Integrative Analyses to Investigate the Link between Microbial Activity and Metabolite Degradation during Anaerobic Digestion

Environmentally-grown aerobic granular sludge performs more complete pharmaceutical biodegradation and wastewater treatment than lab-grown granules

This study evaluated pharmaceutical removal by environmentally-grown aerobic granular sludge (AGS). Most pharmaceutical treatment studies utilize lab-grown AGS, which is cultivated from activated sludge flocs on synthetic media and therefore is likely to possess different physical and microbiological properties than its real-world counterpart. For approximately 70 days, a 60 μg/L mixture of gemfibrozil, diclofenac, and erythromycin was fed to environmentally-grown AGS. Wastewater treatment, granule characteristics, and pharmaceutical fate were monitored. Environmentally-grown granules outperformed their lab-grown counterparts in multiple ways: environmental granules were physically unimpacted by pharmaceuticals, phosphate removal remained complete, and all nitrogen removal processes were unaffected except ammonia oxidation, which was temporarily inhibited by approximately 35%. Most importantly, gemfibrozil was completely biodegraded, a result yet to be observed in any AGS study. Diclofenac and erythromycin removal were minimal and generally below 10%. The families J111, Xanthomonadaceae, OLB5, and Weeksellaceae were uniquely identified as pharmaceutical degraders. Results suggest that environmentally-grown AGS contains rare, but essential, microbial community members missing from lab-grown granules, and these communities enhance environmental granules' resilience during pharmaceutical exposure. Altogether, this study demonstrates that lab-grown AGS may not accurately model the functional capacity of its real-world counterparts.

Microbial Volatile Organic Compounds as Microecological Stability Indicators in Response to Temperature Changes during Anaerobic Digestion

The use of traditional early warning indicators for monitoring anaerobic digestion (AD) is limited, owing to their inability to sensitively reflect microbial performance. Microbial volatile organic compounds (mVOCs) possess distinctive species-specific characteristics, functioning as a communication mechanism between microorganisms at two distinct levels: interspecific and intraspecific, and they can be potential indicators of microbial performance. Therefore, we conducted time-series and comparative nontarget analyses using headspace solid-phase microextraction and high-resolution mass spectrometry to investigate temporal variations in mVOC responses to temperature changes during AD. In total, seventy-six differential mVOCs, playing crucial roles in important material and energy metabolism, signaling, and membrane transport processes throughout AD, were investigated after gradual and pulsed temperature perturbations. These differential mVOCs exhibited high co-occurrences with bacteria and archaea based on 16S rRNA gene sequencing analysis. The study findings suggest that mVOCs can serve as explanatory indicators during AD monitoring, bridging AD process stability, and anaerobic microecology. However, further verification is necessary, owing to the wide range of mVOC types involved.

Microbiome dynamics and products profiles of biowaste fermentation under different organic loads and additives

Biowaste fermentation is a promising technology for low-carbon print bioenergy and biochemical production. Although it is believed that the microbiome determines both the fermentation efficiency and the product profiles of biowastes, the explicit mechanisms of how microbial activity controls fermentation processes remained to be unexplored. The current study investigated the microbiome dynamics and fermentation product profiles of biowaste fermentation under different organic loads (5, 20, and 40 g-VS/L) and with additives that potentially modulate the fermentation process via methanogenesis inhibition (2-bromoethanesulfonate) or electron transfer promotion (i.e., reduced iron, magnetite iron, and activated carbon). The overall fermentation products yields were 440, 373 and 208 CH4-eq/g-VS for low-, medium- and high-load fermentation. For low- and medium-load fermentation, volatile fatty acids (VFAs) were first accumulated and were gradually converted to methane. For high-load fermentation, VFAs were the main fermentation products during the entire fermentation period, accounting for 62% of all products. 16S rRNA-based analyses showed that both 2-bromoethanesulfonate addition and increase of organic loads inhibited the activity of methanogens and promoted the activity of distinct VFA-producing bacterial microbiomes. Moreover, the addition of activated carbon promoted the activity of H2-producing Bacteroides, homoacetogenic Eubacteriaceae and methanogenic Methanosarcinaceae, whose activity dynamics during the fermentation led to changes in acetate and methane production. The current results unveiled mechanisms of microbiome activity dynamics shaping the biowaste fermentation product profiles and provided the fundamental basis for the development of microbiome-guided engineering approaches to modulate biowaste fermentation toward high-value product recovery.

Inhibition of anaerobic digestion by various ammonia sources resulted in subtle differences in metabolite dynamics

The impact of ammonia on anaerobic digestion performance and microbial dynamics has been extensively studied, but the concurrent effect of anions brought by ammonium salt should not be neglected. This paper studied this effect using metabolomics and a time-course statistical framework. Metabolomics provides novel perspectives to study microbial processes and facilitates a more profound understanding at the metabolic level. The advanced statistical framework enables deciphering the complexity of large metabolomics data sets. More specifically, a series of lab-scale batch reactors were set up with different ammonia sources added. Samples of nine time points over the degradation were analyzed with liquid chromatography-mass spectrometry. A filtering procedure was applied to select the promising metabolomic peaks from 1262 peaks, followed by modeling their intensities across time. The metabolomic peaks with similar time profiles were clustered, evidencing the correlation of different biological processes. Differential analysis was performed to seek the differences in metabolite dynamics caused by different anions. Finally, tandem mass spectrometry and metabolite annotation provided further information on the molecular structure and possible metabolic pathways. For example, the consumption of 5-aminovaleric acid, a short-chain fatty acid obtained from l-lysine degradation, was slowed down by phosphates. Overall, by investigating the effect of anions on anaerobic digestion, our study demonstrated the effectiveness of metabolomics in providing detailed information in a set of samples from different experimental conditions. With the statistical framework, the approach enables capturing subtle differences in metabolite dynamics between samples while accounting for the differences caused by time variations.

The role of microbial ecology in improving the performance of anaerobic digestion of sewage sludge

The use of next-generation diagnostic tools to optimise the anaerobic digestion of municipal sewage sludge has the potential to increase renewable natural gas recovery, improve the reuse of biosolid fertilisers and help operators expand circular economies globally. This review aims to provide perspectives on the role of microbial ecology in improving digester performance in wastewater treatment plants, highlighting that a systems biology approach is fundamental for monitoring mesophilic anaerobic sewage sludge in continuously stirred reactor tanks. We further highlight the potential applications arising from investigations into sludge ecology. The principal limitation for improvements in methane recoveries or in process stability of anaerobic digestion, especially after pre-treatment or during co-digestion, are ecological knowledge gaps related to the front-end metabolism (hydrolysis and fermentation). Operational problems such as stable biological foaming are a key problem, for which ecological markers are a suitable approach. However, no biomarkers exist yet to assist in monitoring and management of clade-specific foaming potentials along with other risks, such as pollutants and pathogens. Fundamental ecological principles apply to anaerobic digestion, which presents opportunities to predict and manipulate reactor functions. The path ahead for mapping ecological markers on process endpoints and risk factors of anaerobic digestion will involve numerical ecology, an expanding field that employs metrics derived from alpha, beta, phylogenetic, taxonomic, and functional diversity, as well as from phenotypes or life strategies derived from genetic potentials. In contrast to addressing operational issues (as noted above), which are effectively addressed by whole population or individual biomarkers, broad improvement and optimisation of function will require enhancement of hydrolysis and acidogenic processes. This will require a discovery-based approach, which will involve integrative research involving the proteome and metabolome. This will utilise, but overcome current limitations of DNA-centric approaches, and likely have broad application outside the specific field of anaerobic digestion.

Production of biochar from crop residues and its application for anaerobic digestion

Anaerobic digestion (AD) is a viable and cost-effective method for converting organic waste into usable renewable energy. The efficiency of organic waste digestion, nonetheless, is limited due to inhibition and instability. Accordingly, biochar is an effective method for improving the efficiency of AD by adsorbing inhibitors, promoting biogas generation and methane concentration, maintaining process stability, colonizing microorganisms selectively, and mitigating the inhibition of volatile fatty acids and ammonia. This paper reviews the features of crop waste-derived biochar and its application in AD systems. Four critical roles of biochar in AD systems were identified: maintaining pH stability, promoting hydrolysis, enhancing the direct interspecies electron transfer pathway, and supporting microbial development. This work also highlights that the interaction between biochar dose, amount of organic component in the substrate, and inoculum-to-substrate ratio should be the focus of future research before deploying commercial applications.

Anaerobic digestion challenges and resource recovery opportunities from land-based aquaculture waste and seafood processing byproducts: A review

The unprecedented demand for seafood has resulted in land-based recirculating aquaculture systems (RAS), a highly intensive but sustainable fish farming method. However, intensification also results in concentrated waste streams of fecal matter and uneaten feed. Harvesting and processing vast quantities of fish also leads to the production of byproducts, further creating disposal challenges for fish farms. Recent research indicates that anaerobic digestion (AD), often used for waste treatment in agricultural and wastewater industries, may provide a viable solution. Limited research on AD of freshwater, brackish, and saline wastewater from RAS facilities and co-digestion of seafood byproducts has shown promising results but with considerable operational and process stability issues. This review discusses challenges to AD due to low solid concentrations, salinity, low carbon/nitrogen ratio, and high lipid content in the waste streams. Opportunities for recovering valuable biomolecules and nutrients through microbial treatment, aquaponics, microalgae, and polyhydroxyalkanoate production are also discussed.

Monitor process state of batch anaerobic digestion in reliance on volatile and semi-volatile metabolome

It has been a challenge to recognize appropriate compounds as indicators for monitoring and early-warning of the anaerobic digestion process. A strategy was initiated to explore the evolution of the panorama profile of volatile and semi-volatile metabolites. Non-target analysis using high-resolution gas chromatography coupled with Orbitrap mass spectrometry was applied to construct a time-series molecular fingerprint of 218 metabolites classified in 14 categories. Alkanes accounted for the main part in early and late stages of methanization and aromatic compounds were the major in middle stage. Spearman correlation analysis and partial least squares analysis unwind that Trichococcus (1.49%-83.96%) was positively related to most of metabolites at early and middle stages, while Brevundimonas (0%-24.04%) was positively related to acylamide at late stage. This indicated that microbial volatile organic compounds were possible to serve as biochemical indicators for anaerobic digestion performance and to build nexus of "what" (metabolites), "who" (microorganism), and "how" (kinetics).

The challenges of monitoring and manipulating anaerobic microbial communities

Mixed anaerobic microbial communities are a key component in valorization of waste biomass via anaerobic digestion. Similar microbial communities are important as soil and animal microbiomes and have played a critical role in shaping the planet as it is today. Understanding how individual species within communities interact with others and their environment is important for improving performance and potential applications of an inherently green technology. Here, the challenges associated with making measurements critical to assessing the status of anaerobic microbial communities are considered. How these measurements could be incorporated into control philosophies and augment the potential of anaerobic microbial communities to produce different and higher value products from waste materials are discussed. The benefits and pitfalls of current genetic and molecular approaches to measuring and manipulating anaerobic microbial communities and the challenges which should be addressed to realise the potential of this exciting technology are explored.

Organic waste conversion through anaerobic digestion: A critical insight into the metabolic pathways and microbial interactions

Anaerobic digestion is a promising method for energy recovery through conversion of organic waste to biogas and other industrial valuables. However, to tap the full potential of anaerobic digestion, deciphering the microbial metabolic pathway activities and their underlying bioenergetics is required. In addition, the behavior of organisms in consortia along with the analytical abilities to kinetically measure their metabolic interactions will allow rational optimization of the process. This review aims to explore the metabolic bottlenecks of the microbial communities adopting latest advances of profiling and ¹³C tracer-based analysis using state of the art analytical platforms (GC, GC-MS, LC-MS, NMR). The review summarizes the phases of anaerobic digestion, the role of microbial communities, key process parameters of significance, syntrophic microbial interactions and the bottlenecks that are critical for optimal bioenergetics and enhanced production of valuables. Considerations into the designing of efficient synthetic microbial communities as well as the latest advances in capturing their metabolic cross talk will be highlighted. The review further explores how the presence of additives and inhibiting factors affect the metabolic pathways. The critical insight into the reaction mechanism covered in this review may be helpful to optimize and upgrade the anaerobic digestion system.

Time-course analysis of metabolomic and microbial responses in anaerobic digesters exposed to ammonia

Omics longitudinal studies are effective experimental designs to inform on the stability and dynamics of microbial communities in response to perturbations, but time-course analytical frameworks are required to fully exploit the temporal information acquired in this context. In this study we investigate the influence of ammonia on the stability of anaerobic digestion (AD) microbiome with a new statistical framework. Ammonia can severely reduce AD performance. Understanding how it affects microbial communities development and the degradation progress is a key operational issue to propose more stable processes. Thirty batch digesters were set-up with different levels of ammonia. Microbial community structure and metabolomic profiles were monitored with 16 S-metabarcoding and GCMS (gas-chromatography-mass-spectrometry). Digesters were first grouped according to similar degradation performances. Within each group, time profiles of OTUs and metabolites were modelled, then clustered into similar time trajectories, evidencing for example a syntrophic interaction between Syntrophomonas and Methanoculleus that was maintained up to 387 mg FAN/L. Metabolites resulting from organic matter fermentation, such as dehydroabietic or phytanic acid, decreased with increasing ammonia levels. Our analytical framework enabled to fully account for time variability and integrate this parameter in data analysis.

Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles

The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.