Response of Microbial Community to Induced Failure of Anaerobic Digesters Through Overloading With Propionic Acid Followed by Process Recovery

Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions

Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L-1 day-1 at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol-1 propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.

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.

Evolving tolerance of Yarrowia lipolytica to hydrothermal liquefaction aqueous phase waste

Hydrothermal liquefaction (HTL) is an emerging method for thermochemical conversion of wet organic waste and biomass into renewable biocrude. HTL also produces an aqueous phase (HTL-AP) side stream containing 2-4% light organic compounds that require treatment. Although anaerobic digestion (AD) of HTL-AP has shown promise, lengthy time periods were required for AD microbial communities to adapt to metabolic inhibitors in HTL-AP. An alternative for HTL-AP valorization was recently demonstrated using two engineered strains of Yarrowia lipolytica, E26 and Diploid TAL, for the overproduction of lipids and the polyketide triacetic acid lactone (TAL) respectively. These strains tolerated up to 10% HTL-AP (v/v) in defined media and up to 25% (v/v) HTL-AP in rich media. In this work, adaptive laboratory evolution (ALE) of these strains increased the bulk population tolerance for HTL-AP to up to 30% (v/v) in defined media and up to 35% (v/v) for individual isolates in rich media. The predominate organic acids within HTL-AP (acetic, butyric, and propionic) were rapidly consumed by the evolved Y. lipolytica strains. A TAL-producing isolate (strain 144-3) achieved a nearly 3-fold increase in TAL titer over the parent strain while simultaneously reducing the chemical oxygen demand (COD) of HTL-AP containing media. Fermentation with HTL-AP as the sole nutrient source demonstrated direct conversion of waste into TAL at 10% theoretical yield. Potential genetic mutations of evolved TAL production strains that could be imparting tolerance were explored. This work advances the potential of Y. lipolytica to biologically treat and simultaneously extract value from HTL wastewater. KEY POINTS: • Adaptive evolution of two Y. lipolytica strains enhanced their tolerance to waste. • Y. lipolytica reduces chemical oxygen demand in media containing waste. • Y. lipolytica can produce triacetic acid lactone directly from wastewater.

Fate of intracellular, extracellular polymeric substances-associated, and cell-free antibiotic resistance genes in anaerobic digestion of thermally hydrolyzed sludge

Thermal hydrolysis of sludge is a promising approach to mitigate antibiotic resistance genes (ARGs) propagation in anaerobic digestion (AD). Although ARGs in sludge may be fractioned into intracellular, extracellular polymeric substance (EPS)-associated, and cell-free ARGs, the fate of these different fractions in AD has never been investigated. This study presents a detailed characterization of intracellular and extracellular ARGs in AD of sludge thermally hydrolyzed at 90 °C and 140 °C. EPS-associated ARGs represented the major fraction of the total extracellular ARGs in all samples, while its lowest abundance was observed for thermal hydrolysis at 140 °C along with the lowest EPS levels. The results suggested a positive correlation between EPS-associated ARGs with intracellular and cell-free ARGs. Furthermore, various EPS components, such as proteins and e-DNA, were positively correlated with β-lactam resistance genes. sul1 dominated all samples as an EPS-associated resistance gene. These results provide new insights into the significance of different ARGs fractions in their overall dissemination in AD integrated with thermal hydrolysis.

Molecular biology and modeling analysis reveal functional roles of propionate to acetate ratios on microbial syntrophy and competition in electro-assisted anaerobic digestion

This study examined the significance of propionate to acetate (HPr/HAc) ratios on microbial syntrophy and competition in microbial electrolysis cell-assisted anaerobic digestion (MEC-AD). In addition to molecular biology and phylogenetic analysis, a numerical MEC-AD model was developed by modifying Anaerobic Digestion Model No.1 to predict the effects of different HPr/HAc ratios (0.5, 1.5, 2.5, and 5). The HPr/HAc ratios of 0.5 and 1.5 maintained efficient syntrophy among electroactive bacteria, hydrogenotrophic methanogens, and homoacetogens, leading to higher methane yields. In contrast, higher HPr/HAc ratios of 2.5 and 5 were detrimental to methanogenesis. Both microbial community analysis and numerical modeling results suggested that higher propionate levels could promote the enrichment of H₂-utilizing acetogens, thereby triggering their competition with hydrogenotrophic methanogens. Moreover, protein fraction in extracellular polymeric substances and the relative expression of genes associated with extracellular electron transfer in both anode and cathode biofilms were markedly decreased with increasing HPr/HAc ratios, indicating partial inhibition of microbial electroactivity. Overall, these results illuminate deep insight into anaerobic syntrophy, contributing to the process kinetics and methane yields in MEC-AD systems. Furthermore, from a practical viewpoint, the results can also be helpful in effective control of MEC-AD operation without propionate accumulation.

The effect of substituting energy crop with agricultural waste on the dynamics of bacterial communities in a two-stage anaerobic digester

The replacement of energy crops with agricultural waste in biogas production through anaerobic digestion (AD) is both an environmentally sustainable and economically profitable strategy. However, the change of feeding mix in AD might result in nutrient imbalance or increase of the ammonium concentration, negatively affecting the activity of the microbes responsible for the process. In the present study the structure and dynamics of the bacterial communities of a full-scale two-stage AD plant, composed of a hydrolysis/acidogenesis (H) and an acetogenesis/methanogenesis (M) tanks, was monitored during feedstock substitution. Energy crop (triticale) was replaced by poultry manure litter and olive mill pomace. The increase percentage of poultry manure litter (up to 8.6%) and olive mill pomace (up to 30.5%) in the recipe incremented the total solids (up to 21% in H) and, consequently, the nitrogen content in the digestate (6.7 g N/kg in the solid fraction in H and 4-5 g NH₄⁺-N/L in the liquid fraction). This favored the growth of Lactococcus sp. with consequent increment of lactate production (∼ 1 mg L^-1 last two days of the survey) and the establishment of Weissella and Lactobacillus spp. Syntrophic acetate-oxidizers, including Syntrophaceticus (6% ± 1.7%), were detected manly in M but were negatively affected by the addition of the poultry manure litter, while the sulfate-reducing bacteria correlated with the variations of the volatile fatty acids. Planctomycetes putatively capable of anammox process were also found in the H during the first two days of the survey and accounted for 0.3 ± 0.01% of the total bacterial community. The stability of the process during feedstock change is the result of the shift of bacterial populations of different functional groups that showed peculiar adaptation patterns in the two stages of the plant.

Propagation of antibiotic resistance genes during anaerobic digestion of thermally hydrolyzed sludge and their correlation with extracellular polymeric substances

The positive impact of the thermal hydrolysis process (THP) of sewage sludge on antibiotic resistance genes (ARGs) removal during anaerobic digestion (AD) has been reported in the literature. However, little information is available on how changes in different extracellular polymeric substances (EPS) due to THP can influence ARG propagation during AD. This study focused on systematically correlating EPS components and ARG abundance in AD of sewage sludge pretreated with THP (80 °C, 110 °C, 140 °C, 170 °C). THP under different conditions improved sludge solubilization followed by improved methane yields in the biochemical methane potential (BMP) test. The highest methane yield of 275 ± 11.5 ml CH₄/g COD was observed for THP-140 °C, which was 40.5 ± 2.5% higher than the control. Increasing THP operating temperatures showed a non-linear response of ARG propagation in AD due to the rebound effect. The highest ARGs removal in AD was achieved with THP at 140 °C. The multivariate analysis showed that EPS polysaccharides positively correlated with most ARGs and integrons, except for macrolides resistance genes. In contrast, EPS protein was only strongly correlated with β-lactam resistance genes. These results suggest that manipulating THP operating conditions targeting specific EPS components will be critical to effectively mitigating the dissemination of particular ARG types in AD.

Key microbial clusters and environmental factors affecting the removal of antibiotics in an engineered anaerobic digestion system

To identify the key microbial clusters and influencing factors involved in antibiotic removal from engineered anaerobic digestion (AD) systems, the dynamic characteristics of antibiotics, physiochemical factors, microbial communities and functional genes were investigated by 16S rRNA and metagenome sequencing. The results showed that antibiotic removal occurred mainly in the first 21 days, and sulfonamides had the highest removal rate. The key microbial clusters related to the biodegradation of antibiotics consisted mainly of Firmicutes and Bacteroidetes. The key enzymes consisted of deaminases, peptidases, C-N ligases, decarboxylases and alkyl-aryl transferases. Structural equation modelling indicated that low concentrations of propionic acid promoted the biodegradation activities of key microbial clusters in the first 21 days, but their activities were inhibited by the accumulated propionic acid after 21 days. Thus, propionic acid should be regulated in engineered AD systems to prevent the adverse effect of acid inhibition on antibiotic-degrading bacteria.

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.

Carboxylic acids production via anaerobic fermentation: Microbial communities' responses to stepwise and direct hydraulic retention time decrease

Carboxylic acids, traditionally produced from fossil fuels, might be generated from renewable biomass resources via anaerobic fermentation. Considering that the microbial activity of this bioprocess is ruled by the imposed hydraulic retention time (HRT), this investigation explored the relationship between process stability and microbial community. Stepwise and direct HRT reduction strategies were assessed in terms of waste bioconversion into volatile fatty acids (VFAs). Microbial community dynamics revealed a microbial specialization along the HRT decrease. The direct implementation of low HRT resulted in drastic microbial fluctuations, leading to process failure at HRT below 6 days. Stepwise strategy for HRT reduction favored microbial adaptation, supporting maximum bioconversions efficiencies (32 % VFA_COD/tCOD_in) at low HRT values (HRT 4 days). Microbial similarity analysis revealed Clostridiales, Lactobacillales and Bacteroidales orders as keystone microorganisms involved in VFAs production, being responsible for protein degradation and propionic acid accumulation.

Syntrophic propionate-oxidizing bacteria in methanogenic systems

The mutual nutritional cooperation underpinning syntrophic propionate degradation provides a scant amount of energy for the microorganisms involved, so propionate degradation often acts as a bottleneck in methanogenic systems. Understanding the ecology, physiology and metabolic capacities of syntrophic propionate-oxidizing bacteria (SPOB) is of interest in both engineered and natural ecosystems, as it offers prospects to guide further development of technologies for biogas production and biomass-derived chemicals, and is important in forecasting contributions by biogenic methane emissions to climate change. SPOB are distributed across different phyla. They can exhibit broad metabolic capabilities in addition to syntrophy (e.g. fermentative, sulfidogenic and acetogenic metabolism) and demonstrate variations in interplay with cooperating partners, indicating nuances in their syntrophic lifestyle. In this review, we discuss distinctions in gene repertoire and organization for the methylmalonyl-CoA pathway, hydrogenases and formate dehydrogenases, and emerging facets of (formate/hydrogen/direct) electron transfer mechanisms. We also use information from cultivations, thermodynamic calculations and omic analyses as the basis for identifying environmental conditions governing propionate oxidation in various ecosystems. Overall, this review improves basic and applied understanding of SPOB and highlights knowledge gaps, hopefully encouraging future research and engineering on propionate metabolism in biotechnological processes.

High-rate blackwater anaerobic digestion under septic tank conditions with the amendment of biosolids-derived biochar synthesized at different temperatures

Septic tanks have been widely used for blackwater treatment in developing countries, while high-rate septic tanks with improved methane recovery are yet to be achieved. This study investigated biosolids-derived biochar (synthesized at 300℃, 425℃, and 550℃) as an additive for developing high-rate septic tanks. The experiments were conducted with anaerobic bioreactors operated with synthetic blackwater under septic tank conditions. All biochar amended reactors demonstrated a steady increase in daily methane production for increasing OLR from 0.08 to 3 g COD/L/d. The control reactor showed significant process disturbances at OLRs ≥ 2 g COD/L/d with an accumulation of volatile fatty acids followed by pH drop. At OLR of 3 g COD/L/d, the daily methane production from biochar amended reactors was ~ 4.3 times higher than the control (300 vs. 70 mL per day). Biochar addition established a robust microbiome consisted of a higher abundance of hydrogenotrophic and acetoclastic methanogens and hydrogen-producing fermentative bacteria.