Comparison of the microbial communities in solid-state anaerobic digestion (SS-AD) reactors operated at mesophilic and thermophilic temperatures

Application of next-generation sequencing methods for microbial monitoring of anaerobic digestion of lignocellulosic biomass

The anaerobic digestion of lignocellulosic wastes is considered an efficient method for managing the world's energy shortages and resolving contemporary environmental problems. However, the recalcitrance of lignocellulosic biomass represents a barrier to maximizing biogas production. The purpose of this review is to examine the extent to which sequencing methods can be employed to monitor such biofuel conversion processes. From a microbial perspective, we present a detailed insight into anaerobic digesters that utilize lignocellulosic biomass and discuss some benefits and disadvantages associated with the microbial sequencing techniques that are typically applied. We further evaluate the extent to which a hybrid approach incorporating a variation of existing methods can be utilized to develop a more in-depth understanding of microbial communities. It is hoped that this deeper knowledge will enhance the reliability and extent of research findings with the end objective of improving the stability of anaerobic digesters that manage lignocellulosic biomass.

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste

Anaerobic digestion (AnD) is a microbiological process that converts organic waste materials into biogas. Because of its high methane content, biogas is a combustible energy source and serves as an important environmental technology commonly used in the management of animal waste generated on large animal farms. Much work has been done on hardware design and process engineering for the generation of biogas. However, little is known about the complexity of the microbiology in this process. In particular, how microbes interact in the digester and eventually breakdown and convert organic matter into biogas is still regarded as a "black box." We used 16S rRNA sequencing as a tool to study the microbial community in laboratory hog waste digesters under tightly controlled conditions, and systematically unraveled the distinct interaction networks of two microbial communities from mesophilic (MAnD) and thermophilic anaerobic digestion (TAnD). Under thermophilic conditions, the well-known association between hydrogen-producing bacteria, e.g., Ruminococcaceae and Prevotellaceae, and hydrotrophic methanogens, Methanomicrobiaceae, was reverse engineered by their interactive topological niches. The inferred interaction network provides a sketch enabling the determination of microbial interactive relationships that conventional strategy of finding differential taxa was hard to achieve. This research is still in its infancy, but it can help to depict the dynamics of microbial ecosystems and to lay the groundwork for understanding how microorganisms cohabit in the anaerobic digester.

Solid anaerobic digestion batch with liquid digestate recirculation and wet anaerobic digestion of organic waste: Comparison of system performances and identification of microbial guilds

Solid anaerobic digestion batch (SADB) with liquid digestate recirculation and wet anaerobic digestion of organic waste were experimentally investigated. SADB was operated at an organic loading rate (OLR) of 4.55kgVS/m³day, generating about 252NL CH₄/kgVS, whereas the wet digester was operated at an OLR of 0.9kgVS/m³day, generating about 320NL CH₄/kgVS. The initial total volatile fatty acids concentrations for SADB and wet digestion were about 12,500mg/L and 4500mg/L, respectively. There were higher concentrations of ammonium and COD for the SADB compared to the wet one. The genomic analysis performed by high throughput sequencing returned a number of sequences for each sample ranging from 110,619 to 373,307. More than 93% were assigned to the Bacteria domain. Seven and nine major phyla were sequenced for the SADB and wet digestion, respectively, with Bacteroidetes, Firmicutes and Proteobacteria being the dominant phyla in both digesters. Taxonomic profiles suggested a methanogenic pathway characterized by a relevant syntrophic acetate-oxidizing metabolism mainly in the liquid digestate of the SADB. This result also confirms the benefits of liquid digestate recirculation for improving the efficiency of AD performed with high solids (>30%w/w) content.

Effects of geographic area, feedstock, temperature, and operating time on microbial communities of six full-scale biogas plants

The objective of this study was to investigate the effect of different animal feedings operated in two distinct PDO (protected designation of origin) cheese production areas (Parmigiano Reggiano and Grana Padano) on the microbiome of six full-scale biogas plants, by means of Illumina sequencing and qPCR techniques. The effects of feedstock (cattle slurry manure, energy crops, agro-industrial by-products), temperature (mesophilic/thermophilic), and operating time were also examined, as were the relationships between the predominant bacterial and archaeal taxa and process parameters. The different feedstocks and temperatures strongly affected the microbiomes. A more biodiverse archaeal population was highlighted in Parmigiano Reggiano area plants, suggesting an influence of the different animal feedings. Methanosarcina and Methanosaeta showed an opposite distribution among anaerobic plants, with the former found to be related to ammonium concentration. The Methanoculleus genus was more abundant in the thermophilic digester whereas representation of the Thermotogales order correlated with hydraulic retention time.

Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

Comparison of microbial communities during the anaerobic digestion of Gracilaria under mesophilic and thermophilic conditions

Mesophilic and thermophilic anaerobic digesters (MD and TD, respectively) utilizing Gracilaria and marine sediment as the substrate and inoculum, respectively, were compared by analyzing their performances and microbial community changes. During three successive transfers, the average cumulative methane yields in the MD and TD were 222.6 ± 17.3 mL CH4/g volatile solids (VS) and 246.1 ± 11 mL CH4/g VS, respectively. The higher hydrolysis rate and acidogenesis in the TD resulted in a several fold greater accumulation of volatile fatty acids (acetate, propionate, and butyrate) followed by a larger pH drop with a prolonged recovery than in the MD. However, the operational stability between both digesters remained comparable. Pyrosequencing analyses revealed that the MD had more complex microbial diversity indices and microbial community changes than the TD. Interestingly, Methanomassiliicoccales, the seventh methanogen order was the predominant archaeal order in the MD along with bacterial orders of Clostridiales, Bacteriodales, and Synergistales. Meanwhile, Coprothermobacter and Methanobacteriales dominated the bacterial and archaeal community in the TD, respectively. Although the methane yield is comparable, both MD and TD show a different profile of pH, VFA and the microbial communities.

Thermophilic Dry Methane Fermentation of Distillation Residue Eluted from Ethanol Fermentation of Kitchen Waste and Dynamics of Microbial Communities

Thermophilic dry methane fermentation is advantageous for feedstock with high solid content. Distillation residue with 65.1 % moisture content was eluted from ethanol fermentation of kitchen waste and subjected to thermophilic dry methane fermentation, after adjusting the moisture content to 75 %. The effect of carbon to nitrogen (C/N) ratio on thermophilic dry methane fermentation was investigated. Results showed that thermophilic dry methane fermentation could not be stably performed for >10 weeks at a C/N ratio of 12.6 and a volatile total solid (VTS) loading rate of 1 g/kg sludge/d; however, it was stably performed at a C/N ratio of 19.8 and a VTS loading rate of 3 g/kg sludge/d with 83.4 % energy recovery efficiency. Quantitative PCR analysis revealed that the number of bacteria and archaea decreased by two orders of magnitude at a C/N ratio of 12.6, whereas they were not influenced at a C/N ratio of 19.8. Microbial community analysis revealed that the relative abundance of protein-degrading bacteria increased and that of organic acid-oxidizing bacteria and acetic acid-oxidizing bacteria decreased at a C/N ratio of 12.6. Therefore, there was accumulation of NH₄⁺ and acetic acid, which inhibited thermophilic dry methane fermentation.

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

BACKGROUND

One of the most promising technologies to sustainably produce energy and to mitigate greenhouse gas emissions from combustion of fossil energy carriers is the anaerobic digestion and biomethanation of organic raw material and waste towards biogas by highly diverse microbial consortia. In this context, the microbial systems ecology of thermophilic industrial-scale biogas plants is poorly understood.

RESULTS

The microbial community structure of an exemplary thermophilic biogas plant was analyzed by a comprehensive approach comprising the analysis of the microbial metagenome and metatranscriptome complemented by the cultivation of hydrolytic and acido-/acetogenic Bacteria as well as methanogenic Archaea. Analysis of metagenome-derived 16S rRNA gene sequences revealed that the bacterial genera Defluviitoga (5.5 %), Halocella (3.5 %), Clostridium sensu stricto (1.9 %), Clostridium cluster III (1.5 %), and Tepidimicrobium (0.7 %) were most abundant. Among the Archaea, Methanoculleus (2.8 %) and Methanothermobacter (0.8 %) were predominant. As revealed by a metatranscriptomic 16S rRNA analysis, Defluviitoga (9.2 %), Clostridium cluster III (4.8 %), and Tepidanaerobacter (1.1 %) as well as Methanoculleus (5.7 %) mainly contributed to these sequence tags indicating their metabolic activity, whereas Hallocella (1.8 %), Tepidimicrobium (0.5 %), and Methanothermobacter (<0.1 %) were transcriptionally less active. By applying 11 different cultivation strategies, 52 taxonomically different microbial isolates representing the classes Clostridia, Bacilli, Thermotogae, Methanomicrobia and Methanobacteria were obtained. Genome analyses of isolates support the finding that, besides Clostridium thermocellum and Clostridium stercorarium, Defluviitoga tunisiensis participated in the hydrolysis of hemicellulose producing ethanol, acetate, and H2/CO2. The latter three metabolites are substrates for hydrogentrophic and acetoclastic archaeal methanogenesis.

CONCLUSIONS

Obtained results showed that high abundance of microorganisms as deduced from metagenome analysis does not necessarily indicate high transcriptional or metabolic activity, and vice versa. Additionally, it appeared that the microbiome of the investigated thermophilic biogas plant comprised a huge number of up to now unknown and insufficiently characterized species.

Mechanism and Effect of Temperature on Variations in Antibiotic Resistance Genes during Anaerobic Digestion of Dairy Manure

Animal manure comprises an important reservoir for antibiotic resistance genes (ARGs), but the variation in ARGs during anaerobic digestion at various temperatures and its underlying mechanism remain unclear. Thus, we performed anaerobic digestion using dairy manure at three temperature levels (moderate: 20 °C, mesophilic: 35 °C, and thermophilic: 55 °C), to analyze the dynamics of ARGs and bacterial communities by quantitative PCR and 16S rRNA gene sequencing. We found that 8/10 detected ARGs declined and 5/10 decreased more than 1.0 log during thermophilic digestion, whereas only four and five ARGs decreased during moderate and mesophilic digestion, respectively. The changes in ARGs and bacterial communities were similar under the moderate and mesophilic treatments, but distinct from those in the thermophilic system. Potential pathogens such as Bacteroidetes, Proteobacteria, and Corynebacterium were removed by thermophilic digestion but not by moderate and mesophilic digestion. The bacterial community succession was the dominant mechanism that influenced the variation in ARGs and integrons during anaerobic digestion. Thermophilic digestion decreased the amount of mesophilic bacteria (Bacteroidetes and Proteobacteria) carrying ARGs. Anaerobic digestion generally decreased the abundance of integrons by eliminating the aerobic hosts of integrons (Actinomycetales and Bacilli). Thermophilic anaerobic digestion is recommended for the treatment and reuse of animal manure.

Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens

Poultry litter is a mixture of bedding materials and enteric bacteria excreted by chickens, and it is typically reused for multiple growth cycles in commercial broiler production. Thus, bacteria can be transmitted from one growth cycle to the next via litter. However, it remains poorly understood how litter reuse affects development and composition of chicken gut microbiota. In this study, the effect of litter reuse on the microbiota in litter and in chicken gut was investigated using 2 litter management regimens: fresh vs. reused litter. Samples of ileal mucosa and cecal digesta were collected from young chicks (10 days of age) and mature birds (35 days of age). Based on analysis using DGGE and pyrosequencing of bacterial 16S rRNA gene amplicons, the microbiota of both the ileal mucosa and the cecal contents was affected by both litter management regimen and age of birds. Faecalibacterium, Oscillospira, Butyricicoccus, and one unclassified candidate genus closely related to Ruminococcus were most predominant in the cecal samples, while Lactobacillus was predominant in the ileal samples at both ages and in the cecal samples collected at day 10. At days 10 and 35, 8 and 3 genera, respectively, in the cecal luminal microbiota differed significantly in relative abundance between the 2 litter management regimens. Compared to the fresh litter, reused litter increased predominance of halotolerant/alkaliphilic bacteria and Faecalibacterium prausnitzii, a butyrate-producing gut bacterium. This study suggests that litter management regimens affect the chicken GI microbiota, which may impact the host nutritional status and intestinal health.

Solid-state anaerobic digestion of lignocellulosic biomass: Recent progress and perspectives

Solid-state anaerobic digestion (SS-AD), which has gained popularity in the past decade as an environmentally friendly and cost-effective technology for extracting energy from various types of lignocellulosic biomass, is reviewed in this paper. According to data of biomass and methane yields of lignocellulosic feedstocks, crop residues have the highest methane production potential in the U.S., followed by the organic fraction of municipal solid waste (OFMSW), forestry waste, and energy crops. Methane yield and process stability of SS-AD can be improved by different strategies, such as co-digestion with other organic wastes, pretreatment of lignocellulosic biomass, and optimization of operating parameters. Different models for SS-AD have been developed, and insights into SS-AD processes have been obtained via microbial community analysis, microscope imaging, and tracer techniques. Future research and development in SS-AD, including feedstock identification and co-digestion, feedstock storage and pretreatment, SS-AD reactor development, digestate treatment, and value-added production, are recommended.

Biotic and abiotic dynamics of a high solid-state anaerobic digestion box-type container system

A solid-state anaerobic digestion box-type container system for biomethane production was observed in 12 three-week batch fermentations. Reactor performance was monitored using physico-chemical analysis and the methanogenic community was identified using ANAEROCHIP-microarrays and quantitative PCR. A resilient community was found in all batches, despite variations in inoculum to substrate ratio, feedstock quality, and fluctuating reactor conditions. The consortia were dominated by mixotrophic Methanosarcina that were accompanied by hydrogenotrophic Methanobacterium, Methanoculleus, and Methanocorpusculum. The relationship between biotic and abiotic variables was investigated using bivariate correlation analysis and univariate analysis of variance. High amounts of biogas were produced in batches with high copy numbers of Methanosarcina. High copy numbers of Methanocorpusculum and extensive percolation, however, were found to negatively correlate with biogas production. Supporting these findings, a negative correlation was detected between Methanocorpusculum and Methanosarcina. Based on these results, this study suggests Methanosarcina as an indicator for well-functioning reactor performance.

Performance and microbial communities of a batch anaerobic reactor treating liquid and high-solid sludge at thermophilic conditions

HS-AD with TS of 20% achieved similar reactor utilization efficiency as that in L-AD, and enriched hydrogenotrophic methanogensMethanoculleus.

Impact of different ratios of feedstock to liquid anaerobic digestion effluent on the performance and microbiome of solid-state anaerobic digesters digesting corn stover

The objective of this study was to understand how the non-microbial factors of L-AD effluent affected the microbiome composition and successions in the SS-AD digesters using both Illumina sequencing and qPCR quantification of major genera of methanogens. The SS-AD digesters started with a feedstock/total effluent (F/Et) ratio 2.2 (half of the effluent was autoclaved) performed stably, while the SS-AD digesters started with a 4.4 F/Et ratio (no autoclaved effluent) suffered from digester acidification, accumulation of volatile fatty acids, and ceased biogas production two weeks after startup. Some bacteria and methanogens were affected by non-microbial factors of the L-AD fluent. Alkalinity, the main difference between the two F/Et ratios, may be the crucial factor when SS-AD digesters were started using L-AD effluent.

Anaerobic treatment of rice winery wastewater in an upflow filter packed with steel slag under different hydraulic loading conditions

Rice-washing drainage (RWD), a strong organic wastewater, was anaerobically treated using an upflow filter filled with blast-furnace slag. The continuous performance of the reactor was examined at varying hydraulic retention times (HRTs). The reactor achieved 91.7% chemical oxygen demand removal (CODr) for a 10-day HRT (0.6 g COD/Ld organic loading rate) and maintained fairly stable performance until the HRT was shortened to 2.2 days (CODr > 84%). Further decreases in HRT caused process deterioration (CODr < 50% and pH < 5.5 for a 0.7-day HRT). The methane production rate increased with decreasing HRT to reach the peak level for a 1.3-day HRT, whereas the yield was significantly greater for 3.4-day or longer HRTs. The substrate removal and methane production kinetics were successfully evaluated, and the generated kinetic models produced good performance predictions. The methanogenic activity of the reactor likely relies on the filter biofilm, with Methanosaeta being the main driver.

Effect of salinity on methanogenic propionate degradation by acclimated marine sediment-derived culture

Degradation of propionate under high salinity is needed for biomethane production from salt-containing feedstocks. In this study, marine sediment-derived culture was evaluated to determine the effect of salinity on methanogenic propionate degradation. Microbes in marine sediments were subjected to fed-batch cultivation on propionate for developing acclimatized cultures. The rate of propionate degradation increased eightfold during 10 rounds of cultivation. Microbial community composition was determined through pyrosequencing of 16S rRNA gene amplicons after 10 rounds of cultivation. Taxa analysis was conducted for the reads obtained by pyrosequencing. Known propionate degraders were undetectable in the acclimated culture. Comparison of bacterial taxa in the original sediment with those in the acclimated culture revealed that the populations of four bacterial taxa were significantly increased during acclimation. Methanolobus was the predominant archaea genus in the acclimated culture. The propionate degradation rate of the acclimated culture was not affected by salinity of up to equivalent of 1.9 % NaCl. The rate decreased at higher salinity levels and was more than 50 % of the maximum rate even at equivalent of 4.3 % NaCl.

Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities

Methanogenic Archaea produce approximately one billion tons of methane annually, but their biology remains largely unknown. This is partially due to the large phylogenetic and phenotypic diversity of this group of organisms, which inhabit various anoxic environments including peatlands, freshwater sediments, landfills, anaerobic digesters and the intestinal tracts of ruminants. Research is also hampered by the inability to cultivate methanogenic Archaea. Therefore, biodiversity studies have relied on the use of 16S rRNA and mcrA [encoding the α subunit of the methyl coenzyme M (methyl-CoM) reductase] genes as molecular markers for the detection and phylogenetic analysis of methanogens. Here, we describe four novel molecular markers that should prove useful in the detailed analysis of methanogenic consortia, with a special focus on methylotrophic methanogens. We have developed and validated sets of degenerate PCR primers for the amplification of genes encoding key enzymes involved in methanogenesis: mcrB and mcrG (encoding β and γ subunits of the methyl-CoM reductase, involved in the conversion of methyl-CoM to methane), mtaB (encoding methanol-5-hydroxybenzimidazolylcobamide Co-methyltransferase, catalyzing the conversion of methanol to methyl-CoM) and mtbA (encoding methylated [methylamine-specific corrinoid protein]:coenzyme M methyltransferase, involved in the conversion of mono-, di- and trimethylamine into methyl-CoM). The sensitivity of these primers was verified by high-throughput sequencing of PCR products amplified from DNA isolated from microorganisms present in anaerobic digesters. The selectivity of the markers was analyzed using phylogenetic methods. Our results indicate that the selected markers and the PCR primer sets can be used as specific tools for in-depth diversity analyses of methanogenic consortia.