Determination of the fractions of syntrophically oxidized acetate in a mesophilic methanogenic reactor through an (12)C and (13)C isotope-based kinetic model

Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants

Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H₂/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.

Identification of partial denitrification granulation enhanced by low C/N ratio in the aspect of metabolomics and quorum sensing

Partial denitrification granular sludge (PDGS) and denitrification granular sludge (DGS) play an important role in nitrogen removal from wastewater. However, the inherent cause of aggregation capacity related to the ratio of COD to nitrogen (COD/N) is still unclear. In this study, metabolomics analysis was combined with microbiological analyses, granular performance and extracellular polymeric substances (EPS) structure to explore the granulation mechanism at different influent COD/N ratios. The results showed that the higher COD/N ratio selectively enhanced the gluconeogenesis pathway, purine and pyrimidine metabolism pathway, resulting in more extracellular polysaccharide (PS) excretion and floc sludge. The absence of carbon source weakened tricarboxylic acid cycle (TCA) reaction, resulting in NAD⁺ and ADP decrease, nitrite accumulation and change of microbial community structure. The amino acids biosynthesis pathway was enhanced under low COD/N ratio, which promoted the hydrophobicity of EPS. PDGS had stronger Acyl-homoserine lactones (AHLs)-based quorum sensing (QS) than DGS during the operational period. CO8-HSL, C8-HSL and C6-HSL, as the main form of AHLs, played a dominating role in DGS and PDGS. Batch tests illustrated that adding AHLs obviously improved the synthesis of the amino acids, threonine (Thr), tryptophan (Trp), methionine (Met) and glycine (Gly). Dosing AHLs regulated PS synthesis only at a high COD/N ratio. The glucose-6P, glycerate-3p and UDP-Glc were up-regulated only in DSG, which increased the hydrophilic groups in EPS. The results not only provided the new insights into the metabolism of denitrifying granular sludge, but also indicated the application potential of the technologies regarding start-up and operation of granule sludge.

Characterizing the growing microorganisms at species level in 46 anaerobic digesters at Danish wastewater treatment plants: A six-year survey on microbial community structure and key drivers

Anaerobic digestion (AD) is a key technology at many wastewater treatment plants (WWTPs) for converting primary and surplus activated sludge to methane-rich biogas. However, the limited number of surveys and the lack of comprehensive datasets have hindered a deeper understanding of the characteristics and associations between key variables and the microbial community composition. Here, we present a six-year survey of 46 anaerobic digesters, located at 22 WWTPs in Denmark, which is the first and largest known study of the microbial ecology of AD at WWTPs at a regional scale. For three types of AD (mesophilic, mesophilic with thermal hydrolysis pretreatment, and thermophilic), we present the typical value range of 12 key parameters including operational variables and performance parameters. High-resolution bacterial and archaeal community analyses were carried out at species level using amplicon sequencing of >1,000 samples and the new ecosystem-specific MiDAS 3 reference database. We detected 42 phyla, 1,600 genera, and 3,584 species in the bacterial community, where 70% of the genera and 93% of the species represented environmental taxa that were only classified based on MiDAS 3 de novo placeholder taxonomy. More than 40% of the bacterial species were found not to grow in the mesophilic and thermophilic digesters and were only present due to immigration with the feed sludge. Ammonium concentration was the main driver shaping the bacterial community while temperature and pH were main drivers for the archaea in the three types of ADs. Sub-setting for the growing microbes improved significantly the correlation analyses and revealed the main drivers for the presence of specific species. Within mesophilic digesters, feed sludge composition and other key parameters (organic loading rate, biogas yield, and ammonium concentration) correlated with specific growing species. This survey provides a comprehensive insight into community structure at species level, providing a foundation for future studies of the ecological significance/characteristics and function of the many novel or poorly described taxa.

Biochar for Wastewater Treatment—Conversion Technologies and Applications

Biochar as a stable carbon-rich material shows incredible potential to handle water/wastewater contaminants. Its application is gaining increasing interest due to the availability of feedstock, the simplicity of the preparation methods, and their enhanced physico-chemical properties. The efficacy of biochar to remove organic and inorganic pollutants depends on its surface area, pore size distribution, surface functional groups, and the size of the molecules to be removed, while the physical architecture and surface properties of biochar depend on the nature of feedstock and the preparation method/conditions. For instance, pyrolysis at high temperatures generally produces hydrophobic biochars with higher surface area and micropore volume, allowing it to be more suitable for organic contaminants sorption, whereas biochars produced at low temperatures own smaller pore size, lower surface area, and higher oxygen-containing functional groups and are more suitable to remove inorganic contaminants. In the field of water/wastewater treatment, biochar can have extensive application prospects. Biochar have been widely used as an additive/support media during anaerobic digestion and as filter media for the removal of suspended matter, heavy metals and pathogens. Biochar was also tested for its efficiency as a support-based catalyst for the degradation of dyes and recalcitrant contaminants. The current review discusses on the different methods for biochar production and provides an overview of current applications of biochar in wastewater treatment.

Using stable isotope labeling approach and two dimensional correlation spectroscopy to explore the turnover cycles of different carbon structures in extracellular polymeric substances

Extracellular polymeric substances (EPS) from activated sludge comprise many organic constituents with polysaccharides and proteins as the main components of two different functionalities. Despite a number of previous EPS studies, a fundamental question remained unanswered, namely, whether the different EPS components would have the same turnover cycle (i.e., formation/dissolution) in biological wastewater treatment systems. In this study, we employed a stable isotope labeling approach based on isotope-enriched substrates (i.e., ¹³C-glucose and ¹⁵NH₄Cl) to examine the potential discrepancies in the turnover cycles among different major EPS constituents. Our results, based on substrate consumption in a batch bioreactor, evidenced the existence of differences in carbon and nitrogen cycles within bulk EPS with an earlier replenishment of organic carbon relative to organic nitrogen. The changes in the 13C nuclear magnetic resonance (13C NMR) spectra of EPS with operation clarified the relative differences in the turnover periods among several identified EPS structures with different chemical functionalities. Two-dimensional correlation spectroscopy (2D-COS) on the 13C NMR spectra further showed that the substrate-assimilated carbon functional groups appear to preferably formed within bulk EPS in the order of O-alkyl carbons > amides > α amino acids > aliphatic carbons. This study provides a novel insight into the dissimilar formation rates of different EPS structures after substrate assimilation. This isotope labeling approach can be further applied to determine the mass balance among the substrate, biomass, and bound/soluble EPS within activated sludge systems.

Competition Between Chemolithotrophic Acetogenesis and Hydrogenotrophic Methanogenesis for Exogenous H2/CO2 in Anaerobically Digested Sludge: Impact of Temperature

Anaerobic digestion is a widely applied technology for sewage sludge treatment. Hydrogen and CO₂ are important degradation products, which serve as substrates for both hydrogenotrophic methanogenesis and chemolithotrophic acetogenesis. In order to understand the competition between these processes for H₂/CO₂, sludge samples were incubated under H₂/CO₂ headspace at different temperatures, and analyzed with respect to turnover of H₂, CO₂, CH₄ and acetate including their δ¹³C values. At 15°C, ¹³C-depleted acetate (δ¹³C of -41 to -43‰) and transient acetate accumulation were observed under H₂/CO₂, and CH₄ accumulated with δ¹³C values increasing from -53 to -33‰. The copy numbers of the fhs gene, which is characteristic for acetogenic bacteria, were at 15°C one order of magnitude higher in the H₂/CO₂ incubations than the N₂ control. At 30°C, however, acetate did not accumulate in the H₂/CO₂ incubation and the δ¹³C of CH₄ was very low (-100 to -77‰). At 50°C, isotopically enriched acetate was transiently formed and subsequently consumed followed by the production of ¹³C-depleted CH₄. Collectively, the results indicate a high contribution of chemolithotrophic acetogenesis to H₂/CO₂ utilization at 15°C and 50°C, while H₂/CO₂ was mainly consumed by hydrogenotrophic methanogenesis at 30°C. Fermentative production and methanogenic consumption of acetate were active at 50°C.

Competition Between Chemolithotrophic Acetogenesis and Hydrogenotrophic Methanogenesis for Exogenous H2/CO2 in Anaerobically Digested Sludge: Impact of Temperature

Anaerobic digestion is a widely applied technology for sewage sludge treatment. Hydrogen and CO₂ are important degradation products, which serve as substrates for both hydrogenotrophic methanogenesis and chemolithotrophic acetogenesis. In order to understand the competition between these processes for H₂/CO₂, sludge samples were incubated under H₂/CO₂ headspace at different temperatures, and analyzed with respect to turnover of H₂, CO₂, CH₄ and acetate including their δ¹³C values. At 15°C, ¹³C-depleted acetate (δ¹³C of -41 to -43‰) and transient acetate accumulation were observed under H₂/CO₂, and CH₄ accumulated with δ¹³C values increasing from -53 to -33‰. The copy numbers of the fhs gene, which is characteristic for acetogenic bacteria, were at 15°C one order of magnitude higher in the H₂/CO₂ incubations than the N₂ control. At 30°C, however, acetate did not accumulate in the H₂/CO₂ incubation and the δ¹³C of CH₄ was very low (-100 to -77‰). At 50°C, isotopically enriched acetate was transiently formed and subsequently consumed followed by the production of ¹³C-depleted CH₄. Collectively, the results indicate a high contribution of chemolithotrophic acetogenesis to H₂/CO₂ utilization at 15°C and 50°C, while H₂/CO₂ was mainly consumed by hydrogenotrophic methanogenesis at 30°C. Fermentative production and methanogenic consumption of acetate were active at 50°C.

An explanation of the methanogenic pathway for methane production in anaerobic digestion of nitrogen-rich materials under mesophilic and thermophilic conditions

The impact of temperature on the anaerobic digestion of chicken manure was investigated by studying the process performance and pathway for continuously-fed digesters under mesophilic and thermophilic conditions. The mesophilic digester obtained a 15% higher methane yield compared with the thermophilic digester. Mesophilic and thermophilic digester had free ammonia of 31 and 145 mg/L, respectively. The stable carbon isotope analysis indicated that 41% and 50% of acetate was converted to methane through the syntrophic acetate oxidation and hydrogenotrophic methanogenesis (SAO-HM) pathway under mesophilic and thermophilic conditions, respectively. The genus Pseudomonas represented 10% and 16% under mesophilic and thermophilic conditions, respectively. A high abundance of the methanogens genus Methanoculleus (94% of total methanogens) in mesophilic and the genus Methanothermobacter (96%) in thermophilic digesters indicated they were the main hydrogenotrophic partners in SAO. The present study therefore illustrated that methanogenic pathway shifting, induced by free ammonia, closely correlated to the process performance.