Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities

Enhanced biodegradation of perfluorooctanoic acid in a dual biocatalyzed microbial electrosynthesis system

The toxic perfluorooctanoic acid (PFOA) is widely spread in terrestrial and aquatic habitats owing to its resistance to conventional degradation processes. Advanced techniques to degrade PFOA requires drastic conditions with high energy cost. In this study, we investigated PFOA biodegradation in a simple dual biocatalyzed microbial electrosynthesis system (MES). Different PFOA loadings (1, 5, and 10 ppm) were tested and a biodegradation of 91% was observed within 120 h. Propionate production improved and short-carbon-chain PFOA intermediates were detected, which confirmed PFOA biodegradation. However, the current density decreased, indicating an inhibitory effect of PFOA. High-throughput biofilm analysis revealed that PFOA regulated the microbial flora. Microbial community analysis showed enrichment of the more resilient and PFOA adaptive microbes, including Methanosarcina and Petrimonas. Our study promotes the potential use of dual biocatalyzed MES system as an environment-friendly and inexpensive method to remediate PFOA and provides a new direction for bioremediation research.

Utilization of Macroalgae for the Production of Bioactive Compounds and Bioprocesses Using Microbial Biotechnology

To achieve sustainable development, alternative resources should replace conventional resources such as fossil fuels. In marine ecosystems, many macroalgae grow faster than terrestrial plants. Macroalgae are roughly classified as green, red, or brown algae based on their photosynthetic pigments. Brown algae are considered to be a source of physiologically active substances such as polyphenols. Furthermore, some macroalgae can capture approximately 10 times more carbon dioxide from the atmosphere than terrestrial plants. Therefore, they have immense potential for use in the environment. Recently, macroalgae have emerged as a biomass feedstock for bioethanol production owing to their low lignin content and applicability to biorefinery processes. Herein, we provided an overview of the bioconversion of macroalgae into bioactive substances and biofuels using microbial biotechnology, including engineered yeast designed using molecular display technology.

Study on anaerobic co-digestion of municipal sewage sludge and fruit and vegetable wastes: Methane production, microbial community and three-dimension fluorescence excitation-emission matrix analysis

Constantly increased sewage sludge (SS) and fruit and vegetable wastes (FVW) are becoming the major organic solid wastes in human society. Thus, anaerobic digestion is employed as a low carbon energy strategy to reduce their environmental pollution risk. Anaerobic co-digestion system was developed based on the carbon to nitrogen ratio strategy. Results showed that the daily biogas production was higher in co-digester, and the volumetric biogas production rate (VBPR) significantly enhanced for 1.3 ∼ 3 folds, and the highest VBPR was 2.04 L/L • day with optimal OLR of 2.083 Kg L^-1 d^-1. Analytic results indicated that co-digestion could improve the biodegradable of feedstocks, which transforming to more VFAs and biogas. Compared with mono SS digester, mixed substrates relieved ammonia nitrogen inhibition and enhanced the hydrolytic acidification and methanogenesis. Meanwhile, the excessive humification of organics was suppressed. This study supported the concepts of improving carbon recovery from SS and FVW.

Development of Stable Mixed Microbiota for High Yield Power to Methane Conversion

The performance of a mixed microbial community was tested in lab-scale power-to-methane reactors at 55 °C. The main aim was to uncover the responses of the community to starvation and stoichiometric H2/CO2 supply as the sole substrate. Fed-batch reactors were inoculated with the fermentation effluent of a thermophilic biogas plant. Various volumes of pure H2/CO2 gas mixtures were injected into the headspace daily and the process parameters were followed. Gas volumes and composition were measured by gas-chromatography, the headspace was replaced with N2 prior to the daily H2/CO2 injection. Total DNA samples, collected at the beginning and end (day 71), were analyzed by metagenome sequencing. Low levels of H2 triggered immediate CH4 evolution utilizing CO2/HCO3− dissolved in the fermentation effluent. Biomethanation continued when H2/CO2 was supplied. On the contrary, biomethane formation was inhibited at higher initial H2 doses and concomitant acetate formation indicated homoacetogenesis. Biomethane production started upon daily delivery of stoichiometric H2/CO2. The fed-batch operational mode allowed high H2 injection and consumption rates albeit intermittent operation conditions. Methane was enriched up to 95% CH4 content and the H2 consumption rate attained a remarkable 1000 mL·L−1·d−1. The microbial community spontaneously selected the genus Methanothermobacter in the enriched cultures.

Effect of Dietary Protein Levels on Dynamic Changes and Interactions of Ruminal Microbiota and Metabolites in Yaks on the Qinghai-Tibetan Plateau

To improve performance and optimize rumen function in yaks (Bos grunniens), further knowledge on the appropriate dietary protein levels for ruminal microbiota and the metabolite profiles of yaks in feedlot feeding is necessary. Current understanding of dietary protein requirements, ruminal microbiota, and metabolites is limited. In this study, yaks were fed a low-protein diet (L; 9.64%), middle low-protein diet (ML; 11.25%), middle high-protein diet (MH; 12.48%), or a high-protein diet (H; 13.87%), and the effects of those diets on changes and interactions in ruminal microbiota and metabolites were investigated. Twenty-four female yaks were selected, and the effects on ruminal microbiota and metabolites were investigated using 16s rRNA gene sequencing and gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). Diets containing different protein levels changed the composition of the rumen bacterial community, the H group significantly reduced the diversity of ruminal microbiota (p < 0.05), and the number of shared amplicon sequence variants (ASVs) between the H group and the other three groups was lower, suggesting that the ruminal microbiota community fluctuated more with a high-protein diet. In rumen, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant bacteria at the phylum level, and Bacteroidetes was significantly less abundant in the MH group than in the L and ML groups (p < 0.05). Prevotella_1, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group had the highest abundance at the genus level. Prevotellaceae was enriched in the low-protein groups, whereas Bacteroidales_BS11_gut_group was enriched in the high-protein groups. Rumen metabolite concentrations and metabolic patterns were altered by dietary protein levels: organic acid metabolites, antioxidant-related metabolites, and some plant-derived metabolites showed variation between the groups. Enrichment analysis revealed that significant changes were concentrated in six pathways, including the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and butanoate metabolism. Network analysis showed promotion or restraint relationships between different rumen microbiota and metabolites. Overall, the rumen function was higher in the MH group. This study provides a reference for appropriate dietary protein levels and improves understanding of rumen microbes and metabolites.

Protein biomethanation: insight into the microbial nexus

Biomethanation of carbohydrates (e.g., lignocellulosic biomass) and lipids (e.g., waste oils) has been well studied. However, investigations on the biomethanation of protein-rich biowastes (PRBs) and associated microbial communities have not been reported. This review summarizes the challenges in the metabolic process of anaerobic digestion of PRBs and the microbial instability associated with it. We discuss the diversity of bacterial and archaeal communities via metagenomics under PRB mono- and codigestion. A stable community structure with enhanced metabolic activity is a core factor in PRB biomethanation. The application of strategies such as codigestion of PRBs with carbon-rich biomass and microbial stimulation/augmentation would make PRB biomethanation more feasible.

Illumina sequencing of 16S rRNA genes reveals a unique microbial community in three anaerobic sludge digesters of Dubai

Understanding the microbial communities in anaerobic digesters, especially bacteria and archaea, is key to its better operation and regulation. Microbial communities in the anaerobic digesters of the Gulf region where climatic conditions and other factors may impact the incoming feed are not documented. Therefore, Archaeal and Bacterial communities of three full-scale anaerobic digesters, namely AD1, AD3, and AD5 of the Jebel Ali Sewage water Treatment Plant (JASTP) were analyzed by Illumina sequencing of 16S rRNA genes. Among bacteria, the most abundant genus was fermentative bacteria Acetobacteroides (Blvii28). Other predominant bacterial genera in the digesters included thermophilic bacteria (Fervidobacterium and Coprothermobacter) and halophilic bacteria like Haloterrigena and Sediminibacter. This can be correlated with the climatic condition in Dubai, where the bacteria in the incoming feed may be thermophilic or halophilic as much of the water used in the country is desalinated seawater. The predominant Archaea include mainly the members of the phyla Euryarchaeota and Crenarchaeota belonging to the genus Methanocorpusculum, Metallosphaera, Methanocella, and Methanococcus. The highest population of Methanocorpusculum (more than 50% of total Archaea), and other hydrogenotrophic archaea, is in agreement with the high population of bacterial genera Acetobacteroides (Blvii28) and Fervidobacterium, capable of fermenting organic substrates into acetate and H₂. Coprothermobacter, which is known to improve protein degradation by establishing syntrophy with hydrogenotrophic archaea, is also one of the digesters’ dominant genera. The results suggest that the microbial community in three full-scale anaerobic digesters is different. To best of our knowledge this is the first detailed report from the UAE.

Integrating independent microbial studies to build predictive models of anaerobic digestion inhibition by ammonia and phenol

Anaerobic digestion (AD) is a process that can efficiently degrade organic waste into renewable energies. AD failure is however common as the underpinning microbial mechanisms are highly vulnerable to a wide range of inhibitory compounds. Sequencing technologies enable the identification of microbial indicators of digesters inhibition, but existing studies are limited. They used different inocula, substrates, sites and types of reactors and reported different or contradictory indicators. Our aim was to identify a robust signature of microbial indicators of phenol and ammonia inhibitions across four independent AD microbial studies. To identify such signature, we applied an original multivariate integrative method on two in-house studies, then validated our approach by predicting the inhibitory status of samples from two other studies with more than 90% accuracy. Our approach shows how we can efficiently leverage on existing studies to extract reproducible microbial community patterns and predict AD inhibition to improve AD microbial management.

Microremediation of tannery wastewater by siderophore producing marine bacteria

The present study evaluated the microremediation potential of nine siderophore producing marine bacteria for hazardous raw tannery wastewater from common effluent treatment plant (CETP). Most of the pollutants detected in the wastewater were diminished after the bioremediation process. Further, among the three potent isolates selected for aerobic and anaerobic bioremediation study, Marinobacter hydrocarbonoclasticus demonstrated the highest bioremediation aerobically with a reduction in chromium (88%), sulphate (71%), phosphate (68%) and nitrate (57%). Notably, Nitratireductor kimnyeongensis could attack the effluent under both aerobic and anaerobic conditions as substantiated by statistically significant (p < .05) reduction in the pollutants [chromium (85%), sulphate (63%), Chemical Oxygen Demand (COD) (69%), phosphate (76%)]. From the study it is evident that the pollutant load reduction was achieved under both aerobic and anaerobic conditions, however, aerobic environment was more effective in reducing chromium, Biochemical Oxygen Demand (BOD), sulphate, nitrate and phosphate. The bioremediation efficiency was further confirmed by the bioassay experiments with plant and animal models where higher seed germination, greater plant length and biomass, as well as improved survival rate of Artemia nauplii for bioremediated wastewater was observed as compared to the untreated effluent indicating a significant reduction in toxicity. The results for simultaneous removal of multiple-toxicants thus signify effectiveness and ease of using the robust properties of these marine bacterial strains suggesting their potential application for bioremediation. Hence this could pave a promising way for an environment-friendly and economically feasible clean-up strategy for safer disposal of tannery wastewater.

Effects of pig slurry acidification on methane emissions during storage and subsequent biogas production

In addition to undesirable odorous gases, substantial amounts of greenhouse gases (GHG), particularly methane (CH₄), are generated during the storage of livestock manure. To reduce the CH₄ emissions, first, pig slurry (PS) was stored for 40 d at 30 °C after adjusting the pH at 5.0-7.0 using H₂SO₄ solution. In the control (non-acidified PS), 3.7 kg CO₂ eq./ton PS of CH₄ emissions was detected, which was reduced to 1.8, 0.9, 0.4, 0.2, and 0.1 kg CO₂ eq./ton PS at pH 7.0, 6.5, 6.0, 5.5, and 5.0, respectively. Methanosarcina was found to be the dominant genus (67% of the total archaeal sequence) in the control, whose dominance was reduced as storage pH decreased. The results of ribonucleic acid analysis and specific methanogenic activity test further confirmed the inhibition of indigenous methanogens by acidification. Later, the biochemical CH₄ potential of stored PS was tested. Compared to the control (10.6 L CH₄/L PS), the acidified PS showed higher CH₄ yields of 12.7-14.6 L CH₄/L PS, presumably by keeping degradable organic matters in PS under acidic condition. Among different acidification pHs tested, the maximum amount of GHG reduction was achieved at pH 6.0 by reducing CH₄ emission to +0.4 kg CO₂ eq./ton PS during storage while increasing biogas production potential equivalent to 48.3 kWh/ton PS (-22.5 kg CO₂ eq./ton PS), resulting in a further reduction of (-)9.6 kg CO₂ eq./ton PS compared to the control.

Feeding frequency influences process performance and microbial community composition in anaerobic digesters treating steam exploded food waste

In anaerobic digestion, studies of feeding frequency have produced conflicting results. Hence, the effect of feeding frequency on process variables and microbial community structure was investigated by comparing a laboratory-scale digester fed steam exploded food waste 10 times daily vs. one fed an equivalent amount once daily. The Frequently Fed Digester (FFD) produced on average 20% more methane and had lower effluent concentrations of long-chain fatty acids. Greater daily fluctuations in acetate, pH and biogas production rate could explain the lower specific methane yield and β-oxidation. Feeding frequency also influenced the microbial community whereby Tenericutes (42%) dominated in FFD but Firmicutes (31%) was most abundant in the Daily Fed Digester (DFD). Feeding frequency effects are therefore postulated to occur more often in digesters fed labile feedstocks at high organic loading rates.

Graphene Facilitates Biomethane Production from Protein-Derived Glycine in Anaerobic Digestion

Interspecies electron transfer is a fundamental factor determining the efficiency of anaerobic digestion (AD), which involves syntrophy between fermentative bacteria and methanogens. Direct interspecies electron transfer (DIET) induced by conductive materials can optimize this process offering a significant improvement over indirect electron transfer. Herein, conductive graphene was applied in the AD of protein-derived glycine to establish DIET. The electron-producing reaction via DIET is thermodynamically more favorable and exhibits a more negative Gibbs free energy value (−60.0 kJ/mol) than indirect hydrogen transfer (−33.4 kJ/mol). The Gompertz model indicated that the kinetic parameters exhibited linear correlations with graphene addition from 0.25 to 1.0 g/L, leading to the highest increase in peak biomethane production rate of 28%. Sedimentibacter (7.8% in abundance) and archaea Methanobacterium (71.1%) and Methanosarcina (11.3%) might be responsible for DIET. This research can open up DIET to a range of protein-rich substrates, such as algae.

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Graphene led to an increase in peak bio-CH₄ production rate from glycine by 28%

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Kinetic parameters had linear correlations with graphene addition (0.25–1.0 g/L)

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Direct interspecies electron transfer (DIET) contributed to the improved performance

Microbial community composition and diversity in rice straw digestion bioreactors with and without dairy manure

Anaerobic digestion (AD) uses a range of substrates to generate biogas, including energy crops such as globally abundant rice straw (RS). Unfortunately, RS is high in lignocellulosic material and has high to C:N ratios (~80:1), which makes it (alone) a comparatively poor substrate for AD. Co-digestion with dairy manure (DM) has been promoted as a method for balancing C:N ratios to improve RS AD whilst also treating another farm waste and co-producing a potentially useful fertiliser. However, past co-digestion studies have not directly compared RS AD microbial communities with and without DM additions, which has made it hard to assess all impacts of DM addition to RS AD processes. Here, four RS:DM ratios were contrasted in identical semi-continuous-fed AD bioreactors, and 100% RS was found to produce the highest specific methane yields (112 mL CH4/g VS/day; VS, volatile solids), which is over double yields achieved in the reactor with the highest DM content (30:70 RS:DM by mass; 48 mL CH4/g VS/day). To underpin these data, microbial communities were sequenced and characterised across the four reactors. Dominant operational taxonomic units (OTUs) in the 100% RS unit were Bacteroidetes/Firmicutes, whereas the 30:70 RS:DM unit was dominated by Proteobacteria/Spirochaetes, suggesting major microbial community shifts occur with DM additions. However, community richness was lowest with 100% RS (despite higher specific yields), suggesting particular OTUs may be more important to yields than microbial diversity. Further, ambient VFA and VS levels were significantly higher when no DM was added, suggesting DM-amended reactors may cope better with higher organic loading rates (OLR). Results show that RS AD without DM addition is feasible, although co-digestion with DM will probably allow higher OLRs, resulting in great RS throughput in farm AD units.

Linking the Effect of Antibiotics on Partial-Nitritation Biofilters: Performance, Microbial Communities and Microbial Activities

The emergence and spread of antibiotics resistance in wastewater treatment systems have been pointed as a major environmental health problem. Nevertheless, research about adaptation and antibiotics resistance gain in wastewater treatment systems subjected to antibiotics has not been successfully developed considering bioreactor performance, microbial community dynamics and microbial activity dynamics at the same time. To observe this in autotrophic nitrogen removal systems, a partial-nitritation biofilter was subjected to a continuous loading of antibiotics mix of azithromycin, norfloxacin, trimethoprim, and sulfamethoxazole. The effect of the antibiotics mix over the performance, bacterial communities and bacterial activity in the system was evaluated. The addition of antibiotics caused a drop of ammonium oxidation efficiency (from 50 to 5%) and of biomass concentration in the bioreactor, which was coupled to the loss of ammonium oxidizing bacteria Nitrosomonas in the bacterial community from 40 to 3%. Biomass in the partial nitritation biofilter experienced a sharp decrease of about 80% due to antibiotics loading, but the biomass adapted and experienced a growth by stabilization under antibiotics feeding. During the experiment several bacterial genera appeared, such as Alcaligenes, Paracoccus, and Acidovorax, clearly dominating the bacterial community with >20% relative abundance. The system reached around 30% ammonium oxidation efficiency after adaptation to antibiotics, but no effluent nitrite was found, suggesting that dominant antibiotics-resistant phylotypes could be involved in nitrification–denitrification metabolisms. The activity of ammonium oxidation measured as amoA and hao gene expression dropped a 98.25% and 99.21%, respectively, comparing the system before and after the addition of antibiotics. On the other hand, denitrifying activity increased as observed by higher expression of nir and nos genes (83.14% and 252.54%, respectively). In addition, heterotrophic nitrification cyt c-551 was active only after the antibiotics addition. Resistance to the antibiotics was presumably given by ermF, carA and msrA for azithromycin, mutations of the gyrA and grlB for norfloxacin, and by sul123 genes for sulfamethoxazole. Joined physicochemical and microbiological characterization of the system were used to investigate the effect of the antibiotics over the bioprocess. Despite the antibiotics resistance, activity of Bacteria decreased while the activity of Archaea and Fungi increased.

A critical review on the interaction of substrate nutrient balance and microbial community structure and function in anaerobic co-digestion

Anaerobic co-digestion generally results in a higher yield of biogas than mono-digestion, hence co-digestion has become a topic of general interest in recent studies of anaerobic digestion. Compared with mono-digestion, co-digestion utilizes multiple substrates. The balance of substrate nutrient in co-digestion comprises better adjustments of C/N ratio, pH, moisture, trace elements, and dilution of toxic substances. All of these changes could result in positive shifts in microbial community structure and function in the digestion processes and consequent augmentation of biogas production. Nevertheless, there have been few reviews on the interaction of nutrient and microbial community in co-digestions. The objective of this review is to investigate recent achievements and perspectives on the interaction of substrate nutrient balance and microbial community structure and function. This may provide valuable information on the optimization of combinations of substrates and prediction of bioreactor performance.

Importance of inoculum source and initial community structure for biogas production from agricultural substrates

This study evaluated the importance of inoculum source for start-up and operation of biogas processes. Three different inocula with different community structure were used to initiate six laboratory continuous stirred tank reactor (CSTR) processes operated with a grass manure mixture as substrate. The processes were evaluated by chemical and microbiological analysis, by targeting the overall bacterial community and potential cellulose-degrading bacteria. As expected, the results showed a large difference in community structure in the inocula and in process performance during the first hydraulic retention time (HRT). However, the performance and overall microbial community structure became similar in the reactors over time. An inoculum from a high-ammonia process, characterized by low diversity and low degradation efficiency, took the longest time to reach stability and final methane yield. The overall bacterial community was mainly shaped by the operating conditions but, interestingly, potential cellulose-degrading bacteria seemed mainly to originate from the substrate.

Effects of co-inoculating rice straw with ruminal microbiota and anaerobic sludge: digestion performance and spatial distribution of microbial communities

Ruminal microbiota (RM) were co-inoculated with anaerobic sludge (AS) at different ratios to study the digestion of rice straw in batch experiments. The CH₄ yield reached 273.64 mL/g volatile solid (VS) at a co-inoculum ratio of 1:1. The xylanase and cellulase activities were 198.88-212.88 and 24.51-29.08 U/mL in co-inoculated samples, respectively, and were significantly different compared to the results for single inoculum (p < 0.05). Higher ratios of AS enhanced acetoclastic methanogenesis, and propionate accumulation could be the main reason for the longer lag phase observed in samples with a higher RM ratio. The microbial compositions were clearly altered after digestion. Fibrobacter, Ruminococcus and Butyrivibrio from the rumen did not settle in the co-inoculated system, whereas Clostridiales members became the main polysaccharide degraders. Microbial interactions involving hydrolytic bacteria and acetoclastic methanogens in the residue were considered to be significant for hydrolysis activities and methane production. Syntrophy involving propionate oxidizers with associated methanogens occurred in the liquid phase. Our findings provide a better understanding of the anaerobic digestion of rice straw that is driven by specific microbial populations.

Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities

In order to investigate the long-term stability on the performance of the anaerobic digestion process, a laboratory-scale continuous stirred-tank reactor (CSTR) was operated for 1100 days with sunflower harvested in a heavy metal contaminated site. Changes of microbial communities during digestion were identified using pyrosequencing. According to the results, soluble heavy metal concentrations were lower than the reported inhibitory level and the reactor performance remained stable up to OLR of 2.0g-VS/L/day at HRT of 20days. Microbial communities commonly found in anaerobic digestion for cellulosic biomass were observed and stably established with respect to the substrate. Thus, the balance of microbial metabolism was maintained appropriately and anaerobic digestion seems to be feasible for disposal of heavy metal-containing crop residues from phytoremediation sites.