in paddy soil were increased by both pig manure and organic fertilizer application, and pig manure had a bigger impact than organic manure.

Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production

An estimated 25 million tons of animal manure is produced globally every year, causing considerable impact to the environment. These impacts can be managed through the use of anaerobic digestion (AD) This process achieves waste degradation through enzymatic activity, the efficiency of the AD process is directly related to microorganisms that produce these enzymes. Biomethane potential (BMP) assays remain the standard theoretical framework to pre-determine biogas yield and have been used to determine the feasibility of substrates or their combination for biogas production. However, an integrated approach that combines substrate choice and co-digestion would provide an improvement to the current predictive models. PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) addresses the limitations of assays in this regard. In this paper, the biochemical functions of horse, cow, and pig manures are predicted. A total of 135 predicted KEGG Orthologies (KOs) showed amino acids, carbohydrate, energy, lipid, and xenobiotic metabolisms in all the samples. Linear discriminant analysis (LDA) combined with the effect size measurements (LEfSe), showed that fructose, mannose, amino acid and nucleotide sugar, phosphotransferase (PST) as well as starch and sucrose metabolisms were significantly higher in horse manure samples. 36 of the KOs were related to the acidogenesis and/or acetogenesis AD stages. Extended bar plots showed that 11 significant predictions were observed for horse-cow, while 5 were predicted for horse-pig and for cow-pig manures. Based on these predictions, the AD process can be enhanced through co-digestion strategies that takes into account the predicted metabolic contributions of the manure samples. The results supported the BMP calculations for the samples in this study. Biogas yields can be improved if this combined approach is employed in routine analysis before co-digesting different substrates.

In-situ alkaline enhanced two-stage anaerobic digestion system for waste cooking oil and sewage sludge co-digestion

Anaerobic digestion is a promising way for resource recovery from waste cooking oil (WCO) due to its high bio-methanation potential. In-situ mild alkaline (pH 8) enhanced two-stage continuous stirred tank reactors (ALK-2-CSTRs) were implemented to explore its efficiency in co-digesting WCO and sewage sludge with stepwise increase of WCO in the co-substrates. Results demonstrate that the ALK-2-CSTRs effectively promoted methane yield from the co-substrates via promoting hydrolysis, long chain fatty acids (LCFAs) degradation and protecting methanogens from exposure to high concentration of LCFAs directly. The maximum methane yield of the ALK-2-CSTRs is 39.2% higher than that of a single stage CSTR system at the optimal feed mixture of 45:55 (WCO:SS [VS]). The thermophilic operation applied to the stage-1 of the ALK-2-CSTRs failed to improve the methane yield when the methanogenic performance was stable; while upon WCO overloaded, the elevated temperature mitigated the deterioration of methanogenesis by stimulating the bioconversion of the toxic LCFAs, especially the unsaturated oleic acid. Microbial community analysis reveals the ALK-2-CSTRs stimulated the growth of lipolytic bacteria and hydrogenotrophic methanogens, which suggests the hydrogenotrophic methanogenic pathway was promoted. Cost evaluation demonstrates the economical superiority of the ALK-2-CSTR over the prevailing strategies developed for enhancing methane yield from the co-substrates.

Simultaneous carbon dioxide reduction and enhancement of methane production in biogas via anaerobic digestion of cornstalk in continuous stirred-tank reactors: The influences of biochar, environmental parameters, and microorganisms

The composition of biogas produced by anaerobic digestion (AD) is typically not ideal due to high CO₂ content. In the study, cottonwood biochar was used as an enhanced mediator for the continuously stirred tank reactor AD of cornstalk. The effects of substrate loading and biochar dosage on biogas composition, volatile fatty acids (VFAs), NH₃-N, and microbial community characteristics were systematically explored. The results showed that the highest volumetric biogas production rate with biochar was 1.40 L/L/d, at the same time, the CO₂ content in the biogas decreased by 5.90%, while the CH₄ content increased by 7.40%, compared with the values in AD without biochar. Moreover, VFAs were degraded effectively, in particular, the propionic acid concentration decreased by 55.7%. Besides, microbial abundance had positive correlations with environmental parameters. This study could provide valuable information for both the elucidation of strengthening mechanisms of biochar and further large-scale engineering application.

Addition of a carbon fiber brush improves anaerobic digestion compared to external voltage application

Two methods were examined to improve methane production efficiency in anaerobic digestion (AD) based on adding a large amount of surface area using a single electrically conductive carbon brush, or by adding electrodes as done in microbial electrolysis cells (MECs) to form a hybrid AD-MEC. To examine the impact of surface area relative to electrodes, AD reactors were fitted with a single large brush without electrodes (FB), half a large brush with two electrodes with an applied voltage (0.8 V) and operated in closed circuit (HB-CC) or open circuit (HB-OC) mode, or only two electrodes with a closed circuit and no large brush (NB-CC) (equivalent to an MEC). The three configurations with a half or full brush all had improved performance as shown by 57-82% higher methane generation rate parameters in the Gompertz model compared to NB-CC. The retained biomass was much higher in the reactors with large brush, which likely contributed to the rapid consumption of volatile fatty acids (VFAs) and therefore improved AD performance. A different microbial community structure was formed in the large-size brushes compared to the electrodes. Methanothrix was predominant in the biofilm of large-size carbon brush, while Geobacter (anode) and Methanobacterium (cathode) were highly abundant in the electrode biofilms. These results demonstrate that adding a high surface area carbon fiber brush will be a more effective method of improving AD performance than using MEC electrodes with an applied voltage.

Comparative Analysis of Bacterial and Archaeal Community Structure in Microwave Pretreated Thermophilic and Mesophilic Anaerobic Digesters Utilizing Mixed Sludge under Organic Overloading

The effects of microwave (MW) pretreatment were investigated by six anaerobic digesters operated under thermophilic and mesophilic conditions at high organic loading rates (4.9–5.7 g volatile solids/L/d). The experiments and analyses were mainly designed to reveal the impact of MW pretreatment and digester temperatures on the process stability and microbial community structure by correlating the composition of microbial populations with volatile fatty acid (VFA) concentrations. A slight shift from biogas production (with a reasonable methane content) to VFA accumulation was observed in the thermophilic digesters, especially in the MW-irradiated reactors. Microbial population structure was assessed using a high-throughput sequencing of 16S rRNA gene on the MiSeq platform. Microbial community structure was slightly affected by different MW pretreatment conditions, while substantially affected by the digester temperature. The phylum Bacteroidetes proliferated in the MW-irradiated mesophilic digesters by resisting high-temperature MW (at 160 °C). Hydrogenotrophic methanogenesis (mostly the genus of Methanothermobacter) was found to be a key route of methane production in the thermophilic digesters, whereas aceticlastic methanogenesis (mostly the genus of Methanosaeta) was the main pathway in the mesophilic digesters.

Anaerobic microbial communities can influence algal growth and nutrient removal from anaerobic digestate

The objective of this work was to test the impact of anaerobic digester microorganisms on algal growth, composition, and nutrient removal from digestate. Culture studies were carried out to determine the impacts of the microbial community on treatment of poultry litter anaerobic digestate by two strains of green algae: Auxenochlorella protothecoides and Chlorella sorokiniana. The results showed that the community doubled the growth of A. protothecoides but had no impact on C. sorokiniana growth. A similar result was observed for nutrient removal where the microbial community increased the capacity of A. protothecoides to remove ammonium and phosphate. The impact of the microbial community on biomass composition was minimal for both algae types.