Use of real-time PCR for group-specific quantification of aceticlastic methanogens in anaerobic processes: population dynamics and community structures

In-situ methane enrichment in anaerobic digestion of food waste slurry by nano zero-valent iron: Long-term performance and microbial community succession

In this work, nano zero-valent iron (nZVI) was added to a lab-scale continuous stirring tank reactor (CSTR) for food waste slurry treatment, and the effect of dosing rate and dosage of nZVI were attempted to be changed. The results showed that anaerobic digestion (AD) efficiency and biomethanation stability were optimum under the daily dosing and dosage of 0.48 g/gTCOD. The average daily methane (CH4) yield reached 495.38 mL/gTCOD, which was 43.65% higher than that at control stage, and the maximum CH4 content reached 95%. However, under single dosing rate conditions, high nZVI concentrations caused microbial cell rupture and loosely bound extracellular polymeric substances (LB-EPS) precipitation degradation. The daily dosing rate promoted the hydrogenotrophic methanogenesis pathway, and the activity of coenzyme F420 increased by 400.29%. The microbial analysis indicated that daily addition of nZVI could promote the growth of acid-producing bacteria (Firmicutes and Bacteroidetes) and methanogens (Methanothrix).

Low biological phosphorus removal from effluents treated by slow sand filters

The legislation for environment protection requires strict controls of the wastewater releasing in water bodies. The wastewater treatment plants (WWTP) have been used for organic matter degradation; however, the residual total phosphorus (TP) removal has not been efficient. TP and nitrogen present in wastewater are associated to eutrophication of water bodies and algae growth. Therefore, this study discusses the efficiency of phosphorus removal by a slow filter (SF), complementary to a WWTP and the microbial community involved. The results showed that the use of SF, with or without macrophytes, is not suitable to remove TP. Spatial variation in microbial communities distributed in three distinct zones was identified in the SF. Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes covered the hydrolytic and fermentative bacteria. The acetogenesis, nitrification, and denitrification, as well as the removal of phosphorus from the effluent, were performed by representatives affiliated to different groups. Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria among these, Dokdonella sp., Frateuria sp., Comamonas sp., Diaphorobacter sp., Nitrosospira sp., Ferruginibacter sp., Flavobacterium sp., and the uncultured OD1 were the most abundant bacteria in the SF. The low efficiency for TP removing from SF effluents can be explained by the low abundance of phosphorus accumulating organisms (PAOs), with the association of the low concentration of biodegradable organic matter in the inlet effluent. Therefore, the alternative to using SF as a complement to WWTPs, as recommended by some Brazilian environmental agencies, did not prove to be viable and new approaches must be evaluated. KEY POINTS: • The phosphorus removal was performed by a slow filter system in a WWTP but obtained a low efficiency. • Microbial spatial variation was distributed into distinct zones from slow filter. • Low abundance of PAOs was observed due to the low availability of organic matter.

Development of real-time PCR methods for the quantification of Methanoculleus, Methanosarcina and Methanobacterium in anaerobic digestion

Anaerobic digestion is a growing technology to manage organic waste and produce bioenergy. To promote this technology, it is essential to know, at the molecular level, the dynamics of microbial communities, specifically the methanogenic community. In the present study, three primer pairs were selected from seven primer pairs which were designed and tested with different concentrations and conditions to detect Methanosarcina, Methanoculleus and Methanobacterium by real-time PCR based on the SYBR Green System. The functionality of the developed methods was demonstrated by the high linear relationship of the standard curves, and the specificity of each primer was empirically verified by testing DNA isolated from methane-producing and non-producing strains. These assays also exhibited good repeatability and reproducibility, which indicates the robustness of the methods. The described primers were successfully used to investigate the methanogenic communities of 10 samples from an anaerobic co-digestion. The genus Methanosarcina was the dominant methanogenic group.

Long-term effectiveness of bioaugmentation with rumen culture in continuous anaerobic digestion of food and vegetable wastes under feed composition fluctuations

Biogas plants treating food waste (FW) often experience feed load and composition fluctuations. In Korea, vegetable waste from the preparation of kimchi comprises over 20% of the total FW production during the Kimjang season. The large production of Kimjang waste (KW) can cause mechanical and operational problems in FW digesters. This study investigated the long-term effectiveness of bioaugmentation with rumen culture (38 months) in an anaerobic reactor co-digesting FW with varying amounts of KW. The bioaugmented reactor maintained better and stabler performance under recurrent fluctuations in feed characteristics than a non-bioaugmented control reactor, particularly under high ammonia conditions. Bioaugmentation increased microbial diversity, thereby improving the resilience of the microbial community. Some augmented microorganisms, especially Methanosarcina, likely played an important role in it. The results suggest that the proposed bioaugmentation strategy may provide a means to effectively treat and valorize KW-and potentially other seasonal lignocellulosic wastes-by co-digestion with FW.

Exploration of microbial communities contributing to effective methane production from scum under anaerobic digestion

Scum is formed by the adsorption of long-chain fatty acids (LCFAs) onto biomass surface in anaerobic digestion of oily substrates. Since scum is a recalcitrant substrate to be digested, it is disposed via landfilling or incineration, which results in biomass washout and a decrease in methane yield. The microbes contributing to scum degradation are unclear. This study aimed to investigate the cardinal microorganisms in anaerobic scum digestion. We pre-incubated a sludge with scum to enrich scum-degrading microbes. Using this sludge, a 1.3-times higher methane conversion rate (73%) and a faster LCFA degradation compared with control sludge were attained. Then, we analyzed the cardinal scum-degrading microbes in this pre-incubated sludge by changing the initial scum-loading rates. Increased 16S rRNA copy numbers for the syntrophic fatty-acid degrader Syntrophomonas and hydrogenotrophic methanogens were observed in scum high-loaded samples. 16S rRNA amplicon sequencing indicated that Syntrophomonas was the most abundant genus in all the samples. The amino-acid degrader Aminobacterium and hydrolytic genera such as Defluviitoga and Sporanaerobacter became more dominant as the scum-loading rate increased. Moreover, phylogenic analysis on Syntrophomonas revealed that Syntrophomonas palmitatica, which is capable of degrading LCFAs, related species became more dominant as the scum-loading rate increased. These results indicate that a variety of microorganisms that degrade LCFAs, proteins, and sugars are involved in effective scum degradation.

The Impact of Antimicrobial Substances on the Methanogenic Community during Methane Fermentation of Sewage Sludge and Cattle Slurry

This study showed the effect of amoxicillin (AMO), and oxytetracycline (OXY) at a concentration of 512 µg mL−1, and sulfamethoxazole (SMX), and metronidazole (MET) at a concentration of 1024 µg mL−1 on the efficiency of anaerobic digestion (AD) of sewage sludge (SS) and cattle slurry (CS). The production of biogas and methane (CH4) content, and the concentration of volatile fatty acids (VFAs) was analyzed in this study. Other determinations included the concentration of the mcrA gene, which catalyzes the methanogenesis, and analysis of MSC and MST gene concentration, characteristic of the families Methanosarcinaceae and Methanosaetaceae (Archaea). Both substrates differed in the composition of microbial communities, and in the sensitivity of these microorganisms to particular antimicrobial substances. Metronidazole inhibited SS fermentation to the greatest extent (sixfold decrease in biogas production and over 50% decrease in the content of CH4). The lowest concentrations of the mcrA gene (106 gD−1) were observed in CS and SS digestates with MET. A decline in the number of copies of the MSC and MST genes was noted in most of the digestate samples with antimicrobials supplementation. Due to selective pressure, antimicrobials led to a considerably lowered efficiency of the AD process and induced changes in the structure of methanogenic biodiversity.

Non-sterile fermentation of food waste with indigenous consortium and yeast - Effects on microbial community and product spectrum

This work presents examples of non-sterile mixed culture fermentation of food waste with a cultivated indigenous consortium (IC) gained from food waste, which produces lactic and acetic acids, combined with Saccharomyces cerevisiae, which produces ethanol. All results are flanked by microbial analysis to monitor changes in microbial community. At pH 6 and inoculated with yeast or IC, or both mixed sugars conversion was equal to 71%, 51%, or 67%, respectively. Under pH unregulated conditions metabolic yields were 71%, 67%, or up to 81%. While final titer of acetic acid was not affected by pH (100-200 mM), ethanol and lactic acid titers were. Using mixed culture and pH 6, sugars were almost equally used for formation of ethanol and lactic acid (400-500 mM). However, under pH unregulated conditions 80% of the substrate was converted into ethanol (900-1000 mM).

Dynamic shifts within volatile fatty acid-degrading microbial communities indicate process imbalance in anaerobic digesters

Buildup of volatile fatty acids (VFAs) in anaerobic digesters (ADs) often results in acidification and process failure. Understanding the dynamics of microbial communities involved in VFA degradation under stable and overload conditions may help optimize anaerobic digestion processes. In this study, five triplicate mesophilic completely mixed AD sets were operated at different organic loading rates (OLRs; 1-6 g chemical oxygen demand [COD] L_R^-1day^-1), and changes in the composition and abundance of VFA-degrading microbial communities were monitored using amplicon sequencing and taxon-specific quantitative PCRs, respectively. AD sets operated at OLRs of 1-4 g COD L_R^-1day^-1 were functionally stable throughout the operational period (120 days) whereas process instability (characterized by VFA buildup, pH decline, and decreased methane production rate) occurred in digesters operated at ≥ 5 g COD L_R^-1day^-1. Though microbial taxa involved in propionate (Syntrophobacter and Pelotomaculum) and butyrate (Syntrophomonas) degradation were detected across all ADs, their abundance decreased with increasing OLR. The overload conditions also inhibited the proliferation of the acetoclastic methanogen, Methanosaeta, and caused a microbial community shift to acetate oxidizers (Tepidanaerobacter acetatoxydans) and hydrogenotrophic methanogens (Methanoculleus). This study's results highlight the importance of operating ADs with conditions that promote the maintenance of microbial communities involved in VFA degradation.

Correlations between microbial population dynamics, bamA gene abundance and performance of anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol

The relevant microorganims driving efficiency changes in anaerobic digestion of phenol remains uncertain. In this study correlations were established between microbial population and the process performance in an anaerobic sequencing batch reactor (ASBR) treating increasing concentrations of phenol (from 120 to 1200 mg L^-1). Sludge samples were taken at different operational stages and microbial community dynamics was analyzed by 16S rRNA sequencing. In addition, bamA gene was quantified in order to evaluate the dynamics of anaerobic aromatic degraders. The microbial community was dominated by Anaerolineae, Bacteroidia, Clostridia, and Methanobacteria classes. Correlation analysis between bamA gene copy number and phenol concentration were highly significant, suggesting that the increase of aromatic degraders targeted by bamA assay was due to an increase in the amount of phenol degraded over time. The incremental phenol concentration affected hydrogenotrophic archaea triggering a linear decrease of Methanobacterium and the growth of Methanobrevibacter. The best performance in the reactor was at 800 mg L^-1 of phenol. At this stage, the highest relative abundances of Syntrophorhabdus, Chloroflexus, Smithella, Methanolinea and Methanosaeta were observed and correlated positively with initial degradation rate, suggesting that these microorganisms are relevant players to maintain a good performance in the ASBR.

Temperature Effects on Methanogenesis and Sulfidogenesis during Anaerobic Digestion of Sulfur-Rich Macroalgal Biomass in Sequencing Batch Reactors

Methanogenesis and sulfidogenesis, the major microbial reduction reactions occurring in the anaerobic digestion (AD) process, compete for common substrates. Therefore, the balance between methanogenic and sulfidogenic activities is important for efficient biogas production. In this study, changes in methanogenic and sulfidogenic performances in response to changes in organic loading rate (OLR) were examined in two digesters treating sulfur-rich macroalgal waste under mesophilic and thermophilic conditions, respectively. Both methanogenesis and sulfidogenesis were largely suppressed under thermophilic relative to mesophilic conditions, regardless of OLR. However, the suppressive effect was even more significant for sulfidogenesis, which may suggest an option for H₂S control. The reactor microbial communities developed totally differently according to reactor temperature, with the abundance of both methanogens and sulfate-reducing bacteria being significantly higher under mesophilic conditions. In both reactors, sulfidogenic activity increased with increasing OLR. The findings of this study help to understand how temperature affects sulfidogenesis and methanogenesis during AD.

Enhanced biogas production and in situ ammonia recovery from food waste using a gas-membrane absorption anaerobic reactor

A novel GAs-Membrane Absorption anaerobic Reactor (GAMAR) was developed by combining gas-membrane absorption system with anaerobic digestion. A gas-permeable expanded polytetrafluoroethylene (ePTFE) membrane was submerged in the anaerobic reactor. Free ammonia could transfer through the gas-permeable membrane and be recovered by acidic solution. The free ammonia concentration was lower than 40 mgN L^-1 in GAMAR, which alleviated ammonia inhibition. Meanwhile free ammonia concentration up 70 mgN L^-1 in the reference reactor inhibited methanogens and led to unstable operation. The volumetric biogas production rate of GAMAR was 2.83 m³ m^-3 d^-1, and 58% higher than the reference reactor. Long term use of membrane led to membrane fouling and hydrophobicity loss. The contact angle of membrane decreased from 105.9 ± 1.2° to 97.6 ± 6.3° after 43 d. The abundance of methanogens in GAMAR was 1.8-2.1 times higher than that in the reference reactor, which was in accordance with the higher biogas production rate in GAMAR.

Effect of different initial low pH conditions on biogas production, composition, and shift in the aceticlastic methanogenic population

Anaerobic digestion (AD) reactors often encounter low pH inhibition during startup and high organic loading periods. The use of a large amount of NaOH in order to raise and buffer the low pH, is reported to be inhibitory to methanogens. In order to address this problem, we acclimatized aceticlastic methanogens to low pH. Methanogens were successfully acclimatized to initial low pH down to 3.5 in a lengthy, five months, acclimatization period. The aceticlastic methanogen, Methanothrix soehngenii which was 96.3% of the total methanogenic population at pH 4.5 and 86.75% at pH 3.5, demonstrated that they were the most tolerant aceticlastic methanogens to low pH. After acclimatization, methane yield at pH 4.5 was comparable to neutral pH. Methanosaeta maintained its dominance over Methanosarcina at an elevated level of acetate (66 mM), and a negative correlation was observed between them. There was a positive correlation between the CH₄ content and pH.

Weak magnetic field significantly enhances methane production from a digester supplemented with zero valent iron

Weak magnetic field (WMF) provided by a magnet was proposed to enhance CH₄ production from a swine manure-fed digester supplemented with micron-sized zero valent iron (ZVI). Compared to the control without ZVI addition and WMF application (R_Control), treatments that included ZVI only (R_ZVI) and coupled WMF with ZVI (R_ZVI/WMF) increased the CH₄ production by 77.0% and 124.5%, respectively. As evidenced by the elevated levels of total soluble iron, WMF apparently promoted the corrosion of ZVI, providing extra H₂ for hydrogenotrophic methanogenesis and creating a more reductive environment to reduce propionic-type fermentation. Microbial analysis results revealed that the relative abundance of Methanothrix (capable of accepting electrons) in R_ZVI/WMF were 75.1% higher than that in R_ZVI. Essentially, WMF application promoted the direct interspecies electron transfer-based methanogenesis by (1) providing more electrons as the direct substrate, and (2) inducing Lorentz force to facilitate the mass transfer between the released electrons and the methanogens.

An electrode-assisted anaerobic digestion process for the production of high-quality biogas

Biogas is a sustainable, renewable energy source generated from organic waste degradation during anaerobic digestion (AD). AD is applied for treating different types of wastewater, mostly containing high organic load. However, AD practice is still limited due to the low quality of the produced biogas. Upgrading biogas to natural gas quality (>90% CH₄) is essential for broad applications. Here, an innovative bio-electrochemically assisted AD process was developed, combining wastewater treatment and biogas upgrading. This process was based on a microbial electrolysis cell (MEC) that produced hydrogen from wastewater at a relatively high efficiency, followed by high-rate anaerobic systems for completing biodegradation of organic matter and an in situ bio-methanation process. Results showed that CH₄ production yield was substantially improved upon coupling of the MEC with the AD system. Interestingly, CH₄ production yield increase was most notable once circulation between AD and MEC was applied, while current density was not markedly affected by the circulation rates. The microbial community analysis confirmed that the MEC enhanced hydrogen production, leading to the enrichment of hydrogenotrophic methanogens. Thus, directing soluble hydrogen from the MEC to AD is plausible, and has great potential for biogas upgrading, avoiding the need for direct hydrogen harvesting.

Growth Characteristics and Thermodynamics of Syntrophic Acetate Oxidizers

Syntrophic acetate oxidation (SAO) plays a pivotal role in biogas production processes when aceticlastic methanogens are inhibited. Despite the importance of SAO, the metabolic interactions and syntrophic growth of the organisms involved are still poorly understood. Therefore, we studied growth parameters and interactions within constructed defined cocultures comprising the methanogen Methanoculleus bourgensis and one, or several, of the syntrophic acetate oxidizers Syntrophaceticus schinkii, [ Clostridium] ultunense, and Tepidanaerobacter acetatoxydans and a novel, uncharacterized bacterium. Cultivation experiments in a design-of-experiment approach revealed positive effects on methane production rate of increased ammonium levels (up to 0.2 M), temperature (up to 45 °C), and acetate concentrations (0.15-0.30 M). Molecular analyses and thermodynamic calculations demonstrated close interlinkages between the microorganisms, with available energies of -10 kJ/mol for acetate oxidation and -20 kJ/mol for hydrogenotrophic methanogenesis. The estimated generation time varied between 3 and 20 days for all syntrophic microorganisms involved, and the acetate minimum threshold level was 0.40-0.45 mM. The rate of methanogenesis depended on the SAO bacteria present in the culture. These data are beneficial for interpretation of SAO prevalence and competiveness against aceticlastic methanogens in anaerobic environments.

Temporal variation in bacterial and methanogenic communities of three full-scale anaerobic digesters treating swine wastewater

To investigate the effects of temporal variations of process parameters on microbial community structures in the two types of full-scale anaerobic digester treating swine wastewater, three full-scale anaerobic digesters were monitored. An anaerobic filter (AF)-type digester located in Gong-Ju (GJ) showed the highest COD removal among three digesters and maintained stable efficiency. A digester in Hong-Seong (HS) was of the same type as it GJ and showed improved efficiency over the sampling period. A continuously stirred tank reactor (CSTR)-type digester in Soon-Cheon (SC) showed decreasing efficiency due to a high residual concentration of VFAs and NH₄⁺. These process efficiencies were closely correlated to the Simpson indices of the methanogenic communities. Genera Bacillus, Methanosaeta, and Methanospirillum that have filamentous morphology were dominant in both AF-type digesters, but genera Acholeplasma, Methanosarcina, and Methanoculleus that have spherical or coccoid morphology were dominantly abundant in the CSTR-type digester. Correlation between populations suggests a possible syntrophic relationship between genera Desulfobulbus and Methanosaeta in digesters GJ and HS.

Enhancing syntrophic associations among Clostridium butyricum, Syntrophomonas and two types of methanogen by zero valent iron in an anaerobic assay with a high organic loading

The impacts of ZVI on microbial community diversity in an anaerobic assay with high organic loading were investigated. The relative abundance of bacteria, archaea, and the functional methyl coenzyme-M reductase (mcrA) gene were investigated using high-throughput sequencing, and variations in their quantity were determined by qPCR. The results showed that ZVI significantly increased both the relative abundance and quantity of Methanobacteriales and Methanosarcinales during hydrogenotrophic and acetoclastic methanogenesis. The relative abundance of syntrophic Methanobacteriales at the hydrolysis and acidogenesis stages resulted in H₂ partial pressure decrease through an interspecies hydrogen transfer (IHT) network, which further induced butyric conversion to acetic by Syntrophomonas. The primary microbial metabolism then converted to acetoclastic methanogensis in the assay with ZVI addition. The short duration of this process and high relative abundance of Syntrophomonas, Clostridium butyricum and Methanosarcinales potentially indicated the existence of a novelty syntrophic mechanism for extracellular electron transfer, which promoted CH₄ generation.

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.

Microbial stress mediated intercellular nanotubes in an anaerobic microbial consortium digesting cellulose

The anaerobic digestion process is a multi - step reaction dependent on concerted activities such as exchange of metabolites among physiologically different microbial communities. This study investigated the impact of iron oxide nanoparticles on the anaerobic sludge microbiota. It was shown there were three distinct microbial phases following addition of the nanoparticles: microbial stress and cell death of approximately one log order of magnitude, followed by microbial rewiring, and recovery. Furthermore, it was noted that cellular stress led to the establishment of intercellular nanotubes within the microbial biomass. Intercellular nanotube - mediated communication among genetically engineered microorganisms and ad hoc assembled co - cultures have been previously reported. This study presents evidence of intercellular nanotube formation within an environmental sample - i.e., anaerobic sludge microbiota subjected to stress. Our observations suggested a mode of microbial communication in the anaerobic digestion process not previously explored and which may have implications on bioreactor design and microbial functions.

Biogas generation in anaerobic wastewater treatment under tetracycline antibiotic pressure

The effect of tetracycline (TC) antibiotic on biogas generation in anaerobic wastewater treatment was studied. A lab-scale Anaerobic Baffled Reactor (ABR) with three compartments was used. The reactor was operated with synthetic wastewater in the absence of TC and in the presence of 250 μg/L TC for 90 days, respectively. The removal rate of TC, volatile fatty acids (VFAs), biogas compositions (hydrogen (H₂), methane (CH₄), carbon dioxide (CO₂)), and total biogas production in each compartment were monitored in the two operational conditions. Results showed that the removal rate of TC was 14.97–67.97% in the reactor. The presence of TC had a large negative effect on CH₄ and CO₂ generation, but appeared to have a positive effect on H₂ production and VFAs accumulation. This response indicated that the methanogenesis process was sensitive to TC presence, but the acidogenesis process was insensitive. This suggested that the presence of TC had less influence on the degradation of organic matter but had a strong influence on biogas generation. Additionally, the decrease of CH₄ and CO₂ generation and the increase of H₂ and VFAs accumulation suggest a promising strategy to help alleviate global warming and improve resource recovery in an environmentally friendly approach.

Methane production improvement by modulation of solid phase immersion in dry batch anaerobic digestion process: Dynamic of methanogen populations

Several 60L dry batch anaerobic digestion (AD) reactors were implemented with or without liquid reserve on cattle manure. The immersed part modulation of cattle manure increased the methane flow of about 13%. The quantitative real time PCR and the optimized DNA extraction were implemented and validated to characterize and quantify the methanogen dynamic in dry batch AD process. Final quantities of methanogens converged toward the same level in several inocula at the end of AD. Methanogen dynamic was shown by dominance of Methanosarcinaceae for acetotrophic methanogens and Methanobacteriales for the hydrogenotrophic methanogens. Overall, methanogens populations were stabilized in liquid phase, except Methanosaetaceae. Solid phase was colonized by Methanomicrobiales and Methanosarcinaceae populations giving a support to biofilm development. The methane increase could be explained by a raise of Methanosarcinaceae population in presence of a total contact between solid and liquid phases. Methanosarcinaceae was a bio-indicator of the methane production.

Performance and microbial community variations in thermophilic anaerobic digesters treating OTC medicated cow manure under different operational conditions

This study aimed to determine the fate and effect of oxytetracycline (OTC) and its metabolites during thermophilic anaerobic digestion of cow manure. OTC-medicated and non-medicated digesters were operated at 55°C with different volatile solids (VS) concentrations (4% and 6%) and mixing rates (90 and 120rpm). OTC and its metabolites were measured by HPLC and LC/MS/MS, respectively. Microbial community dynamics were monitored by denaturing gradient gel electrophoresis (DGGE) and real-time PCR (qPCR). Approximately 2mg/L initial OTC concentration caused 10-30% inhibition on biogas production and higher inhibition was observed as mixing rate increased. DGGE results indicated that OTC caused a shift in bacterial community structure and several species became dominant with time. Archaeal community decreased throughout the digestion period. RNA based qPCR analyses showed that gene copy numbers of bacteria and Methanomicrobiales declined in all digesters whereas gene copy numbers of Methanobacteriales and Methanosarcinales increased in high mixing rate digesters.

Piezo-tolerant natural gas-producing microbes under accumulating pCO2

BACKGROUND

It is known that a part of natural gas is produced by biogenic degradation of organic matter, but the microbial pathways resulting in the formation of pressurized gas fields remain unknown. Autogeneration of biogas pressure of up to 20 bar has been shown to improve the quality of biogas to the level of biogenic natural gas as the fraction of CO₂ decreased. Still, the pCO₂ is higher compared to atmospheric digestion and this may affect the process in several ways. In this work, we investigated the effect of elevated pCO₂ of up to 0.5 MPa on Gibbs free energy, microbial community composition and substrate utilization kinetics in autogenerative high-pressure digestion.

RESULTS

In this study, biogas pressure (up to 2.0 MPa) was batch-wise autogenerated for 268 days at 303 K in an 8-L bioreactor, resulting in a population dominated by archaeal Methanosaeta concilii, Methanobacterium formicicum and Mtb. beijingense and bacterial Kosmotoga-like (31% of total bacterial species), Propioniferax-like (25%) and Treponema-like (12%) species. Related microorganisms have also been detected in gas, oil and abandoned coal-bed reservoirs, where elevated pressure prevails. After 107 days autogeneration of biogas pressure up to 0.50 MPa of pCO₂, propionate accumulated whilst CH₄ formation declined. Alongside the Propioniferax-like organism, a putative propionate producer, increased in relative abundance in the period of propionate accumulation. Complementary experiments showed that specific propionate conversion rates decreased linearly from 30.3 mg g^-1 VS_added day^-1 by more than 90% to 2.2 mg g^-1 VS_added day^-1 after elevating pCO₂ from 0.10 to 0.50 MPa. Neither thermodynamic limitations, especially due to elevated pH₂, nor pH inhibition could sufficiently explain this phenomenon. The reduced propionate conversion could therefore be attributed to reversible CO₂-toxicity.

CONCLUSIONS

The results of this study suggest a generic role of the detected bacterial and archaeal species in biogenic methane formation at elevated pressure. The propionate conversion rate and subsequent methane production rate were inhibited by up to 90% by the accumulating pCO₂ up to 0.5 MPa in the pressure reactor, which opens opportunities for steering carboxylate production using reversible CO₂-toxicity in mixed-culture microbial electrosynthesis and fermentation.Graphical abstractThe role of pCO₂ in steering product formation in autogenerative high pressure digestion.

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.

Dairy manure resource recovery utilizing two-stage anaerobic digestion - Implications of solids fractionation

Dairy manure management is increasingly becoming an environmental challenge. In this regard, manure anaerobic digestion (AD) can be applied to address environmental concerns; however, dairy manure AD remains economically uncompetitive. Ongoing research is focused on enhanced resource recovery from manure, including maximizing AD methane yield through a novel multi-stage AD configuration. Research presented herein centered on the hypothesis that separately digesting fine and coarse solids from fermented dairy manure would improve methane production; the hypothesis was disproven. While maximum methane concentration was realized on fine solids, combined solids AD yielded enhanced VS destruction. The diverse combined-solids substrate enriched for a more heterogeneous bacterial/archaeal consortium that balanced fermentation and methanogenesis to yield maximum product (methane). However, results suggest that targeted AD of the fat-rich fine solids could be a more optimal approach for processing manure; alternate (non-AD) methods could then be applied to extract value from the fibrous fraction.

Improved Monitoring of Semi-Continuous Anaerobic Digestion of Sugarcane Waste: Effects of Increasing Organic Loading Rate on Methanogenic Community Dynamics

The anaerobic digestion of filter cake and its co-digestion with bagasse, and the effect of gradual increase of the organic loading rate (OLR) from start-up to overload were investigated. Understanding the influence of environmental and technical parameters on the development of particular methanogenic pathway in the biogas process was an important aim for the prediction and prevention of process failure. The rapid accumulation of volatile organic acids at high OLR of 3.0 to 4.0 gvs·L⁻¹·day⁻¹ indicated strong process inhibition. Methanogenic community dynamics of the reactors was monitored by stable isotope composition of biogas and molecular biological analysis. A potential shift toward the aceticlastic methanogenesis was observed along with the OLR increase under stable reactor operating conditions. Reactor overloading and process failure were indicated by the tendency to return to a predominance of hydrogenotrophic methanogenesis with rising abundances of the orders Methanobacteriales and Methanomicrobiales and drop of the genus Methanosarcina abundance.

Use of PCR-DGGE based molecular methods to assessment of microbial diversity during anaerobic treatment of antibiotic combinations

As it is currently often not know how anaerobic bioreactors, e.g. for biogas production, react if the substrate is contaminated by toxic compounds like antibiotics. This study evaluated how anaerobic sequencing batch reactors were affected by amendments of different antibiotics and stepwise increasing concentrations. The compositions of microbial community were determined in the seed sludge using 16S rRNA gene clone libraries and PCR-DGGE analyses were used for the detection of microbial community changes upon antibiotics additions. According to PCR-DGGE results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors. Assessment of DGGE data is also useful for suggesting the potential to control ultimate microbial community structure, especially derived from Gram-negative bacteria, through bioaugmentation to successful for antibiotic biodegradation.

Dominant and novel clades of Candidatus Accumulibacter phosphatis in 18 globally distributed full-scale wastewater treatment plants

Here we employed quantitative real-time PCR (qPCR) assays for polyphosphate kinase 1 (ppk1) and 16S rRNA genes to assess relative abundances of dominant clades of Candidatus Accumulibacter phosphatis (referred to Accumulibacter) in 18 globally distributed full-scale wastewater treatment plants (WWTPs) from six countries. Accumulibacter were not only detected in the 6 WWTPs performing biological phosphorus removal, but also inhabited in the other 11 WWTPs employing conventional activated sludge (AS) with abundances ranging from 0.02% to 7.0%. Among the AS samples, clades IIC and IID were found to be dominant among the five Accumulibacter clades. The relative abundance of each clade in the Accumulibacter lineage significantly correlated (p < 0.05) with the influent total phosphorus and chemical oxygen demand instead of geographical factors (e.g. latitude), which showed that the local wastewater characteristics and WWTPs configurations could be more significant to determine the proliferation of Accumulibacter clades in full-scale WWTPs rather than the geographical location. Moreover, two novel Accumulibacter clades (IIH and II-I) which had not been previously detected were discovered in two enhanced biological phosphorus removal (EBPR) WWTPs. The results deepened our understanding of the Accumulibacter diversity in environmental samples.

Application of real-time PCR to determination of combined effect of antibiotics on Bacteria, Methanogenic Archaea, Archaea in anaerobic sequencing batch reactors

This study evaluated the long-term effects of erythromycin-tetracycline-sulfamethoxazole (ETS) and sulfamethoxazole-tetracycline (ST) antibiotic combinations on the microbial community and examined the ways in which these antimicrobials impact the performance of anaerobic reactors. Quantitative real-time PCR was used to determine the effect that different antibiotic combinations had on the total and active Bacteria, Archae and Methanogenic Archae. Three primer sets that targeted metabolic genes encoding formylterahydrofolate synthetase, methyl-coenzyme M reductase and acetyl-coA synthetase were also used to determine the inhibition level on the mRNA expression of the homoacetogens, methanogens and specifically acetoclastic methanogens, respectively. These microorganisms play a vital role in the anaerobic degradation of organic waste and targeting these gene expressions offers operators or someone at a treatment plant the potential to control and the improve the anaerobic system. The results of the investigation revealed that acetogens have a competitive advantage over Archaea in the presence of ETS and ST combinations. Although the efficiency with which methane production takes place and the quantification of microbial populations in both the ETS and ST reactors decreased as antibiotic concentrations increased, the ETS batch reactor performed better than the ST batch reactor. According to the expression of genes results, the syntrophic interaction of acetogens and methanogens is critical to the performance of the ETS and ST reactors. Failure to maintain the stability of these microorganisms resulted in a decrease in the performance and stability of the anaerobic reactors.

Development and validation of a multiplex reverse transcription quantitative PCR (RT-qPCR) assay for the rapid detection of Citrus tristeza virus, Citrus psorosis virus, and Citrus leaf blotch virus

A single real-time multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay for the simultaneous detection of Citrus tristeza virus (CTV), Citrus psorosis virus (CPsV), and Citrus leaf blotch virus (CLBV) was developed and validated using three different fluorescently labeled minor groove binding qPCR probes. To increase the detection reliability, coat protein (CP) genes from large number of different isolates of CTV, CPsV and CLBV were sequenced and a multiple sequence alignment was generated with corresponding CP sequences from the GenBank and a robust multiplex RT-qPCR assay was designed. The capacity of the multiplex RT-qPCR assay in detecting the viruses was compared to singleplex RT-qPCR designed specifically for each virus and was assessed using multiple virus isolates from diverse geographical regions and citrus species as well as graft-inoculated citrus plants infected with various combination of the three viruses. No significant difference in detection limits was found and specificity was not affected by the inclusion of the three assays in a multiplex RT-qPCR reaction. Comparison of the viral load for each virus using singleplex and multiplex RT-qPCR assays, revealed no significant differences between the two assays in virus detection. No significant difference in Cq values was detected when using one-step and two-step multiplex RT-qPCR detection formats. Optimizing the RNA extraction technique for citrus tissues and testing the quality of the extracted RNA using RT-qPCR targeting the cytochrome oxidase citrus gene as an RNA specific internal control proved to generate better diagnostic assays. Results showed that the developed multiplex RT-qPCR can streamline viruses testing of citrus nursery stock by replacing three separate singleplex assays, thus reducing time and labor while retaining the same sensitivity and specificity. The three targeted RNA viruses are regulated pathogens for California's mandatory "Section 3701: Citrus Nursery Stock Pest Cleanliness Program". Adopting a compatible multiplex RT-qPCR testing protocol for these viruses as well as other RNA and DNA regulated pathogens will provide a valuable alternative tool for virus detection and efficient program implementation.

Optimization of volatile fatty acids and hydrogen production from Saccharina japonica: acidogenesis and molecular analysis of the resulting microbial communities

Response surface methodology (RSM) was used to optimize the production of volatile fatty acids (VFAs) and hydrogen from mixed anaerobic cultures of Saccharina japonica with respect to two independent variables: methanogenic inhibitor concentration and temperature. The effects of four methanogenic inhibitors on acidogenic processes were tested, and qualitative microbial analyses were carried out. Escherichia, Acinetobacter, and Clostridium were the most predominant genera in samples treated with chloroform (CHCl3), iodoform (CHI3), 2-bromoethanesulfonate (BES), or β-cyclodextrin (β-CD), respectively. RSM showed that the production of VFAs reached a peak of 12.5 g/L at 38.6 °C in the presence of 7.4 g/L β-CD; these were the conditions under which hydrogen production was also nearly maximal. The quantitative polymerase chain reaction (qPCR) showed that shifts in the bacterial community population correlated with the concentrations of β-CD indicating that this compound effectively inhibited methanogens.

Absolute quantification of individual biomass concentrations in a methanogenic coculture

Identification of individual biomass concentrations is a crucial step towards an improved understanding of anaerobic digestion processes and mixed microbial conversions in general. The knowledge of individual biomass concentrations allows for the calculation of biomass specific conversion rates which form the basis of anaerobic digestion models. Only few attempts addressed the absolute quantification of individual biomass concentrations in methanogenic microbial ecosystems which has so far impaired the calculation of biomass specific conversion rates and thus model validation. This study proposes a quantitative PCR (qPCR) approach for the direct determination of individual biomass concentrations in methanogenic microbial associations by correlating the native qPCR signal (cycle threshold, Ct) to individual biomass concentrations (mg dry matter/L). Unlike existing methods, the proposed approach circumvents error-prone conversion factors that are typically used to convert gene copy numbers or cell concentrations into actual biomass concentrations. The newly developed method was assessed and deemed suitable for the determination of individual biomass concentrations in a defined coculture of Desulfovibrio sp. G11 and Methanospirillum hungatei JF1. The obtained calibration curves showed high accuracy, indicating that the new approach is well suited for any engineering applications where the knowledge of individual biomass concentrations is required.

Microbial examination of anaerobic sludge adaptation to animal slurry

The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

Microbial ecology of anaerobic digesters: the key players of anaerobiosis

Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO₂. The conversions of complex organic compounds to CH₄ and CO₂ are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed.

The use of agricultural substrates to improve methane yield in anaerobic co-digestion with pig slurry: effect of substrate type and inclusion level

Anaerobic co-digestion of pig slurry with four agricultural substrates (tomato, pepper, persimmon and peach) was investigated. Each agricultural substrate was tested in co-digestion with pig slurry at four inclusion levels: 0%, 15%, 30% and 50%. Inclusion levels consisted in the replacement of the volatile solids (VS) from the pig slurry with the VS from the agricultural substrate. The effect of substrate type and inclusion level on the biochemical methane potential (BMP) was evaluated in a batch assay performed at 35 °C for 100 days. Agricultural substrate's chemical composition was also analyzed and related with BMP. Additionally, Bacteria and Archaea domains together with the four main methanogenic archaeal orders were quantified using quantitative real-time TaqMan polymerase chain reaction (qPCR) at the end of the experiment to determine the influence of agricultural substrate on sludge's microbial composition. Results showed that vegetable substrates (pepper and tomato) had higher lipid and protein content and lower carbohydrates than fruit substrates (persimmon and peach). Among substrates, vegetable substrates showed higher BMP than fruit substrates. Higher BMP values were obtained with increasing addition of agricultural substrate. The replacement of 50% of VS from pig slurry by tomato and pepper increased BMP in 41% and 44%, respectively compared with pig slurry only. Lower increments in BMP were achieved with lower inclusion levels. Results from qPCR showed that total bacteria and total archaea gene concentrations were similar in all combinations tested. Methanomicrobiales gene concentrations dominated over the rest of individual archaeal orders.

Microbial diversity and dynamics during methane production from municipal solid waste

The objectives of this study were to characterize development of bacterial and archaeal populations during biodegradation of municipal solid waste (MSW) and to link specific methanogens to methane generation. Experiments were conducted in three 0.61-m-diameter by 0.90-m-tall laboratory reactors to simulate MSW bioreactor landfills. Pyrosequencing of 16S rRNA genes was used to characterize microbial communities in both leachate and solid waste. Microbial assemblages in effluent leachate were similar between reactors during peak methane generation. Specific groups within the Bacteroidetes and Thermatogae phyla were present in all samples and were particularly abundant during peak methane generation. Microbial communities were not similar in leachate and solid fractions assayed at the end of reactor operation; solid waste contained a more abundant bacterial community of cellulose-degrading organisms (e.g., Firmicutes). Specific methanogen populations were assessed using quantitative polymerase chain reaction. Methanomicrobiales, Methanosarcinaceae, and Methanobacteriales were the predominant methanogens in all reactors, with Methanomicrobiales consistently the most abundant. Methanogen growth phases coincided with accelerated methane production, and cumulative methane yield increased with increasing total methanogen abundance. The difference in methanogen populations and corresponding methane yield is attributed to different initial cellulose and hemicellulose contents of the MSW. Higher initial cellulose and hemicellulose contents supported growth of larger methanogen populations that resulted in higher methane yield.

Primer evaluation and adaption for cost-efficient SYBR Green-based qPCR and its applicability for specific quantification of methanogens

In the present study nine promising primer sets, targeting Archaea and methanogenic Archaea in particular, were evaluated in silico, in vitro and in situ concerning specificity, accuracy and applicability in end-point (ep-) and especially quantitative (q-)PCR research. The main goal was to adapt and evaluate already adapted primer sets, which were partially designed in combination with TaqMan probes, in substantially cheaper SYBR Green-based qPCR applications. An initial 16S rRNA gene bank-based in silico evaluation revealed high coverage potentials for all primers within targeted groups, ranging from 71 to 90%, except the Methanosaeta specific set showing a low potential of 37%. Mentionable cross-reacting potentials could be detected for the Methanothermobacter, Methanomicrobiales and Methanoculleus sets. The in vitro evaluation with selected reference organisms revealed a specific behavior for most primer sets, while the Methanosarcina and Methanothermobacter sets showed most problematic cross-reactions in epPCR application. We were able to show that primers for detecting the total archaeal community, methanogenic orders Methanosarcinales, Methanobacteriales, Methanococcales and the genus Methanoculleus performed in a highly specific way and allowed an accurate quantification of targeted organisms without the use of expensive TaqMan probes. However, primer pairs designed for detecting Methanomicrobiales, Methanothermobacter, Methanosarcina and Methanosaeta are not suitable for SYBR Green applications. The reliability of in situ quantifications was assessed for a typical methanogenic community, derived from a thermophilic fermenter, and confirmed via denaturing gradient gel band quantification and sequencing. Thereby, we revealed high abundances of methanogenic Archaea, mainly comprising Methanoculleus and Methanosarcinales, while Methanobacteriales only formed a minor fraction.

Monitoring methanogenic population dynamics in a full-scale anaerobic digester to facilitate operational management

Microbial populations in a full-scale anaerobic digester fed on food waste were monitored over an 18-month period using qPCR. The digester exhibited a highly dynamic environment in which methanogenic populations changed constantly in response to availability of substrates and inhibitors. The methanogenic population in the digester was dominated by Methanosaetaceae, suggesting that aceticlastic methanogenesis was the main route for the production of methane. Sudden losses (69%) in Methanosaetaceae were followed by a build-up of VFAs which were subsequently consumed when populations recovered. A build up of ammonium inhibited Methanosaetaceae and resulted in shifts from acetate to hydrogen utilization. Addition of trace elements and alkalinity when propionate levels were high stimulated microbial growth. Routine monitoring of microbial populations and VFAs provided valuable insights into the complex processes occurring within the digester and could be used to predict digester stability and facilitate digester optimization.