Microbial analysis in biogas reactors suffering by foaming incidents

Evaluation of the optimal sewage sludge pre-treatment technology through continuous reactor operation: Process performance and microbial community insights

This study investigated the impact of two low-temperature thermal pre-treatments on continuous anaerobic reactors' performance, sequentially fed with sludge of different total solids content (∼3 % and ∼6 %) and subjected to progressively increasing Organic Loading Rates (OLR) from 1.0 to 2.5 g volatile solids/(LReactor⋅day). Assessing pre-treatments' influence on influent sludge characteristics revealed enhanced organic matter hydrolysis, facilitating sludge solubilization and methanogenesis; volatile fatty acids concentration also increased, particularly in pre-treated sludge of ∼6 % total solids, indicating improved heating efficiency under increased solids content. The reactor fed with sludge pre-treated at 45 °C for 48 h and 55 °C for an extra 48 h exhibited the highest methane yield under all applied OLRs, peaking at 240 ± 3.0 mL/g volatile solids at the OLR of 2.5 g volatile solids/(LReactor⋅day). 16S rRNA gene sequencing demonstrated differences in the reactors' microbiomes as evidence of sludge thickening and the different pre-treatments applied, which promoted the release of organic matter in diverse concentrations and compositions. Finally, the microbial analysis revealed that specific foam-related genera increased in abundance in the foam layer of reactors' effluent bottles, dictating their association with the sludge foaming incidents that occurred inside the reactors during their operation at 2.0 g volatile solids/(LReactor⋅day).

Multi-scale analysis of the foaming mechanism in anaerobic digestion of food waste: From physicochemical parameter, microbial community to metabolite response

Foaming is a key issue that threatens the efficient and stable operation of the anaerobic digestion process. This study introduced three disturbances to induce foaming and explored the responses of physicochemical parameters, microbial communities, and metabolites to reveal the foaming mechanism. Under the three disturbance conditions, extracellular polymeric substances (EPS)-related parameters are significantly positively correlated with foam height, and EPS may cause foam by lowering the surface tension. Microorganisms that are more tolerant to high acid or high ammonia stress environments were identified after foaming, and they could resist the stress environment by producing more EPS. The up-regulated expression of sphingomyelin or ceramide was discovered after foaming, involved in the signal molecular transduction process of cell apoptosis or necrosis, which might be related to EPS production. Pantothenic acid involved in pantothenate and CoA biosynthesis pathways was down-regulated expression after foaming, which might be related to the hindered degradation of EPS. The response of multi-scale parameters in the foaming process shows that EPS is the key factor in foaming events.

Eubacterium coprostanoligenes and Methanoculleus identified as potential producers of metabolites that contribute to swine manure foaming

AIM

Swine manure foaming is a major problem, causing damage to property, livestock, and people. Here, we identified the main chemicals and microbes that contribute to foaming.

METHODS AND RESULTS

Foaming and non-foaming swine manure were sampled from farms in Iowa and Illinois. Targeted and untargeted metabolomics analyses identified chemical markers that differed between foaming and non-foaming manure and between manure layers. Microbial community analysis and metagenomics were performed on a subset of samples. Foam contained significantly higher levels of total bile acids and long chain fatty acids like palmitic, stearic and oleic acid than the other manure layers. Foam layers also had significantly higher levels of ubiquinone 9 and ubiquinone 10. The slurry layer of foaming samples contained more alanine, isoleucine/leucine, diacylglycerols (DG), phosphtatidylethanolamines, and vitamin K2, while ceramide was significantly increased in the slurry layer of non-foaming samples. Eubacterium coprostanoligenes and Methanoculleus were more abundant in foaming samples, and E. coprostanoligenes was significantly correlated with levels of DG. Genes involved in diacylglycerol biosynthesis and in the biosynthesis of branched-chain hydrophobic amino acids were overrepresented in foaming samples.

CONCLUSIONS

A mechanism for manure foaming is hypothesized in which proliferation of Methanoculleus leads to excessive production of methane, while production of DG by E. coprostanoligenes and hydrophobic proteins by Methanosphaera stadtmanae facilitates bubble formation and stabilization.

SIGNIFICANCE AND IMPACT OF STUDY

While some chemical and biological treatments have been developed to treat swine manure foaming, its causes remain unknown. We identified key microbes and metabolites that correlate with foaming and point to possible roles of other factors like animal feed.

Foaming mechanisms and control strategies during the anaerobic digestion of organic waste: A critical review

Foaming is a problem that affects the efficient and stable operation of the anaerobic digestion process. Characterizing foaming mechanisms and developing early warning and foaming control methods is thus critically important. This review summarizes the correlation of process parameters, state parameters, and microbial communities with foaming in anaerobic digesters; discusses the applicability of the above-mentioned multi-scale parameters and foaming potential evaluation methods for the prediction of foaming risk; and introduces the principles and practical applications of antifoaming and defoaming methods. Multiple causes of foaming in anaerobic digestion systems have been identified, but a generalizable foaming mechanism has yet to be described. Further study of the correlation between extracellular polymeric substances and soluble microbial products and foaming may provide new insights into foaming mechanisms. Monitoring the foaming potential (including the volume expansion potential) is an effective approach for estimating the risk of foaming. An in-situ monitoring system for determining the foaming potential in anaerobic digestion sites could provide an early warning of foaming risk. Antifoaming methods based on operating parameter management and process regulation help prevent foaming from the source, and biological defoaming methods are highly targeted and efficient, which is a promising research direction. Clarifying foaming mechanisms will aid the development of active antifoaming methods and efficient biological defoaming methods.

Feeding strategies of continuous biomethanation processes during increasing organic loading with lipids or glucose for avoiding potential inhibition

Anaerobic co-digestion is a promising solution for nutrients balance and improvement of methane production in anaerobic digestion (AD) processes. However, the knowledge about the effects of different co-substrates in manure-based AD, and different feeding strategies, on the process performance and the methanogenic microbiome pathway, are still missing. Therefore, under harsh and slow stepwise increase of organic loading rate (OLR), by addition of lipids and carbohydrates as co-substrates in continuous reactors, this study elucidated their effect on methane production and methanogenic microbiome. The results showed that, when OLR increased by adding lipids, a severe inhibition due to accumulated long-chain fatty acids (LCFA) was observed, while no significant inhibition was obtained by addition of glucose. Additionally, the LCFA inhibition in the reactor fed with lipid was alleviated by slow stepwise feeding strategy that enriched aceticlastic Methanosarcina thermophile and Methanosaeta concilii, and hydrogenotrophic Methanobacterium methanogens.

Identification of microorganisms responsible for foam formation in mesophilic anaerobic digesters treating surplus activated sludge

Foaming is a common operational problem in anaerobic digestion (AD) systems, where hydrophobic filamentous microorganisms are usually considered to be the major cause. However, little is known about the identity of foam-stabilising microorganisms in AD systems, and control measures are lacking. This study identified putative foam forming microorganisms in 13 full-scale mesophilic digesters located at 11 wastewater treatment plants in Denmark, using 16S rRNA gene amplicon sequencing with species-level resolution and fluorescence in situ hybridization (FISH) for visualization. A foaming potential aeration test was applied to classify the digester sludges according to their foaming propensity. A high foaming potential for sludges was linked to the abundance of species from the genus Candidatus Microthrix, immigrating with the feed stream (surplus activated sludge), but also to several novel phylotypes potentially growing in the digester. These species were classified to the genera Ca. Brevefilum (Ca. B. fermentans) and Tetrasphaera (midas_s_5), the families ST-12K33 (midas_s_22), and Rikenellaceae (midas_s_141), and the archaeal genus Methanospirillum (midas_s_2576). Application of FISH showed that these potential foam-forming organisms all had a filamentous morphology. Additionally, it was shown that concentrations of ammonium and total nitrogen correlated strongly to the presence of foam-formers. This study provided new insight into the identity of putative foam-forming microorganisms in mesophilic AD systems, allowing for the subsequent surveillance of their abundances and studies of their ecology. Such information will importantly inform the development of control measures for these problematic microorganisms.

Correlating sludge constituents with digester foaming risk using sludge foam potential and rheology

Foam potential and viscometer ramp tests (VRTs) were conducted for three municipal wastewater treatment plants to determine if these methods can relate to mechanisms of foaming to physical and biological constituents in sludge. At all plants, digester volatile solids (VS) concentration correlated (R² > 0.41) with increases in plastic viscosity, a VRT parameter corresponding to foaming risk. Plastic viscosity also correlated with foam-causing bacteria Gordonia (R² = 0.38). Foam potential test values increased with Microthrix parvicella (R²> 0.28). For one plant, suspected foam-causing bacteria Mycobacterium negatively correlated with parameters representing foam risk. Microscopic filament counting correlated (R² = 0.97) with quantitative polymerase chain reaction (qPCR) for Gordonia, suggesting that the more accessible counting method can reliably quantify foam-causing bacteria. Foam potential tests and VRTs resulted in plant-specific correlations with foam-related constituents. Therefore, these tests may provide useful evidence when investigating causes of digester foam events.

A novel hydraulic biogas digester controlling the scum formation in batch and semi-continuous tests using banana stems

Scum formation is a widespread phenomenon and causes serious damage in straw biogas digesters. A 10-L novel hydraulic conical digester for controlling scum was developed in this work and compared with a hydraulic cylindrical digester that simulated the conventional digester. After 30 d of batch and 120 d of semi-continuous fermentations using banana stems, the scum volumes of in cylindrical digesters were 4.12 and 2.12 times that in the conical digesters, respectively. The conical digesters increased biogas production by 5.7% and 11.6% in batch and semi-continuous tests, respectively. The VS removal of feedstock in conical digesters were 5.6 and 7.2% greater than for the batch and semi-continuous cylindrical, respectively. The microbial diversity and evenness were higher in conical than cylindrical digesters. The results demonstrated that conical shape was an effective structure for controlling scum formation and improving biogas production.

Metagenomic analysis and characterization of acidogenic microbiome and effect of pH on organic acid production

Organic acid production including lactate and acetate is an economically attractive technology that has gained momentum worldwide over the past years. These series of action need to be performed by an esoteric and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. In this study, we analyzed the bioma from bioreactors with various pH conditions of 4.0, 5.0 and 6.0 (R₁, R₂ and R₃), respectively, involved in acidogenic digestion for stable production of various organic acids by means of high-throughput Illumina sequencing, disclosing thousands of genes and extracting more than 53 microbial genomes. At pH 5.0, the hydrolysis reaction was enhanced and thus the lactic acid fermentation was stably improved to 45.96 mm/L and acetic acid to 73.77 mm/L. R₂ was found with the most suitable pH condition for stable organic acids production as Lactobacilli and Bifidobacteria were the major members. Both the members have the key roles in heterofermentation and produce higher transcripts of key encoding enzymes involved in the dominant heterofermentation pathways.

Methods for quantification of growth and productivity in anaerobic microbiology and biotechnology

Anaerobic microorganisms (anaerobes) possess a fascinating metabolic versatility. This characteristic makes anaerobes interesting candidates for physiological studies and utilizable as microbial cell factories. To investigate the physiological characteristics of an anaerobic microbial population, yield, productivity, specific growth rate, biomass production, substrate uptake, and product formation are regarded as essential variables. The determination of those variables in distinct cultivation systems may be achieved by using different techniques for sampling, measuring of growth, substrate uptake, and product formation kinetics. In this review, a comprehensive overview of methods is presented, and the applicability is discussed in the frame of anaerobic microbiology and biotechnology.

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies

In the past few years, many studies investigated the anaerobic digestion microbiome by means of 16S rRNA amplicon sequencing. Results obtained from these studies were compared to each other without taking into consideration the followed procedure for amplicons preparation and data analysis. This negligence was mainly due to the lack of knowledge regarding the biases influencing specific steps of the microbiome investigation process. In the present study, the main technical aspects of the 16S rRNA analysis were checked giving special attention to the approach used for high throughput sequencing. More specifically, the microbial compositions of three laboratory scale biogas reactors were analyzed before and after addition of sodium oleate by sequencing the microbiome with three different approaches: 16S rRNA amplicon sequencing, shotgun DNA and shotgun RNA. This comparative analysis revealed that, in amplicon sequencing, abundance of some taxa (Euryarchaeota and Spirochaetes) was biased by the inefficiency of universal primers to hybridize all the templates. Reliability of the results obtained was also influenced by the number of hypervariable regions under investigation. Finally, amplicon sequencing and shotgun DNA underestimated the Methanoculleus genus, probably due to the low 16S rRNA gene copy number encoded in this taxon.

Investigation of foaming causes in three mesophilic food waste digesters: reactor performance and microbial analysis

Foaming negatively affects anaerobic digestion of food waste (FW). To identify the causes of foaming, reactor performance and microbial community dynamics were investigated in three mesophilic digesters treating FW. The digesters were operated under different modes, and foaming was induced with several methods. Proliferation of specific bacteria and accumulation of surface active materials may be the main causes of foaming. Volatile fatty acids (VFAs) and total ammonia nitrogen (TAN) accumulated in these reactors before foaming, which may have contributed to foam formation by decreasing the surface tension of sludge and increasing foam stability. The relative abundance of acid-producing bacteria (Petrimonas, Fastidiosipila, etc.) and ammonia producers (Proteiniphilum, Gelria, Aminobacterium, etc.) significantly increased after foaming, which explained the rapid accumulation of VFAs and NH4+ after foaming. In addition, the proportions of microbial genera known to contribute to foam formation and stabilization significantly increased in foaming samples, including bacteria containing mycolic acid in cell walls (Actinomyces, Corynebacterium, etc.) and those capable of producing biosurfactants (Corynebacterium, Lactobacillus, 060F05-B-SD-P93, etc.). These findings improve the understanding of foaming mechanisms in FW digesters and provide a theoretical basis for further research on effective suppression and early warning of foaming.

Microbial population dynamics in urban organic waste anaerobic co-digestion with mixed sludge during a change in feedstock composition and different hydraulic retention times

Microbial communities play an essential role in the biochemical pathways of anaerobic digestion processes. The correlations between microorganisms' relative abundance and anaerobic digestion process parameters were investigated, by considering the effect of different feedstock compositions and hydraulic retention times (HRTs). Shifts in microbial diversity and changes in microbial community richness were observed by changing feedstock composition from mono-digestion of mixed sludge to co-digestion of food waste, grass clippings and garden waste with mixed sludge at HRT of 30, 20, 15 and 10 days. Syntrophic acetate oxidation along with hydrogenotrophic methanogenesis, mediated by Methanothermobacter, was found to be the most prevalent methane formation pathway, with the only exception of 10 days' HRT, in which Methanosarcina was the most dominant archaea. Significantly, the degradation of complex organic polymers was found to be the most active process, performed by members of S1 (Thermotogales), Thermonema and Lactobacillus in a reactor fed with a high share of food waste. Conversely, Thermacetogenium, Anaerobaculum, Ruminococcaceae, Porphyromonadaceae and the lignocellulosic-degrading Clostridium were the significantly more abundant bacteria in the reactor fed with an increased share of lignocellulosic biomass in the form of grass clippings and garden waste. Finally, microbes belonging to Coprothermobacter, Syntrophomonas and Clostridium were correlated significantly with the specific methane yield obtained in both reactors.

Foam-forming bacteria in activated sludge effectively reduced by rotifers in laboratory- and real-scale wastewater treatment plant experiments

Lecane inermis rotifers were shown to diminish sludge bulking due to their ability to ingest the filamentous bacteria in activated sludge. To determine if rotifers are also able to control branched actinomycetes, we investigated three other Lecane species (Monogononta). In a week-long experiment, only Lecane tenuiseta significantly reduced the density of Microthrix parvicella and Type 0092 filaments, but in a 2-week experiment, actinomycetes were significantly reduced by most of the tested monogonont rotifers: L. inermis, Lecane decipiens and Lecane pyriformis. Rotifers L. inermis originating from the mass culture were artificially introduced into real-scale wastewater treatment plant (WWTP) in two series. The WWTP was monitored for 1 year. Rotifer inoculation resulted in diminishing of M. parvicella and actinomycete abundance. The experiments showed that different species of rotifers vary in their effectiveness at limiting various types of filamentous organisms. This is the first report demonstrating that one of the most troublesome bacteria, branched actinomycetes, which cause heavy foaming in bioreactors, can be controlled by rotifers. Knowledge of the consumers of filamentous bacteria that inhabit activated sludge could help WWTP operators overcome bulking and foaming through environmentally friendly methods.

Impact of fiber source and feed particle size on swine manure properties related to spontaneous foam formation during anaerobic decomposition

Foam accumulation in deep-pit manure storage facilities is of concern for swine producers because of the logistical and safety-related problems it creates. A feeding trial was performed to evaluate the impact of feed grind size, fiber source, and manure inoculation on foaming characteristics. Animals were fed: (1) C-SBM (corn-soybean meal): (2) C-DDGS (corn-dried distiller grains with solubles); and (3) C-Soybean Hull (corn-soybean meal with soybean hulls) with each diet ground to either fine (374 μm) or coarse (631 μm) particle size. Two sets of 24 pigs were fed and their manure collected. Factors that decreased feed digestibility (larger grind size and increased fiber content) resulted in increased solids loading to the manure, greater foaming characteristics, more particles in the critical particle size range (2-25 μm), and a greater biological activity/potential.

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

BACKGROUND

Biogas production is an economically attractive technology that has gained momentum worldwide over the past years. Biogas is produced by a biologically mediated process, widely known as "anaerobic digestion." This process is performed by a specialized and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. Deciphering the complex microbial community engaged in this process is interesting both for unraveling the network of bacterial interactions and for applicability potential to the derived knowledge.

RESULTS

In this study, we dissect the bioma involved in anaerobic digestion by means of high throughput Illumina sequencing (~51 gigabases of sequence data), disclosing nearly one million genes and extracting 106 microbial genomes by a novel strategy combining two binning processes. Microbial phylogeny and putative taxonomy performed using >400 proteins revealed that the biogas community is a trove of new species. A new approach based on functional properties as per network representation was developed to assign roles to the microbial species. The organization of the anaerobic digestion microbiome is resembled by a funnel concept, in which the microbial consortium presents a progressive functional specialization while reaching the final step of the process (i.e., methanogenesis). Key microbial genomes encoding enzymes involved in specific metabolic pathways, such as carbohydrates utilization, fatty acids degradation, amino acids fermentation, and syntrophic acetate oxidation, were identified. Additionally, the analysis identified a new uncultured archaeon that was putatively related to Methanomassiliicoccales but surprisingly having a methylotrophic methanogenic pathway.

CONCLUSION

This study is a pioneer research on the phylogenetic and functional characterization of the microbial community populating biogas reactors. By applying for the first time high-throughput sequencing and a novel binning strategy, the identified genes were anchored to single genomes providing a clear understanding of their metabolic pathways and highlighting their involvement in anaerobic digestion. The overall research established a reference catalog of biogas microbial genomes that will greatly simplify future genomic studies.

Biogas Upgrading via Hydrogenotrophic Methanogenesis in Two-Stage Continuous Stirred Tank Reactors at Mesophilic and Thermophilic Conditions

This study proposes an innovative setup composed by two stage reactors to achieve biogas upgrading coupling the CO2 in the biogas with external H2 and subsequent conversion into CH4 by hydrogenotrophic methanogenesis. In this configuration, the biogas produced in the first reactor was transferred to the second one, where H2 was injected. This configuration was tested at both mesophilic and thermophilic conditions. After H2 addition, the produced biogas was upgraded to average CH4 content of 89% in the mesophilic reactor and 85% in the thermophilic. At thermophilic conditions, a higher efficiency of CH4 production and CO2 conversion was recorded. The consequent increase of pH did not inhibit the process indicating adaptation of microorganisms to higher pH levels. The effects of H2 on the microbial community were studied using high-throughput Illumina random sequences and full-length 16S rRNA genes extracted from the total sequences. The relative abundance of archaeal community markedly increased upon H2 addition with Methanoculleus as dominant genus. The increase of hydrogenotrophic methanogens and syntrophic Desulfovibrio and the decrease of aceticlastic methanogens indicate a H2-mediated shift toward the hydrogenotrophic pathway enhancing biogas upgrading. Moreover, Thermoanaerobacteraceae were likely involved in syntrophic acetate oxidation with hydrogenotrophic methanogens in absence of aceticlastic methanogenesis.

Counteracting foaming caused by lipids or proteins in biogas reactors using rapeseed oil or oleic acid as antifoaming agents

Foaming is one of the major operational problems in biogas plants, and dealing with foaming incidents is still based on empirical practices. Various types of antifoams are used arbitrarily to combat foaming in biogas plants, but without any scientific support this action can lead to serious deterioration of the methanogenic process. Many commercial antifoams are derivatives of fatty acids or oils. However, it is well known that lipids can induce foaming in manure based biogas plants. This study aimed to elucidate the effect of rapeseed oil and oleic acid on foam reduction and process performance in biogas reactors fed with protein or lipid rich substrates. The results showed that both antifoams efficiently suppressed foaming. Moreover rapeseed oil resulted in stimulation of the biogas production. Finally, it was reckoned that the chemical structure of lipids, and more specifically their carboxylic ends, is responsible for their foam promoting or foam counteracting behaviour. Thus, it was concluded that the fatty acids and oils could suppress foaming, while salt of fatty acids could generate foam.

Bioaugmentation of biogas production by a hydrogen-producing bacterium

The rate-limiting nature of the hydrogen concentration prevailing in the anaerobic digester has been recognized, but the associated alterations in the microbial community are unknown. In response to the addition of Enterobacter cloacae cells in laboratory anaerobic digesters, the level of biogas production was augmented. Terminal restriction fragment length polymorphism (T-RFLP) and real-time polymerase chain reaction (Real-Time PCR) were used to study the survival of mesophilic hydrogen-producing bacteria and the effects of their presence on the composition of the other members of the bacterial community. E. cloacae proved to maintain a stable cell number and to influence the microbial composition of the system. Bioaugmentation by a single strain added to the natural biogas-producing microbial community was demonstrated. The community underwent pronounced changes as a result of the relatively slight initial shift in the microbiological system, responding sensitively to the alterations in local hydrogen concentration.

Effects of feedstock ratio and organic loading rate on the anaerobic mesophilic co-digestion of rice straw and pig manure

In order to investigate the effects of feedstock ratio and organic loading rate (OLR) on the anaerobic mesophilic co-digestion of rice straw (RS) and pig manure (PM), batch bottle tests (2.5L) were carried out at volatile solid (VS) ratios of 0:1, 1:2, 1:1, 2:1, and 1:0 (RS/PM), and continuous bench experiments (40L) were carried out at OLRs of 3.0, 3.6, 4.2, 4.8, 6.0, 8.0, and 12.0kg VS/(m(3)d) with optimal VS ratio. The results showed that the optimal ratio was 1:1 in terms of biogas yield. Stable biogas production with an average specific biogas production of 413L/kg VS was obtained at an OLR of 3-8kg VS/(m(3)d). Anaerobic co-digestion was severely inhibited by the accumulation of volatile fatty acids when the OLR was 12kg VS/(m(3)d). Further, light and serious foaming were observed at OLR of 8 and 12kg VS/(m(3)d), respectively.

Effects of feedstock ratio and organic loading rate on the anaerobic mesophilic co-digestion of rice straw and cow manure

In order to investigate the effects of feedstock ratio and organic loading rate (OLR) on the anaerobic mesophilic co-digestion of rice straw (RS) and cow manure (CM), batch tests (2.5L) were carried out at volatile solid (VS) ratios of 0:1, 1:2, 1:1, 2:1, and 1:0 (RS/CM), and continuous bench experiments (40 L) were carried out at OLRs of 3.0, 3.6, 4.2, 4.8, 6.0, 8.0, and 12.0 kg VS/(m(3) d) with optimal VS ratio. The optimal VS ratio was found to be 1:1. Stable and efficient co-digestion with average specific biogas production of 383.5L/kg VS and volumetric biogas production rate of 2.30 m(3)/(m(3) d) was obtained at an OLR of 6 kg VS/(m(3) d). Anaerobic co-digestion was severely inhibited by the accumulation of volatile fatty acids instead of ammonia when the OLR was 12 kg VS/(m(3) d). Further, significant foaming was observed at OLR ⩾ 8 kg VS/(m(3) d).

Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition

The anaerobic digestion process is often inhibited by alteration of substrates and/or organic overload. This study aimed to elucidate changes of microbial ecology in biogas reactors upon radical changes of substrates and to determine their importance to process imbalance. For this reason, continuously fed reactors were disturbed with pulses of proteins, lipids and carbohydrates and the microbial ecology of the reactors were characterized by 16S rRNA gene sequencing before and after the imposed changes. The microbial composition of the three reactors, initially similar, diverged greatly after substrate change. The greatest increase in diversity was observed in the reactor supplemented with carbohydrates and the microbial community became dominated by lactobacilli, while the lowest corresponded to the reactor overfed with proteins, where only Desulfotomaculum showed significant increase. The overall results suggest that feed composition has a decisive impact on the microbial composition of the reactors, and thereby on their performance.