Distinctive responses of metabolically active microbiota to acidification in a thermophilic anaerobic digester

Metagenomics analysis of microbial community distribution in large-scale and step-by-step purification system of swine wastewater

Biological treatment is one of the most widely used methods to treat swine wastewater in wastewater treatment plants. The microbial community plays an important role in the swine slurry treatment system. However, limited information is available regarding the correlation between pollutant concentration and dominant microbial community in swine wastewater. This work aimed to study the profiling of microbial communities and their abundance in the 40 M³/day large-scale and step-by-step treatment pools of swine wastewater. Metagenome sequencing was applied to study the changes of microbial community structure in biochemical reaction pools. The results showed that in the heavily polluted pools, it was mainly Proteobacteria, Cyanobacteria, Chlorella and other strains that could tolerate high concentration of ammonia nitrogen to remove nitrogen and absorb chemical oxygen demand (COD). In the moderately polluted pools, Nitrospirae, Actinobacteria and other strains further cooperated to purify swine wastewater. In the later stage, the emergence of Brachionus indicated the reduction of water pollution. The dominant microbes and their abundance changed with the purification of swine wastewater in different stages. Moreover, the dominant microflora of swine wastewater treatment pools at all levels reflected little difference in phylum classification level, while in genus classification level, the dominant microflora manifested great difference. Findings demonstrated that the microorganisms maintained ecological balance and absorbed the nutrients in the swine wastewater treatment pools, so as to play the role of purifying sewage. Therefore, the stepwise purification of swine wastewater can be realized by adding bacteria and microalgae of different genera.

Simultaneous production of hydrogen-methane and spatial community succession in an anaerobic baffled reactor treating corn starch processing wastewater

Corn starch processing wastewater (CSPW) is a high-strength organic wastewater and biological treatment is considered as the dominant process. The present work investigated the effects of pH on the bioenergy production and spatial succession of microbial community in an anaerobic baffled reactor (ABR) treating CSPW. The results showed that above 90.5% of COD removal and above 16.6 L d^-1 of methane were achieved at the influent pHs of 8.0 and 7.0 under organic loading rate of 4.0 kg COD·m^-3·L^-1 condition. Further decreasing the influent pH to 6.0 resulted in the COD removal decreased to 89.7%. Besides, 9.2 L d^-1 of hydrogen and 13.0 L d^-1 of methane were obtained. There was significant difference in the volatile fatty acids profiles during the variation of pH. Illumina Miseq sequencing showed that Clostridium, Ethanoligenens, Megasphaera, Prevotella and Trichococcus with relative abundance of 2.1%∼28.1% were the dominant hydrogen-producing bacteria in C1. Methanogens (Methanothrix and Methanobacterium) dominated in the last three compartments. Function predicted analysis revealed that the abundance of metabolic-related gene families containing carbohydrate, amino acids and energy in the last three compartments were higher than that in C1. A deduced biodegradation model of CSPW in ABR revealed that the anaerobic sludge in C1 mainly produced hydrogen. Microbial population in C3 was responsible for COD removal and methane production. The redundancy analysis revealed that hydrogen production was highly correlated with some hydrogen-producing bacteria in C1, whereas methane production was positively correlated with microbial group in C2∼ C4.

Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community

Acetogens play a very important role in anaerobic digestion and are essential in ensuring process stability. Despite this, targeted studies of the acetogenic community in biogas processes remain limited. Some efforts have been made to identify and understand this community, but the lack of a reliable molecular analysis strategy makes the detection of acetogenic bacteria tedious. Recent studies suggest that screening of bacterial genetic material for formyltetrahydrofolate synthetase (FTHFS), a key marker enzyme in the Wood-Ljungdahl pathway, can give a strong indication of the presence of putative acetogens in biogas environments. In this study, we applied an acetogen-targeted analyses strategy developed previously by our research group for microbiological surveillance of commercial biogas plants. The surveillance comprised high-throughput sequencing of FTHFS gene amplicons and unsupervised data analysis with the AcetoScan pipeline. The results showed differences in the acetogenic community structure related to feed substrate and operating parameters. They also indicated that our surveillance method can be helpful in the detection of community changes before observed changes in physico-chemical profiles, and that frequent high-throughput surveillance can assist in management towards stable process operation, thus improving the economic viability of biogas plants. To our knowledge, this is the first study to apply a high-throughput microbiological surveillance approach to visualise the potential acetogenic population in commercial biogas digesters.

Anaerobic co-digestion of spent coconut copra with cow urine for enhanced biogas production

Laboratory-scale bioreactors were used to co-digest spent coconut copra (SCC) and cow urine (CU) as a co-substrate (SCC + CU) in a batch mode under thermophilic condition (45 ± 2°C) in order to enhance biogas production. The effect of CU pretreatment on the performance indicators (biogas and biomethane yields, total solids (TS), and volatile solids (VS) reduction, pH and volatile fatty acids (VFAs) concentrations) were also examined. This was compared with mono-digestion of SCC. The experiment was performed with different mixing ratios in reactors labelled as follows: A = 75 g SCC + 5 ml CU; B = 70 g SCC + 10 ml CU; C = 65 g SCC + 15 ml CU; and D (control) = 80 g SCC at a hydraulic retention time of 42 days. Co-digestion (SCC + CU) significantly improved anaerobic digestion (AD) performance resulting in a threefold and fivefold increase in biogas and biomethane production, respectively, with concomitant TS (44.9-57.7%) and VS (55.4-60.3%) removal efficiencies. But for mono-digestion (control experiment), all CU treated and co-digestion assays showed pH stability ranging between 6.6 and 7.4 and VFAs' concentrations ranging from 15-330 mgL^-1. By acting as a buffer, CU effectively enhanced the AD performance of SCC as demonstrated in this study.

Strategies for recovery of imbalanced full-scale biogas reactor feeding with palm oil mill effluent

Background

Full-scale biogas production from palm oil mill effluent (POME) was inhibited by low pH and highly volatile fatty acid (VFA) accumulation. Three strategies were investigated for recovering the anaerobic digestion (AD) imbalance on biogas production, namely the dilution method (tap water vs. biogas effluent), pH adjustment method (NaOH, NaHCO₃, Ca(OH)₂, oil palm ash), and bioaugmentation (active methane-producing sludge) method. The highly economical and feasible method was selected and validated in a full-scale application.

Results

The inhibited sludge from a full-scale biogas reactor could be recovered within 30–36 days by employing various strategies. Dilution of the inhibited sludge with biogas effluent at a ratio of 8:2, pH adjustment with 0.14% w/v NaOH, and 8.0% w/v oil palm ash were considered to be more economically feasible than other strategies tested (dilution with tap water, or pH adjustment with 0.50% w/v Ca(OH)₂, or 1.25% NaHCO₃ and bioaugmentation) with a recovery time of 30–36 days. The recovered biogas reactor exhibited a 35–83% higher methane yield than self-recovery, with a significantly increased hydrolysis constant (k_H) and specific methanogenic activity (SMA). The population of Clostridium sp., Bacillus sp., and Methanosarcina sp. increased in the recovered sludge. The imbalanced full-scale hybrid cover lagoon reactor was recovered within 15 days by dilution with biogas effluent at a ratio of 8:2 and a better result than the lab-scale test (36 days).

Conclusion

Dilution of the inhibited sludge with biogas effluent could recover the imbalance of the full-scale POME-biogas reactor with economically feasible and high biogas production performance.

Soil-Derived Inocula Enhance Methane Production and Counteract Common Process Failures During Anaerobic Digestion

Although soil-borne methanogens are known to be highly diverse and adapted to extreme environments, their application as potential (anaerobic) inocula to improve anaerobic digestion has not been investigated until now. The present study aimed at evaluating if soil-derived communities can be beneficial for biogas (methane, CH₄) production and endure unfavorable conditions commonly associated with digestion failure. Nine study sites were chosen and tested for suitability as inoculation sources to improve biogas production via in situ measurements (CH₄ fluxes, physical and chemical soil properties, and abundance of methanogens) and during a series of anaerobic digestions with (a) combinations of both sterile or unsterile soil and diluted fermenter sludge, and (b) pH-, acetate-, propionate-, and ammonium-induced disturbance. Amplicon sequencing was performed to assess key microbial communities pivotal for successful biogas production. Four out of nine tested soil inocula exerted sufficient methanogenic activity and repeatedly allowed satisfactory CH₄/biogas production even under deteriorated conditions. Remarkably, the significantly highest CH₄ production was observed using unsterile soil combined with sterile sludge, which coincided with both a higher relative abundance of methanogens and predicted genes involved in CH₄ metabolism in these variants. Different bacterial and archaeal community patterns depending on the soil/sludge combinations and disturbance variations were established and these patterns significantly impacted CH₄ production. Methanosarcina spp. seemed to play a key role in CH₄ formation and prevailed even under stressed conditions. Overall, the results provided evidence that soil-borne methanogens can be effective in enhancing digestion performance and stability and, thus, harbor vast potential for further exploitation.

Synergistic effects of co-trace elements on anaerobic co-digestion of food waste and sewage sludge at high organic load

Trace elements play an indispensable role in stabilizing the performance of anaerobic co-digestion (Co-AD) of food waste (FW) and sewage sludge (SS) at greater organic load (OL). The results of high organic-loaded reactors showed that the stability of the system failed due to the buildup of volatile fatty acid (VFA) and ammonia. At the OL of 6.5 g/L, the stability of the system failed due to the buildup of propionic acid. The optimum dosage of Fe (5000 mg/L), Ni (200 mg/L), Zn (320 mg/L), and Mo (2.2 mg/L) was experimentally determined and added to reduce the inhibition condition. Consequently, the propionic acid concentration, which was above 1500 mg/L reduced to under 500 mg/L during Co-AD. Hence, higher biogas production, and biodegradability of 236 ± 23 mL/g VS, and 41.75%, respectively, were obtained. Increasing OL (9.5 g/L), the stability of the system was hindered due to only the buildup of ammonia (up to 188 ± 6 NH₃-N mg/L). Therefore, the trace elements of Cu (250 mg/L) and Co (3 mg/L) were experimentally determined and added into the Co-AD to diminish ammonia accumulation and process instability. The experimental results showed that at OL of 14 g/L, biogas production, low ammonia concentration and biodegradability of 332 ± 21 mL/g VS, and 70 NH3-N mg/L, and 57.89%, respectively, were achieved. However, the performance and stability of the system failed at the higher OL due to the more increased ammonia and VFA concentration, and the greater dosages of trace elements did not enhance the process stability.

Detection of early imbalances in semi-continuous anaerobic co-digestion process based on instantaneous biogas production rate

The aim of this study was to investigate the use of biogas production rate kinetics for the monitoring of anaerobic co-digestion. Recent extensive studies of degradation pathways showed that acetoclastic methanogenesis is not always the main pathway. Hydrogenotrophic methanogenesis and syntrophic acetate oxidation can also dominate, mostly for operating conditions with high concentrations of ammonia or volatile fatty acids … These conditions are also known to cause instability in the digester's operation especially in co-digestion due to substrate variability. Therefore, co-digestion experiments were conducted with several co-substrates using a continuously stirred 35-L tank reactor. Degradation pathways and their potential shifts were identified by monitoring variations in biogas production rate kinetics using a principal component analysis model. The shifts in the degradation pathways were used to monitor the process. These shift points were found to provide early warnings of instabilities in the anaerobic co-digestion process.

A Methanogenic Consortium Was Active and Exhibited Long-Term Survival in an Extremely Acidified Thermophilic Bioreactor

Acid crisis characterized by acid accumulation and/or low pH is a common reason for the failure of anaerobic digestion (AD), which is usually applied for wastewater and waste treatment. Acid-tolerant methanogens are rarely reported to be active in the artificial anaerobic digester. In this study, we observed that the thermophilic methanogenesis by a consortium in the form of flocs and not granules could still be recovered during long-term operation at acetate concentration of up to 104 mM and pH 5.5 by adjusting the pH gradually or directly to pH 5.5 or 5.0. The acclimation process involving the gradual decrease in pH could enhance the resistance of the consortium against extreme acidification. The stable isotopic signature analysis of biogas revealed that Methanosarcina, which produced methane through acetoclastic methanogenesis (AM) pathway, was the predominant methane producer when the pH was decreased gradually to 5.0. Meanwhile, the abundance of Coprothermobacter increased with a decrease in pH. Contrastingly, when directly subjected to an environment of pH 5.5 and 104 mM acetate (15.84-mM free acetic acid) after a 42-day lag phase, Methanothermobacter was the predominant methanogen. Methanothermobacter initiated methane production through the hydrogenotrophic pathway and formed syntrophic relationship/consortium with the potential acetate-oxidizing bacteria, Thermacetogenium and Coprothermobacter. Comparative metagenomic and metatranscriptomic analysis on this self-adapted and acid-tolerant consortium revealed that the genes, such as GroEL, DnaK, CheY, and flagellum-related genes (FlaA, FlgE, and FliC) from Anaerobaculum, Thermacetogenium, and Coprothermobacter were highly overexpressed in response to system acidification. Microbial self-adaptation patterns (community structure adjustment, methanogenesis pathway shift, and transcriptional regulation) of thermophilic methanogenic consortium to gradual and sudden acidification were evaluated by integrated stable isotopic signature and comparative meta-omic approaches. The study elucidated the acid-resistant mechanism of thermophilic methanogenic consortium and deepened our knowledge of the function, interaction, and microbial characteristics of Methanosarcina, Methanothermobacter, and Coprothermobacter under extreme acidic environment.

The hydraulic retention time influences the abundance of Enterobacter, Clostridium and Lactobacillus during the hydrogen production from food waste

The influence of hydraulic retention time (HRT) on the microbial communities was evaluated in an anaerobic sequencing batch reactor (AnSBR) using organic waste from a restaurant as the substrate. The relationship among Lactobacillus, Clostridium and Bacillus as key micro-organisms on hydrogen production from organic solid waste was studied. The effect of the HRT (8-48 h) on the hydrogen production and the microbial community was evaluated. Quantitative PCR was applied to determine the abundance of bacteria (in particular, Enterobacter, Clostridium and Lactobacillus genera). An AnSBR fermentative reactor was operated for 111 cycles, with carbohydrate and organic matter removal efficiencies of 80 ± 15·42% and 22·1 ± 4·49% respectively. The highest percentage of hydrogen in the biogas (23·2 ± 11·1 %), and the specific production rate (0·42 ± 0·16 mmol H₂ gVS_added ^-1 d^-1 ) were obtained at an HRT of 48 h. The decrease in the HRT generated an increase in the hydrogen production rate but decreasing the content of the hydrogen in the gas. HRT significantly influence the abundance of Enterobacter, Clostridium and Lactobacillus during the hydrogen production from food waste leading the hydrogen production as well as the metabolic pathways. The microbial analysis revealed a direct relationship between the HRT and the presence of fermentative bacteria (Enterobacter, Clostridium and Lactobacillus genera). Clostridium sp. predominated at an HRT of 48 h, while Enterobacter and Lactobacillus predominated at HRTs between 8 and 24 h. SIGNIFICANCE AND IMPACT OF THE STUDY: Significance and Impact of the Study: It was demonstrated that hydrogen production using food waste was influenced by the hydraulic retention time (HRT), and closely related to changes in microbial communities together with differences in metabolic patterns (e.g. volatile fatty acids, lactate, etc.). The decrease in the HRT led to the dominance of lactic acid bacteria within the microbial community whereas the increase in HRT favoured the emergence of Clostridium bacteria and the increase in acetic and butyric acids. Statistical data analysis revealed a direct relationship existing between the HRT and the microbial community composition in fermentative bacteria. This study provides new insight into the relationship between the bioprocess operation and the microbial community to understand better and control the biohydrogen production.

Energy performance evaluation of ultrasonic pretreatment of organic solid waste in a pilot-scale digester

It has been proven that ultrasonic pretreatment (UP) has positive effect on biogas generation from previous lab-scale studies. However, that is not always the case in larger scale processes. The purpose of this study was to evaluate the effectiveness of UP to biogas generation in terms of anaerobic digestion process and energy efficiency. Parameters including total solids (TS) and ultrasonic treatment operational parameters of organic solid waste (OSW) resulted from our past lab scale UP studies were applied in this study. OSW with 6-10% TS was treated using a lab-scale ultrasonic processor using various power densities (0.2-0.6 W/mL) at different time periods up to 30 min. Results of lab scale confirmed that OSW with 6% TS sonicated with 0.2 W/mL power density in 30 min gave the best outcome for the pilot scale experiment. To simulate the condition of an actual scale, in addition to energy analysis, two different organic loading rates (OLR), namely 500 and 1500 gVS/m³day were examined. The pilot digester was fed with OSW with or without the pretreatment based on the aforementioned specifications. The results showed that UP effectively improves biogas generation in terms of quantity and quality (CH₄/CO₂). Furthermore, it decreases the time to reach the maximum cumulative biogas volume comparing to the untreated feed. The key achievement of this research has confirmed that although the relative increase in the energy gain by the influence of UP was more remarkable under the 500 gVS/m³day OLR, energy analysis showed a better energy gain and energy benefit as well as jumping in biogas yield up to 80% for UP treated OSW under 1500 gVS/m³day OLR.

A Review of the Processes, Parameters, and Optimization of Anaerobic Digestion

Anaerobic digestion is a technology that has been used by humans for centuries. Anaerobic digestion is considered to be a useful tool that can generate renewable energy and significant research interest has arisen recently. The underlying theory of anaerobic digestion has been established for decades; however, a great deal of current research is directed towards the optimization of anaerobic digestion under diverse digestion conditions. This review provides a summary of the processes underlying anaerobic digestion, commonly-utilized measurements of anaerobic sludge, operating parameters of anaerobic digesters, and methods of acceleration and optimization used to improve process efficiency. Recent developments in addition to older research are considered to provide a general but comprehensive summary of accumulated knowledge in the theory of anaerobic digestion, as well as considerations in the efficient operation of digesters. We have determined that the numerous factors pertinent to the design and operation of batch-based anaerobic digesters must each be considered to ensure the maximum efficiency and cost-effectiveness of a digester provided its respective operating conditions.

Assessing Methanogenic Archaeal Community in Full Scale Anaerobic Sludge Digester Systems in Dubai, United Arab Emirates

Introduction:

Anaerobic digestion for methane production comprises of an exceptionally diverse microbial consortium, a profound understanding about which is still constrained. In this study, the methanogenic archaeal communities in three full-scale anaerobic digesters of a Municipal Wastewater Treatment Plant were analyzed by Fluorescence in situ hybridization and quantitative real-time Polymerase Chain Reaction (qPCR) technique.

Methods & Materials:

Fluorescence in situ hybridization (FISH) was performed to detect and quantify the methanogenic Archaea in the sludge samples whereas qPCR was carried out to support the FISH analysis. Multiple probes targeting domain archaea, different orders and families of Archaea were used for the studies.

Results and Discussion:

In general, the aceticlastic organisms (Methanosarcinaceae & Methanosaetaceae) were more abundant than the hydrogenotrophic organisms (Methanobacteriales, Methanomicrobiales, Methanobacteriaceae & Methanococcales). Both FISH and qPCR indicated that family Methanosaetaceae was the most abundant suggesting that aceticlastic methanogenesis is probably the dominant methane production pathway in these digesters.

Conclusion:

Future work involving high-throughput sequencing methods and correlating archaeal communities with the main operational parameters of anaerobic digesters will help to obtain a better understanding of the dynamics of the methanogenic archaeal community in wastewater treatment plants in United Arab Emirates (UAE) which in turn would lead to improved performance of anaerobic sludge digesters.

Sugar beet silage as highly flexible feedstock for on demand biogas production

On demand biogas production is a great option to complement solar and wind power for the energy revolution. Alternatives like feedstock management are important in order to avoid expensive and complex adjustments for gas storage systems. The use of sugar beet silage (S) is a good option because it mainly contains carbohydrates that are easily degradable. Anaerobic digestion was performed for 63 days in four completely stirred tank reactors (CSTR) with different ratios of maize silage (M) and S. M given every hour was used as a base load for the fermentation and S was given two times a day every 12h. Biogas and methane production rates were measured every 5min in order to achieve data with high resolution. Also, pH value, VFA/TIC values and volatile fatty acids were measured during the experiment. The process remained stable in CSTR1 (M:S1:0), CSTR2 (M:S6:1) and CSTR3 (M:S3:1). Instabilities occurred in CSTR4 (M:S1:3) after an operation time of 33 days. Nevertheless, methane yields more than doubled for CSTR3 within 5min after the input of S. Use of sugar beet as a feedstock for biogas production is a further application for this agricultural commodity.

Performance and stability of an expanded granular sludge bed reactor modified with zeolite addition subjected to step increases of organic loading rate (OLR) and to organic shock load (OSL)

This paper shows the effect of organic shock loads (OSLs) on the anaerobic digestion (AD) of synthetic swine wastewater using an expanded granular sludge bed (EGSB) reactor modified with zeolite. Two reactors (R1 and R2), each with an effective volume of 3.04 L, were operated for 180 days at a controlled temperature of 30 °C and hydraulic retention time of 12 h. In the case of R2, 120 g of zeolite was added. The reactors were operated with an up-flow velocity of 6 m/h. The evolution of pH, total Kjeldahl nitrogen, chemical oxygen demand (COD) and volatile fatty acids (VFAs) was monitored during the AD process with OSL and increases in the organic loading rate (OLR). In addition, the microbial composition and changes in the structure of the bacterial and archaeal communities were assessed. The principal results demonstrate that the presence of zeolite in an EGSB reactor provides a more stable process at higher OLRs and after applying OSL, based on both COD and VFA accumulation, which presented with significant differences compared to the control. Denaturing gradient gel electrophoresis band profiles indicated differences in the populations of Bacteria and Archaea between the R1 and R2 reactors, attributed to the presence of zeolite.

Improved methane production from sugarcane vinasse with filter cake in thermophilic UASB reactors, with predominance of Methanothermobacter and Methanosarcina archaea and Thermotogae bacteria

Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability. We used UASB reactors in a two-stage configuration, with OLRs up to 45gCODL^-1d^-1, and obtained methane production as high as 3LL^-1d^-1. Quantitative PCR indicated balanced amounts of bacteria and archaea in the sludge (10⁹-10¹⁰copiesg^-1VS), and of the predominant archaea orders, Methanobacteriales and Methanosarcinales (10⁶-10⁸copiesg^-1VS). 16S rDNA sequencing also indicated the thermophilic Thermotogae as the most abundant class of bacteria in the sludge.

Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation

The evolution and population dynamics of complex anaerobic microbial communities in anaerobic digesters were investigated during stable operation and recovery after prolonged starvation. Three thermophilic reactor systems fed with cattle manure were operated continuously in parallel for 167days. Significant changes in the microbial communities were observed for both the bacterial and archaeal populations as the reactor systems were subjected to changing feeding regimes. The ecosystems developed from being relatively similar in structure to more specialised communities, with large population shifts within the acetogenic and methanogenic communities, which appeared to shift towards the hydrogenotrophic methanogenesis pathway. All reactor systems showed signs of adaptation to a harsher environment under high VFA, H₂S and ammonia concentrations, but remained at a lower degree of stability after 45days of recovery compared to stable period of operation before starvation.

Characterisation of winery wastewater from continuous flow settling basins and waste stabilisation ponds over the course of 1 year: implications for biological wastewater treatment and land application

Wineries generate 0.2 to 4 L of wastewater per litre of wine produced. Many cellars make use of irrigation as a means of disposal, either directly or after storage. In order to consider the potential downstream impacts of storage/no storage, this study critically compared the seasonal organic and inorganic composition of fresh winery effluent with effluent that had been stored in waste stabilisation ponds. Ethanol and short chain volatile fatty acids were the main contributors to chemical oxygen demand (COD), with average concentrations of 2,086 and 882 mgCOD/L, respectively. Total phenolics were typically present in concentrations <100 mg/L. The concentration of sodium from cleaning agents was higher in the non-crush season, while the converse was true for organics. The effluent was nitrogen-deficient for biological treatment, with COD:N ratios of 0.09 to 1.2. There was an accumulation of propionic and butyric acid during storage. The composition of the pond effluent was more stable in character, and it is possible that bacterial and algal nitrogen fixation in such systems may enhance biological wastewater treatment by natural nitrogen supplementation. It is therefore recommended that if land requirements can be met, winery effluent should be stored in ponds prior to treatment.

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions

Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

A balanced microbiota efficiently produces methane in a novel high-rate horizontal anaerobic reactor for the treatment of swine wastewater

A novel combination of structurally simple, high-rate horizontal anaerobic reactors installed in series was used to treat swine wastewater. The reactors maintained stable pH, alkalinity, and volatile acid levels. Removed chemical oxygen demand (COD) represented 68% of the total, and the average specific methane production was 0.30L CH4 (g removed CODtot)(-1). In addition, next-generation sequencing and quantitative real-time PCR analyses were used to explore the methane-producing Archaea and microbial diversity. At least 94% of the sludge diversity belong to the Bacteria and Archaea, indicating a good balance of microorganisms. Among the Bacteria the Proteobacteria, Bacteroidetes and Firmicutes were the most prevalent phyla. Interestingly, up to 12% of the sludge diversity belongs to methane-producing orders, such as Methanosarcinales, Methanobacteriales and Methanomicrobiales. In summary, this system can efficiently produce methane and this is the first time that horizontal anaerobic reactors have been evaluated for the treatment of swine wastewater.

Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery

BACKGROUND

Volatile fatty acid intoxication (acidosis), a common process failure recorded in anaerobic reactors, leads to drastic losses in methane production. Unfortunately, little is known about the microbial mechanisms underlining acidosis and the potential to recover the process. In this study, triplicate mesophilic anaerobic reactors of 100 L were exposed to acidosis resulting from an excessive feeding with sugar beet pulp and were compared to a steady-state reactor.

RESULTS

Stable operational conditions at the beginning of the experiment initially led to similar microbial populations in the four reactors, as revealed by 16S rRNA gene T-RFLP and high-throughput amplicon sequencing. Bacteroidetes and Firmicutes were the two dominant phyla, and although they were represented by a high number of operational taxonomic units, only a few were dominant. Once the environment became deterministic (selective pressure from an increased substrate feeding), microbial populations started to diverge between the overfed reactors. Interestingly, most of bacteria and archaea showed redundant functional adaptation to the changing environmental conditions. However, the dominant Bacteroidales were resistant to high volatile fatty acids content and low pH. The severe acidosis did not eradicate archaea and a clear shift in archaeal populations from acetotrophic to hydrogenotrophic methanogenesis occurred in the overfed reactors. After 11 days of severe acidosis (pH 5.2 ± 0.4), the process was quickly recovered (restoration of the biogas production with methane content above 50 %) in the overfed reactors, by adjusting the pH to around 7 using NaOH and NaHCO3.

CONCLUSIONS

In this study we show that once the replicate reactors are confronted with sub-optimal conditions, their microbial populations start to evolve differentially. Furthermore the alterations of commonly used microbial parameters to monitor the process, such as richness, evenness and diversity indices were unsuccessful to predict the process failure. At the same time, we tentatively propose the replacement of the dominant Methanosaeta sp. in this case by Methanoculleus sp., to be a potential warning indicator of acidosis.

Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities

Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia.

Isolation of microorganisms involved in reduction of crystalline iron(III) oxides in natural environments

Reduction of crystalline Fe(III) oxides is one of the most important electron sinks for organic compound oxidation in natural environments. Yet the limited number of isolates makes it difficult to understand the physiology and ecological impact of the microorganisms involved. Here, two-stage cultivation was implemented to selectively enrich and isolate crystalline iron(III) oxide reducing microorganisms in soils and sediments. Firstly, iron reducers were enriched and other untargeted eutrophs were depleted by 2-years successive culture on a crystalline ferric iron oxide (i.e., goethite, lepidocrocite, hematite, or magnetite) as electron acceptor. Fifty-eight out of 136 incubation conditions allowed the continued existence of microorganisms as confirmed by PCR amplification. High-throughput Illumina sequencing and clone library analysis based on 16S rRNA genes revealed that the enrichment cultures on each of the ferric iron oxides contained bacteria belonging to the Deltaproteobacteria (mainly Geobacteraceae), followed by Firmicutes and Chloroflexi, which also comprised most of the operational taxonomic units (OTUs) identified. Venn diagrams indicated that the core OTUs enriched with all of the iron oxides were dominant in the Geobacteraceae while each type of iron oxides supplemented selectively enriched specific OTUs in the other phylogenetic groups. Secondly, 38 enrichment cultures including novel microorganisms were transferred to soluble-iron(III) containing media in order to stimulate the proliferation of the enriched iron reducers. Through extinction dilution-culture and single colony isolation, six strains within the Deltaproteobacteria were finally obtained; five strains belonged to the genus Geobacter and one strain to Pelobacter. The 16S rRNA genes of these isolates were 94.8-98.1% identical in sequence to cultured relatives. All the isolates were able to grow on acetate and ferric iron but their physiological characteristics differed considerably in terms of growth rate. Thus, the novel strategy allowed to enrich and isolate novel iron(III) reducers that were able to thrive by reducing crystalline ferric iron oxides.

Ultra-high-sensitivity stable-isotope probing of rRNA by high-throughput sequencing of isopycnic centrifugation gradients

Stable isotope probing (SIP) of rRNA directly identifies microorganisms assimilating an isotopically labelled substrate. High-throughput DNA sequencing is available for label screening at high resolution and high sensitivity, yet its effectiveness and validity remain to be clarified. Here, we investigated whether the detection sensitivity of rRNA-SIP could be improved by using Illumina sequencing in place of terminal restriction fragment length polymorphism (T-RFLP) analysis. A dilution series of (13) C-labelled RNA from Escherichia coli (1-0.0001%) and unlabelled RNA from Bacillus subtilis was density separated and fractionated. Illumina sequencing of isopycnic centrifugation gradients was able to detect (13) C-labelled RNA in the heaviest fraction with a buoyant density of 1.798 g ml(-1) even at the mixing ratio of 0.001%, whereas the detection ability of T-RFLP was not lower than 0.5%. Quantitative reverse transcription polymerase chain reaction of the density-separated RNAs showed that (13) C-labelled RNAs at mixing ratios of 0.05-0.001% had definitely accumulated in the heaviest fraction. Consequently, high-throughput sequencing provided up to 500-fold higher sensitivity for screening of (13) C-labelled RNA than T-RFLP. Ultra-high-sensitivity rRNA-SIP represents a clear advance towards a more complete understanding of microbial ecosystem function, including the ecophysiology of rare microorganisms in various natural environments.

Bacterial community dynamics in a swine wastewater anaerobic reactor revealed by 16S rDNA sequence analysis

Anaerobic digestion is a microbiological process of converting organic wastes into digestate and biogas in the absence of oxygen. In practice, disturbance to the system (e.g., organic shock loading) may cause imbalance of the microbial community and lead to digester failure. To examine the bacterial community dynamics after a disturbance, this study simulated an organic shock loading that doubled the chemical oxygen demand (COD) loading using a 4.5L swine wastewater anaerobic completely stirred tank reactor (CSTR). Before the shock (loading rate=0.65gCOD/L/day), biogas production rate was about 1-2L/L/day. After the shock, three periods representing increased biogas production rates were observed during days 1-7 (∼4.0L/L/day), 13 (3.3L/L/day), and 21-23 (∼6.1L/L/day). For culture-independent assessments of the bacterial community composition, the 454 pyrosequencing results indicated that the community contained >2500 operational taxonomic units (OTUs) and was dominated by three phyla: Bacteroidetes, Firmicutes, and Proteobacteria. The shock induced dynamic changes in the community composition, which was re-stabilized after approximately threefold hydraulic retention time (HRT). Intriguingly, upon restabilization, the community composition became similar to that observed before the shock, rather than reaching a new equilibrium.

Investigation into the effect of high concentrations of volatile fatty acids in anaerobic digestion on methanogenic communities

A study was conducted to determine whether differences in the levels of volatile fatty acids (VFAs) in anaerobic digester plants could result in variations in the indigenous methanogenic communities. Two digesters (one operated under mesophilic conditions, the other under thermophilic conditions) were monitored, and sampled at points where VFA levels were high, as well as when VFA levels were low. Physical and chemical parameters were measured, and the methanogenic diversity was screened using the phylogenetic microarray ANAEROCHIP. In addition, real-time PCR was used to quantify the presence of the different methanogenic genera in the sludge samples. Array results indicated that the archaeal communities in the different reactors were stable, and that changes in the VFA levels of the anaerobic digesters did not greatly alter the dominating methanogenic organisms. In contrast, the two digesters were found to harbour different dominating methanogenic communities, which appeared to remain stable over time. Real-time PCR results were inline with those of microarray analysis indicating only minimal changes in methanogen numbers during periods of high VFAs, however, revealed a greater diversity in methanogens than found with the array.

Involvement of a novel fermentative bacterium in acidification in a thermophilic anaerobic digester

Acidification results from the excessive accumulation of volatile fatty acids and the breakthrough of buffering capacity in anaerobic digesters. However, little is known about the identity of the acidogenic bacteria involved. Here, we identified an active fermentative bacterium during acidification in a thermophilic anaerobic digester by sequencing and phylogenetic analysis of isotopically labeled rRNA. The digestion sludge retrieved from the beginning of pH drop in the laboratory-scale anaerobic digester was incubated anaerobically at 55 °C for 4 h during which ¹³C-labeled glucose was supplemented repeatedly. ¹³CH₄ and ¹³CO₂ were produced after substrate addition. RNA extracts from the incubated sludge was density-separated by ultracentrifugation, and then bacterial communities in the density fractions were screened by terminal restriction fragment length polymorphism and clone library analyses based on 16S rRNA transcripts. Remarkably, a novel lineage within the genus Thermoanaerobacterium became abundant with increasing the buoyant density and predominated in the heaviest fraction of RNA. The results in this study indicate that a thermoacidophilic bacterium exclusively fermented the simple carbohydrate glucose, thereby playing key roles in acidification in the thermophilic anaerobic digester.

Inhibitory effects of ferrihydrite on a thermophilic methanogenic community

The addition of ferrihydrite to methanogenic microbial communities obtained from a thermophilic anaerobic digester suppressed methanogenesis in a dose-dependent manner. The amount of reducing equivalents consumed by the reduction of iron was significantly smaller than that expected from the decrease in the production of CH4, which suggested that competition between iron-reducing microorganisms and methanogens was not the most significant cause for the suppression of methanogenesis. Microbial community analyses revealed that the presence of ferrihydrite markedly affected the bacterial composition, but not the archaeal composition. These results indicate that the presence of ferrihydrite directly and indirectly suppresses thermophilic methanogenesis.

Digestion performance and microbial community in full-scale methane fermentation of stillage from sweet potato-shochu production

Sweet potato shochu is a traditional Japanese spirit produced mainly in the South Kyushu area in Japan. The amount of stillage reaches approximately 8 x 10(5) tons per year. Wastewater mainly containing stillage from the production of sweet potato-shochu was treated thermophilically in a full-scale treatment plant using fixed-bed reactors (8 reactors x 283 m3). Following the addition of Ni2+ and Co2+, the reactors have been stably operated for six years at a high chemical oxygen demand (COD) loading rate of 14 kg/(m3 x day). Analysis of coenzyme content and microbial communities indicated that similar microbial communities were present in the liquid phase and on the fiber carriers installed in reactors. Bacteria in the phyla Firmicutes as well as Bacteroidetes were dominant bacteria, and Methanosarcina thermophila as well as Methanothermobacter crinale were dominant methanogens in the reactors. This study reveals that stillage from sweet potato-shochu production can be treated effectively in a full-scale fixed-bed reactor under thermophilic conditions with the help of Ni2+ and Co2+. The high diversity of bacterial community and the coexistence of both aceticlastic and hydrogenotrophic methanogens contributed to the excellent fermentation performance.

Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata

The class Thermoplasmata harbors huge uncultured archaeal lineages at the order level, so-called Groups E2 and E3. A novel archaeon Kjm51a affiliated with Group E2 was enriched from anaerobic sludge in the present study. Clone library analysis of the archaeal 16S rRNA and mcrA genes confirmed a unique archaeal population in the enrichment culture. The 16S rRNA gene-based phylogeny revealed that the enriched archaeon Kjm51a formed a distinct cluster within Group E2 in the class Thermoplasmata together with Methanomassiliicoccus luminyensis B10^T and environmental clone sequences derived from anaerobic digesters, bovine rumen, and landfill leachate. Archaeon Kjm51a showed 87.7% 16S rRNA gene sequence identity to the closest cultured species, M. luminyensis B10^T, indicating that archaeon Kjm51a might be phylogenetically novel at least at the genus level. In fluorescence in situ hybridization analysis, archaeon Kjm51a was observed as coccoid cells completely corresponding to the archaeal cells detected, although bacterial rod cells still coexisted. The growth of archaeon Kjm51a was dependent on the presence of methanol and yeast extract, and hydrogen and methane were produced in the enrichment culture. The addition of 2-bromo ethanesulfonate to the enrichment culture completely inhibited methane production and increased hydrogen concentration, which suggested that archaeon Kjm51a is a methanol-reducing hydrogenotrophic methanogen. Taken together, we propose the provisional taxonomic assignment, named Candidatus Methanogranum caenicola, for the enriched archaeon Kjm51a belonging to Group E2. We also propose to place the methanogenic lineage of the class Thermoplasmata in a novel order, Methanomassiliicoccales ord. nov.

Detection of active, potentially acetate-oxidizing syntrophs in an anaerobic digester by flux measurement and formyltetrahydrofolate synthetase (FTHFS) expression profiling

Syntrophic oxidation of acetate, so-called reversed reductive acetogenesis, is one of the most important degradation steps in anaerobic digesters. However, little is known about the genetic diversity of the micro-organisms involved. Here we investigated the activity and composition of potentially acetate-oxidizing syntrophs using a combinatorial approach of flux measurement and transcriptional profiling of the formyltetrahydrofolate synthetase (FTHFS) gene, an ecological biomarker for reductive acetogenesis. During the operation of a thermophilic anaerobic digester, volatile fatty acids were mostly depleted, suggesting a high turnover rate for dissolved H(2), and hydrogenotrophic methanogens were the dominant archaeal members. Batch cultivation of the digester microbiota with (13)C-labelled acetate indicated that syntrophic oxidation accounted for 13.1-21.3 % of methane production from acetate. FTHFS genes were transcribed in the absence of carbon monoxide, methoxylated compounds and inorganic electron acceptors other than CO(2), which is implicated in the activity of reversed reductive acetogenesis; however, expression itself does not distinguish whether biosynthesis or biodegradation is functioning. The mRNA- and DNA-based terminal RFLP and clone library analyses indicated that, out of nine FTHFS phylotypes detected, the FTHFS genes from the novel phylotypes I-IV in addition to the known syntroph Thermacetogenium phaeum (i.e. phylotype V) were specifically expressed. These transcripts arose from phylogenetically presumed homoacetogens. The results of this study demonstrate that hitherto unidentified phylotypes of homoacetogens are responsible for syntrophic acetate oxidation in an anaerobic digester.