Direct characterization of methanogens in two high-rate anaerobic biological reactors

Comparison of mesophilic and thermophilic anaerobic digestions of thermal hydrolysis pretreated swine manure: Process performance, microbial communities and energy balance

Anaerobic digestion (AD) of swine manure (SM) commonly shows low biogas output and unsatisfactory economic performance. In this study, thermophilic AD (TAD, 50 ± 1 °C) was combined with thermal hydrolysis pretreatment (THP, 170 °C/10 bar), to investigate its potential for maximizing biogas yield, securing successful digestion and microbial diversity, as well as improving energy balance. Four lab-scale continuously stirred tank reactors were operated for 300 days and compared with each other, i.e., reactor 1 (raw SM fed in mesophilic AD: RSM-MAD), reactor 2 (THP-treated SM fed in MAD: TSM-MAD), reactor 3 (RSM-TAD), and reactor 4 (TSM-TAD). The results showed that THP was efficient to increase methane production of SM, TSM-TAD mode led to the highest methane yield (129.8 ± 40.5 mL-CH₄/g-VS/day) among the tests (p < 0.05). Although TAD was more likely to induce free ammonia (> 700 mg/L) or volatile fatty acids (> 6000 mg/L) accumulation compared with MAD in start-up phase, TSM-TAD treatment mode behaved a sustainable digestion process in a long-term operation. For TSM-TAD scenario, higher Shannon-Weaver (3.873) and lower Simpson index (0.061) indicated this mode ensured and enlarged the diversity of bacteria communities. Phylum Bathyarchaeota was dominant (59.3%-90.0%) in archaea community, followed by Euryarchaeota in the four reactors. RSM-MAD treatment mode achieved the highest energy output (4.65 GJ/day), TSM-TAD was less effective (-17.38 GJ/day) due to increased energy demands. Thus improving the energetic efficiency of THP units is recommended for the development of TSM-TAD treatment mode.

Shifts in methanogenic subpopulations measured with antibody probes in a fixed-bed loop anaerobic bioreactor treating sulfite evaporator condensate

A fixed-bed loop, high-rate anaerobic bioreactor treating sulfite evaporator condensate was sampled when it reached steady state and afterwards following perturbations during a 14-month period. By using immunotechnology, it was observed that shifts in methanogenic subpopulations occurred in association with perturbations, such as restarting and relocating the biomass into a different tank. Methanogens related to Methanobacterium bryantii MoHG and Methanobrevibacter smithii ALI were numerous throughout the observation period, while Methanosarcina mazei S6 and Methanosarcina thermophila TM1 were found in the early and late samples, respectively. Also, Methanobacterium formicicum was more numerous at the top portion of the bioreactor, while Methanobrevibacter arboriphilus AZ and DC were at the bottom. Sample formalinization required for prolonged storage proved suitable for antigen preservation.

Performances and microbial features of a granular activated carbon packed-bed biofilm reactor capable of an efficient anaerobic digestion of olive mill wastewaters

Anaerobic digestion of olive mill wastewaters is generally performed in anaerobic contact bioreactors where the removal of toxic phenols is often unsatisfactory. In the present work we show that a granular activated carbon packed-bed biofilm reactor can be successfully used to achieve effective and reproducible wastewater decontamination even at high organic loads. A comparison of 16S rRNA gene sequences of the inoculum and of biomass samples from different districts of the reactor revealed enrichment of specific microbial populations, probably minor members of the inoculum and/or of the olive mill wastewaters. They mainly consisted of the members of Proteobacteria, Flexibacter-Cytophaga-Bacteroides, and sulphate-reducing bacteria. The dominant sequence among Archaea (70% of clones) was closely related to Methanobacterium formicicum.

Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea

Although of limited metabolic diversity, methanogenic archaea or methanogens possess great phylogenetic and ecological diversity. Only three types of methanogenic pathways are known: CO(2)-reduction, methyl-group reduction, and the aceticlastic reaction. Cultured methanogens are grouped into five orders based upon their phylogeny and phenotypic properties. In addition, uncultured methanogens that may represent new orders are present in many environments. The ecology of methanogens highlights their complex interactions with other anaerobes and the physical and chemical factors controlling their function.

Temporal change of composition and potential activity of the thermophilic archaeal community during the composting of organic material

To date, composting has been regarded as an aerobic process but it has been shown that composting piles are often sources of atmospheric methane. In order to gain a more comprehensive view on the diversity of methanogenic Archaea in compost, gas chromatographical methods and molecular cloning were used to study relationships of thermophilic archaeal communities and changes in methane production potential during compost maturation. According to the thermophilic methane production potential, wide differences could be detected between differently aged compost materials. In material derived from 3- and 4-week-old piles, low and no thermophilic methane production potential, respectively, was observed at 50 degrees C. Material from a 6-week-old pile showed the maximum methane production. With compost maturation, the production slowly decreased again with 6 weeks, 8 weeks, and mature compost showing an optimum methane production potential at 60 degrees C. At 70 degrees C, only 6-week-old material showed a comparable high production of methane. The 16S rRNA-based phylogenetic surveys revealed an increase of archaeal diversity with compost maturation. In the 6-week-old material, 86% of the sequences in the archaeal 16S rRNA library had the highest sequence similarities to Methanothermobacter spp. and the remaining 14% of the clones were related to Methanosarcina thermophila. Quantification of methanogens in 6-week-old material, on the basis of the methane production rate, resulted in values of about 2x10(7) cells per gram fresh weight. In 8-week-old and mature compost material, the proportion of sequences similar to Methanothermobacter spp. decreased to 34% and 0%, respectively. The mature compost material showed the highest variation in identified sequences, although 33% could be assigned to as yet uncultured Archaea (e.g. Rice cluster I, III, and IV). Our results indicate that compost harbours a diverse community of thermophilic methanogens, with changing composition during the maturation process, presumably due to altered pile conditions. Likewise, compost may act as a potential carrier for thermophilic methanogens in temperate soils because it is widely used as a soil amendment.

Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing

The diversity of Archaea in anaerobic digesters was characterized by strand conformation polymorphism (SSCP) analysis and the sequencing of 16S rDNA genes. The 44 digesters sampled, located in eight different countries, treated effluents from agriculture, the food processing and petro-chemical industries, pulp and paper plant, breweries, slaughterhouses and municipal waste. All the existing processes were represented among the samples (fixed-film, fluidized bed, stirred-tank, UASB, sequential batch reactor, lagoon). Single strand conformation polymorphism analysis targeting the V3 region of 16S rDNA revealed between four to six distinct archaeal peaks per digester. The diversity of dominant Archaea in the 44 digesters was estimated as 23 different 16S rDNA sequences. Cloning of archaeal 16S rRNA genes from 11 distinct total genomic DNA, screening of clones by SSCP and the sequencing of 170 of them made it possible to characterize these SSCP peaks. All the sequences retrieved were members of the Euryarchaeaota subdomain. Furthermore, most of the sequences retrieved were very close to already known and cultivated strains or to environmental clones. The most frequent archaeal sequences were close to Methanosaeta concilii and to a 16S rDNA clone vadinDC06 located in the Methanobacterium clade (84% and 73% of digesters respectively). The other sequences were members of the Methanobacteriales and the Methanomicrobiales families. Only one sequence was far from any sequence of the database and it could be grouped with several sequences of environmental clones. Each digester harboured between two to nine archaeal sequences with only one of them corresponding to a putative acetate-utilizing species. Furthermore, the process in the digesters appeared to play a part in the distribution of archaeal diversity.

Molecular biology of stress genes in methanogens: potential for bioreactor technology

Many agents of physical, chemical, or biological nature, have the potential for causing cell stress. These agents are called stressors and their effects on cells are due to protein denaturation. Cells, microbes, for instance, perform their physiological functions and survive stress only if they have their proteins in the necessary concentrations and shapes. To be functional a protein shape must conform to a specific three-dimensional arrangement, named the native configuration. When a stressor (e.g., temperature elevation or heat shock, decrease in pH, hypersalinity, heavy metals) hits a microbe, it causes proteins to lose their native configuration, which is to say that stressors cause protein denaturation. The cell mounts an anti-stress response: house-keeping genes are down-regulated and stress genes are activated. Among the latter are the genes that produce the Hsp70(DnaK), Hsp60, and small heat protein (sHsp) families of stress proteins. Hsp70(DnaK) is part of the molecular chaperone machine together with Hsp40(DnaJ) and GrpE, and Hsp60 is a component of the chaperonin complex. Both the chaperone machine and the chaperonins play a crucial role in assisting microbial proteins to reach their native, functional configuration and to regain it when it is partially lost due to stress. Proteins that are denatured beyond repair are degraded by proteases so they do not accumulate and become a burden to the cell. All Archaea studied to date possess chaperonins but only some methanogens have the chaperone machine. A recent genome survey indicates that Archaea do not harbor well conserved equivalents of the co-chaperones trigger factor, Hip, Hop, BAG-1, and NAC, although the data suggest that Archaea have proteins related to Hop and to the NAC alpha subunit whose functions remain to be elucidated. Other anti-stress means involve osmolytes, ion traffic, and formation of multicellular structures. All cellular anti-stress mechanisms depend on genes whose products are directly involved in counteracting the effects of stressors, or are regulators. The latter proteins monitor and modulate gene activity. Biomethanation depends on the concerted action of at least three groups of microbes, the methanogens being one of them. Their anti-stress mechanisms are briefly discussed in this Chapter from the standpoint of their role in biomethanation with emphasis on their potential for optimizing bioreactor performance. Bioreactors usually contain stressors that come with the influent, or are produced during the digestion process. If the stressors reach levels above those that can be dealt with by the anti-stress mechanisms of the microbes in the bioreactor, the microbes will die or at least cease to function. The bioreactor will malfunction and crash. Manipulation of genes involved in the anti-stress response, particularly those pertinent to the synthesis and regulation of the Hsp70(DnaK) and Hsp60 molecular machines, is a promising avenue for improving the capacity of microbes to withstand stress, and thus to continue biomethanation even when the bioreactor is loaded with harsh waste. The engineering of methanogenic consortia with stress-resistant microbes, made on demand for efficient bioprocessing of stressor-containing effluents and wastes, is a tangible possibility for the near future. This promising biotechnological development will soon become a reality due to the advances in the study of the stress response and anti-stress mechanisms at the molecular and genetic levels.

Single strand conformation polymorphism monitoring of 16S rDNA Archaea during start-up of an anaerobic digester

A laboratory-scale continuously mixed anaerobic digester was inoculated with a mix of anaerobic sludge and fed with glucose. The start-up strategy was progressive and chemical analyses were done to evaluate digester performance from day 1 to day 107. In parallel, Archaeal community dynamics were monitored by SSCP analysis of the V3 region of 16S rDNA genes and further characterized by partial sequencing of 16S rDNA genes. At day 1 the inoculum contained at least five distinct Archaeal peaks close to known methanogenic species. The dominant peak was very close to Methanosaeta concilli, the remaining species being members of the Methanobacteriales and Methanomicrobiales. A rapid shift of the Archaeal population was observed during the experiment. At day 21 Methanobacterium formicicum, which was not detected at day 1, became the dominant methanogenic species in the bioreactor and remained so until the end of the experiment.

Application of anaerobic fluidized bed reactors in wastewater treatment: a review

During the past ten years, anaerobic process has become a popular technology for treating concentrated effluents. Research and development programmes led by both engineers and microbiologists have resulted in a better understanding of the microbiology of anaerobic reactions and reactor design for anaerobic processes. Considerable progress has been achieved in the development of high rate anaerobic reactors with several configurations for treating concentrated industrial effluents. In this review, attention is paid to highlighting the conceptual and full scale developments of anaerobic fluidized bed reactors, in respect of process performance, design concepts, start‐up of the reactor, stability of the system with respect to various operating parameters, reactor configurations, comparison with competing reactor designs for concentrated industrial effluents and kinetics and modelling of reactor systems.

An improved enzyme-linked immunosorbent assay for whole-cell determination of methanogens in samples from anaerobic reactors

An enzyme-linked immunosorbent assay was developed for the detection of whole cells of methanogens in samples from anaerobic continuously stirred tank digesters treating slurries of solid waste. The assay was found to allow for quantitative analysis of the most important groups of methanogens in samples from anaerobic digesters in a reproducible manner. Polyclonal antisera against eight strains of methanogens were employed in the test. The specificities of the antisera were increased by adsorption with cross-reacting cells. The reproducibility of the assay depended on the use of high-quality microtiter plates and the addition of dilute hydrochloric acid to the samples. In an experiment on different digester samples, the test demonstrated a unique pattern of different methanogenic strains present in each sample. The limited preparatory work required for the assay and the simple assay design make the test well suited for routine analysis of large numbers of samples and thus for process surveillance during operation of biogas digesters.

Examination of Bacterial Characteristics of Anaerobic Membrane Bioreactors in Three Pilot-Scale Plants for Treating Low-Strength Wastewater by Application of the Colony-Forming-Curve Analysis Method

Characteristic sludge ecosystems arising in anaerobic membrane bioreactors of three pilot-scale plants treating low-strength (less than 1 g of biological oxygen demand per liter) sewage or soybean-processing wastewater were examined by analysis of the colony-forming-curves (CFC) obtained by counting colonies at suitable intervals. The wastewaters, containing high amounts of suspended solids (SS) (SS/chemical oxygen demand ratio, 0.51 to 0.80), were treated by using two types of bioreactors: (i) a hydrolyzation reactor for solubilization and acidification of SS in wastewater and (ii) a methane fermentation reactor for producing methane. The colony counts for the two sewage treatment plants continued to increase even after 3 weeks of incubation, whereas those for soybean-processing wastewater reached an approximately constant level within 3 weeks of incubation. The CFCs were analyzed by correlating the rate of colony appearance on roll tubes with the physiological types of bacteria present in the bioreactors. It was found that there were large numbers of slow-colony-forming anaerobic bacteria within the bioreactors and that the viable populations consisted of a few groups with different growth rates. It is considered that the slow-growing colonies appearing after 10 days of incubation were the dominant microflora in the sewage treated by hydrolyzation reactors. In particular, highly concentrated sludge (30.0 g of mixed-liquor volatile SS per liter) retained by the membrane separation module contained a large number of such bacteria. Slow-growing colonies of these bacteria could be counted by using a sludge extract medium prepared from only the supernatant of autoclaved sludge. In addition, the highest colony counts were almost always obtained with the sludge extract medium, meaning that most of the anaerobic bacteria in these sludges have complex nutrient requirements for growth. This report also indicates the usefulness of application of the CFC analysis method to the study of bacterial populations of anaerobic treatment systems.

Microbial attachment and growth in fixed-film reactors: Process startup considerations

Optimal steady-state performance of any biofilm reactor requires a fully developed and mature biofilm. During fixed-film reactor startup phase, biofilm is in process of development and accordingly, process performance is difficult to quantify. Environmental, cellular and surface factors greatly influence the process of biofilm formation during reactor startup. Improved knowledge of nutritional, toxicological and environmental requirements of wastewater degrading microorganisms has helped define optimal microbial growth conditions. In case of anaerobic fixed film reactors the startup is hindered by low microbial growth rates, strict environmental requirements and limited ability of methanogens to adhere and form fixed biofilms. These obstacles could be overcome by proper support media selection and formulation of appropriate inoculation procedures and startup strategies.

Diversity and Population Dynamics of Methanogenic Bacteria in a Granular Consortium

Upflow anaerobic sludge blanket bioreactor granules were used as an experimental model microbial consortium to study the dynamics and distribution of methanogens. Immunologic methods revealed a considerable diversity of methanogens that was greater in mesophilic granules than in the same granules 4 months after a temperature shift from 38 to 55°C. During this period, the sizes of the methanogenic subpopulations changed with distinctive profiles after the initial reduction caused by the shift. Methanogens antigenically related to Methanobrevibacter smithii PS and ALI, Methanobacterium hungatei JF1, and Methanosarcina thermophila TM1 increased rapidly, reached a short plateau, and then fell to lower concentrations that persisted for the duration of the experiment. A methanogen related to Methanogenium cariaci JR1 followed a similar profile at the beginning, but it soon diminished below detection levels. Methanothrix rods weakly related to the strain Opfikon increased rapidly, reaching a high-level, long-lasting plateau. Two methanogens related to Methanobrevibacter arboriphilus AZ and Methanobacterium thermoautotrophicum ΔH emerged from very low levels before the temperature shift and multiplied to attain their highest numbers 4 months after the shift. Histochemistry and immunohistochemistry revealed thick layers, globular clusters, and lawns of variable density which were distinctive of the methanogens related to M. thermoautotrophicum ΔH, M. thermophila TM1, and M. arboriphilus AZ and M. soehngenii Opfikon, respectively, in thin sections of granules grown at 55°C for 4 months. Mesophilic granules showed a different pattern of methanogenic subpopulations.

Quantitative Microbiological Analysis of Bacterial Community Shifts in a High-Rate Anaerobic Bioreactor Treating Sulfite Evaporator Condensate

The bacterial population of a high-rate, anaerobic, fixed-bed loop reactor treating sulfite evaporator condensate from the pulp industry was studied over a 14-month period. This period was divided into seven cycles that included a startup at the beginning of each cycle. Some 82% of the total biomass was immobilized on and between the porous glass rings filling the reactor. The range of the total number of microorganisms in these biofilms was 2 × 10 9 to 7 × 10 9 cells per ml. Enumeration and characterization by microbiological methods and by phase-contrast, epifluorescence, and electron microscopy showed that the samples consisted mainly of the following methanogens: a Methanobacterium sp., a Methanosarcina sp., a Methanobrevibacter sp., and a Methanothrix sp., as well as furfural-degrading sulfate-reducing bacteria resembling Desulfovibrio furfuralis. Viable counts of hydrogenotrophic methanogens were relatively stable (mostly within the range of 3.2 × 10 8 to 7.5 × 10 8 cells per ml), but Methanobrevibacter cells increased from <5 to 30% of the total hydrogenotrophic count after transfer of the fixed bed into a second reactor vessel. Acetotrophic methanogens reached their highest numbers of 1.3 × 10 8 to 2.6 × 10 8 cells per ml in the last fermentation cycles. They showed a morphological shift from sarcinalike packets in early samples to single coccoid forms in later phases of the fermentation. Furfural-degrading sulfate reducers reached counts of 1 × 10 7 to 5.8 × 10 7 cells per ml. The distribution of the chief metabolic groups between free fluid and biofilms was analyzed in the fifth fermentation cycle: 4.5 times more furfural degraders were found in the free fluid than in the biofilms. In contrast, 5.8 times more acetotrophic and 16.6 times more hydrogenotrophic methanogens were found in the biofilms than in the free liquid. The data concerning time shifts of morphotypes among the trophic groups of methanogens corroborated the trends observed by using immunological assays on the same samples.