Microbial community structure and methanogenic activity during start-up of psychrophilic anaerobic digesters treating synthetic industrial wastewaters

Optimizing the hydrolysis-acidification stage in municipal wastewater treatment: comparison of immobilized fillers and granular sludge

The decomposition of organic macromolecules in sewage currently benefits substantially from hydrolysis-acidification. The full use of its qualities can help domestic sewage to biodegrade more quickly, which promotes the subsequent aerobic reactions. This study evaluated the hydrolysis-acidification performance of granular sludge and filler in residential sewage. Both forms were highly effective at producing volatile fatty acids (VFAs) at the beginning of the reaction, but the granular sludge gradually disintegrated over time, particularly at low temperatures. The production of VFAs decreased (68.08 mg/L), and the effluent dissolved organic nitrogen (DON) increased (6.23 mg/L). However, the effluent of fillers remained at a lower level (1.3 mg/L) and produced more VFAs (74.13 mg/L). High-throughput sequencing revealed that the filler included a greater quantity of hydrolytic-acidifying bacteria than the granular sludge, which resulted in higher performance. In this study, the optimal form of utilizing hydrolytic acidifying bacteria was discussed to provide a theoretical basis to improve the full utilization of organic matter in domestic sewage and the removal of as much total nitrogen as possible.

Propidium monoazide - polymerase chain reaction reveals viable microbial community shifts in anaerobic membrane bioreactors treating domestic sewage at low temperature

An anaerobic membrane bioreactor (AnMBR) treated domestic sewage at 15 °C under different hydraulic retention time (HRT) conditions (6, 12, 16, and 24 h). Propidium monoazide (PMA)-PCR excluded microorganisms without intact cell membranes, focusing on the viable microbial community in anaerobic digestion. The results showed that the 6-hour HRT had poor treatment performance: low chemical oxygen demand removal efficiency (below 80%) and high mean trans-membrane pressure and flux (15 kPa and 9.4 L/(m2 h)). Comparatively, PMA-PCR combined with next-generation sequencing improved the identification of microbial changes compared to conventional 16S rRNA gene sequencing. HRT influenced microorganisms in the hydrolysis and acid-production stages, including carbohydrate-degrading bacteria such as Bifidobacterium and Prevotella 1. Remarkably, a comparison with an AnMBR at 25 °C showed Proteobacteria to be the main cause of membrane fouling in the low-temperature AnMBR, with most operational taxonomic units negatively correlated with HRT and solids retention time.

Research trends and strategies for the improvement of anaerobic digestion of food waste in psychrophilic temperatures conditions

The organic fraction of municipal solid waste is mainly composed of food waste (FW), and traditional disposal practices for this fraction are generally considered to have negative environmental and economic impacts. However, the organic characteristics of this fraction could also be exploited through the anaerobic digestion of FW (FW-AD), which represents unique advantages, including the reduction of the area required for final disposal and environmental pollution and the same time the generation of renewable energy (mainly methane gas), and a by-product for agricultural use (digestate) due to its high nutrient content. Although approximately 88% of the world's population resides in areas with temperatures below 8 °C, psychrophilic conditions (temperatures below 20 °C) have hardly been studied, while mesophilic (66%) and thermophilic (27%) ranges were found to be more common than psychrophilic FW-AD (7%). The latter condition could decrease microbial activity and organic matter removal, which could affect biogas production and even make AD unfeasible. To improve the efficiency of the psychrophilic FW-AD process, there are strategies such as: measurement of physical properties as particle size, rheological characteristics (viscosity, consistency index and substrate behavior index), density and humidity, bioaugmentation and co-digestion with other substrates, use of inocula with psychrophilic methanogenic communities, reactor heating and modification of reactor configurations. However, these variables have hardly been studied in the context of psychrophilic conditions and future research should focus on evaluating the influence of these variables on FW-AD under psychrophilic conditions. Through a bibliometric analysis, this paper has described and analyzed the FW-AD process, with a focus on the psychrophilic conditions (<20 °C) so as to identify advances and future research trends, as well as determine strategies toward improving the anaerobic process under low temperature conditions.

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Temperature has a great influence on anaerobic digestion of food waste (FW-AD).

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Studies on the psychrophilic condition are limited, warranting further research.

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Physical properties of the substrate and inoculum influence psychrophilic FW-AD.

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The use of inocula adapted to low temperatures could increase biogas production.

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Changes in reactor configurations could improve biogas yield at low temperature.

Conductive biofilms in up-flow anaerobic sludge blanket enhanced biomethane recovery from municipal sewage under ambient temperatures

The feasibility of municipal sewage treatment in laboratory-scale up-flow anaerobic sludge blankets was investigated in this work. Unlike previous studies, granular activated carbon (conductive) or sponge (non-conductive) was introduced to hollow plastic balls as carriers and suspended in the middle and upper layers of the reactors. The two bioreactors were operated at four different hydraulic retention times (stepwise reduced from 24 h to 8 h) for 100 days at ∼18 °C. The conductive-amended treatment was more effective than the non-conductive treatment in enhancing reactor performance. Interestingly, in the reactor containing conductive carriers, microorganisms enriched in the conductive biofilm were also dominant in the suspended sludge. In the reactor containing sponge carriers, the dominant microorganisms differed between the non-conductive biofilm and the suspended sludge. This study underlines that the enrichment of functional microbial communities and the positive impacts of biofilm on suspended sludge are the keys to improving biomethane recovery.

Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater

An ecogenomic analysis of the methanogenic microbial community in a laboratory-scale up-flow anaerobic sludge blanket (UASB) reactor treating soy sauce-processing wastewater revealed a synergistic metabolic network. Granular sludge samples were collected from the UASB reactor operated under psychrophilic (20°C) conditions with a COD removal rate >75%. A 16S rRNA gene amplicon sequencing-based microbial community analysis classified the major microbial taxa as Methanothrix, Methanobacterium, Pelotomaculaceae, Syntrophomonadaceae, Solidesulfovibrio, and members of the phyla Synergistota and Bacteroidota. Draft genomes of dominant microbial populations were recovered by metagenomic shotgun sequencing. Metagenomic- and metatranscriptomic-assisted metabolic reconstructions indicated that Synergistota- and Bacteroidota-related organisms play major roles in the degradation of amino acids. A metagenomic bin of the uncultured Bacteroidales 4484-276 clade encodes genes for proteins that may function in the catabolism of phenylalanine and tyrosine under microaerobic conditions. Syntrophomonadaceae and Pelotomaculaceae oxidize fatty acid byproducts presumably derived from the degradation of amino acids in syntrophic association with aceticlastic and hydrogenotrophic methanogen populations. Solidesulfovibrio organisms are responsible for the reduction of sulfite and may support the activity of hydrogenotrophic methanogens and other microbial populations by providing hydrogen and ammonia using nitrogen fixation-related proteins. Overall, functionally diverse anaerobic organisms unite to form a metabolic network that performs the complete degradation of amino acids in the psychrophilic methanogenic microbiota.

Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles

The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take place via a non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods, i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types, i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method's features i.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.

Effects of storage temperature on CH4 emissions from cattle manure and subsequent biogas production potential

CH₄ is one of the main greenhouse gases (GHGs) generated from agricultural sector, and a significant amount of it is emitted during the storage of livestock manure. To mitigate the CH₄ emissions, strong acid addition to the manure was attempted, which is only applicable to slurry-type manure. On the other hand, lowering the storage temperature could be an effective method to reduce the CH₄ emissions, particularly applicable to solid-type manure. In this study, cattle manure (CM) with a high-solid content (TS > 30%) was stored at different temperatures (15-35 °C) for 80 d. The highest CH₄ emissions of 375.1 kg CO₂ eq./ton VS was observed at 35 °C, and this was reduced to less than half at ≤20 °C. Like the difference in CH₄ emissions, the degradation of organic matter showed a similar trend. The maximum VS reduction of 29% was observed at 35 °C, while only 8% reduction was observed at 15 °C. Results from microbial community analyses and specific methanogenic activity tests indicated that hydrogenotrophic methanogens were the dominant indigenous CH₄-producers, and the abundance of psychrophilic methanogens increased with decreasing temperature. The conservation of organic matter at low temperature led to an increase in biogas production potential from 25 to 43 L CH₄/kg CM. It was calculated that the GHGs emissions from electricity consumption for cooling CM below 25 °C can be offset by mitigating CH₄ emissions during storage but increasing in subsequent biogas production potential of CM. Compared at 35 °C, 91.6 kg CO₂ eq./ton CM of GHGs reduction can be attained at 15 °C.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

Soil incubation studies with Cry1Ac protein indicate no adverse effect of Bt crops on soil microbial communities

Bt crops that are transgenic crops engineered to produce Bt toxins which occur naturally with Bacillus thuringiensis (Bt) have been widely planted and its environmental risk assessment has been heavily debated. The effects of Bt crops on soil microbial communities are possible through changing the quantity and quality of C inputs and potential toxic activity of Bt protein on soil organisms. To date, the direct effects of Bt protein on soil microorganisms is unclear. Here we added Cry1Ac, one of the most commonly used Bt protein in Bt crops, to the soil and monitored changes in soil bacterial, fungal and archaeal diversities and community structures using ribosomal DNA-fingerprinting method, as well as their population sizes by real-time PCR over a 100-day period. Despite the fact that variations were observed in the indices of evenness, diversity and population sizes of bacteria, fungi and archaea with different Cry1Ac addition rates up to 100ngg^-1 soil, the indices of soil microbial diversities and evennesses did not significantly shift with Cry1Ac protein addition, nor did population sizes change over time. The diversities of the dominant bacteria, fungi and archaea were not significantly changed, given Cry1Ac protein addition rates over a period of 100 days. These results suggested that Bt protein derived by cultivations of transgenic Bt crops is unlikely to cause transient or even persisting significant changes in soil microorganisms in field.

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

The production of biogas by anaerobic digestion (AD) of agricultural residues, organic wastes, animal excrements, municipal sludge, and energy crops has a firm place in sustainable energy production and bio-economy strategies. Focusing on the microbial community involved in biomass conversion offers the opportunity to control and engineer the biogas process with the objective to optimize its efficiency. Taxonomic profiling of biogas producing communities by means of high-throughput 16S rRNA gene amplicon sequencing provided high-resolution insights into bacterial and archaeal structures of AD assemblages and their linkages to fed substrates and process parameters. Commonly, the bacterial phyla Firmicutes and Bacteroidetes appeared to dominate biogas communities in varying abundances depending on the apparent process conditions. Regarding the community of methanogenic Archaea, their diversity was mainly affected by the nature and composition of the substrates, availability of nutrients and ammonium/ammonia contents, but not by the temperature. It also appeared that a high proportion of 16S rRNA sequences can only be classified on higher taxonomic ranks indicating that many community members and their participation in AD within functional networks are still unknown. Although cultivation-based approaches to isolate microorganisms from biogas fermentation samples yielded hundreds of novel species and strains, this approach intrinsically is limited to the cultivable fraction of the community. To obtain genome sequence information of non-cultivable biogas community members, metagenome sequencing including assembly and binning strategies was highly valuable. Corresponding research has led to the compilation of hundreds of metagenome-assembled genomes (MAGs) frequently representing novel taxa whose metabolism and lifestyle could be reconstructed based on nucleotide sequence information. In contrast to metagenome analyses revealing the genetic potential of microbial communities, metatranscriptome sequencing provided insights into the metabolically active community. Taking advantage of genome sequence information, transcriptional activities were evaluated considering the microorganism's genetic background. Metaproteome studies uncovered enzyme profiles expressed by biogas community members. Enzymes involved in cellulose and hemicellulose decomposition and utilization of other complex biopolymers were identified. Future studies on biogas functional microbial networks will increasingly involve integrated multi-omics analyses evaluating metagenome, transcriptome, proteome, and metabolome datasets.

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.

Quantifying the percentage of methane formation via acetoclastic and syntrophic acetate oxidation pathways in anaerobic digesters

Ammonia concentration is one of the key factors influencing the methanogenic community composition and dominant methanogenic pathway in anaerobic digesters. This study adopted a radiolabelling technique using [2-¹⁴C] acetate to investigate the relationship between total ammonia nitrogen (TAN) and the methanogenic pathway. The radiolabelling experiments determined the ratio of ¹⁴CO₂ and ¹⁴CH₄ in the biogas which was used to quantitatively determine the percentage of CH₄ derived from acetoclastic and syntrophic acetate oxidation routes, respectively. This technique was performed on a selection of mesophilic digesters representing samples of low to high TAN concentrations (0.2-11.1gkg^-1 wet weight). In high TAN digesters, the ratio between ¹⁴CO₂ and ¹⁴CH₄ was in the range 2.1-3.0; indicating 68-75% of methane was produced via the hydrogenotrophic route; whereas in low ammonia samples the ratio was 0.1-0.3, indicating 9-23% of methane was produced by the hydrogenotrophic route. These findings have been confirmed further by phylogenetic studies.

Evaluation of an up-flow anaerobic sludge bed (UASB) reactor containing diatomite and maifanite for the improved treatment of petroleum wastewater

Novel diatomite (R1) and maifanite (R2) were utilized as support materials in an up-flow anaerobic sludge bed (UASB) reactor for the treatment of recalcitrant petroleum wastewater. At high organic loadings (11kg-COD/m³·d), these materials were efficient at reducing COD (92.7% and 93.0%) in comparison with controls (R0) (88.4%). Higher percentages of large granular sludge (0.6mm or larger) were observed for R1 (30.3%) and R2 (24.6%) compared with controls (22.6%). The larger portion of granular sludge provided a favorable habitat that resulted in greater microorganism diversity. Increased filamentous bacterial communities are believed to have promoted granular sludge formation promoting a conductive environment for stimulation methanogenic Archaea. These communities had enhanced pH tolerance and produced more methane. This study illustrates a new potential use of diatomite and maifanite as support materials in UASB reactors for increased efficiency when treating refractory wastewaters.

Detection of acidification limit in anaerobic membrane bioreactors at ambient temperature

High-volume, low-strength industrial wastewaters constitute a large potential for biogas production, which could be realized by membrane bioreactors operating at the ambient temperature of the wastewater. However, the start-up of low-temperature anaerobic processes using unadapted inoculum can be sensitive to overloading, which results in acidification. This study assessed if a novel acidification limit test can be used to identify stable organic loading rates as well as process over-loading. The test is based on easy-to-apply batch experiments for determination of the hydrolysis rate constant and the specific methanogenic activity of the acetotrophic and hydrogenotrophic pathways. For evaluation, two anaerobic membrane bioreactors, treating synthetic dairy wastewater at an ambient temperature of 24 °C, were used with a slow or a rapid start-up regime, respectively. Tests for hydrolysis rate and methanogenic activity were performed throughout the experiment and were used to calculate acidification limits for each system throughout the start-up. The acidification limit test was able to successfully identify both stable operation of one reactor and process failure of the other reactor as the organic loading rate increased. The reactor failure was caused by over-loading the acetotrophic pathway and coincided with microbial changes observed in real-time PCR and moving window analysis. Overall, the acidification limit tests seem promising as an easy applicable method for estimating what organic loading rate can be utilized, without risking acidification of anaerobic systems.

Process parameters and changes in the microbial community patterns during the first 240 days of an agricultural energy crop digester

Commercial biogas production takes place by complex microbial communities enclosed in controlled "technical ecosystems". Once established, the communities tend to be resilient towards disturbances, although the relative abundance of their members may vary. The start-up phase, during which the community establishes itself, is therefore decisive for the later performance of the reactor. In this study, we followed the first 240 days of a standard agricultural energy crop digester consisting of a 400 m(3) plug flow fermenter and a 1000 m(3) agitated post digester, operated at 40-45 °C. The feed consisted of corn and later grass silage augmented by ground wheat. Changes in both the eubacterial and methanogenic archaeal communities were followed by automated ribosomal intergenic spacer analysis (ARISA). In addition the copy number of the methyl-coenzyme reductase A (mcrA)-genes found in all known methanogens were followed by quantitative PCR, while selected samples from two phases-one early, one late-of the community structure development were subjected to high throughput sequencing. Biogas volume and composition (CH4, CO2, H2, H2S, O2), pH, ammonia-N, and volatile fatty acids (VFA), were measured as part of the routine process control. VFA/TIC values were calculated on this basis. Whereas the total gas production of the plant established itself at about 2500 m(3) biogas per day within the first months, the composition of the microbial communities showed distinct spatial and temporal differences over the investigated time period. Absolute values for DNA isolation procedures are difficult to certify, hence comparative results on community structures obtained using standardized ARISA with identical primers are of value. Moreover, ARISA patterns can be statistically analyzed to identify distinct subgroups and transitions between them as well as serial correlations. Thereby the microbial community and its structural development can be correlated with statistical relevance to changes in operational (feed) and process parameters (pH-value, biogas composition). In particular when augmented by deep sequencing data of judiciously chosen samples, this allows a hitherto unknown level of insight into the performance of technical biogas plants.

Microbial community dynamics in an anaerobic biofilm reactor treating heavy oil refinery wastewater

We have established an anaerobic biofilm reactor (AnBR) for treating heavy oil refinery wastewater at the field scale for the first time.

Low-temperature anaerobic digestion is associated with differential methanogenic protein expression

Anaerobic digestion (AD) is an attractive wastewater treatment technology, leading to the generation of recoverable biofuel (methane). Most industrial AD applications, carry excessive heating costs, however, as AD reactors are commonly operated at mesophilic temperatures while handling waste streams discharged at ambient or cold temperatures. Consequently, low-temperature AD represents a cost-effective strategy for wastewater treatment. The comparative investigation of key microbial groups underpinning laboratory-scale AD bioreactors operated at 37, 15 and 7°C was carried out. Community structure was monitored using 16S rRNA clone libraries, while abundance of the most prominent methanogens was investigated using qPCR. In addition, metaproteomics was employed to access the microbial functions carried out in situ. While δ-Proteobacteria were prevalent at 37°C, their abundance decreased dramatically at lower temperatures with inverse trends observed for Bacteroidetes and Firmicutes. Methanobacteriales and Methanosaeta were predominant at all temperatures investigated while Methanomicrobiales abundance increased at 15°C compared to 37 and 7°C. Changes in operating temperature resulted in the differential expression of proteins involved in methanogenesis, which was found to occur in all bioreactors, as corroborated by bioreactors' performance. This study demonstrated the value of employing a polyphasic approach to address microbial community dynamics and highlighted the functional redundancy of AD microbiomes.

Co-occurence of Crenarchaeota, Thermoplasmata and methanogens in anaerobic sludge digesters

16S rRNA Crenarchaeota and Thermoplasmata sequences retrieved from 22 anaerobic digesters were analysed. 4.8 and 0.53 % of archaeal sequences were simultaneously affiliated to these lineages. A core of 2 operational taxonomic units (OTUs) representing 0.6 to -33.6 % of all archaeal sequences were defined for the Crenarchaeotes and identified to already known but not yet cultivable organisms in almost half of the digesters sampled. For the Thermoplasmata, apparently less abundant with 0.7 to -4.7 % of the archaeal sequences, 3 OTUs were identified. We showed here that Crenarchaeotes coexist with methanogens and are particularly abundant when Arch I lineage (also called WSA2 by Hugenholtz) is dominant in digesters. Moreover, Thermoplasmata were detected when Crenarchaeota were present. Interactions between methanogens, Crenarchaeotea and Thermoplamata were thus discussed.

Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control

Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

Effect of sulfate on low-temperature anaerobic digestion

The effect of sulfate addition on the stability of, and microbial community behavior in, low-temperature anaerobic expanded granular sludge bed-based bioreactors was investigated at 15°C. Efficient bioreactor performance was observed, with chemical oxygen demand (COD) removal efficiencies of >90%, and a mean SO²⁻₄ removal rate of 98.3%. In situ methanogensis appeared unaffected at a COD: SO²⁻₄ influent ratio of 8:1, and subsequently of 3:1, and was impacted marginally only when the COD: SO²⁻₄ ratio was 1:2. Specific methanogenic activity assays indicated a complex set of interactions between sulfate-reducing bacteria (SRB), methanogens and homoacetogenic bacteria. SO²⁻₄ addition resulted in predominantly acetoclastic, rather than hydrogenotrophic, methanogenesis until >600 days of SO²⁻₄-influenced bioreactor operation. Temporal microbial community development was monitored by denaturation gradient gel electrophoresis (DGGE) of 16S rRNA genes. Fluorescence in situ hybridizations (FISH), qPCR and microsensor analysis were combined to investigate the distribution of microbial groups, and particularly SRB and methanogens, along the structure of granular biofilms. qPCR data indicated that sulfidogenic genes were present in methanogenic and sulfidogenic biofilms, indicating the potential for sulfate reduction even in bioreactors not exposed to SO²⁻₄. Although the architecture of methanogenic and sulfidogenic granules was similar, indicating the presence of SRB even in methanogenic systems, FISH with rRNA targets found that the SRB were more abundant in the sulfidogenic biofilms. Methanosaeta species were the predominant, keystone members of the archaeal community, with the complete absence of the Methanosarcina species in the experimental bioreactor by trial conclusion. Microsensor data suggested the ordered distribution of sulfate reduction and sulfide accumulation, even in methanogenic granules.

Dynamics of microbial communities in untreated and autoclaved food waste anaerobic digesters

This study describes the microbial community richness and dynamics of two semi-continuously stirred biogas reactors during a time-course study of 120 days. The reactors were fed with untreated and autoclaved (160 °C, 6.2 bar) food waste. The microbial community was analysed using a bacteria- and archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism (T-RFLP) approach. Compared with the archaeal community, the structures and functions of the bacterial community were found to be more complex and diverse. With the principal coordinates analysis it was possible to separate both microbial communities with 75 and 50% difference for bacteria and archaea, respectively, in the two reactors fed with the same waste but with different pretreatment. Despite the use of the same feeding material, anaerobic reactors showed a distinct community profile which could explain the differences in methane yield (2-17%). The community composition was highly dynamic for bacteria and archaea during the entire studied period. This study illustrates that microbial communities are dependent on feeding material and that correlations among specific bacterial and archaeal T-RFs can be established.

Changes in the Archaea microbial community when the biogas fermenters are fed with protein-rich substrates

Terminal restriction fragment length polymorphism (T-RFLP) was applied to study the changes in the composition of the methanogens of biogas-producing microbial communities on adaptation to protein-rich monosubstrates such as casein and blood. Specially developed laboratory scale (5-L) continuously stirred tank reactors have been developed and used in these experiments. Sequencing of the appropriate T-RF fragments selected from a methanogen-specific (mcrA gene-based) library revealed that the methanogens responded to the unconventional substrates by changing the community structure. T-RFLP of the 16S rDNA gene confirmed the findings.

Treatment of wastewater from coffee bean processing in anaerobic fixed bed reactors with different support materials: performance and kinetic modeling

An evaluation was performed of three upflow anaerobic fixed bed reactors for the treatment of wastewater from coffee bean processing (WCP). The supports used were: blast furnace cinders, polyurethane foam and crushed stone with porosities of 53, 95 and 48%, respectively. The testing of these 139.5 L reactors consisted of increasing the COD of the influent (978; 2401 and 4545 mg L(-1)), while maintaining the retention time of 1.3 days. For the maximum COD applied, the reactor filled with foam presented removals of 80% (non-filtered samples) and 83% (filtered samples). The greater performance of the reactor filled with foam is attributed to its porosity, which promoted greater collection of biomass. From the results, it could be concluded that the reactors presented satisfactory performance, especially when using the foam as a support. Furthermore, the modified Stover-Kincannon and second order for multicomponent substrate degradation models were successfully used to develop a model of the experimental data.

Recent developments in anaerobic membrane reactors

Anaerobic membrane reactors (AnMBRs) have recently evolved from aerobic MBRs, with the membrane either external or submerged within the reactor, and can achieve high COD removals (~98%) at hydraulic retention times (HRTs) as low as 3 h. Since membranes stop biomass being washed out, they can enhance performance with inhibitory substrates, at psychrophilic/thermophilic temperatures, and enable nitrogen removal via Anammox. Fouling is important, but addition of activated carbon or resins/precipitants can remove soluble microbial products (SMPs)/colloids and enhance flux. Due to their low energy use and solids production, and solids free effluent, they can enhance nutrient and water recycling. Nevertheless, more work is needed to: compare fouling between aerobic and anaerobic systems; determine how reactor operation influences fouling; evaluate the effect of different additives on membrane fouling; determine whether nitrogen removal can be incorporated into AnMBRs; recover methane solubility from low temperatures effluents; and, establish sound mass and energy balances.

Microbial community structure and dynamics in anaerobic fluidized-bed and granular sludge-bed reactors: influence of operational temperature and reactor configuration

Methanogenic community structure and dynamics were investigated in two different, replicated anaerobic wastewater treatment reactor configurations [inverted fluidized bed (IFB) and expanded granular sludge bed (EGSB)] treating synthetic dairy wastewater, during operating temperature transitions from 37°C to 25°C, and from 25°C to 15°C, over a 430-day trial. Non-metric multidimensional scaling (NMS) and moving-window analyses, based on quantitative real-time PCR data, along with denaturing gradient gel electrophoresis (DGGE) profiling, demonstrated that the methanogenic communities developed in a different manner in these reactor configurations. A comparable level of performance was recorded for both systems at 37°C and 25°C, but a more dynamic and diverse microbial community in the IFB reactors supported better stability and adaptative capacity towards low temperature operation. The emergence and maintenance of particular bacterial genotypes (phylum Firmicutes and Bacteroidetes) was associated with efficient protein hydrolysis in the IFB, while protein hydrolysis was inefficient in the EGSB. A significant community shift from a Methanobacteriales and Methanosaetaceae towards a Methanomicrobiales-predominated community was demonstrated during operation at 15°C in both reactor configurations.

Low-temperature (7 °C) anaerobic treatment of a trichloroethylene-contaminated wastewater: microbial community development

The feasibility of low-temperature (7 °C) anaerobic digestion for the treatment of a trichloroethylene (TCE) contaminated wastewater was investigated. Two expanded granular sludge bed (EGSB) bioreactors (R1 and R2) were employed for the mineralisation of a synthetic volatile fatty acid based wastewater at an initial organic loading rate (OLR) of 3 kg COD m(-3) d(-1), and an operating temperature of 15 °C. Successive reductions in OLR to 0.75 kg COD m(-3) d(-1), and operational temperature to 7 °C, resulted in stable bioreactor operation by day 417, with COD removal efficiency and biogas CH(4) content ≥ 74%, for both bioreactors. Subsequently, the influent to R1 was supplemented with increasing concentrations (10, 20, 30 mg l(-1)) of TCE, while R2 acted as a control. At an influent TCE concentration of 30 mg l(-1), although phase average TCE removal rates of 79% were recorded, a sustained decrease in R1 performance was observed, with COD removal of 6%, and % biogas CH(4) of 3% recorded on days 595 and 607, respectively. Specific methanogenic activity (SMA) assays identified a general shift from acetate- to hydrogen-mediated methanogenesis in both R1 and R2 biomass, while toxicity assays confirmed an increased sensitivity of the acetoclastic community in R1 to TCE and dichloroethylene (DCE), which contributed to acetate accumulation. Quantitative Polymerase Chain Reaction (qPCR) analysis of the methanogenic community confirmed the dominance of hydrogenotrophic methanogens in both R1 and R2, representing 71-89% of the total methanogenic population, however acetoclastic Methanosaeta were the dominant organisms, based on 16S rRNA gene clone library analysis of reactor biomass. The greatest change in the bacterial community, as demonstrated by UPGMA analysis of DGGE banding profiles, was observed in R1 biomass between days 417 and 609, although 88% similarity was retained between these sampling points.

Potential impact of process parameters upon the bacterial diversity in the mesophilic anaerobic digestion of beet silage

The impact of the process parameters hydraulic retention time (HRT), organic loading rate (OLR) and substrate upon bacterial diversity was analyzed. Therefore, a controlled anaerobic fermentation (1755 days) of beet silage, only initially inoculated with manure, was monitored by the amplified "ribosomal DNA" restriction analysis. More than 85% of detected operational taxonomic units (OTUs) could not be assigned to described Bacteria. In contrast to studies analyzing the digestion of energy crops in the presence of manure, Chloroflexi were detected, whereas Clostridia and Chloroflexi were identified as persistent groups. Both groups are known as potential hydrogen producers or users. Species distribution patterns for Firmicutes, Bacteroidetes, Synergistetes and Thermotogae were not clearly linked to process parameters. The presence of Planctomycetes, Actinobacteria and Alcaligenaceae was related to long HRTs and short OLRs, while Acidobacteria were governed by short HRTs and high OLRs, respectively. The impact of substrate variations on diversity was minute.

A metaproteomic approach gives functional insights into anaerobic digestion

AIMS

The objective of this work was to provide functional evidence of key metabolic pathways important for anaerobic digestion processes through the identification of highly expressed proteins in a mixed anaerobic microbial consortium.

METHODS AND RESULTS

The microbial communities from an anaerobic industrial-like wastewater treatment bioreactor were characterized using phylogenetic analyses and metaproteomics. Clone libraries indicated that the bacterial community in the bioreactor was diverse while the archaeal population was mainly composed of Methanocorpusculum-like (76%) micro-organisms. Three hundred and eighty-eight reproducible protein spots were obtained on 2-D gels, of which 70 were excised and 33 were identified. The putative functions of the proteins detected in the anaerobic bioreactor were related to cellular processes, including methanogenesis from CO(2) and acetate, glycolysis and the pentose phosphate pathway. Metaproteomics also indicated, by protein assignment, the presence of specific micro-organisms in the bioreactor. However, only a limited overlap was observed between the phylogenetic and metaproteomic analyses.

CONCLUSIONS

This study provides some direct evidence of the microbial activities taking place during anaerobic digestion.

SIGNIFICANCE AND IMPACT OF STUDY

This study demonstrates metaproteomics as a useful tool to uncover key biochemical pathways underpinning specific anaerobic bioprocesses.

Methanogenic community development in anaerobic granular bioreactors treating trichloroethylene (TCE)-contaminated wastewater at 37 °C and 15 °C

Four expanded granular sludge bed (EGSB) bioreactors were seeded with a mesophilically-grown granular sludge and operated in duplicate for mesophilic (37 °C; R1 & R2) and low- (15°; R3 & R4) temperature treatment of a synthetic volatile fatty acid (VFA) based wastewater (3 kg COD m(-3) d(-1)) with one of each pair (R1 & R3) supplemented with increasing concentrations of trichloroethylene (TCE; 10, 20, 40, 60 mg l(-1)) and one acting as a control. Bioreactor performance was evaluated by % COD removal efficiency and % biogas methane (CH(4)) content. Quantitative Polymerase Chain Reaction (qPCR) was used to investigate the methanogenic community composition and dynamics in the bioreactors during the trial, while specific methanogenic activity (SMA) and toxicity assays were utilized to investigate the activity and TCE/dichloroethylene (DCE) toxicity thresholds of key trophic groups, respectively. At both 37 °C and 15 °C, TCE levels of 60 mg l(-1) resulted in the decline of % COD removal efficiencies to 29% (Day 235) and 37% (Day 238), respectively, and in % biogas CH(4) to 54% (Day 235) and 5% (Day 238), respectively. Despite the inhibitory effect of TCE on the anaerobic digestion process, the main drivers influencing methanogenic community development, as determined by qPCR and Non-metric multidimensional scaling analysis, were (i) wastewater composition and (ii) operating temperature. At the apical TCE concentration both SMA and qPCR of methanogenic archaea suggested that acetoclastic methanogens were somewhat inhibited by the presence of TCE and/or its degradation derivatives, while competition by dechlorinating organisms may have limited the availability of H(2) for hydrogenotrophic methanogenesis. In addition, there appeared to be an inverse correlation between SMA levels and TCE tolerance, a finding that was supported by the analysis of the inhibitory effect of TCE on two additional biomass sources. The results indicate that low-temperature anaerobic digestion is a feasible approach for the treatment of TCE-containing wastewater.

Rapid acclimation of methanogenic granular sludge into denitrifying sulfide removal granules

Rapid formation of denitrifying sulfide removal granules is of practical interest to start up an expanded granular sludge bed reactor for wastewater treatment. This study demonstrates that methanogenic granules can be easily acclimated into DSR granules in one day, removing all 1.30 kg m(-3) d(-1) sulfide and converting >90% of 0.56 kg-Nm(-3)d(-1) nitrate into di-nitrogen gas. Under high loadings, reactor performance, however, declined. Under high loading rates, sulfide first inhibited the heterotrophic denitrifier (Caldithrix sp.), thereby accumulating nitrite in the system; the autotrophic denitrifier (Pseudomonas sp. C23) was then inhibited by accumulated nitrite, leading to breakdown of the entire DSR process.

Anaerobic biological treatment of alginate production wastewaters in a pilot-scale expended granular sludge bed reactor under moderate to low temperatures

Psychrophilic anaerobic digestion recently has been demonstrated as a cost-effective option for the treatment of a range of wastewater categories. In this study, the treatment of alginate production wastewaters was carried out in a pilot-scale expended granular sludge bed (EGSB) reactor. After a 40-day startup with two inocula, a 163-day experiment was run, from moderate to low temperatures, to treat seaweed-based-production wastewater. The results showed that inoculating with the active granular sludge instead of flocculent biomass can remarkably speed up the startup, and, at applied organic loading rates of 1.5 to 3.0 kg chemical oxygen demand (COD)/m3 x d, COD removal efficiencies of 55.4 to 72.6% were achieved. The volatile suspended solids ratio decreased slowly with operation time, as a result of the extremely slow growth rates of microorganisms and the accumulation of inorganic substances. Morphological examination and particle-size distribution of the granules revealed their tendency to disintegrate. Inorganic precipitates, microorganism shift, and substrate limitations may have contributed to it.

Spatial structure and persistence of methanogen populations in humic bog lakes

Patterns of diversity within methanogenic archaea in humic bog lakes are quantified over time and space to determine the roles that spatial isolation and seasonal mixing play in structuring microbial populations. The protein encoding gene mcrA is used as a molecular marker for the detection of fine-scale differences between methanogens in four dimictic bog lakes in which the water column is mixed twice a year and one meromictic lake that is permanently stratified. Although similar sequences are observed in each bog lake, each lake has its own characteristic set of persisting sequence types, indicating that methanogen populations are delimited either by low migration between the anaerobic hypolimnia or by lake-specific selection. The meromictic lake is differentiated from all other lakes and contains sequences with a higher degree of microdiversity than the dimictic lakes. By relating the structure of diversity to the depth of each bog lake, we propose the hypothesis that the deeper parts of the water column favor microdiversification of methanogens, whereas the periodically disturbed water column of shallower dimictic lakes promote genetically more diverse methanogen communities.

Diversity of methanogenic archaea in a biogas reactor fed with swine feces as the mono-substrate by mcrA analysis

Methanogenesis from the biomass in the anoxic biogas reactors is catalyzed by syntrophic cooperation between anaerobic bacteria, syntrophic acetogenic bacteria and methanogenic archaea. Understanding of microbial community composition within the biogas reactors may improve the methane production from biomass fermentation. In this study, methanogenic archaea diverity of a biogas reactor supplied with swine feces as mono-substrate under mesophilic conditions was investigated. Community composition was determined by analysis of methyl coenzyme reductase subunit A gene (mcrA) clone library consisting of 123 clones. Statistical analysis of mcrA library indicated that all major groups of methanogens from our biogas reactor were detected. In the library, 57.7% clones were affiliated to Methanobacteriales, 34.2% to Methanomicrobiales, 2.4% to Methanosarcinales and about 5.7% clones belonged to unclassified euryarchaeota. Over 90% of the methanogenic archaea from our biogas reactor were postulated to be hydrogenotrophic methanogens. Comparing with other previous studies reporting that hydrogenotrophic methanogens are dominant species in the biogas plants, this study firstly reported that Methanobacteriales instead of Methanomicrobiales are the most predominant methanogenic archaea in the biogas reactor fed with swine feces as sole substrate.

Microbial community structure and population dynamics of granules developed in expanded granular sludge bed (EGSB) reactors for the anaerobic treatment of low-strength wastewater at low temperature

The anaerobic biological treatment of sucrose-based, low-strength wastewater was investigated in expanded granular sludge bed (EGSB) reactors at low temperatures over a 300-day trial period. During the trial, the operating temperature was lowered in a stepwise manner from 20 degrees C to 5 degrees C. As a result, the reactors exhibited sufficient performances until 10 degrees C operation. The COD removal rate was 3.1-3.8 kgCOD m(-3) day(-1) at 10 degrees C. In particular, the COD removal rate increased gradually through the low-temperature operation; indeed, the later stages of the 10 degrees C operation attained a rate similar to those achieved at 20 degrees C and 15 degrees C. This finding is especially practical for applications of psychrophilic methane fermentation. Additionally, the structure of the microbial community in the granular sludge was analyzed by clone analysis based on 16S rRNA genes and fluorescence in situ hybridization (FISH). As a result, the percentage of the phylum Firmicutes, which were assumed to be Anaerobivrio sp. and Lactococcus sp., greatly increased from 0.7% to 8.0% of the total cells, especially in the surface layer of the granular sludge. These bacteria would contribute to the degradation of the sucrose substrate anaerobically at ambient temperatures. Moreover, the results suggest that a Methanospirillum species, which is a H2-utilizing methanogen, increased from 0.5% to 6.7% during the low-temperature incubation, with a significant increase of methanogenic activity from H2/CO2 at 20 degrees C. Thus, the Methanospirillum species detected in this study may have a key role as hydrogen scavenger during hydrogen-metabolism in low-temperature conditions.

Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis

AIMS

The Archaea diversity was evaluated in an agricultural biogas plant supplied with cattle liquid manure and maize silage under mesophilic conditions.

METHODS AND RESULTS

Two different genes (16S rRNA; methyl-coenzyme-M-reductase, MCR) targeted by three different PCR primer sets were selected and used for the construction of three clone libraries comprising between 104 and 118 clones. The clone libraries were analysed by restriction fragment polymorphism (RFLP). Between 11 and 31 operational taxonomic units (OTUs) were detected and assigned to orders Methanomicrobiales, Methanosarcinales and Methanobacteriales. Over 70% of all Archaea OTUs belong to the order Methanomicrobiales which mostly include hydrogenotrophic methanogens. Acetotrophic methanogens were detected in minor rates. Similar relative values were obtained by a quantitative real-time PCR analysis.

CONCLUSIONS

The results implied that in this biogas plant the most of the methane formation resulted from the conversion of H(2) and CO(2).

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reports, for the first time, a molecular analysis of the archaeal community in this type of agricultural biogas plants. Therein the hydrogenotrophic methanogenesis seems to be the major pathway of methane formation. These results are in contrast with the common thesis that in biogas fermentations the primary substrate for methanogenesis is acetate.

Long-term (1,243 days), low-temperature (4-15 degrees C), anaerobic biotreatment of acidified wastewaters: bioprocess performance and physiological characteristics

The feasibility of long-term (>3 years), low-temperature (4-15 degrees C) and anaerobic bioreactor operation, for the treatment of acidified wastewater, was investigated. A hybrid, expanded granular sludge bed-anaerobic filter bioreactor was seeded with a mesophilic inoculum and employed for the mineralization of moderate-strength (3.75-10 kg chemical oxygen demand (COD)m(-3)) volatile fatty acid-based wastewaters at 4-15 degrees C. Bioprocess performance was assessed in terms of COD removal efficiency (CODRE), methane biogas concentration, and yield, and biomass retention. Batch specific methanogenic activity assays were performed to physiologically characterise reactor biomass. Despite transient disimprovements, CODRE and methane biogas concentrations exceeded 80% and 65%, respectively, at an applied organic loading rate (OLR) of 10 kgCODm(-3)d(-1) between 9.5 and 15 degrees C (sludge loading rate (SLR), 0.6 kgCOD kg[VSS](-1)d(-1)). Over 50% of the granular sludge bed was lost to disintegration during operation at 9.5 degrees C, warranting a reduction in the applied OLR to 3.75-5 kgCODm(-3)d(-1) (SLR, c. 0.4-0.5kgCOD kg[VSS](-1)d(-1)). From that point forward, remarkably stable and efficient performance was observed during operation at 4-10 degrees C, with respect to CODRE (>or=82%), methane biogas concentration (>70%) and methane yields (>4l(Methane)d(-1)), suggesting the adaptation of our mesophilic inoculum to psychrophilic operating conditions. Physiological activity assays indicated the development of psychroactive syntrophic and methanogenic populations, including the emergence of putatively psychrophilic propionate-oxidising and hydrogenotrophic methanogenic activity. The data suggest that mesophilic inocula can physiologically adapt to sub-optimal operational temperatures: treatment efficiencies and sludge loading rates at 4 degrees C (day, 1243) were comparable to those achieved at 15 degrees C (day 0). Furthermore, long-term, low-temperature bioreactor operation may act as a selective enrichment for psychrophilic methanogenic activity from mesophilic inocula. The observed efficient and stable bioprocess performance highlights the potential for long-term, low-temperature bioreactor operation.

Phylogenetic comparison of the methanogenic communities from an acidic, oligotrophic fen and an anaerobic digester treating municipal wastewater sludge

Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.