Microbial trophic interactions and mcrA gene expression in monitoring of anaerobic digesters

Fe-Mn binary oxides improve the methanogenic performance and reduce the environmental health risks associated with antibiotic resistance genes during anaerobic digestion

Increasing evidence indicates that metal oxides can improve the methanogenic performance during anaerobic digestion (AD) of piggery wastewater. However, the impacts of composite metal oxides on the methanogenic performance and risk of antibiotic resistance gene (ARG) transmission during AD are not fully understood. In this study, different concentrations of Fe-Mn binary oxides (FMBO at 0, 250, 500, and 1000 mg/L) were added to AD to explore the effects of FMBO on the process. The methane yield was 7825.1 mL under FMBO at 250 mg/L, 35.2% higher than that with FMBO at 0 mg/L. PICRUSt2 functional predictions showed that FMBO promoted the oxidation of acetate and propionate, and the production of methane from the substrate, as well as increasing the abundances of most methanogens and genes encoding related enzymes. Furthermore, under FMBO at 250 mg/L, the relative abundances of 14 ARGs (excluding tetC and sul2) and four mobile gene elements (MGEs) decreased by 24.7% and 55.8%, respectively. Most of the changes in the abundances of ARGs were explained by microorganisms, especially Bacteroidetes (51.20%), followed by MGEs (11.98%). Thus, the methanogenic performance of AD improved and the risk of horizontal ARG transfer decreased with FMBO, especially at 250 mg/L.

Mechanism of action of single and mixed antibiotics during anaerobic digestion of swine wastewater: Microbial functional diversity and gene expression analysis

The mechanism by which antibiotics in swine wastewater affect anaerobic digestion (AD) remains unclear. Herein, we investigated how single and mixed antibiotics affect AD in swine wastewater. Both single and mixed antibiotics stimulated methane production at actual concentrations of 0.5-2 mg/L. Low-dose antibiotics (0.5 mg/L) exerted the most significant stimulatory effect on methane production, which increased by 211.63% (single) and 60.93% (mixed), respectively. However, an increased dose decreased the stimulatory effect on methane production. Overall, single antibiotics were more beneficial for methane production than mixed antibiotics since single antibiotics could promote the conversion of propionic and butyric acid, while mixed antibiotics inhibited the process. Microbial community analysis showed that single and mixed antibiotics could also lead to large changes in functional acidogens, ultimately leading to changes in methanogenic pathways.

Comparative Transcriptomics Sheds Light on Remodeling of Gene Expression during Diazotrophy in the Thermophilic Methanogen Methanothermococcus thermolithotrophicus

Some marine thermophilic methanogens are able to perform energy-consuming nitrogen fixation despite deriving only little energy from hydrogenotrophic methanogenesis. We studied this process in Methanothermococcus thermolithotrophicus DSM 2095, a methanogenic archaeon of the order Methanococcales that contributes to the nitrogen pool in some marine environments. We successfully grew this archaeon under diazotrophic conditions in both batch and fermenter cultures, reaching the highest cell density reported so far. Diazotrophic growth depended strictly on molybdenum and, in contrast to other diazotrophs, was not inhibited by tungstate or vanadium. This suggests an elaborate control of metal uptake and a specific metal recognition system for the insertion into the nitrogenase cofactor. Differential transcriptomics of M. thermolithotrophicus grown under diazotrophic conditions with ammonium-fed cultures as controls revealed upregulation of the nitrogenase machinery, including chaperones, regulators, and molybdate importers, as well as simultaneous upregulation of an ammonium transporter and a putative pathway for nitrate and nitrite utilization. The organism thus employs multiple synergistic strategies for uptake of nitrogen nutrients during the early exponential growth phase without altering transcription levels for genes involved in methanogenesis. As a counterpart, genes coding for transcription and translation processes were downregulated, highlighting the maintenance of an intricate metabolic balance to deal with energy constraints and nutrient limitations imposed by diazotrophy. This switch in the metabolic balance included unexpected processes, such as upregulation of the CRISPR-Cas system, probably caused by drastic changes in transcription levels of putative mobile and virus-like elements. IMPORTANCE The thermophilic anaerobic archaeon M. thermolithotrophicus is a particularly suitable model organism to study the coupling of methanogenesis to diazotrophy. Likewise, its capability of simultaneously reducing N₂ and CO₂ into NH₃ and CH₄ with H₂ makes it a viable target for biofuel production. We optimized M. thermolithotrophicus cultivation, resulting in considerably higher cell yields and enabling the successful establishment of N₂-fixing bioreactors. Improved understanding of the N₂ fixation process would provide novel insights into metabolic adaptations that allow this energy-limited extremophile to thrive under diazotrophy, for instance, by investigating its physiology and uncharacterized nitrogenase. We demonstrated that diazotrophic growth of M. thermolithotrophicus is exclusively dependent on molybdenum, and complementary transcriptomics corroborated the expression of the molybdenum nitrogenase system. Further analyses of differentially expressed genes during diazotrophy across three cultivation time points revealed insights into the response to nitrogen limitation and the coordination of core metabolic processes.

Delineating the Drivers and Functionality of Methanogenic Niches within an Arid Landfill

Microbial communities mediate the transformation of organic matter within landfills into methane (CH₄). Yet their ecological role in CH₄ production is rarely evaluated. To characterize the microbiome associated with this biotransformation, the overall community and methanogenic Archaea were surveyed in an arid landfill using leachate collected from distinctly aged landfill cells (i.e., younger, intermediate, and older). We hypothesized that distinct methanogenic niches exist within an arid landfill, driven by geochemical gradients that developed under extended and age-dependent waste biodegradation stages. Using 16S rRNA and mcrA gene amplicon sequencing, we identified putative methanogenic niches as follows. The order Methanomicrobiales was the most abundant order in leachate from younger cells, where leachate temperature and propionate concentrations were measured at 41.8°C ± 1.7°C and 57.1 ± 10.7 mg L⁻¹. In intermediate-aged cells, the family Methanocellaceae was identified as a putative specialist family under intermediate-temperature and -total dissolved solid (TDS) conditions, wherein samples had a higher alpha diversity index and near CH₄ concentrations. In older-aged cells, accumulating metals and TDS supported Methanocorpusculaceae, “Candidatus Bathyarchaeota,” and “Candidatus Verstraetearchaeota” operational taxonomic units (OTUs). Consistent with the mcrA data, we assayed methanogenic activity across the age gradient through stable isotopic measurements of δ¹³C of CH₄ and δ¹³C of CO₂. The majority (80%) of the samples’ carbon fractionation was consistent with hydrogenotrophic methanogenesis. Together, we report age-dependent geochemical gradients detected through leachate in an arid landfill seemingly influencing CH₄ production, niche partitioning, and methanogenic activity.

IMPORTANCE Microbiome analysis is becoming common in select municipal and service ecosystems, including wastewater treatment and anaerobic digestion, but its potential as a microbial-status-informative tool to promote or mitigate CH₄ production has not yet been evaluated in landfills. Methanogenesis mediated by Archaea is highly active in solid-waste microbiomes but is commonly neglected in studies employing next-generation sequencing techniques. Identifying methanogenic niches within a landfill offers detail into operations that positively or negatively impact the commercial production of methane known as biomethanation. We provide evidence that the geochemistry of leachate and its microbiome can be a variable accounting for ecosystem-level (coarse) variation of CH₄ production, where we demonstrate through independent assessments of leachate and gas collection that the functional variability of an arid landfill is linked to the composition of methanogenic Archaea.

Long-Term, Simultaneous Impact of Antimicrobials on the Efficiency of Anaerobic Digestion of Sewage Sludge and Changes in the Microbial Community

The aim of this study was to evaluate the influence of simultaneous, long-term exposure to increasing concentrations of three classes of antimicrobials (β-lactams, fluoroquinolones and nitroimidazoles) on: (1) the efficiency of anaerobic digestion of sewage sludge, (2) qualitative and quantitative changes in microbial consortia that participate in methane fermentation, and (3) fate of antibiotic resistance genes (ARGs). Long-term supplementation of sewage sludge with a combination of metronidazole, amoxicillin and ciprofloxacin applied at different doses did not induce significant changes in process parameters, including the concentrations of volatile fatty acids (VFAs), or the total abundance of ARGs. Exposure to antibiotics significantly decreased methane production and modified microbial composition. The sequencing analysis revealed that the abundance of OTUs characteristic of Archaea was not correlated with the biogas production efficiency. The study also demonstrated that the hydrogen-dependent pathway of methylotrophic methanogenesis could significantly contribute to the stability of anaerobic digestion in the presence of antimicrobials. The greatest changes in microbial biodiversity were noted in substrate samples exposed to the highest dose of the tested antibiotics, relative to control. The widespread use of antimicrobials increases antibiotic concentrations in sewage sludge, which may decrease the efficiency of anaerobic digestion, and contribute to the spread of antibiotic resistance (AR).

Microbiological insights into anaerobic digestion for biogas, hydrogen or volatile fatty acids (VFAs): a review

In the past decades, considerable attention has been directed toward anaerobic digestion (AD), which is an effective biological process for converting diverse organic wastes into biogas, volatile fatty acids (VFAs), biohydrogen, etc. The microbial bioprocessing takes part during AD is of substantial significance, and one of the crucial approaches for the deep and adequate understanding and manipulating it toward different products is process microbiology. Due to highly complexity of AD microbiome, it is critically important to study the involved microorganisms in AD. In recent years, in addition to traditional methods, novel molecular techniques and meta-omics approaches have been developed which provide accurate details about microbial communities involved AD. Better understanding of process microbiomes could guide us in identifying and controlling various factors in both improving the AD process and diverting metabolic pathway toward production of selective bio-products. This review covers various platforms of AD process that results in different final products from microbiological point of view. The review also highlights distinctive interactions occurring among microbial communities. Furthermore, assessment of these communities existing in the anaerobic digesters is discussed to provide more insights into their structure, dynamics, and metabolic pathways. Moreover, the important factors affecting microbial communities in each platform of AD are highlighted. Finally, the review provides some recent applications of AD for the production of novel bio-products and deals with challenges and future perspectives of AD.

The impact of antimicrobials on the efficiency of methane fermentation of sewage sludge, changes in microbial biodiversity and the spread of antibiotic resistance

The study was designed to simultaneously evaluate the influence of high doses (512-1024 µg/g) the most commonly prescribed antimicrobials on the efficiency of anaerobic digestion of sewage sludge, qualitative and quantitative changes in microbial consortia responsible for the fermentation process, the presence of methanogenic microorganisms, and the fate of antibiotic resistance genes (ARGs). The efficiency of antibiotic degradation during anaerobic treatment was also determined. Metronidazole, amoxicillin and ciprofloxacin exerted the greatest effect on methane fermentation by decreasing its efficiency. Metronidazole, amoxicillin, cefuroxime and sulfamethoxazole were degraded in 100%, whereas ciprofloxacin and nalidixic acid were least susceptible to degradation. The most extensive changes in the structure of digestate microbiota were observed in sewage sludge exposed to metronidazole, where a decrease in the percentage of bacteria of the phylum Bacteroidetes led to an increase in the proportions of bacteria of the phyla Firmicutes and Proteobacteria. The results of the analysis examining changes in the concentration of the functional methanogen gene (mcrA) did not reflect the actual efficiency of methane fermentation. In sewage sludge exposed to antimicrobials, a significant increase was noted in the concentrations of β-lactam, tetracycline and fluoroquinolone ARGs and integrase genes, but selective pressure was not specific to the corresponding ARGs.

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

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

Waste to Energy: A Focus on the Impact of Substrate Type in Biogas Production

Anaerobic digestion is an efficient technology for a sustainable conversion of various organic wastes such as animal manure, municipal solid waste, agricultural residues and industrial waste into biogas. This technology offers a unique set of benefits, some of which include a good waste management technique, enhancement in the ecology of rural areas, improvement in health through a decrease of pathogens and optimization of the energy consumption of communities. The biogas produced through anaerobic digestion varies in composition, but it consists mainly of carbon dioxide methane together with a low quantity of trace gases. The variation in biogas composition are dependent on some factors namely the substrate type being digested, pH, operating temperature, organic loading rate, hydraulic retention time and digester design. However, the type of substrate used is of greater interest due to the direct dependency of microorganism activities on the nutritional composition of the substrate. Therefore, the aim of this review study is to provide a detailed analysis of the various types of organic wastes that have been used as a substrate for the sustainable production of biogas. Biogas formation from various substrates reported in the literature were investigated, an analysis and characterization of these substrates provided the pro and cons associated with each substrate. The findings obtained showed that the methane yield for all animal manure varied from 157 to 500 mL/gVS with goat and pig manure superseding the other animal manure whereas lignocellulose biomass varied from 160 to 212 mL/gVS. In addition, organic municipal solid waste and industrial waste showed methane yield in the ranges of 143–516 mL/gVS and 25–429 mL/gVS respectively. These variations in methane yield are primarily attributed to the nutritional composition of the various substrates.

Recognition of core microbial communities contributing to complex organic components degradation during dry anaerobic digestion of chicken manure

Microbial metabolism of complex organic components can drive different microbial communities, which is significant to the process of dry anaerobic digestion (AD). However, possible mechanisms between organic components and the corresponding microbial communities during the process of dry AD is poorly investigated. Results showed that the microbial species affecting the degradation of organic components were 69 nodes (13.3%) in the hydrolysis stage, hemicellulose was mainly degraded by Methanobacterium (2.3%), with a degradation rate of 35.0%. In the acetogenesis stage, the microbial species were 27 nodes (10.3%), hemicellulose was mainly degraded by LK-44f (0.1%) and Treponema (0.3%), with a degradation rate of 52.2%. In the methanogenesis stage, the microbial species were 10 nodes (4.8%), polysaccharide was mainly degraded by Ureibacillus (0.1%), with a degradation rate of 46.9%. The study provides theoretical support for the rapid degradation of complex components by segment-oriented regulation.

Acetate promotes microbial reductive debromination of tetrabromobisphenol A during the startup phase of anaerobic wastewater sludge bioreactors

The detection of increasing concentrations of tetrabromobisphenol A (TBBPA) in wastewater treatment plants is raising concerns as TBBPA has been identified as a potentially toxic flame retardant. The objectives of this study were to evaluate the effect of acetate biostimulation on TBBPA microbial reductive debromination, and the response of anaerobic sludge associated microbial communities repeatedly exposed to TBBPA. Results indicate that the bulk of the microbial community did not experience significant shifts as a result of TBBPA exposure, and that only a small fraction of the community responded to the presence of TBBPA. Taxa most likely responsible for TBBPA transformation affiliated to Clostridiales and the wastewater sludge group Blvii28. The biostimulating effect of acetate was only observed during reactor startup, when acetogenesis was likely not yet occurring. However, when acetate likely started to be microbially generated in the reactor, acetate addition resulted in a slight but significant inhibiting effect on TBBPA transformation. A significant increase of hydrogenotrophic methanogens in the TBBPA-spiked reactor overtime implies that TBBPA degraders were not in direct competition with methanogens for H₂. These results strongly suggest that TBBPA degrading taxa might have been primarily using acetate as an electron donor for the reductive debromination of TBBPA.

Microbiota of a Full-scale UASB Reactor Treating Brewery Wastewater Using Illumina MiSeq Sequencing

Background:

The efficiency of biological wastewater treatment plant is determined by bacterial metabolism. There are data on the effect of operational parameters on microbial consortia present in laboratory scale reactor. However, knowledge on the full-scale reactor is still limited at present, hence the need to define the relations between the microbial structure and the performance of full-scale reactor.

Objective:

In this study, the microbial community structure in a full-scale UASB reactor treating brewery wastewater was assessed using metagenomics Next-Generation Sequencing technique.

Method:

Granular sludge samples were collected from the UASB reactor treating brewery wastewater and extracted genomic DNA was amplified using barcoded bacterial primer sets targeting V3-V4 region of the 16S rRNA genes on sequencing Illumina MiSeq platform.

Results:

The taxonomic analysis revealed the abundance of bacteria (~95%) with considerable Archaea community (~2%) in the granular sludge. After trimming, 18 bacterial phyla, 29 orders, 36 families and 44 genera were recovered from the 48,488 sequences reads of the 16S rRNA genes analysed, where the most abundant community belongs to Firmicutes, Bacteroidetes, Synergistetes and Proteobacteria phyla.

Conclusion:

For a sustainable bioenergy generation, understanding the mechanisms of anaerobic system in relation to microbial community is an important factor to increase the production of biogas production during wastewater treatment. To the best of our knowledge, this report is one of the studies that explored and described bacterial diversity and community structure of a full-scale UASB reactor treating brewery wastewater using high-throughput sequencing. This study provides insight into the dominant microbial community and their phylogenetic diversity in biogas producing reactor.

Electron Fluxes in Biocathode Bioelectrochemical Systems Performing Dechlorination of Chlorinated Aliphatic Hydrocarbons

Bioelectrochemical systems (BESs) are regarded as a promising approach for the enhanced dechlorination of chlorinated aliphatic hydrocarbons (CAHs). However, the electron distribution and transfer considering dechlorination, methanogenesis, and other bioprocesses in these systems are little understood. This study investigated the electron fluxes in biocathode BES performing dechlorination of three typical CAHs, 1,1,2,2-tetrachloroethene (PCE), 1,1,2-trichloroethene (TCE) and 1,2-dichloroethane (1,2-DCA). Anaerobic sludge was inoculated to cathode and biocathode was acclimated by the direct acclimation and selection. The constructed biocathode at −0.26 V had significantly higher dechlorination efficiency (E_24h > 99.0%) than the opened circuit (E_24h of 17.2–27.5%) and abiotic cathode (E_24h of 5.5–10.8%), respectively. Cyclic voltammetry analysis demonstrated the enhanced cathodic current and the positive shift of onset potential in the cathodic biofilm. Under autotrophic conditions with electrons from the cathode as sole energy source (columbic efficiencies of 80.4–90.0%) and bicarbonate as sole carbon source, CAHs dechlorination efficiencies were still maintained at 85.0 ± 2.0%, 91.4 ± 1.8%, and 84.9 ± 3.1% for PCE, TCE, and 1,2-DCA, respectively. Cis-1,2-dichloroethene was the final product for PCE and TCE, while 1,2-DCA went through a different dechlorination pathway with the non-toxic ethene as the final metabolite. Methane was the main by-product of the heterotrophic biocathode, and methane production could be enhanced to some extent by electrochemical stimulation. The various electron fluxes originating from the cathode and oxidation of organic substrates might be responsible for the enhanced CAHs dechlorination, while methane generation and bacterial growth would probably reduce the fraction of electrons provided for CAH dechlorination. The study deals with the dechlorination and competitive bioprocesses in CAH-dechlorinating biocathodes with a focus on electron fluxes.

Metatranscriptomics reveals a differential temperature effect on the structural and functional organization of the anaerobic food web in rice field soil

BACKGROUND

The expected increase in global surface temperature due to climate change may have a tremendous effect on the structure and function of the anaerobic food web in flooded rice field soil. Here, we used the metatranscriptomic analysis of total RNA to gain a system-level understanding of this temperature effect on the methanogenic food web.

RESULTS

Mesophilic (30 °C) and thermophilic (45 °C) food web communities had a modular structure. Family-specific rRNA dynamics indicated that each network module represents a particular function within the food webs. Temperature had a differential effect on all the functional activities, including polymer hydrolysis, syntrophic oxidation of key intermediates, and methanogenesis. This was further evidenced by the temporal expression patterns of total bacterial and archaeal mRNA and of transcripts encoding carbohydrate-active enzymes (CAZymes). At 30 °C, various bacterial phyla contributed to polymer hydrolysis, with Firmicutes decreasing and non-Firmicutes (e.g., Bacteroidetes, Ignavibacteriae) increasing with incubation time. At 45 °C, CAZyme expression was solely dominated by the Firmicutes but, depending on polymer and incubation time, varied on family level. The structural and functional community dynamics corresponded well to process measurements (acetate, propionate, methane). At both temperatures, a major change in food web functionality was linked to the transition from the early to late stage. The mesophilic food web was characterized by gradual polymer breakdown that governed acetoclastic methanogenesis (Methanosarcinaceae) and, with polymer hydrolysis becoming the rate-limiting step, syntrophic propionate oxidation (Christensenellaceae, Peptococcaceae). The thermophilic food web had two activity stages characterized first by polymer hydrolysis and followed by syntrophic oxidation of acetate (Thermoanaerobacteraceae, Heliobacteriaceae, clade OPB54). Hydrogenotrophic Methanocellaceae were the syntrophic methanogen partner, but their population structure differed between the temperatures. Thermophilic temperature promoted proliferation of a new Methanocella ecotype.

CONCLUSIONS

Temperature had a differential effect on the structural and functional continuum in which the methanogenic food web operates. This temperature-induced change in food web functionality may not only be a near-future scenario for rice paddies but also for natural wetlands in the tropics and subtropics.

Influence of food waste addition over microbial communities in an Anaerobic Membrane Bioreactor plant treating urban wastewater

Notorious changes in microbial communities were observed during and after the joint treatment of wastewater with Food Waste (FW) in an Anaerobic Membrane Bioreactor (AnMBR) plant. The microbial population was analysed by high-throughput sequencing of the 16S rRNA gene and dominance of Chloroflexi, Firmicutes, Synergistetes and Proteobacteria phyla was found. The relative abundance of these potential hydrolytic phyla increased as a higher fraction of FW was jointly treated. Moreover, whereas Specific Methanogenic Activity (SMA) rose from 10 to 51 mL CH₄ g^-1 VS, Methanosarcinales order increased from 34.0% over 80.0% of total Archaea, being Methanosaeta the dominant genus. The effect of FW over AnMBR biomass was observed during the whole experience, as methane production rose from 49.2 to 144.5 L CH₄ · kg^-1 influent COD. Furthermore, biomethanization potential was increased over 82% after the experience. AnMBR technology allows the established microbial community to remain in the bioreactor even after the addition of FW, improving the anaerobic digestion of urban wastewater.

Defluviitalea raffinosedens sp. nov., a thermophilic, anaerobic, saccharolytic bacterium isolated from an anaerobic batch digester treating animal manure and rice straw

A thermophilic, anaerobic, fermentative bacterium, strain A6T, was obtained from an anaerobic batch digester treating animal manure and rice straw. Cells were Gram-stain-positive, slightly curved rods with a size of 0.6-1×2.5-8.2 µm, non-motile and produced terminal spores. The temperature, pH and NaCl concentration ranges for growth were 40-60 °C, 6.5-8.0 and 0-15.0 g l-1, with optimum growth noted at 50-55 °C, pH 7.5 and in the absence of NaCl, respectively. Yeast extract was required for growth. d-Glucose, maltose, d-xylose, d-galactose, d-fructose, d-ribose, lactose, raffinose, sucrose, d-arabinose, cellobiose, d-mannose and yeast extract were used as carbon and energy sources. The fermentation products from glucose were ethanol, lactate, acetate, propionate, butyrate, valerate, iso-butyrate, iso-valerate, H2 and CO2. The G+C content of the genomic DNA was 36.6 mol%. The predominant fatty acids were C16 : 0, iso-C17 : 1, C14 : 0, C16 : 1ω7c, C16 : 0 N-alcohol and C13 : 0 3-OH. Respiratory quinones were not detected. The polar lipid profile comprised phosphoglycolipids, phospholipids, glycolipids, a diphosphatidylglycerol, a phosphatidylglycerol and an unidentified lipid. Phylogenetic analyses of the 16S rRNA gene sequence indicated that the strain was closely related to Defluviitalea saccharophila DSM 22681T with a similarity of 96.0 %. Based on the morphological, physiological and taxonomic characterization, strain A6T is considered to represent a novel species of the genus Defluviitalea, for which the name Defluviitalea raffinosedens sp. nov. is proposed. The type strain is A6T (=DSM 28090T=ACCC 19951T).

Diversity of microbial carbohydrate-active enzymes in Danish anaerobic digesters fed with wastewater treatment sludge

BACKGROUND

Improved carbohydrate-active enzymes (CAZymes) are needed to fulfill the goal of producing food, feed, fuel, chemicals, and materials from biomass. Little is known about how the diverse microbial communities in anaerobic digesters (ADs) metabolize carbohydrates or which CAZymes that are present, making the ADs a unique niche to look for CAZymes that can potentiate the enzyme blends currently used in industry.

RESULTS

Enzymatic assays showed that functional CAZymes were secreted into the AD environments in four full-scale mesophilic Danish ADs fed with primary and surplus sludge from municipal wastewater treatment plants. Metagenomes from the ADs were mined for CAZymes with Homology to Peptide Patterns (HotPep). 19,335 CAZymes were identified of which 30% showed 50% or lower identity to known proteins demonstrating that ADs make up a promising pool for discovery of novel CAZymes. A function was assigned to 54% of all CAZymes identified by HotPep. Many different α-glucan-acting CAZymes were identified in the four metagenomes, and the most abundant family was glycoside hydrolase family 13, which contains α-glucan-acting CAZymes. Cellulytic and xylanolytic CAZymes were also abundant in the four metagenomes. The cellulytic enzymes were limited almost to endoglucanases and β-glucosidases, which reflect the large amount of partly degraded cellulose in the sludge. No dockerin domains were identified suggesting that the cellulytic enzymes in the ADs studied operate independently. Of xylanolytic CAZymes, especially xylanases and β-xylosidase, but also a battery of accessory enzymes, were present in the four ADs.

CONCLUSIONS

Our findings suggest that the ADs are a good place to look for novel plant biomass degrading and modifying enzymes that can potentiate biological processes and provide basis for production of a range of added-value products from biorefineries.

Incubation of innovative methanogenic communities to seed anaerobic digesters

The methanogenic communities in alternative inocula and their potential to increase CH₄ production in mesophilic and psychrophilic dairy manure-based anaerobic digesters were examined. Quantitative-PCR and terminal restriction fragment length polymorphism (T-RFLP) profiles were used to determine archaeal and methanogenic community changes when three inocula (wetland sediment (WS), landfill leachate (LL), and mesophilic digestate (MD)) were incubated at 15, 25, and 35 °C for 91 and 196 days. After each incubation period, the inocula were used in biochemical methane potential (BMP) tests at the incubation temperatures. There was no significant correlation between inoculum mcrA gene copy numbers and CH₄ produced in BMP tests, suggesting that population size was not a distinguishing characteristic for predicting CH₄ production. Archaeal composition in LL and WS reactors generally converged with MD reactors after incubation at 25 and 35 °C for 196 days. These MD reactors had high relative abundance of TRF 302, likely Methanosaetaceae, and low acetic acid (0.62-1.61 mM). At 15 °C incubation, most reactors were associated with high acetic acid (1.61-133.6 mM) and dominated by TRF 199, likely Methanosarcinaceae. The LL reactor incubated at 25 °C for 91 days had higher relative abundance of TRF 199 and produced significantly higher CH₄ than WS and MD reactors in BMP test. In the future, it may be possible to create enrichment cultures that favor particular methanogens and use them as inoculum to benefit digesters at low mesophilic temperatures. Our data provides evidence that tailoring the archaeal community could benefit digesters operating under different conditions.

Overcoming organic and nitrogen overload in thermophilic anaerobic digestion of pig slurry by coupling a microbial electrolysis cell

The combination of the anaerobic digestion (AD) process with a microbial electrolysis cell (MEC) coupled to an ammonia stripping unit as a post-treatment was assessed both in series operation, to improve the quality of the effluent, and in loop configuration recirculating the effluent, to increase the AD robustness. The MEC allowed maintaining the chemical oxygen demand removal of the whole system of 46±5% despite the AD destabilization after doubling the organic and nitrogen loads, while recovering 40±3% of ammonia. The AD-MEC system, in loop configuration, helped to recover the AD (55% increase in methane productivity) and attained a more stable and robust operation. The microbial population assessment revealed an enhancement of AD methanogenic archaea numbers and a shift in eubacterial population. The AD-MEC combined system is a promising strategy for stabilizing AD against organic and nitrogen overloads, while improving the quality of the effluent and recovering nutrients for their reutilization.

Characterization and Adaptation of Anaerobic Sludge Microbial Communities Exposed to Tetrabromobisphenol A

The increasing occurrence of tetrabromobisphenol A (TBBPA) in the environment is raising questions about its potential ecological and human health impacts. TBBPA is microbially transformed under anaerobic conditions to bisphenol A (BPA). However, little is known about which taxa degrade TBBPA and the adaptation of microbial communities exposed to TBBPA. The objectives of this study were to characterize the effect of TBBPA on microbial community structure during the start-up phase of a bench-scale anaerobic sludge reactor, and identify taxa that may be associated with TBBPA degradation. TBBPA degradation was monitored using LC/MS-MS, and the microbial community was characterized using Ion Torrent sequencing and qPCR. TBBPA was nearly completely transformed to BPA via reductive debromination in 55 days. Anaerobic reactor performance was not negatively affected by the presence of TBBPA and the bulk of the microbial community did not experience significant shifts. Several taxa showed a positive response to TBBPA, suggesting they may be associated with TBBPA degradation. Some of these taxa had been previously identified as dehalogenating bacteria including Dehalococcoides, Desulfovibrio, Propionibacterium, and Methylosinus species, but most had not previously been identified as having dehalogenating capacities. This study is the first to provide in-depth information on the microbial dynamics of anaerobic microbial communities exposed to TBBPA.

Biogas Production: Microbiology and Technology

Biogas, containing energy-rich methane, is produced by microbial decomposition of organic material under anaerobic conditions. Under controlled conditions, this process can be used for the production of energy and a nutrient-rich residue suitable for use as a fertilising agent. The biogas can be used for production of heat, electricity or vehicle fuel. Different substrates can be used in the process and, depending on substrate character, various reactor technologies are available. The microbiological process leading to methane production is complex and involves many different types of microorganisms, often operating in close relationships because of the limited amount of energy available for growth. The microbial community structure is shaped by the incoming material, but also by operating parameters such as process temperature. Factors leading to an imbalance in the microbial community can result in process instability or even complete process failure. To ensure stable operation, different key parameters, such as levels of degradation intermediates and gas quality, are often monitored. Despite the fact that the anaerobic digestion process has long been used for industrial production of biogas, many questions need still to be resolved to achieve optimal management and gas yields and to exploit the great energy and nutrient potential available in waste material. This chapter discusses the different aspects that need to be taken into consideration to achieve optimal degradation and gas production, with particular focus on operation management and microbiology.

Substrate Type and Free Ammonia Determine Bacterial Community Structure in Full-Scale Mesophilic Anaerobic Digesters Treating Cattle or Swine Manure

The microbial-mediated anaerobic digestion (AD) process represents an efficient biological process for the treatment of organic waste along with biogas harvest. Currently, the key factors structuring bacterial communities and the potential core and unique bacterial populations in manure anaerobic digesters are not completely elucidated yet. In this study, we collected sludge samples from 20 full-scale anaerobic digesters treating cattle or swine manure, and investigated the variations of bacterial community compositions using high-throughput 16S rRNA amplicon sequencing. Clustering and correlation analysis suggested that substrate type and free ammonia (FA) play key roles in determining the bacterial community structure. The COD: NH4+-N (C:N) ratio of substrate and FA were the most important available operational parameters correlating to the bacterial communities in cattle and swine manure digesters, respectively. The bacterial populations in all of the digesters were dominated by phylum Firmicutes, followed by Bacteroidetes, Proteobacteria and Chloroflexi. Increased FA content selected Firmicutes, suggesting that they probably play more important roles under high FA content. Syntrophic metabolism by Proteobacteria, Chloroflexi, Synergistetes and Planctomycetes are likely inhibited when FA content is high. Despite the different manure substrates, operational conditions and geographical locations of digesters, core bacterial communities were identified. The core communities were best characterized by phylum Firmicutes, wherein Clostridium predominated overwhelmingly. Substrate-unique and abundant communities may reflect the properties of manure substrate and operational conditions. These findings extend our current understanding of the bacterial assembly in full-scale manure anaerobic digesters.

Analysis of methane-producing and metabolizing archaeal and bacterial communities in sediments of the northern South China Sea and coastal Mai Po Nature Reserve revealed by PCR amplification of mcrA and pmoA genes

Communities of methanogens, anaerobic methanotrophic archaea and aerobic methanotrophic bacteria (MOB) were compared by profiling polymerase chain reaction (PCR)-amplified products of mcrA and pmoA genes encoded by methyl-coenzyme M reductase alpha subunit and particulate methane monooxygenase alpha subunit, respectively, in sediments of northern South China Sea (nSCS) and Mai Po mangrove wetland. Community structures representing by mcrA gene based on 12 clone libraries from nSCS showed separate clusters indicating niche specificity, while, Methanomicrobiales, Methanosarcinales clades 1,2, and Methanomassiliicoccus-like groups of methanogens were the most abundant groups in nSCS sediment samples. Novel clusters specific to the SCS were identified and the phylogeny of mcrA gene-harboring archaea was updated. Quantitative polymerase chain reaction was used to detect mcrA gene abundance in all samples: similar abundance of mcrA gene in the surface layers of mangrove (3.4∼3.9 × 10⁶ copies per gram dry weight) and of intertidal mudflat (5.5∼5.8 × 10⁶ copies per gram dry weight) was observed, but higher abundance (6.9 × 10⁶ to 1.02 × 10⁸ copies per gram dry weight) was found in subsurface samples of both sediment types. Aerobic MOB were more abundant in surface layers (6.7∼11.1 × 10⁵ copies per gram dry weight) than the subsurface layers (1.2∼5.9 × 10⁵ copies per gram dry weight) based on pmoA gene. Mangrove surface layers harbored more abundant pmoA gene than intertidal mudflat, but less pmoA genes in the subsurface layers. Meanwhile, it is also noted that in surface layers of all samples, more pmoA gene copies were detected than the subsurface layers. Reedbed rhizosphere exhibited the highest gene abundance of mcrA gene (8.51 × 10⁸ copies per gram dry weight) and pmoA gene (1.56 × 10⁷ copies per gram dry weight). This study investigated the prokaryotic communities responsible for methane cycling in both marine and coastal wetland ecosystems, showing the distribution characteristics of mcrA gene-harboring communities in nSCS and stratification of mcrA and pmoA gene diversity and abundance in the Mai Po Nature Reserve.

Effects of 17β-estradiol on typical greenhouse gas emissions in aquatic anaerobic ecosystem

Anaerobic microecosystems designed with different concentrations of 17β-estradiol (17β-E2) (0.0-10,000.0 ng/L) were simulated in this study. The influence of different concentrations of 17β-E2 on the emissions of typical greenhouse gases (CH4 and CO2) in simulated anaerobic microecosystems is analyzed to primarily explore the relationship between 17β-E2 and such emissions in aquatic anaerobic ecosystems. The results showed that 17β-E2 could promote or significantly stimulate aquatic anaerobic micro-organisms' production of CH4. The degree and the promotion time of CH4 production were both enhanced with the increase of 17β-E2 concentration. Furthermore, under higher concentration of 17β-E2 (≥500.0 ng/L), the increasing tendency of aquatic anaerobic microbial populations' activity and the function of methanogenic activity under corresponding experimental conditions had a synchronous relationship.