Biomethane potential of industrial paper wastes and investigation of the methanogenic communities involved

BACKGROUND

Cellulose-containing waste products from the agricultural or industrial sector are potentially one of the largest sources of renewable energy on earth. In this study, the biomethane potential (BMP) of two types of industrial paper wastes, wood and pulp residues (WR and PR, respectively), were evaluated under both mesophilic and thermophilic conditions, and various pretreatment methods were applied in the attempt to increase the methane potential during anaerobic digestion. The methanogenic community composition was investigated with denaturing gradient gel electrophoresis (DGGE) and the ANAEROCHIP microarray, and dominant methanogens were quantitated using quantitative PCR.

RESULTS

All pretreatments investigated in this study with the exception of the alkaline pretreatment of PR were found to increase the BMP of two paper industry wastes. However, the low recalcitrance level of the PR resulted in the pretreatments being less effective in increasing BMP when compared with those for WR. These results were supported by the physico-chemical data. A combined application of ultrasound and enzymatic pretreatment was found to be the best strategy for increasing methane yields. The retention time of substrates in the reactors strongly influenced the BMP of wastes subjected to the different pretreatments. In sludges from both paper wastes subjected to the various pretreatments, mixotrophic Methanosarcina species were found to dominate the community, accompanied by a consortium of hydrogenotrophic genera.

CONCLUSIONS

Pretreating industrial paper wastes could be a potentially viable option for increasing the overall degradation efficiency and decreasing reactor retention time for the digestion of complex organic matter such as lignocellulose or hemicellulose. This would help reduce the environmental burden generated from paper production. Although there were minor differences in the methanogenic communities depending on the temperature of anaerobic digestion, there was little effect of substrate and pretreatment type on the community composition. Thus, methanogen community dynamics would not seem to be an appropriate indicator regarding BMP in the AD processes investigated.

Co-composting of biowaste and wood ash, influence on a microbially driven-process

A trial at semi-industrial scale was conducted to evaluate the effect of wood ash amendment on communal biowaste in a composting process and on the final composts produced. For this purpose, three treatments including an unamended control (C0) and composts with additions of 6% (C6), and 12% (C12) of wood ash (w/w) were studied, and physico-chemical parameters as well as microbial activity and community composition were investigated. At the end of the process, composts were tested for toxicity and quality, and microbial physiological activity. The influence of ash addition on compost temperature, pH, microbial activity and composition was stronger during the early composting stages and diminished with time, whereby composts became more similar. Using the COMPOCHIP microarray, a reduction in the pathogenic genera Listeria and Clostridium was observed, which together with the temperature increases of the composting process helped in the hygienisation of composts. Lactobacillus species were also affected, such that reduced hybridisation signals were observed with increased ash addition, due to the increased pH values in amended composts. Organic matter mineralisation was also increased through ash addition, and no negative effects on the composting process were observed. The nutrient content of the final products was increased through the addition of ash, and no toxic effects were observed. Nonetheless, greater concentrations of heavy metals were found in composts amended with more ash, which resulted in a downgrading of the compost quality according to the Austrian Compost Ordinance. Thus, regulation of both input materials and end-product quality is essential in optimising composting processes.

Methane yields and methanogenic community changes during co-fermentation of cattle slurry with empty fruit bunches of oil palm

The biomethane potential and structural changes of the methanogenic community in a solid-state anaerobic digestion process co-digesting cattle slurry and empty fruit bunches were investigated under mesophilic (37°C) and thermophilic (55°C) conditions. Phylogenetic microarrays revealed the presence of two hydrogenotrophic genera (Methanoculleus and Methanobrevibacter) and one acetoclastic genus (Methanosarcina). Methanosarcina numbers were found to increase in both mesophilic and thermophilic treatments of empty fruit bunches. Methanobrevibacter, which dominated in the cattle slurry, remained constant during anaerobic digestion (AD) at 37°C and decreased in numbers during digestion at 55°C. Numbers of Methanoculleus remained constant at 37°C and increased during the thermophilic digestion. Physicochemical data revealed non-critical concentrations for important monitoring parameters such as total ammonia nitrogen, free ammonia nitrogen and volatile fatty acids in all treatments after AD. The biomethane potential of empty fruit bunches was higher under thermophilic conditions than under mesophilic conditions.

Investigation into the effect of high concentrations of volatile fatty acids in anaerobic digestion on methanogenic communities

A study was conducted to determine whether differences in the levels of volatile fatty acids (VFAs) in anaerobic digester plants could result in variations in the indigenous methanogenic communities. Two digesters (one operated under mesophilic conditions, the other under thermophilic conditions) were monitored, and sampled at points where VFA levels were high, as well as when VFA levels were low. Physical and chemical parameters were measured, and the methanogenic diversity was screened using the phylogenetic microarray ANAEROCHIP. In addition, real-time PCR was used to quantify the presence of the different methanogenic genera in the sludge samples. Array results indicated that the archaeal communities in the different reactors were stable, and that changes in the VFA levels of the anaerobic digesters did not greatly alter the dominating methanogenic organisms. In contrast, the two digesters were found to harbour different dominating methanogenic communities, which appeared to remain stable over time. Real-time PCR results were inline with those of microarray analysis indicating only minimal changes in methanogen numbers during periods of high VFAs, however, revealed a greater diversity in methanogens than found with the array.

Compost: its role, mechanism and impact on reducing soil-borne plant diseases

Soil-borne plant pathogens are responsible for causing many crop plant diseases, resulting in significant economic losses. Compost application to agricultural fields is an excellent natural approach, which can be taken to fight against plant pathogens. The application of organic waste products is also an environmentally friendly alternative to chemical use, which unfortunately is the most common approach in agriculture today. This review analyses pioneering and recent compost research, and also the mechanisms and mode of action of compost microbial communities for reducing the activity of plant pathogens in agricultural crops. In addition, an approach for improving the quality of composts through the microbial communities already present in the compost is presented. Future agricultural practices will almost definitely require integrated research strategies to help combat plant diseases.

Coffee husk composting: an investigation of the process using molecular and non-molecular tools

Various parameters were measured during a 90-day composting process of coffee husk with cow dung (Pile 1), with fruit/vegetable wastes (Pile 2) and coffee husk alone (Pile 3). Samples were collected on days 0, 32 and 90 for chemical and microbiological analyses. C/N ratios of Piles 1 and 2 decreased significantly over the 90 days. The highest bacterial counts at the start of the process and highest actinobacterial counts at the end of the process (Piles 1 and 2) indicated microbial succession with concomitant production of compost relevant enzymes. Denaturing gradient gel electrophoresis of rDNA and COMPOCHIP microarray analysis indicated distinctive community shifts during the composting process, with day 0 samples clustering separately from the 32 and 90-day samples. This study, using a multi-parameter approach, has revealed differences in quality and species diversity of the three composts.

Changes in the microbial communities during co-composting of digestates

Anaerobic digestion is a waste treatment method which is of increasing interest worldwide. At the end of the process, a digestate remains, which can gain added value by being composted. A study was conducted in order to investigate microbial community dynamics during the composting process of a mixture of anaerobic digestate (derived from the anaerobic digestion of municipal food waste), green wastes and a screened compost (green waste/kitchen waste compost), using the COMPOCHIP microarray. The composting process showed a typical temperature development, and the highest degradation rates occurred during the first 14 days of composting, as seen from the elevated CO2 content in the exhaust air. With an exception of elevated nitrite and nitrate levels in the day 34 samples, physical-chemical parameters for all compost samples collected during the 63 day process indicated typical composting conditions. The microbial communities changed over the 63 days of composting. According to principal component analysis of the COMPOCHIP microarray results, compost samples from the start of the experiment were found to cluster most closely with the digestate and screened compost samples. The green waste samples were found to group separately. All starting materials investigated were found to yield fewer and lower signals when compared to the samples collected during the composting experiment.

Biotic and abiotic processes contribute to successful anaerobic degradation of cyanide by UASB reactor biomass treating brewery waste water

In contrast to the general aerobic detoxification of industrial effluents containing cyanide, anaerobic cyanide degradation is not well understood, including the microbial communities involved. To address this knowledge gap, this study measured anaerobic cyanide degradation and the rearrangements in bacterial and archaeal microbial communities in an upflow anaerobic sludge blanket (UASB) reactor biomass treating brewery waste water using bio-methane potential assays, molecular profiling, sequencing and microarray approaches. Successful biogas formation and cyanide removal without inhibition were observed at cyanide concentrations up to 5 mg l(-1). At 8.5 mg l(-1) cyanide, there was a 22 day lag phase in microbial activity, but subsequent methane production rates were equivalent to when 5 mg l(-1) was used. The higher cumulative methane production in cyanide-amended samples indicated that part of the biogas was derived from cyanide degradation. Anaerobic degradation of cyanide using autoclaved UASB biomass proceeded at a rate more than two times lower than when UASB biomass was not autoclaved, indicating that anaerobic cyanide degradation was in fact a combination of simultaneous abiotic and biotic processes. Phylogenetic analyses of bacterial and archaeal 16S rRNA genes for the first time identified and linked the bacterial phylum Firmicutes and the archaeal genus Methanosarcina sp. as important microbial groups involved in cyanide degradation. Methanogenic activity of unadapted granulated biomass was detected at higher cyanide concentrations than reported previously for the unadapted suspended biomass, making the aggregated structure and predominantly hydrogenotrophic nature of methanogenic community important features in cyanide degradation. The combination of brewery waste water and cyanide substrate was thus shown to be of high interest for industrial level anaerobic cyanide degradation.

Archaeal community dynamics and abiotic characteristics in a mesophilic anaerobic co-digestion process treating fruit and vegetable processing waste sludge with chopped fresh artichoke waste

This study evaluated the feasibility of obtaining methane in anaerobic digestion (AD) from the waste products generated by the processing of fruit and vegetables. During the first phase (0-55 d) of the AD using sludge from fruit and vegetable processing, an average value of 244±88 L kg(-1) dry matter d(-1)of biogas production was obtained, and methane content reached 65% of the biogas. Co-digestion with chopped fresh artichoke wastes in a second phase (55-71 d) enhanced biogas production, and resulted in an average value of 354±68 L kg(-1) dry matter d(-1), with higher methane content (more than 70%). The archaeal community involved in methane production was studied using the ANAEROCHIP microarray and real-time PCR. Results indicated that species of Methanosaeta and Methanosarcina were important during the AD process. Methanosarcina numbers increased after the addition of chopped fresh artichoke, while Methanosaeta numbers decreased.

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year.

Treatment alternatives of slaughterhouse wastes, and their effect on the inactivation of different pathogens: a review

Slaughterhouse wastes are a potential reservoir of bacterial, viral, prion and parasitic pathogens, capable of infecting both animals and humans. A quick, cost effective and safe disposal method is thus essential in order to reduce the risk of disease following animal slaughter. Different methods for the disposal of such wastes exist, including composting, anaerobic digestion (AD), alkaline hydrolysis (AH), rendering, incineration and burning. Composting is a disposal method that allows a recycling of the slaughterhouse waste nutrients back into the earth. The high fat and protein content of slaughterhouse wastes mean however, that such wastes are an excellent substrate for AD processes, resulting in both the disposal of wastes, a recycling of nutrients (soil amendment with sludge), and in methane production. Concerns exist as to whether AD and composting processes can inactivate pathogens. In contrast, AH is capable of the inactivation of almost all known microorganisms. This review was conducted in order to compare three different methods of slaughterhouse waste disposal, as regards to their ability to inactivate various microbial pathogens. The intention was to investigate whether AD could be used for waste disposal (either alone, or in combination with another process) such that both energy can be obtained and potentially hazardous materials be disposed of.

Characterisation of source-separated household waste intended for composting

Large-scale composting of source-separated household waste has expanded in recent years in the Nordic countries. One problem can be low pH at the start of the process. Incoming biowaste at four composting plants was characterised chemically, physically and microbiologically. The pH of food waste ranged from 4.7 to 6.1 and organic acid concentration from 24 to 81 mmol kg(-1). The bacterial diversity in the waste samples was high, with all samples dominated by Gammaproteobacteria, particularly Pseudomonas and Enterobacteria (Escherichia coli, Klebsiella, Enterobacter). Lactic acid bacteria were also numerically important and are known to negatively affect the composting process because the lactic acid they produce lowers the pH, inhibiting other bacteria. The bacterial groups needed for efficient composting, i.e. Bacillales and Actinobacteria, were present in appreciable amounts. The results indicated that start-up problems in the composting process can be prevented by recycling bulk material and compost.

Design and testing of real-time PCR primers for the quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of uncultured methanogens

In this study, 16S rRNA gene primers were designed to complement the suite of already available PCR primers for the detection of different methanogens involved in biogas production through anaerobic digestion by SYBR Green real-time PCR. Primers designed for use in TaqMan real-time PCR for the organisms Methanosaeta, Methanosarcina, and Methanoculleus have been described previously; however, we found that (i) the Methanoculleus primers were not specific to members of the genus and that (ii) the Methanosarcina primers did not work specifically with SYBR Green real-time PCR. Thus, we designed new primers for these and other methanogens, and we optimized SYBR Green real-time PCR assays. Primers were tested by end-point and real-time PCR, and they were found to work specifically and sensitively. Application of these primers will allow the detection and quantification of Methanoculleus, Methanosarcina, Methanothermobacter, and a group of yet uncultured archaea from anaerobic habitats.

Application of COMPOCHIP microarray to investigate the bacterial communities of different composts

A microarray spotted with 369 different 16S rRNA gene probes specific to microorganisms involved in the degradation process of organic waste during composting was developed. The microarray was tested with pure cultures, and of the 30,258 individual probe-target hybridization reactions performed, there were only 188 false positive (0.62%) and 22 false negative signals (0.07%). Labeled target DNA was prepared by polymerase chain reaction amplification of 16S rRNA genes using a Cy5-labeled universal bacterial forward primer and a universal reverse primer. The COMPOCHIP microarray was applied to three different compost types (green compost, manure mix compost, and anaerobic digestate compost) of different maturity (2, 8, and 16 weeks), and differences in the microorganisms in the three compost types and maturity stages were observed. Multivariate analysis showed that the bacterial composition of the three composts was different at the beginning of the composting process and became more similar upon maturation. Certain probes (targeting Sphingobacterium, Actinomyces, Xylella/Xanthomonas/Stenotrophomonas, Microbacterium, Verrucomicrobia, Planctomycetes, Low G + C and Alphaproteobacteria) were more influential in discriminating between different composts. Results from denaturing gradient gel electrophoresis supported those of microarray analysis. This study showed that the COMPOCHIP array is a suitable tool to study bacterial communities in composts.

Molecular analysis of bacterial community succession during prolonged compost curing

The compost environment consists of complex organic materials that form a habitat for a rich and diverse microbial community. The aim of this research was to study the dynamics of microbial communities during the compost-curing phase. Three different methods based on 16S rRNA gene sequence were applied to monitor changes in the microbial communities: (1) denaturing gradient gel electrophoresis of PCR-generated rRNA gene fragments; (2) partial rRNA gene clone libraries; and (3) a microarray of oligonucleotide probes targeting rRNA gene sequences. All three methods indicated distinctive community shifts during curing and the dominant species prevailing during the different curing stages were identified. We found a successional transition of different bacterial phylogenetic groups during compost curing. The Proteobacteria were the most abundant phylum in all cases. The Bacteroidetes and the Gammaproteobacteria were ubiquitous. During the midcuring stage, Actinobacteria were dominant. Different members of nitrifying bacteria and cellulose and macromolecule-degrading bacteria were found throughout the curing process. In contrast, pathogens were not detected. In the cured compost, bacterial population shifts were still observed after the compost organic matter and other biochemical properties had seemingly stabilized.

Identification of anammox bacteria in a full-scale deammonification plant making use of anaerobic ammonia oxidation

The existence of anaerobic ammonia-oxidizing (anammox) bacteria was postulated in the late 1970s. Approximately 20 years later, these lithotrophic members of the nitrogen cycle were identified as deep-branching members of the planctomycetes. Recently, full-scale implementation of biological deammonification was successfully achieved in the DEMON reactor at the wastewater treatment plant in Strass, Austria. The sludge of this reactor contains red granules and brownish flocs that can be physically separated. The two fractions yielded different banding patterns in denaturing gradient gel electrophoresis of PCR products obtained with primer sets targeting the 16S rRNA genes of planctomycetes. Comparative analysis of partial sequences of almost full-length 16S rRNA gene clones obtained from the granules and flocs confirms the differences in the community composition of the two fractions. The sequences retrieved from the red granules were 93% similar to those of Candidatus Brocadia anammoxidans, a bacterium known to catalyze the anaerobic ammonia oxidation.

Microbial community related to volatile organic compound (VOC) emission in household biowaste

Malodorous emissions and potentially pathogenic microorganisms which develop during domestic organic waste collection are not only a nuisance but may also pose health risks. The aim of the present study was to determine whether the presence of specific microorganisms in biowastes is directly related to the composition of the emitted volatile organic compounds (VOCs). The succession of microbial communities during 16 days of storage in organic waste collection bins was studied by denaturing gradient gel electrophoresis (DGGE) of amplified 16S ribosomal DNA in parallel with a classical cultivation and isolation approach. Approximately 60 different bacterial species and 20 different fungal species were isolated. Additionally, some bacterial species were identified through sequencing of excised DGGE bands. Proton transfer reaction mass spectrometry (PTR-MS) was used to detect VOCs over the sampling periods, and co-inertia analyses of VOC concentrations with DGGE band intensities were conducted. Positive correlations, indicating production of the respective VOC or enhancement of microbial growth, and negative correlations, indicating the use of, or microbial inhibition by the respective compound, were found for the different VOCs. Measurement of the VOC emission pattern from a pure culture of Lactococcus lactis confirmed the positive correlations for the protonated masses 89 (tentatively identified as butyric acid), 63 (tentatively identified as dimethylsulfide), 69 (likely isoprene) and 73 (likely butanone).

Comparison of different labeling methods for the production of labeled target DNA for microarray hybridization

Different labeling methods were studied to compare various approaches to the preparation of labeled target DNA for microarray experiments. The methods under investigation included a post-PCR labeling method using the Klenow fragment and a DecaLabel DNA labeling kit, the use of a Cy3-labeled forward primer in the PCR, generating either double-stranded or single-stranded PCR products, and the incorporation of Cy3-labeled dCTPs in the PCR. A microarray that had already been designed and used for the detection of microorganisms in compost was used in the study. PCR products from the organisms Burkholderia cepacia and Staphylococcus aureus were used in the comparison study, and the signals from the probes for these organisms analyzed. The highest signals were obtained when using the post-PCR labeling method, although with this method, more non-specific hybridizations were found. Single-stranded PCR products that had been labeled by the incorporation of a Cy3-labeled forward primer in the PCR were found to give the next highest signals upon hybridization for a majority of the tested probes, with less non-specific hybridizations. Hybridization with double-stranded PCR product labeled with a Cy3-labeled forward primer, or labeled by the incorporation of Cy3-labeled dCTPs resulted in acceptable signal to noise ratios for all probes except the UNIV 1389a and Burkholderia genus probes, both located toward the 3' end of the 16S rRNA gene. The comparison of the different DNA labeling methods revealed that labeling via the Cy3-forward primer approach is the most appropriate of the studied methods for the preparation of labeled target DNA for our purposes.

Design, development, and use of molecular primers and probes for the detection of Gluconacetobacter species in the pink sugarcane mealybug

Molecular tools for the species-specific detection of Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens from the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homiptera: Pseudococcidae) were developed and used in polymerase chain reactions (PCR) and in fluorescence in situ hybridizations (FISH) to better understand the microbial diversity and the numerical significance of the acetic acid bacteria in the PSMB microenvironment. The presence of these species in the PSMB occurred over a wide range of sites, but not in all sites in sugarcane-growing areas of Queensland, Australia, and was variable over time. Molecular probes for use in FISH were also designed for the three acetic acid bacterial species, and shown to be specific only for the target species. Use of these probes in FISH of "squashed" whole mealybugs indicated that these acetic acid bacteria species represent only a small proportion of the microbial population of the PSMB. Despite the detection of Glac. sacchari, Glac. diazotrophicus, and Glac. liquefaciens by PCR from different mealybugs isolated at various times and from various sugarcane-growing areas in Queensland, Australia, these bacteria do not appear to be significant commensals in the PSMB environment.

Design and application of an oligonucleotide microarray for the investigation of compost microbial communities

A microarray consisting of oligonucleotide probes targeting variable regions of the 16S rRNA gene was designed and tested for the investigation of microbial communities in compost. Probes were designed for microorganisms that have been previously reported in the composting process and for plant, animal and human pathogens. The oligonucleotide probes were between 17 and 25 bp in length and included mostly species-specific sequences. Validation of probe specificity and optimization of hybridization conditions were conducted using fluorescently labeled 16S rRNA gene PCR products of pure culture strains. A labeling method employing a Cy3 or Cy5-labeled forward primer together with a phosphate-conjugated reverse primer for the production of single stranded DNA after a digestion step was optimised and used to label target DNA. A combination of two different DNA extraction methods using both physical and chemical lysis was found to give the best DNA yields. Increased hybridization signal intensities were obtained for probes modified with a 12 mer T-spacer. The microarray was found to have a detection limit of 10(3) cells, although in compost spiking experiments, the detection limit was reduced to 10(5) cells. The application of the microarray to compost samples indicated the presence of Streptococcus, Acinetobacter lwoffii, and Clostridium tetani in various compost samples. The presence of A. lwoffii in those compost samples was confirmed by PCR using primers specific for the organism. The aim of this study was to develop a molecular tool that would allow screening for the presence or absence of different microorganisms within compost samples.