The alkaloid gramine in the anaerobic digestion process-inhibition and adaptation of the methanogenic community

Comprehending the impact of berberine on anaerobic digestion of waste activated sludge

Berberine is a natural isoquinoline alkaloid performing wide-spectrum antimicrobial and antiviral effects like antibiotics. Its production generates berberine containing wastewater, and berberine adsorbed on waste activated sludge (WAS) will unavoidably enter the anaerobic digestion (AD) system while its impact on the AD process is unknown. Our research found that berberine of 20 mg/L (BBR20) slightly enhanced the methane yield (4.2 ± 0.6%) under mesophilic condition (35.0 ± 1.0 °C). However, 100 and 500 mg/L (BBR100 and BBR500) depressed methane production by 17.3 ± 4.3% and 83.2 ± 0.4%; meanwhile more soluble chemical oxygen demand (SCOD) including volatile fatty acid (VFA), protein, and polysaccharide were left in the fermentation broth, which led to an increase in sludge reduction. 88.3 ± 0.09%-99.1 ± 0.04% of berberine was distributed in the sludge phase and could be efficiently removed even under a high berberine level of 500 mg/L during the AD process. Exposure to different berberine concentrations promoted sludge dissolution and triggered more sludge extracellular polymeric substances (EPS) being dissolved. Lower berberine concentration (20 mg/L) enhanced acidification and methanogenesis steps, resulting in a final methane generation increase. While hydrolysis, acidification and methanogenesis processes were all inhibited by 100 and 500 mg/L berberine. Microbial analysis revealed that the main acid-producing bacteria genera were changed as Bacteroidetes vadinHA17 dominated in control, BBR20 and BBR100 groups, was replaced by Petrimonas in BBR500. Additionally, Methanosaeta, as a strict acetoclastic methanogen, was suppressed under exposure to 100 and 500 mg/L berberine. Accordingly, the declined abundance of archaea genera consuming acetic acid caused more VFA accumulation and less methane production in BBR100 and BBR500 groups.

A New Fluorescence Detection Method for Tryptophan- and Tyrosine-Derived Allelopathic Compounds in Barley and Lupin

Barley (Hordeum vulgare) is one of the most widely cultivated crops for feedstock and beer production, whereas lupins (Lupinus spp.) are grown as fodder and their seeds are a source of protein. Both species produce the allelopathic alkaloids gramine and hordenine. These plant-specialized metabolites may be of economic interest for crop protection, depending on their tissue distribution. However, in high concentrations they pose a health risk to humans and animals that feed on them. This study was carried out to develop and validate a new method for monitoring these alkaloids and their related metabolites using fluorescence detection. Separation was performed on an HSS T3 column using slightly acidified water-acetonitrile eluents. Calibration plots expressed linearity over the range 0.09-100 pmol/µL for gramine. The accuracy and precision ranged from 97.8 to 123.4%, <7% RSD. The method was successfully applied in a study of the natural range of abundance of gramine, hordenine and their related metabolites, AMI, tryptophan and tyramine, in 22 barley accessions and 10 lupin species. This method provides accurate and highly sensitive chromatographic separation and detection of tryptophan- and tyrosine-derived allelochemicals and is an accessible alternative to LC-MS techniques for routine screening.

Epicuticular wax of sweet sorghum influenced the microbial community and fermentation quality of silage

Epicuticular wax, as secondary metabolites (hydrophobic compounds) covering plant surface, plays important roles in protecting plants from abiotic and biotic stresses. However, whether these compounds will influence fermentation process of silage is still not clear. In this study, two sweet sorghum cultivars with varying epicuticular wax on sheath (bloom), Yajin 2 (YJ, less bloom), and Jintian (JT, dense bloom), were harvested at flowering and maturing stages, and ensiled with or without bloom, aiming to evaluate the effects of bloom on fermentation quality, feed nutrition and microbial community. The bloom was collected manually with de-waxed cotton and extracted with chloroform. The results showed that the bloom reduced the concentrations of water-soluble carbohydrate and crude protein of the two cultivars at both stages, reduced lactic acid (LA) for YJ at both stages and for JT at flowering stage, and increased LA for JT at mature stage. The α-diversity of bacterial communities of the silage fermentation with bloom was significantly lower than that without bloom. Bloom increased the abundance of Lactobacillus, reduced that of Bacillus and Weissella, and significant correlations were observed between fermentative qualities and bacterial abundances. However, decreased diversity of bacterial community and the contents of LA implied that shifts in bacterial community might exert negative effects on silage fermentation. Our results suggest that bloom wax could alter the microbial community composition of ensiled sweet sorghums, which thus influence the fermentation qualities.

Modification of wheat straw to improve the caproate production in a cell immobilized system

Wheat straw is a favorable cell carrier in the caproate fermentation system, yet its smooth surface limits the biofilm formation. In this study, the modification of wheat straw was conducted using three different chemical methods and the influence of its modified surface on the caproate fermentation was investigated. Results showed that the sodium hydroxide was the optimum reagent for modification of wheat straw, where both the external and internal surfaces were effectively modified, resulting in 34.4% increased specific surface area. The highest caproate production of 21.1 g/L was obtained in fed-batch fermentation, which was ascribed to the formation of a thick biofilm on the modified carrier. Moreover, the crystallinity index of the carrier increased during the fed-batch fermentation, implying that the modified wheat straw was a stable matrix for cell immobilization. This study provides an effective way for efficient caproate production through modification of wheat straw.

Differential Impact of Plant Secondary Metabolites on the Soil Microbiota

Plant metabolites can shape the microbial community composition in the soil. Two indole metabolites, benzoxazolinone (BOA) and gramine, produced by different Gramineae species, and quercetin, a flavonoid synthesized by many dicot species, were studied for their impacts on the community structure of field soil bacteria. The three plant metabolites were directly added to agricultural soil over a period of 28 days. Alterations in bacterial composition were monitored by next generation sequencing of 16S rRNA gene PCR products and phospholipid fatty acid analysis. Treatment of the soil with the plant metabolites altered the community composition from phylum to amplicon sequence variant (ASV) level. Alpha diversity was significantly reduced by BOA or quercetin, but not by gramine. BOA treatment caused a decrease of the relative abundance of 11 ASVs, while only 10 ASVs were increased. Gramine or quercetin treatment resulted in the increase in relative abundance of many more ASVs (33 or 38, respectively), most of them belonging to the Proteobacteria. Isolation and characterization of cultivable bacteria indicated an enrichment in Pseudarthrobacter or Pseudomonas strains under BOA/quercetin or BOA/gramine treatments, respectively. Therefore, the effects of the treatments on soil bacteria were characteristic for each metabolite, with BOA exerting a predominantly inhibitory effect, with only few genera being able to proliferate, while gramine and quercetin caused the proliferation of many potentially beneficial strains. As a consequence, BOA or gramine biosynthesis, which have evolved in different barley species, is accompanied with the association of distinct bacterial communities in the soil, presumably after mutual adaptation during evolution.

Untargeted Metabolite Profiling for Screening Bioactive Compounds in Digestate of Manure under Anaerobic Digestion

Untargeted metabolite profiling was performed on chicken manure (CHM), swine manure (SM), cattle manure (CM), and their respective digestate by XCMS coupled with MetaboAnalyst programs. Through global chemical profiling, the chemical characteristics of different digestates and types of manure were displayed during the anaerobic digestion (AD) process. As the feed for AD, CM had less easily-degradable organics, SM contained the least O-alkyls and anomerics of carbohydrates, and CHM exhibited relatively lower bio-stability. The derived metabolite pathways of different manure during the AD process were identified by MetaboAnalyst. Twelve, 8, and 5 metabolic pathways were affected by the AD process in CHM, SM, and CM, respectively. Furthermore, bioactive compounds of digestate were detected, such as amino acids (L-arginine, L-ornithine, L-cysteine, and L-aspartate), hormones (L-adrenaline, 19-hydroxy androstenedione, and estrone), alkaloids (tryptamine and N-methyltyramine), and vitamin B5, in different types of manure and their digestates. The combination of XCMS and MetaboAnalyst programs can be an effective strategy for metabolite profiling of manure and its anaerobic digestate under different situations.

Syngas-aided anaerobic fermentation for medium-chain carboxylate and alcohol production: the case for microbial communities

Syngas fermentation has been successfully implemented in commercial-scale plants and can enable the biochemical conversion of the driest fractions of biomass through synthesis gas (H₂, CO₂, and CO). The process relies on optimized acetogenic strains able to reach and maintain high productivity of ethanol and acetate. In parallel, microbial communities have shown to be the best choice for the production of valuable medium-chain carboxylates through anaerobic fermentation of biomass, demanding low technical complexity and being able to realize simultaneous hydrolysis of the substrate. Each of the two technologies benefits from different strong points and has different challenges to overcome. This review discusses the rationales for merging these two seemingly disparate technologies by analyzing previous studies and drawing opinions based on the lessons learned from such studies. For keeping the technical demands of the resulting process low, a case is built for using microbial communities instead of pure strains. For that to occur, a shift from conventional syngas-based to "syngas-aided" anaerobic fermentation is suggested. Strategies for tackling the intricacies of working simultaneously with communities and syngas, such as competing pathways, and thermodynamic aspects are discussed as well as the stoichiometry and economic feasibility of the concept. Overall, syngas-aided anaerobic fermentation seems to be a promising concept for the biorefinery of the future. However, the effects of process parameters on microbial interactions have to be understood in greater detail, in order to achieve and sustain feasible medium-chain carboxylate and alcohol productivity.

16s rRNA gene sequencing and radioisotopic analysis reveal the composition of ammonia acclimatized methanogenic consortia

Different mesophilic and thermophilic methanogenic consortia were acclimatised and enriched to extreme total ammonia (9.0 and 5.0 g NH₄⁺-N L^-1, respectively) and free ammonia (1.0 and 1.4 g NH₃-N L^-1, respectively) levels in this study. [2-¹⁴C] acetate radioisotopic analyses showed the dominance of aceticlastic methanogenesis in all enriched consortia. According to 16S rRNA gene sequencing result, in mesophilic consortia, methylotrophic Methanomassiliicoccus luminyensis was predominant, followed by aceticlastic Methanosarcina soligelidi. A possible scenario explaining the dominance of M. luminyensis includes the use of methylamine produced by Tissierella spp. and biomass build-up by metabolizing acetate. Nevertheless, further studies are needed to pinpoint the exact metabolic pathway of M. luminyensis. In thermophilic consortia, aceticlastic Methanosarcina thermophila was the sole dominant methanogen. Overall, results derived from this study demonstrated the efficient biomethanation ability of these ammonia-tolerant methanogenic consortia, indicating a potential application of these consortia to solve ammonia toxicity problems in future full-scale reactors.

Intermittent fasting for microbes: how discontinuous feeding increases functional stability in anaerobic digestion

BACKGROUND

Demand-driven biogas production could play an important role for future sustainable energy supply. However, feeding a biogas reactor according to energy demand may lead to organic overloading and, thus, to process failures. To minimize this risk, digesters need to be actively steered towards containing more robust microbial communities. This study focuses on acetogenesis and methanogenesis as crucial process steps for avoiding acidification. We fed lab-scale anaerobic digesters with volatile fatty acids under various feeding regimes and disturbances. The resulting microbial communities were analyzed on DNA and RNA level by terminal restriction fragment length polymorphism of the mcrA gene, 16S rRNA gene amplicon sequencing, and a [2-13C]-acetate assay. A modified Anaerobic Digestion Model 1 (ADM1) that distinguishes between the acetoclastic methanogens Methanosaeta and Methanosarcina was developed and fitted using experimental abiotic and biotic process parameters.

RESULTS

Discontinuous feeding led to more functional resilience than continuous feeding, without loss in process efficiency. This was attributed to a different microbial community composition. Methanosaeta dominated the continuously fed reactors, while its competitor Methanosarcina was washed out. With discontinuous feeding, however, the fluctuating acetic acid concentrations provided niches to grow and co-exist for both organisms as shown by transcription analysis of the mcrA gene. Our model confirmed the higher functional resilience due to the higher abundance of Methanosarcina based on its higher substrate uptake rate and higher resistance to low pH values. Finally, we applied our model to maize silage as a more complex and practically relevant substrate and showed that our model is likely transferable to the complete AD process.

CONCLUSIONS

The composition of the microbial community determined the AD functional resilience against organic overloading in our experiments. In particular, communities with higher share of Methanosarcina showed higher process stability. The share of these microorganisms can be purposefully increased by discontinuous feeding. A model was developed that enables derivation of the necessary feeding regime for a more robust community with higher share of Methanosarcina.

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation

Anaerobic digestion (AD) is a complex multi-stage process relying on the activity of highly diverse microbial communities including hydrolytic, acidogenic and syntrophic acetogenic bacteria as well as methanogenic archaea. The lower diversity of methanogenic archaea compared to the bacterial groups involved in AD and the corresponding lack of functional redundancy cause a stronger susceptibility of methanogenesis to unfavorable process conditions such as trace element (TE) deprivation, thus controlling the stability of the overall process. Here, we investigated the effects of a slowly increasing TE deficit on the methanogenic community function in a semi-continuous biogas process. The aim of the study was to understand how methanogens in digester communities cope with TE limitation and sustain their growth and metabolic activity. Two lab-scale biogas reactors fed with distillers grains and supplemented with TEs were operated in parallel for 76 weeks before one of the reactors was subjected to TE deprivation, leading to a decline of cobalt and molybdenum concentrations from 0.9 to 0.2 mg/L, nickel concentrations from 2.9 to 0.8 mg/L, manganese concentrations from 38 to 18 mg/L, and tungsten concentrations from 1.4 to 0.2 mg/L. Amplicon sequencing of mcrA genes revealed Methanosarcina (72%) and Methanoculleus (23%) as the predominant methanogens in the undisturbed reactors. With increasing TE limitation, the relative abundance of Methanosarcina dropped to 67% and a slight decrease of acetoclastic methanogenic activity was observed in batch tests with ¹³C-methyl-labeled acetate, suggesting a shift toward syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Metaproteome analysis revealed abundance shifts of the enzymes involved in methanogenic pathways. Proteins involved in methylotrophic and acetoclastic methanogenesis decreased in abundance while formylmethanofuran dehydrogenase from Methanosarcinaceae increased, confirming our hypothesis of a shift from acetoclastic to hydrogenotrophic methanogenesis by Methanosarcina. Both Methanosarcina and Methanoculleus increased the abundance of N5-methyltetrahydromethanopterin-coenzyme M methyltransferase and methyl-coenzyme M reductase. However, these efforts to preserve the ion motive force for energy conservation were seemingly more successful in Methanoculleus. We conclude that both methanogenic genera use different strategies to stabilize their energy balance under TE limitation. Methanosarcina switched from TE expensive pathways (methylotrophic and acetoclastic methanogenesis) to hydrogenotrophic methanogenesis. Methanoculleus showed a higher robustness and was favored over the more fastidious Methanosarcina, thus stabilizing reactor performance under TE limitation.

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation

Anaerobic digestion (AD) is a complex multi-stage process relying on the activity of highly diverse microbial communities including hydrolytic, acidogenic and syntrophic acetogenic bacteria as well as methanogenic archaea. The lower diversity of methanogenic archaea compared to the bacterial groups involved in AD and the corresponding lack of functional redundancy cause a stronger susceptibility of methanogenesis to unfavorable process conditions such as trace element (TE) deprivation, thus controlling the stability of the overall process. Here, we investigated the effects of a slowly increasing TE deficit on the methanogenic community function in a semi-continuous biogas process. The aim of the study was to understand how methanogens in digester communities cope with TE limitation and sustain their growth and metabolic activity. Two lab-scale biogas reactors fed with distillers grains and supplemented with TEs were operated in parallel for 76 weeks before one of the reactors was subjected to TE deprivation, leading to a decline of cobalt and molybdenum concentrations from 0.9 to 0.2 mg/L, nickel concentrations from 2.9 to 0.8 mg/L, manganese concentrations from 38 to 18 mg/L, and tungsten concentrations from 1.4 to 0.2 mg/L. Amplicon sequencing of mcrA genes revealed Methanosarcina (72%) and Methanoculleus (23%) as the predominant methanogens in the undisturbed reactors. With increasing TE limitation, the relative abundance of Methanosarcina dropped to 67% and a slight decrease of acetoclastic methanogenic activity was observed in batch tests with ¹³C-methyl-labeled acetate, suggesting a shift toward syntrophic acetate oxidation coupled to hydrogenotrophic methanogenesis. Metaproteome analysis revealed abundance shifts of the enzymes involved in methanogenic pathways. Proteins involved in methylotrophic and acetoclastic methanogenesis decreased in abundance while formylmethanofuran dehydrogenase from Methanosarcinaceae increased, confirming our hypothesis of a shift from acetoclastic to hydrogenotrophic methanogenesis by Methanosarcina. Both Methanosarcina and Methanoculleus increased the abundance of N5-methyltetrahydromethanopterin-coenzyme M methyltransferase and methyl-coenzyme M reductase. However, these efforts to preserve the ion motive force for energy conservation were seemingly more successful in Methanoculleus. We conclude that both methanogenic genera use different strategies to stabilize their energy balance under TE limitation. Methanosarcina switched from TE expensive pathways (methylotrophic and acetoclastic methanogenesis) to hydrogenotrophic methanogenesis. Methanoculleus showed a higher robustness and was favored over the more fastidious Methanosarcina, thus stabilizing reactor performance under TE limitation.

Inhibitory Effect of Coumarin on Syntrophic Fatty Acid-Oxidizing and Methanogenic Cultures and Biogas Reactor Microbiomes

Coumarins are widely found in plants as natural constituents having antimicrobial activity. When considering plants that are rich in coumarins for biogas production, adverse effects on microorganisms driving the anaerobic digestion process are expected. Furthermore, coumarin derivatives, like warfarin, which are used as anticoagulating medicines, are found in wastewater, affecting its treatment. Coumarin, the structure common to all coumarins, inhibits the anaerobic digestion process. However, the details of this inhibition are still elusive. Here, we studied the impact of coumarin on acetogenesis and methanogenesis. First, coumarin was applied at four concentrations between 0.25 and 1 g · liter^-1 to pure cultures of the methanogens Methanosarcina barkeri and Methanospirillum hungatei, which resulted in up to 25% less methane production. Acetate production of syntrophic propionate- and butyrate-degrading cultures of Syntrophobacter fumaroxidans and Syntrophomonas wolfei was inhibited by 72% at a coumarin concentration of 1 g · liter^-1 Coumarin also inhibited acetogenesis and acetoclastic methanogenesis in a complex biogas reactor microbiome. When a coumarin-adapted microbiome was used, acetogenesis and methanogenesis were not inhibited. According to amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, the communities of the two microbiomes were similar, although Methanoculleus was more abundant and Methanobacterium less abundant in the coumarin-adapted than in the nonadapted microbiome. Our results suggest that well-dosed feeding with coumarin-rich feedstocks to full-scale biogas reactors while keeping the coumarin concentrations below 0.5 g · liter^-1 will allow adaptation to coumarins by structural and functional community reorganization and coumarin degradation.IMPORTANCE Coumarins from natural and anthropogenic sources have an inhibitory impact on the anaerobic digestion process. Here, we studied in detail the adverse effects of the model compound coumarin on acetogenesis and methanogenesis, which are two important steps of the anaerobic digestion process. Coumarin concentrations lower than 0.5 g · liter^-1 had only a minor impact. Even though similar inhibitory effects can be assumed for coumarin derivatives, little effects on the anaerobic treatment of wastewater are expected where concentrations of coumarin derivatives are lower than 0.5 g · liter^-1 However, when full-scale reactors are fed with coumarin-rich feedstocks, the biogas processes might be inhibited. Hence, these feedstocks should be utilized in a well-dosed manner or after adaptation of the microbial community.

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets

In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application.