Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor

Inoculum source determines the stress resistance of electroactive functional taxa in biofilms: A metagenomic perspective

The inoculum has a crucial impact on bioreactor initialization and performance. However, there is currently a lack of guidance on selecting appropriate inocula for applications in environmental biotechnology. In this study, we applied microbial electrolysis cells (MECs) as models to investigate the differences in the functional potential of electroactive microorganisms (EAMs) within anodic biofilms developed from four different inocula (natural or artificial), using shotgun metagenomic techniques. We specifically focused on extracellular electron transfer (EET) function and stress resistance, which affect the performance and stability of MECs. Community profiling revealed that the family Geobacteraceae was the key EAM taxon in all biofilms, with Geobacter as the dominant genus. The c-type cytochrome gene imcH showed universal importance for Geobacteraceae EET and was utilized as a marker gene to evaluate the EET potential of EAMs. Additionally, stress response functional genes were used to assess the stress resistance potential of Geobacter species. Comparative analysis of imcH gene abundance revealed that EAMs with comparable overall EET potential could be enriched from artificial and natural inocula (P > 0.05). However, quantification of stress response gene copy numbers in the genomes demonstrated that EAMs originating from natural inocula possessed superior stress resistance potential (196 vs. 163). Overall, this study provides novel perspectives on the inoculum effect in bioreactors and offers theoretical guidance for selecting inoculum in environmental engineering applications.

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.

Validation of collection and anaerobic fermentation techniques for measuring prebiotic impact on gut microbiota

BACKGROUND

Defining the ability of prebiotic dietary carbohydrates to influence the composition and metabolism of the gut microbiota is central to defining their health impact in diverse individuals. Many clinical trials are using indirect methods. This study aimed to validate collection and fermentation methods enabling their use in the context of clinical studies.

METHODS AND RESULTS

Parameters tested included stool sample acquisition, storage, and growth conditions. Stool from 3 infants and 3 adults was collected and stored under varying conditions. Samples were cultured anaerobically for two days in the presence of prebiotics, whereupon optical density and pH were measured across time. Whole genome shotgun sequencing and NMR metabolomics were performed. Neither the type of collection vial (standard vial and two different BD anaerobic collection vials) nor cryopreservation (-80 °C or 4 °C) significantly influenced either microbial composition at 16 h of anaerobic culture or the principal components of the metabolome at 8 or 16 h. Metagenomic differences were driven primarily by subject, while metabolomic differences were driven by fermentation sugar (2'-fucosyllactose or dextrose).

CONCLUSIONS

These data identified a feasible and valid approach for prebiotic fermentation analysis of individual samples in large clinical studies: collection of stool microbiota using standard vials; cryopreservation prior to testing; and collecting fermentation read-out at 8 and 16 hr. Thus, fermentation analysis can be a valid technique for testing the effects of prebiotics on human fecal microbiota.

Calcium ion can alleviate ammonia inhibition on anaerobic digestion via balanced-strengthening dehydrogenases and reinforcing protein-binding structure: Model evaluation and microbial characterization

Experimental investigation and model simulation was combined to identify the effect of metal ions on mitigating ammonia inhibition during anaerobic digestion. Five metal ions (Ca, Mg, Cu, Zn, Fe) were tested in reactors with 1 g-glucose/L/d and 5 g-N/L under fed batch operation. Ca addition was considered the optimal approach with a 25% increment in methane production via balanced-strengthening dehydrogenases and reinforcing protein-binding structure. Gene-sequencing results suggested 50% and 15% increment in acetotrophic-related and hydrogenotrophic-related dehydrogenases, respectively, after Ca addition. The Anaerobic Digestion Model No.1 was modified by introducing lactate-related reactions, syntrophic acetate oxidation process, and kinetic equation of metal ions, with satisfactory predictions of methane and intermediates (R² > 0.80). The lowest affinity constant K_{I_MI} value was obtained with Ca supplement, indicating the highest conversion rate of substrates to methane. The model evaluation revealed the balanced ratio on the enzyme contribution of acetotrophic to hydrogenotrophic methanogenesis.

Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste

Future manned space travel will require efficient recycling of nutrients from organic waste back into food production. Microbial systems are a low-energy, efficient means of nutrient recycling, but their use in a life support system requires predictability and reproducibility in community formation and reactor performance. To assess the reproducibility of microbial community formation in fixed-film reactors, we inoculated replicate anaerobic reactors from two methanogenic inocula: a lab-scale fixed-film, plug-flow anaerobic reactor and an acidic transitional fen. Reactors were operated under identical conditions, and we assessed reactor performance and used 16s rDNA amplicon sequencing to determine microbial community formation. Reactor microbial communities were dominated by similar groups, but differences in community membership persisted in reactors inoculated from different sources. Reactor performance overlapped, suggesting a convergence of both reactor communities and organic matter mineralization. The results of this study suggest an optimized microbial community could be preserved and used to start new, or restart failed, anaerobic reactors in a life support system with predictable reactor performance.

Solid state anaerobic digestion of food waste and sewage sludge: Impact of mixing ratios and temperature on microbial diversity, reactor stability and methane yield

Food waste (FW) and sewage sludge (SS) were anaerobically co digested under solid state conditions (Total solids >15%) and observed that mixing ratio of 3:1 and 2:1 is optimum for mesophilic and thermophilic conditions respectively. The VS reduction and methane yield at optimized ratio was 76% and 0.35 L CH₄/(g VS reduced) respectively at mesophilic temperature whereas it was 88% and 0.42 L CH₄/(g VS reduced) at thermophilic temperature. The metagenomic analysis for these cases were done and high throughput DNA sequencing revealed that diversified bacterial groups that participate in the different metabolisms (hydrolysis, acidogenesis and acetogenesis) were mainly dominated by the phylum Firmicutes and Bacteriodetes. Genus Methanothrix is found to be dominant which is capable of generating methane by any methanogenic pathway among all the archaeal communities in the reactors followed by Methanolinea and Methanoculleus. However, it was understood through metagenomic studies that acetotrophic pathway is observed to be the major metabolic pathway in the reactors.

Illumina sequencing of 16S rRNA genes reveals a unique microbial community in three anaerobic sludge digesters of Dubai

Understanding the microbial communities in anaerobic digesters, especially bacteria and archaea, is key to its better operation and regulation. Microbial communities in the anaerobic digesters of the Gulf region where climatic conditions and other factors may impact the incoming feed are not documented. Therefore, Archaeal and Bacterial communities of three full-scale anaerobic digesters, namely AD1, AD3, and AD5 of the Jebel Ali Sewage water Treatment Plant (JASTP) were analyzed by Illumina sequencing of 16S rRNA genes. Among bacteria, the most abundant genus was fermentative bacteria Acetobacteroides (Blvii28). Other predominant bacterial genera in the digesters included thermophilic bacteria (Fervidobacterium and Coprothermobacter) and halophilic bacteria like Haloterrigena and Sediminibacter. This can be correlated with the climatic condition in Dubai, where the bacteria in the incoming feed may be thermophilic or halophilic as much of the water used in the country is desalinated seawater. The predominant Archaea include mainly the members of the phyla Euryarchaeota and Crenarchaeota belonging to the genus Methanocorpusculum, Metallosphaera, Methanocella, and Methanococcus. The highest population of Methanocorpusculum (more than 50% of total Archaea), and other hydrogenotrophic archaea, is in agreement with the high population of bacterial genera Acetobacteroides (Blvii28) and Fervidobacterium, capable of fermenting organic substrates into acetate and H₂. Coprothermobacter, which is known to improve protein degradation by establishing syntrophy with hydrogenotrophic archaea, is also one of the digesters’ dominant genera. The results suggest that the microbial community in three full-scale anaerobic digesters is different. To best of our knowledge this is the first detailed report from the UAE.

Assessment of Gram- and Viability-Staining Methods for Quantifying Bacterial Community Dynamics Using Flow Cytometry

Over the past years, gut microbiota became a major field of interest with increasing reports suggesting its association with a large number of human diseases. In this context, there is a major interest to develop analysis tools allowing simple and cost-effective population pattern analysis of these complex ecosystems to follow changes over time. Whereas sequence-based metagenomics profiling is widely used for microbial ecosystems characterization, it still requires time and specific expertise for analysis. Flow cytometry overcomes these disadvantages, providing key information on communities within hours. In addition, it can potentially be used to select, isolate and cultivate specific bacteria of interest. In this study, we evaluated the culturability of strictly anaerobic bacteria that were stained with a classical Live/Dead staining, and then sorted using flow cytometry under anaerobic conditions. This sorting of “viable” fraction demonstrated that 10–80% of identified “viable” cells of pure cultures of strictly anaerobic bacteria were culturable. In addition, we tested the use of a combination of labeled vancomycin and Wheat Germ Agglutinin (WGA) lectin to discriminate Gram-positive from Gram-negative bacteria in complex ecosystems. After validation on both aerobic/anaerobic facultative and strictly anaerobic bacteria, the staining methods were applied on complex ecosystems, revealing differences between culture conditions and demonstrating that minor pH variations have strong impacts on microbial community structure, which was confirmed by 16S rRNA gene sequencing. This combination of staining methods makes it possible to follow-up evolutions of complex microbial communities, supporting its future use as a rapid analysis tool in various applications. The flow cytometry staining method that was developed has the potential to facilitate the analysis of complex ecosystems by highlighting changes in bacterial communities’ dynamics. It is assumed to be applicable as an efficient and fast approach to improve the control of processes linked to a wide range of ecosystems or known communities of bacterial species in both research and industrial contexts.

Coagulation-flocculation and moving bed biofilm reactor as pre-treatment for water recycling in the petrochemical industry

Water recycling and reuse is of important value in water-using sectors like petrochemical industry. The aim of this research was to optimise the pre-treatment of petrochemical wastewater to undergo a further membrane treatment, with the final objective of water recycling within the same industry. Laboratory coagulation-flocculation tests prior to biological treatment were performed using Actiflo® Veolia commercial technology and an optimal coagulant dose of 30 mg/L ferric chloride was obtained. A bench-scale Moving Bed Biofilm Reactor (MBBR) system with two sequential reactors with working volumes of 5 L was filled with Z-carriers at 35% of their working volume. Organic loading rate (OLR) was varied from 0.2 to 3.25 kg/(m³ d) and the hydraulic retention time (HRT) ranged from 23.4 h to 4.5 h. High soluble chemical oxygen demand (sCOD) removals were obtained in stationary states (80-90%) and the calculated maximum sCOD that the system could degrade was 4.96 ± 0.01 kg/(m³ d) at 23 ± 2 °C. Changes in feed composition did not decrease sCOD removals showing that MBBR is a robust technology and the coagulation-flocculation step could be by-passed. Further removal of total suspended solids (TSS) and turbidity from the MBBR effluent would be required before a reverse osmosis (RO) step could be performed. A biofilm-forming genus, Haliscomenobacter spp., and an oil degrading genus Flavobacterium spp. were found in all the attached biomass samples. Acinetobacter spp. was the major bacterial genera found in suspended biomass. Proteobacteria and Bacteroidetes were the major phyla detected in the carrier samples while Proteobacteria the main one detected in the suspended biomass. The lack of fungal annotated sequences in databases led to a major proportion of fungal sequences being categorized as unclassified Fungi. The results obtained indicate that MBBR is an appropriate technology for hydrocarbon-degrading microorganism growth and, thus, for petrochemical wastewater pre-treatment for water regeneration.

Full-scale anaerobic reactor samples would be more suitable than lab-scale anaerobic reactor and natural samples to inoculate the wheat straw batch anaerobic digesters

This study evaluated the effects of the inocula from natural wetland, lab-scale and full-scale anaerobic reactors on wheat straw anaerobic digestion. Three replicate batch reactors were constructed for each inoculum to investigate the reactor performances and microbial communities. Reactors seeded with full-scale reactor samples were started up most rapidly, achieved the highest methane production, and were recognized as the higher efficient reactors. The dominance of acetoclastic methanogens, including Methanosaeta and Methanoscrina, was crucial for the higher efficient reactors, whereas hydrogenotrophic methanogens were dominant in other reactors. Genus Treponema, which could enhance the cellulose degradation and conduct homoacetogenesis, was first reported to be dominant in the bacterial communities of high efficient reactors. Inoculum sources and process conditions were suggested to be the deterministic factors in shaping the microbial communities in the higher efficient reactors. These findings contribute to the startup of new anaerobic reactors.

Response of sulfate-reducing bacteria and supporting microbial community to persulfate exposure in a continuous flow system

Coupling of chemical oxidation using persulfate with bioremediation has been proposed as a method to increase remedial efficacy at petroleum hydrocarbon contaminated sites. To support this integrated treatment approach, an understanding of persulfate impact on the indigenous microbial community is necessary for system design. As sulfate-reducing bacteria (SRB) are active in most aquifer systems and can utilize the sulfate generated from the degradation of persulfate, this study assessed the impact on SRB and the supporting anaerobic microbial community when exposed to persulfate in a continuous flow system. A series of bioreactors (1000 L) packed with anaerobic aquifer material were operated for an 8 month acclimatization period before being continuously subjected to benzene, toluene, ethylbenzene and xylenes (total BTEX 3 mg L-1). After 2 months, the bioreactors were then exposed to an unactivated persulfate solution (20 g L-1), or an alkaline-activated persulfate solution (20 g L-1, pH 12) then effluent-sampled for 60 days following. A combination of culture and molecular-based techniques were used to monitor SRB presence and structural profiles in the anaerobic SRB-specific and broader microbial community. Post-exposure, the rate of BTEX mass removal remained below pre-exposure values; however, trends suggest that full recovery would be expected. Rebound of SRB-specific and the associated microbial community to pre-exposure levels were observed in all exposed bioreactors. Structural community profiles identified recovery in both microbial species and diversity indices. Findings from this investigation demonstrate robustness of SRB in the presence of a supporting microbial community and, thus, are suitable organisms for target use during bioremediation in an integrated system with persulfate.

Process stability and comparative rDNA/rRNA community analyses in an anaerobic membrane bioreactor with silicon carbide ceramic membrane applications

This study evaluated the feasibility of using a silicon carbide (SiC) anaerobic ceramic membrane bioreactor (AnCMBR) to co-manage domestic wastewater (DWW) and food waste recycling wastewater (FRW). A pilot-scale SiC-AnCMBR was put into operation for 140 days under two different organic loading rates (OLRs): 5 kg COD m^-3 d^-1 (OLR 5) and 3 kg COD m^-3 d^-1 (OLR 3). The organic removal efficiency was 93.5 ± 3.7% over the operational period. Methane production increased significantly after sludge re-seeding at OLR 3. rDNA and rRNA microbial results showed that the active archaeal community was affected by sludge re-seeding, whereas the active bacterial community was not, indicating that a shift in the active archaeal community was responsible for the increased methane production. Our results thus suggest that SiC-AnCMBRs are a promising option for co-managing DWW and FRW.

Roles and correlations of functional bacteria and genes in the start-up of simultaneous anammox and denitrification system for enhanced nitrogen removal

Simultaneous anammox and denitrification (SAD) is a newly developed wastewater treatment process efficient in nitrogen removal, but its underlying microbiological mechanisms during start-up remains unknown. This study investigated the changing patterns of functional bacteria and genes, as well as their correlation during the start-up (260 d) of the SAD systems in two lab-scale up-flow anaerobic sludge blanket bioreactors separately inoculated with anaerobic granular sludge (R1) and aerobic floccular sludge (R2). Results showed that high total nitrogen removal was achieved in the SAD systems of both R1 (88.25%) and R2 (89.42%). High-throughput sequencing of 16S rRNA gene amplicons revealed that Armatimonadetes phylum had a high abundance (44.34%) in R2, while was not detectable in R1 during the anammox stage. However, the SAD bioreactors retained inherent microbial community and the inoculation with different sludge showed less notable effects on their microbial composition. In the SAD systems, Candidatus Brocadia had high abundance in R1 (2.93%) and R2 (4.64%) and played important role in anammox. Network analysis indicated that Denitratisoma and Dokdonella were positively correlated with nitrite reductase genes nirS and nirK (p < 0.05), while Thermomonas and Pseudomonas showing a positive correlation with nitrate reductase gene narG (p < 0.05) were mainly responsible for the nitrate reduction in the SAD systems. Moreover, the overwhelming dominance of narG v.s. napA revealed the crucial roles of respiratory nitrate reduction in the bioreactors. The results extend our knowledge regarding the microbial ecology of the SAD system, which might be practically helpful for application of the process in wastewater treatment.

Preliminary analysis of Chloroflexi populations in full-scale UASB methanogenic reactors

AIMS

The phylum Chloroflexi is frequently found in high abundance in methanogenic reactors, but their role is still unclear as most of them remain uncultured and understudied. Hence, a detailed analysis was performed in samples from five up-flow anaerobic sludge blanket (UASB) full-scale reactors fed different industrial wastewaters.

METHODS AND RESULTS

Quantitative PCR show that the phylum Chloroflexi was abundant in all UASB methanogenic reactors, with higher abundance in the reactors operated for a long period of time, which presented granular biomass. Both terminal restriction fragment length polymorphism and 16S rRNA gene amplicon sequencing revealed diverse Chloroflexi populations apparently determined by the different inocula. According to the phylogenetic analysis, the sequences from the dominant Chloroflexi were positioned in branches where no sequences of the cultured representative strains were placed. Fluorescent in situ hybridization analysis performed in two of the reactors showed filamentous morphology of the hybridizing cells.

CONCLUSIONS

While members of the Anaerolineae class within phylum Chloroflexi were predominant, their diversity is still poorly described in anaerobic reactors. Due to their filamentous morphology, Chloroflexi may have a key role in the granulation in methanogenic UASB reactors.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our results bring new insights about the diversity, stability, dynamics and abundance of this phylum in full-scale UASB reactors which aid in understanding their function within the reactor biomass. However, new methodological approaches and analysis of bulking biomass are needed to completely unravel their role in these reactors. Combining all this knowledge with reactor operational parameters will allow to understand their participation in granulation and bulking episodes and design strategies to prevent Chloroflexi overgrowth.

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community

The impact of the starting inoculum on long-term anaerobic digestion performance, process functionality and microbial community composition remains unclear. To understand the impact of starting inoculum, active microbial communities from four different full-scale anaerobic digesters were each used to inoculate four continuous lab-scale anaerobic digesters, which were operated identically for 295 days. Digesters were operated at 15 days solid retention time, an organic loading rate of 1 g COD L_r^-1 d^-1 (75:25 - cellulose:casein) and 37 °C. Results showed that long-term process performance, metabolic rates (hydrolytic, acetogenic, and methanogenic) and microbial community are independent of the inoculum source. Digesters process performance converged after 80 days, while metabolic rates and microbial communities converged after 120-145 days. The convergence of the different microbial communities towards a core-community proves that the deterministic factors (process operational conditions) were a stronger driver than the initial microbial community composition. Indeed, the core-community represented 72% of the relative abundance among the four digesters. Moreover, a number of positive correlations were observed between higher metabolic rates and the relative abundance of specific microbial groups. These correlations showed that both substrate consumers and suppliers trigger higher metabolic rates, expanding the knowledge of the nexus between microorganisms and functionality. Overall, these results support that deterministic factors control microbial communities in bioreactors independently of the inoculum source. Hence, it seems plausible that a desired microbial composition and functionality can be achieved by tuning process operational conditions.

Metataxonomy and functionality of wood-tar degrading microbial consortia

Wood-tar is a liquid material obtained by wood gasification process, and comprises several polycyclic aromatic hydrocarbons (PAH). Tar biodegradation is a very challenging task, due to its toxicity and to its complex chemistry. The 'microbial resource management' concerns the use of environmental microbial communities potentially able to provide us services. We applied this concept in tar biodegradation. Tar composed by several PAH (including phenanthrene, acenaphthylene and fluorene) was subjected to a biodegradation process in triplicate microcosms spiked with a microbial community collected from PAH-rich soils. In 20 days, 98.9% of tar was mineralized or adsorbed to floccules, while negative controls showed poor PAH reduction. The dynamics of fungal and bacterial communities was assessed through Automated Ribosomal Intergenic Spacer Analysis (ARISA), 454 pyrosequencing of the fungal ITS and of the bacterial 16S rRNA. Quantification of the degrading bacterial communities was performed via quantitative Real Time PCR of the 16S rRNA genes and of the cathecol 2,3-dioxygenase genes. Results showed the importance of fungal tar-degrading populations in the first period of incubation, followed by a complex bacterial dynamical growth ruled by co-feeding behaviors.

Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion

Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel. However, this is labor intensive, especially when measuring biogas production. Commercial solutions for multiplying reactors performing continuous anaerobic digestion exist but are expensive and use comparably large reactor volumes, requiring the preparation of substantial amounts of media. Here, a flexible system of Lab-scale Automated and Multiplexed Anaerobic Chemostat system (LAMACs) with a working volume of 200 mL is introduced. Sterile feeding, biomass wasting and pressure monitoring are automated. One module containing six reactors fits the typical dimensions of a lab bench. Thanks to automation, time required for reactor operation and maintenance are reduced compared to traditional lab-scale systems. Several modules can be used together, and so far the parallel operation of 30 reactors was demonstrated. The chemostats are autoclavable. Parameters like reactor volume, flow rates and operating temperature can be freely set. The robustness of the system was tested in a two-month long experiment in which three inocula in four replicates, i.e., twelve continuous digesters were monitored. Statistically significant differences in the biogas production between inocula were observed. In anaerobic digestion, biogas production and consequently pressure development in a closed environment is a proxy for ecosystem performance. The precision of the pressure measurement is thus crucial. The measured maximum and minimum rates of gas production could be determined at the same precision. The LAMACs is a tool that enables us to put in practice the often-demanded need for replication and rigorous testing in microbial ecology as well as bioprocess engineering.