Methanoculleus spp. as a biomarker of methanogenic activity in swine manure storage tanks

Anaerobic co-biodegradation of polyhydroxyalkanoate and swine manure for volatile fatty acid production: The impact of C/N ratios and microbial dynamics

Polyhydroxyalkanoate (PHA) is the important biodegradable plastic, however, biodegradation of PHA waste in anaerobic environments emits more CH4, a potent greenhouse gas. Bioconversion of PHA waste to useful byproducts - volatile fatty acids (VFAs) is a practical method to upcycle carbon from PHA. In this study, PHA waste was anaerobically co-digested with swine manure (SM) (the typical high nitrogen waste) at different C/N ratios. The results indicate that co-digestion of PHA and SM with a C/N ratio of 32.1 achieved VFA production of 5488 mg COD/L and 0.20 g COD/g VS. No significant differences were found in terms of the highest VFA concentrations between treatments with C/N ratios of 43.4 and 32.1. VFA produciton of 3655 mg COD/L and 0.14 g COD/g VS was achieved at 19 days by adjusting the C/N ratio to 19.2. Four bacteria were identified as dominant microorganisms responsible for converting PHA and SM to VFA.

Mechanistic insights into synergistic facilitation of copper/zinc ions and dewatered swine manure-derived biochar on anaerobic digestion of swine wastewater

Biochar-assisted anaerobic digestion (AD) has been proposed an advanced system for swine wastewater (SW) management. However, the effects of metallic nutrients in SW, such as copper/zinc ions (Cu2+/Zn2+), on the biochar-assisted AD of SW are not well understood. This study investigated the influences of individual Cu2+/Zn2+ or dewatered swine manure-derived biochar, as well as their combined additions, on the AD of SW. The results showed that exposure to 50 mg/L Cu2+/Zn2+ temporary inhibited methane production, but the addition of 20 g/L biochar alleviated this inhibition by shortening the methanogenic lag time and increasing methane yield. Following a period of acclimation, both Cu2+/Zn2+ and biochar promoted methane production, although metagenomic analysis revealed distinct mechanisms underlying their promotion. Cu2+/Zn2+ enhanced ATP processing, including electron exchange between NADH/NAD+ and succinate/fumarate transformation, by 26.0-35.8%. Additionally, the gene encoding Coenzyme M methylation was upregulated by 36.2% along with enrichments of Methanocullus and Methanosarcina, contributing to accelerated hydrolysis and methanogenesis rates by 54.7% and 44.8%, respectively. On the other hand, biochar mainly stimulated bacterial F-type ATPase activities by 28.4%, likely facilitating direct interspecies electron transfer between Geobacter and Methanosarcina for syntrophic methanogenesis. The combined addition of Cu2+/Zn2+ and biochar resulted in "win-win" benefits, significantly increasing the maximum methane production rate from 40.3 mL CH4/d to 53.7 mL CH4/d. Moreover, the introduction of biochar into AD of SW facilitated the transformation of more Cu2+/Zn2+ from a reducible Fe-Mn oxides form to a residual form, which potentially reduced the metallic toxicity of the digestate for soil amendment. The findings of this study provide novel insights into understanding the synergistic impacts of heavy metals and biochar in regulating SW during AD, as well as the management of associated digestate.

Patterns of syntrophic interactions in methanogenic conversion of propionate

Methanogenesis is central to anaerobic digestion processes. The conversion of propionate as a key intermediate for methanogenesis requires syntrophic interactions between bacterial and archaeal partners. In this study, a series of methanogenic enrichments with propionate as the sole substrate were developed to identify microbial populations specifically involved in syntrophic propionate conversion. These rigorously controlled propionate enrichments exhibited functional stability with consistent propionate conversion and methane production; yet, the methanogenic microbial communities experienced substantial temporal dynamics, which has important implications on the understanding of mechanisms involved in microbial community assembly in anaerobic digestion. Syntrophobacter was identified as the most abundant and consistent bacterial partner in syntrophic propionate conversion regardless of the origin of the source culture, the concentration of propionate, or the temporal dynamics of the culture. In contrast, the methanogen partners involved in syntrophic propionate conversion lacked consistency, as the dominant methanogens varied as a function of process condition and temporal dynamics. Methanoculleus populations were specifically enriched as the syntrophic partner at inhibitory levels of propionate, likely due to the ability to function under unfavorable environmental conditions. Syntrophic propionate conversion was carried out exclusively via transformation of propionate into acetate and hydrogen in enrichments established in this study. Microbial populations highly tolerant of elevated propionate, represented by Syntrophobacter and Methanoculleus, are of great significance in understanding methanogenic activities during process perturbations when propionate accumulation is frequently encountered. Key points • Syntrophobacter was the most consistent bacterial partner in propionate metabolism. • Diverse hydrogenotrophic methanogen populations could serve as syntrophic partners. • Methanoculleus emerged as a methanogen partner tolerant of elevated propionate.

Enteric and Fecal Methane Emissions from Dairy Cows Fed Grass or Corn Silage Diets Supplemented with Rapeseed Oil

Simple Summary

In this study, we evaluated methane emissions from dairy cows fed grass or corn silage diets supplemented with rapeseed oil. Enteric methane emissions decreased on adding rapeseed oil to the diet, but methane emissions from feces of dairy cows fed diets supplemented with rapeseed oil did not differ. Thus, no trade-offs were observed between enteric and fecal methane emissions due to forage type or addition of rapeseed oil to diets fed to Swedish dairy cows.

Abstract

This study evaluated potential trade-offs between enteric methane (CH₄) emissions and CH₄ emissions from feces of dairy cows fed grass silage or partial replacement of grass silage with corn silage, both with and without supplementation of rapeseed oil. Measured data for eight dairy cows (two blocks) included in a production trial were analyzed. Dietary treatments were grass silage (GS), GS supplemented with rapeseed oil (GS-RSO), GS plus corn silage (GSCS), and GSCS supplemented with rapeseed oil (GSCS-RSO). Feces samples were collected after each period and incubated for nine weeks to estimate fecal CH₄ emissions. Including RSO (0.5 kg/d) in the diet decreased dry matter intake (DMI) by 1.75 kg/d. Enteric CH₄ emissions were reduced by inclusion of RSO in the diet (on average 473 vs. 607 L/d). In 9-week incubations, there was a trend for lower CH₄ emissions from feces of cows fed diets supplemented with RSO (on average 3.45 L/kg DM) than cows with diets not supplemented with RSO (3.84 L/kg DM). Total CH₄ emissions (enteric + feces, L/d) were significantly lower for the cows fed diets supplemented with RSO. Total fecal CH₄ emissions were similar between treatments, indicating no trade-offs between enteric and fecal CH₄ emissions.

The combination of nutraceuticals and functional feeds as additives modulates gut microbiota and blood markers associated with immune response and health in weanling piglets

This study aimed to evaluate the effects of a combination of feed additives with complementary functional properties on the intestinal microbiota, homocysteine, and vitamins E and B status as well as systemic immune response of weanling piglets. At weaning, 32 litters were assigned to one of the following dietary treatments (DT): 1) conventional diet (CTRL); 2) CTRL diet supplemented with antibiotics (ATB); 3) a cocktail of feed additives containing cranberry extract, encapsulated carvacrol, yeast-derived products, and extra vitamins A, D, E, and B complex (CKTL); or 4) CKTL diet with bovine colostrum in replacement of plasma proteins (CKTL + COL). Within each litter, the piglets with lowest and highest birth weights (LBW and HBW, respectively) and two piglets of medium birth weight (MBW) were identified. The MBW piglets were euthanized at 42 d of age in order to characterize the ileal and colonic microbiota. Blood samples were also collected at weaning and at 42 d of age from LBW and HBW piglets to measure insulin-like growth factor-1 (IGF-1), cysteine, homocysteine, and vitamins E, B₆, and B₁₂, and to characterize the leukocyte populations. At 42 d of age, cytokine production by stimulated peripheral blood mononuclear cells was also measured. In a second experiment, piglets were reared under commercial conditions to evaluate the effects of the DT on the growth performance. At the indicator species analysis, the highest indicator value (IV) for Succinivibrio dextrinosolvens was found in the CKTL group, whereas the highest IV for Lactobacillus reuteri and Faecalibacterium prausnitzii was evidenced in the CKTL + COL group (P < 0.05). Compared with the other DT, CTRL piglets had higher concentrations of homocysteine, whereas the CKTL and CKTL + COL supplementations increased the concentrations of vitamins E and B₁₂ (P < 0.05). DT had no effect on IGF-1 concentration and on blood leukocytes populations; however, compared with HBW piglets, LBW animals had lower values of IGF-1, whereas the percentages of γδ T lymphocytes and T helper were decreased and increased, respectively (P < 0.05). CKTL + COL also improved the growth performance of piglets reared under commercial conditions (P < 0.05). This study highlights the impact of birth weight on piglet systemic immune defenses and the potential of weaning diet supplemented with feed additives and bovine colostrum to modulate the homocysteine metabolism and the intestinal microbiota.

Does overwintering change the inoculum effect on methane emissions from stored liquid manure?

Greenhouse gas (GHG) emissions, especially methane (CH₄ ), from manure storage facilities can be substantial. Methane production requires adapted microbial communities ("inoculum") to be present in the manure. Complete removal of liquid dairy manure (thus removing all inoculum) from storage tanks in the spring has been shown to significantly reduce CH₄ emissions over the following warm season. This study examined whether the same mitigation effect would occur after fall removal of liquid dairy manure. Emissions of CH₄ , nitrous oxide (N₂ O), ammonia (NH₃ ), and CO₂ were measured from six 11.88-m³ tanks equipped with flow-through chambers. There were three inoculated controls (20% inoculum) and three uninoculated treatments, where inoculum was completely removed in the fall/winter (0% inoculum). Direct N₂ O and NH₃ (indirect N₂ O) were minor contributors to the total GHG budget, contributing <2% on a CO₂ equivalent (CO₂ e) basis. Removal of inoculum led to a 34% decrease in total emissions on a CO₂ e basis and to a 29% decrease in the CH₄ conversion factor compared with the inoculated control (0.37 vs. 0.52; p = .01). Overall, removing inoculum in the fall reduced CH₄ emissions from manure storage tanks; however, fall inoculum removal was less effective than in a previous study where inoculum was removed in the spring. The timing of inoculum removal may affect the efficiency of this CH₄ mitigation strategy. However, this method may be impractical for larger manure storage tanks. Further study is required to overcome challenges of time-sensitive, complete inoculum removal from farm-scale storage tanks.

Enhancing hydrogenotrophic activities by zero-valent iron addition as an effective method to improve sulfadiazine removal during anaerobic digestion of swine manure

In this study, the feasibility of Fe⁰ addition for driving sulfadiazine (SDZ) removal during anaerobic digestion of swine manure (SM) was tested. Compared with the Fe⁰-free digesters spiked with 200 mg/L SDZ (R_SDZ), treatments with 5.0 g/L Fe⁰ (R_SDZ/Fe⁰) significantly accelerated and optimized the acidification process by enriching Clostridia and Bacteroidia (key members responsible for VFAs/H₂ production), providing more readily available substrates for methanogenesis. Furthermore, Fe⁰ increased the overall abundance of hydrogenotrophic methanogens, specifically toxicant resistant Methanoculleus and Methanosphaera spp. were selectively enriched, helping achieve a 36.9% higher CH₄ yield and a 26.4% greater total solids removal efficiency. A positive correlation between the solid content and the SDZ concentration adsorbed in SM was observed. The addition of Fe⁰ increased the distribution of SDZ in liquid and facilitated its removal through the enhanced biodegradation and physicochemical processes. Overall, the total SDZ removal efficiency was improved by 86.8% with Fe⁰.

Anaerobic digestion of aqueous phase from pyrolysis of biomass: Reducing toxicity and improving microbial tolerance

Among the products of pyrolysis is an aqueous phase (AP), which contains a significant fraction of carbon but is too dilute to make recovery of this organic content cost-effectively. This study was to explore the use of AP for anaerobic digestion. Different treatment methods including overliming, Fenton's reagent oxidation, bleaching and activated carbon adsorption were investigated to reduce toxicity of AP. Overliming treatment increased biogas production up to 32-fold compared to non-treated AP. Enhancing the tolerance of the bacterial and archaeal community to the AP toxicity was also attempted with a directed evolution method, resulting the microbes' tolerance to AP from 5% to 14%. Directed evolution resulted a major bacterial taxa as Cloacimonetes, Firmicutes, and Chloroflexi, while shifted the predominant archaea shifted from acetoclastic to hydrogenotrophic methanogens. Collectively, the results demonstrated that combining feedstock treatment and directed evolution of the microbial community is an effective way for AP anaerobic digestion.

Methane emissions of manure from dairy cows fed red clover- or corn silage-based diets supplemented with linseed oil

The objective of this study was to investigate the effects of forage source (red clover silage: RCS vs. corn silage: CS) and diet supplementation with linseed oil (LO) on CH₄ emissions of manure from dairy cows. For this purpose, 12 lactating cows were used in a 2 × 2 factorial arrangement of treatments. Cows were fed (ad libitum) RCS- or CS-based diets (forage:concentrate ratio 60:40; dry matter basis) without or with LO addition (4% dry matter). Feces and urine were collected from each cow and mixed with residual sludge obtained from a manure storage structure. Manure was incubated for 17 wk at 20°C under anaerobic conditions (O₂-free N₂) in 500-mL glass bottles. Methane emissions and changes in chemical composition of the manure were monitored during the entire incubation period. The total amount of feces and urine excreted by cows was not affected by dietary treatments and averaged 6.6 kg/d of volatile solids (VS). Compared with manure from cows fed RCS-based diets, maximum CH₄ production potential of manure from cows fed CS-based diets was 54% higher (182 vs. 118 L/kg of VS) throughout the incubation period. Maximum CH₄ production potential from manure also increased (by 17%) when cows were fed LO-supplemented diets compared with those fed nonsupplemented diets. Similar to maximum CH₄ production potential, VS degraded during incubation (i.e., VS loss) was higher from manure from cows fed CS-based diets versus cows fed RCS-based diets (30.6 vs. 22.5%), and increased (+3 percentage units, on average) with the addition of LO to the diets. Ammonia concentration in manure was higher when cows were fed CS-based diets compared with RCS-based diets, and declined with LO supplementation to CS and RCS diets. It is concluded that both dietary forage source and fat supplementation affect maximum CH₄ production potential from manure and this should be taken into account when such dietary options are recommended to mitigate enteric CH₄ emissions from dairy cows.

Microbial community dynamics in anaerobic digesters treating conventional and vacuum toilet flushed blackwater

Decentralized wastewater treatment represents a promising sustainable option for future wastewater management. Blackwater collected from toilets contains high concentrations of organic matter, ideal for energy recovery using anaerobic digestion. Up-flow anaerobic sludge blanket (UASB) reactors treating conventional toilet (CT, 9 L water per flush) and vacuum toilet (VT, 1 L water per flush) blackwater with increments of loadings were successfully operated to steady state in three phases. The organic loading rates were maintained at comparable levels between the two reactors. The methanisation rates were 0.23-0.29 and 0.41-0.48 gCH₄-COD/gfeedCOD in the CT and VT reactors, and the COD removal rates were 72% and 89%, respectively. The enriched microbial consortia and the community dynamics under different loading phases were compared. The rank abundance distributions and alpha-diversity showed that archaeal communities were predominated by mono-enrichments in both CT and VT reactors, while bacterial communities showed lower diversity in the VT reactor. Through principal coordinates analysis (beta-diversity), clear divergences of archaeal and bacterial communities between the CT and VT reactors were revealed, and the archaeal community developed at a slower rate than the bacterial community. The enriched archaea were hydrogenotrophic methanogens, Methanolinea in the CT reactor (56.6%), and Methanogenium in the VT reactor (62.3%). The enriched bacteria were Porphyromonadaceae in both CT (15.9%) and VT (13.4%) reactors, sulfate-reducing bacteria in the CT reactor, and Fibrobacteraceae in the VT reactor (13.8%). Links between enriched consortia and ammonia stress were discussed. Isotope fraction analysis of the biogas showed a slight shift from acetoclastic methanogenesis to hydrogenotrophic methanogenesis. A closer look into the predicted metagenomic functional profiles showed agreeing results, where hydrogenotrophic methanogenesis and fhs gene abundances were higher in the VT reactor. We demonstrated that different blackwater types enriched different microbial consortia, probably due to ammonia concentrations and sulfate loadings, which should be taken into consideration for practical applications.

Effects of tylosin, ciprofloxacin, and sulfadimidine on mcrA gene abundance and the methanogen community during anaerobic digestion of cattle manure

This study evaluated how tylosin (TYL), ciprofloxacin (CIP), and sulfadimidine (SM₂) affected biogas and CH₄ production during anaerobic digestion (AD) via their effects on the key genes related to methane production and the methanogenic community. The results showed that TYL, CIP, and SM₂ reduced the production of methane during AD by 7.5%, 21.9%, and 16.0%, respectively. After AD for five days, CIP strongly inhibited the mcrA gene, where its abundance was 49% less than that in the control. TYL and SM₂ decreased the abundances of Spirochaeta and Fibrobacteres during AD. High-throughput sequencing identified 10 methanogen genera, where Methanocorpusculum, Methanobrevibacter, and Methanosarcina accounted for 99.1% of the total archaeal reads. TYL and SM₂ increased the efficiency of the acetoclastic methanogen pathway (Methanosarcina) by 29.04% and 52.79%, respectively. Redundancy analysis showed that Spirochaeta, Fibrobacteres, and Methanosarcina had positive correlations with CH₄ and mcrA. We found that 30 mg kg^-1 CIP had a strong inhibitory effect on methane production by influencing the abundances of Methanobrevibacter and Methanosarcina during AD.

Impact of seasonal temperature transition, alkalinity and other abiotic factors on the persistence of viruses in swine and dairy manures

Animal manures are a valued source of nutrients for crop production. They frequently do, however, contain zoonotic pathogens including a wide range of viruses. Ideally, manures would be treated prior to land application, reducing the burden of zoonotic viruses, and thus the potential for transmission to adjacent water resources or crops intended for human or animal consumption. In the present study, manure was obtained from four dairy and three swine farms. The manure was incubated anaerobically in the laboratory for 28 weeks at temperatures ranging from 4 to 25 °C, and multiple physical and chemical parameters were monitored. The abundance of various DNA and RNA viruses was measured throughout the incubation by amplifying virus-specific gene targets. A combination of statistical analyses were applied to identify whether the viruses are significantly impacted by temperature transition or affected by other abiotic factors. Temperature had no effect on the persistence of any of the viruses studied. An increase in pH of the manures during the incubation was significantly (P < 0.05) associated with decreased persistence, suggesting that pH manipulation during storage could reduce the abundance of viruses.

Exploring the roles of and interactions among microbes in dry co-digestion of food waste and pig manure using high-throughput 16S rRNA gene amplicon sequencing

BACKGROUND

With the increasing global population and increasing demand for food, the generation of food waste and animal manure increases. Anaerobic digestion is one of the best available technologies for food waste and pig manure management by producing methane-rich biogas. Dry co-digestion of food waste and pig manure can significantly reduce the reactor volume, capital cost, heating energy consumption and the cost of digestate liquid management. It is advantageous over mono-digestion of food waste or pig manure due to the balanced carbon/nitrogen ratio, high pH buffering capacity, and provision of trace elements. However, few studies have been carried out to study the roles of and interactions among microbes in dry anaerobic co-digestion systems. Therefore, this study aimed to assess the effects of different inocula (finished digestate and anaerobic sludge taken from wastewater treatment plants) and substrate compositions (food waste to pig manure ratios of 50:50 and 75:25 in terms of volatile solids) on the microbial community structure in food waste and pig manure dry co-digestion systems, and to examine the possible roles of the previously poorly described bacteria and the interactions among dry co-digestion-associated microbes.

RESULTS

The dry co-digestion experiment lasted for 120 days. The microbial profile during different anaerobic digestion stages was explored using high-throughput 16S rRNA gene amplicon sequencing. It was found that the inoculum factor was more significant in determining the microbial community structure than the substrate composition factor. Significant correlation was observed between the relative abundance of specific microbial taxa and digesters' physicochemical parameters. Hydrogenotrophic methanogens dominated in dry co-digestion systems.

CONCLUSIONS

The possible roles of specific microbial taxa were explored by correlation analysis, which were consistent with the literature. Based on this, the anaerobic digestion-associated roles of 11 bacteria, which were previously poorly understood, were estimated here for the first time. The inoculum played a more important role in determining the microbial community structure than substrate composition in dry co-digestion systems. Hydrogenotrophic methanogenesis was a significant methane production pathway in dry co-digestion systems.

Inhibition of volatile fatty acids on methane production kinetics during dry co-digestion of food waste and pig manure

Compared with wet digestion, dry digestion of organic wastes reduces reactor volume and requires less energy for heating, but it is easily inhibited by high volatile fatty acid (VFA) or ammonia concentration. The inhibition on methane production kinetics during dry co-digestion of food waste and pig manure is rarely reported. The aim of this study was to explore the inhibition mechanisms and the microbial interactions in food waste and pig manure dry co-digestion systems at different inoculum rates (25% and 50% based on volatile solids) and food waste/pig manure ratios (0:100, 25:75, 50:50, 75:25 and 100:0 based on volatile solids). The results showed that the preferable operation conditions were obtained at the inoculum rate of 50% and food waste/pig manure ratio of 50:50, with a specific methane yield of 263 mL/g VS_added. High VFA concentration was the main inhibition factor on methane production, and the threshold VFA inhibition concentrations ranged 16.5-18.0 g/L. Syntrophic oxidation with hydrogenotrophic methanogenesis might be the main methane production pathway in dry co-digestion systems due to the dominance of hydrogenotrophic methanogens in the archaeal community. In conclusion, dry co-digestion of food waste and pig manure is feasible for methane production without pH adjustment and can be operated stably by choosing proper operation conditions.

Pre-treatment and inoculum affect the microbial community structure and enhance the biogas reactor performance in a pilot-scale biodigestion of municipal solid waste

During anaerobic digestion of municipal solid waste, organic matter is converted to methane, carbon dioxide, and other organic and inorganic compounds through a complex cooperation among different microbial groups with different metabolic activities. Here, culture-dependent and independent approaches provided evidence for examining the relationship between bacterial and archaeal communities and methane production in a pilot-scale anaerobic digestion. The abundance of aerobic and anaerobic functional groups of C and N cycles, such as cellulolytic, pectinolytic, amylolytic and proteolytic bacteria, was high at the beginning of the experiment and was drastically decreased after anaerobic digestion. In contrast, the ammonifiers increased in the biogas producing reactors in a higher pH environment. The methanogenic archaeal genera recovered were Methanobrevibacter, Methanobacterium, Methanoculleus and Methanocorpusculum, thus indicating that methane was formed primarily by the hydrogenotrophic pathway in the reactors. Moreover, the mechanical pretreatment effects, as well as the effect of pelleted manure as inoculum, were considered. The highest methane production was detected in the biodigesters with minced organic waste, thus indicating that pre-treatment of a heterogeneous starting matrix was essential for improving biogas production and stabilizing the process.

Growth performance of piglets during the first two weeks of lactation affects the development of the intestinal microbiota

The aim of this study was to evaluate the effect of newborn piglet weight gain during the first 2 weeks of lactation on the luminal and mucosal microbiota of the ileum and colon. The microbiota from high-weight-gain (HWG) and low-weight-gain (LWG) 2-week-old piglets was characterized by amplicon length heterogeneity PCR (LH-PCR) and compared using diversity indices and multivariate statistical analyses. At birth, LWG piglets weighted in average 0.26 kg less than HWG piglets (p = .002). The weight difference between LWG and HWG piglets increased with time and reached 2.1 kg after 16 days of lactation (p < .0001). Based on these growth performance differences, estimated colostrum and milk intake was greater in HWG than in LWG piglets (p < .0001). Analysis of the LH-PCR data of the microbiota using non-metric multidimensional scaling (NMS) and blocked multiresponse permutation procedure (MRBP) revealed that the microbiota of the HWG and LWG piglets tended to differ in ileal mucosa (p = .097) and differed in colonic lumen (p = .024). The microbiota of HWG piglets had higher levels of Bacteroidetes, Bacteroides and Ruminoccocaceae, and lower proportions of Actinobacillus porcinus and Lactobacillus amylovorus when compared with those of LWG piglets. As the weight gain of nursing piglets is highly correlated with the amount of ingested colostrum and milk, the results strongly suggest that colostrum and milk intake in the first 2 weeks of life influenced the development of the gut microbiota.

Identifying methanogen community structures and their correlations with performance parameters in four full-scale anaerobic sludge digesters

Four full-scale mesophilic anaerobic digesters treating waste sludge were monitored to characterize methanogen communities and their relationship with process parameters. The performance of the four digesters were dissimilar with the average chemical oxygen demand removal efficiencies between 24 and 45% and differing pH. Real-time quantitative PCR showed that archaeal 16S rRNA gene concentration ([ARC]) and, more pronouncedly, its ratio to bacterial counterpart ([ARC]/[BAC]) correlated positively with the performance parameters, including the lipid removal efficiency. Pyrosequencing identified 12 methanogen genera, of which Methanolinea, Methansaeta, and Methanospirillum collectively accounted for 79.2% of total archaeal reads. However, Methanoculleus, a numerically minor (1.9±2.6%) taxa, was the most promising biomarker for positive performance, while Methanoregula was abundant in samples with poor performance. These results could be useful for the control and management of anaerobic sludge digestion.

High rate manure supernatant digestion

The study shows that high rate anaerobic digestion may be an efficient way to obtain sustainable energy recovery from slurries such as pig manure. High process capacity and robustness to 5% daily load increases are observed in the 370 mL sludge bed AD reactors investigated. The supernatant from partly settled, stored pig manure was fed at rates giving hydraulic retention times, HRT, gradually decreased from 42 to 1.7 h imposing a maximum organic load of 400 g COD L(-1) reactor d(-1). The reactors reached a biogas production rate of 97 g COD L(-1) reactor d(-1) at the highest load at which process stress signs were apparent. The yield was ∼0.47 g COD methane g(-1) CODT feed at HRT above 17 h, gradually decreasing to 0.24 at the lowest HRT (0.166 NL CH4 g(-1) CODT feed decreasing to 0.086). Reactor pH was innately stable at 8.0 ± 0.1 at all HRTs with alkalinity between 9 and 11 g L(-1). The first stress symptom occurred as reduced methane yield when HRT dropped below 17 h. When HRT dropped below 4 h the propionate removal stopped. The yield from acetate removal was constant at 0.17 g COD acetate removed per g CODT substrate. This robust methanogenesis implies that pig manure supernatant, and probably other similar slurries, can be digested for methane production in compact and effective sludge bed reactors. Denaturing gradient gel electrophoresis (DGGE) analysis indicated a relatively fast adaptation of the microbial communities to manure and implies that non-adapted granular sludge can be used to start such sludge bed bioreactors.

Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

Sequestration of CO₂ in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO₂ building up and also for the in situ potential bioconversion of stored CO₂ to methane. However, the information on these functional microbial communities and the impact of CO₂ storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO₂-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO₂. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO₂ injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO₂ injection and, if so, demonstrated the potential for microbial fixation and conversion of CO₂ into methane in subsurface oil reservoirs.

Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants

The final step of the biogas production process, the methanogenesis, is frequently dominated by members of the genus Methanoculleus. In particular, the species Methanoculleus bourgensis was identified to play a role in different biogas reactor systems. The genome of the type strain M. bourgensis MS2(T), originally isolated from a sewage sludge digestor, was completely sequenced to analyze putative adaptive genome features conferring competitiveness within biogas reactor environments to the strain. Sequencing and assembly of the M. bourgensis MS2(T) genome yielded a chromosome with a size of 2,789,773 bp. Comparative analysis of M. bourgensis MS2(T) and Methanoculleus marisnigri JR1 revealed significant similarities. The absence of genes for a putative ammonium uptake system may indicate that M. bourgensis MS2(T) is adapted to environments rich in ammonium/ammonia. Specific genes featuring predicted functions in the context of osmolyte production were detected in the genome of M. bourgensis MS2(T). Mapping of metagenome sequences derived from a production-scale biogas plant revealed that M. bourgensis MS2(T) almost completely comprises the genetic information of dominant methanogens present in the biogas reactor analyzed. Hence, availability of the M. bourgensis MS2(T) genome sequence may be valuable regarding further research addressing the performance of Methanoculleus species in agricultural biogas plants.

Comparison of DNA extraction kits and modification of DNA elution procedure for the quantitation of subdominant bacteria from piggery effluents with real-time PCR

Four commercial DNA extraction kits and a minor modification in the DNA elution procedure were evaluated for the quantitation of bacteria in pig manure samples. The PowerSoil®, PowerFecal®, NucleoSpin® Soil kits and QIAamp® DNA Stool Mini kit were tested on raw manure samples and on lagoon effluents for their ability to quantify total bacteria and a subdominant bacteria specific of pig manure contamination: Lactobacillus amylovorus. The NucleoSpin® Soil kit (NS kit), and to a lesser extent the PowerFecal® kit were the most efficient methods. Regardless of the kit utilized, the modified elution procedure increased DNA yield in the lagoon effluent by a factor of 1.4 to 1.8. When tested on 10 piggery effluent samples, compared to the QIAamp kit, the NS kit combined with the modified elution step, increased by a factor up to 1.7 log₁₀ the values of the concentration of L. amylovorus. Regardless of the type of manure, the best DNA quality and the highest concentrations of bacteria were obtained using the NS kit combined with the modification of the elution procedure. The method recommended here significantly improved quantitation of subdominant bacteria in manure.

Development of Methanoculleus-specific real-time quantitative PCR assay for assessing methanogen communities in anaerobic digestion

AIM

To develop a Methanoculleus-specific real-time quantitative PCR (RT-qPCR) assay with high coverage and specificity for the analysis of methanogenic populations in anaerobic digestion.

METHODS AND RESULTS

A Methanoculleus-specific primer/probe set for RT-qPCR was designed in this study based on all Methanoculleus 16S rRNA gene sequences in Ribosomal Database Project (RDP) according to TaqMan chemistry. The newly designed primer/probe set was shown to have high coverage and specificity by both in silico and experimental analyses. Amplification efficiency of the Methanoculleus-specific primer/probe set was determined to be ideal for RT-qPCR applications. Subsequent field testing on anaerobic digesters showed that results from RT-qPCR were consistent with those from clone library analysis, validating the accuracy of the RT-qPCR assay.

CONCLUSIONS

The Methanoculleus-specific RT-qPCR assay designed in this study can serve as a rapid and effective tool for the quantification of Methanoculleus populations in anaerobic digestion.

SIGNIFICANCE AND IMPACT OF THE STUDY

Methanoculleus populations represent important members of archaeal communities in methanogenic processes, necessitating the need to develop effective tools to monitor Methanoculleus population abundance. The RT-qPCR developed in this study provides an essential tool for the quantification of Methanoculleus populations in anaerobic digestion and for the understanding of the functions of these methanogens in anaerobic biotransformation.

Application of an early warning indicator and CaO to maximize the time-space-yield of an completely mixed waste digester using rape seed oil as co-substrate

In order to increase the organic loading rate (OLR) and hereby the performance of biogas plants an early warning indicator (EWI-VFA/Ca) was applied in a laboratory-scale biogas digester to control process stability and to steer additive dosing. As soon as the EWI-VFA/Ca indicated the change from stable to instable process conditions, calcium oxide was charged as a countermeasure to raise the pH and to bind long-chain fatty acids (LCFAs) by formation of aggregates. An interval of eight days between two increases of the OLR, which corresponded to 38% of the hydraulic residence time (HRT), was sufficient for process adaptation. An OLR increase by a factor of three within six weeks was successfully used for biogas production. The OLR was increased to 9.5 kg volatile solids (VS) m(-3) d(-1) with up to 87% of fat. The high loading rates affected neither the microbial community negatively nor the biogas production process. Despite the increase of the organic load to high rates, methane production yielded almost its optimum, amounting to 0.9 m(3)(kg VS)(-1). Beneath several uncharacterized members of the phylum Firmicutes mostly belonging to the family Clostridiaceae, a Syntrophomonas-like organism was identified that is known to live in a syntrophic relationship to methanogenic archaea. Within the methanogenic group, microorganisms affiliated to Methanosarcina, Methanoculleus and Methanobacterium dominated the community.

Corn silage in dairy cow diets to reduce ruminal methanogenesis: effects on the rumen metabolically active microbial communities

Methane produced by the methanogenic Archaea that inhabit the rumen is a potent greenhouse gas and represents an energy loss for the animal. Although several strategies have been proposed to mitigate enteric CH4 production, little is known about the effects of dietary changes on the microbial consortia involved in ruminal methanogenesis. Thus, the current study aimed to examine how the metabolically active microbes are affected when dairy cows were fed diets with increasing proportions of corn silage (CS). For this purpose, 9 ruminally cannulated lactating dairy cows were used in a replicated 3 × 3 Latin square design and fed a total mixed ration (60:40 forage:concentrate ratio on a dry matter basis) with the forage portion being either alfalfa silage (0% CS), corn silage (100% CS), or a 50:50 mixture (50% CS). Enteric CH4 production was determined using respiration chambers and total rumen content was sampled for the determination of fermentation characteristics and molecular biology analyses (cDNA-based length heterogeneity PCR, quantitative PCR). The cDNA-based length heterogeneity PCR targeting active microbes revealed similar bacterial communities in cows fed 0% CS and 50% CS diets, whereas important differences were observed between 0% CS and 100% CS diets, including a reduction in the bacterial richness and diversity in cows fed 100% CS diet. As revealed by quantitative PCR, feeding the 100% CS diet increased the number of total bacteria, Prevotella spp., Archaea, and methanogenic activity, though it reduced protozoal number. Meanwhile, increasing the CS proportion in the diet increased propionate concentration but decreased ruminal pH, CH4 production (L/kg of dry matter intake), and concentrations of acetate and butyrate. Based on these microbial and fermentation changes, and because CH4 production was reduced by feeding 100% CS diet, this study shows that the use of cDNA-based quantitative PCR to estimate archaeal growth and activity is not reliable enough to reflect changes in ruminal methanogenesis. A more robust technique to characterize changes in archaeal community structures will help to better understand the microbial process involved in ruminal methanogenesis and, hence, enabling the development of more effective dietary CH4 mitigation strategies.

Diet-induced alterations in total and metabolically active microbes within the rumen of dairy cows

DNA-based techniques are widely used to study microbial populations; however, this approach is not specific to active microbes, because DNA may originate from inactive and/or dead cells. Using cDNA and DNA, respectively, we aimed to discriminate the active microbes from the total microbial community within the rumen of dairy cows fed diets with increasing proportions of corn silage (CS). Nine multiparous lactating Holstein cows fitted with ruminal cannulas were used in a replicated 3×3 Latin square (32-d period; 21-d adaptation) design to investigate diet-induced shifts in microbial populations by targeting the rDNA gene. Cows were fed a total mixed ration with the forage portion being either barley silage (0% CS), a 50∶50 mixture of barley silage and corn silage (50% CS), or corn silage (100% CS). No differences were found for total microbes analyzed by quantitative PCR, but changes were observed within the active ones. Feeding more CS to dairy cows was accompanied by an increase in Prevotella rRNA transcripts (P = 0.10) and a decrease in the protozoal rRNA transcripts (P<0.05). Although they were distributed differently among diets, 78% of the amplicons detected in DNA- and cDNA-based fingerprints were common to total and active bacterial communities. These may represent a bacterial core of abundant and active cells that drive the fermentation processes. In contrast, 10% of amplicons were specific to total bacteria and may represent inactive or dead cells, whereas 12% were only found within the active bacterial community and may constitute slow-growing bacteria with high metabolic activity. It appears that cDNA-based analysis is more discriminative to identify diet-induced shifts within the microbial community. This approach allows the detection of diet-induced changes in the microbial populations as well as particular bacterial amplicons that remained undetected using DNA-based methods.

Identification of Methanoculleus spp. as active methanogens during anoxic incubations of swine manure storage tank samples

Methane emissions represent a major environmental concern associated with manure management in the livestock industry. A more thorough understanding of how microbial communities function in manure storage tanks is a prerequisite for mitigating methane emissions. Identifying the microorganisms that are metabolically active is an important first step. Methanogenic archaea are major contributors to methanogenesis in stored swine manure, and we investigated active methanogenic populations by DNA stable isotope probing (DNA-SIP). Following a preincubation of manure samples under anoxic conditions to induce substrate starvation, [U-(13)C]acetate was added as a labeled substrate. Fingerprint analysis of density-fractionated DNA, using length-heterogeneity analysis of PCR-amplified mcrA genes (encoding the alpha subunit of methyl coenzyme M reductase), showed that the incorporation of (13)C into DNA was detectable at in situ acetate concentrations (~7 g/liter). Fingerprints of DNA retrieved from heavy fractions of the (13)C treatment were primarily enriched in a 483-bp amplicon and, to a lesser extent, in a 481-bp amplicon. Analyses based on clone libraries of the mcrA and 16S rRNA genes revealed that both of these heavy DNA amplicons corresponded to Methanoculleus spp. Our results demonstrate that uncultivated methanogenic archaea related to Methanoculleus spp. were major contributors to acetate-C assimilation during the anoxic incubation of swine manure storage tank samples. Carbon assimilation and dissimilation rate estimations suggested that Methanoculleus spp. were also major contributors to methane emissions and that the hydrogenotrophic pathway predominated during methanogenesis.