Microbial communities in 9 full-scale biogas reactors
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB11422 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1074710.fastq.gz | Fastqsanger.gz | |||
| ERR1074720.fastq.gz | Fastqsanger.gz | |||
| ERR1074730.fastq.gz | Fastqsanger.gz | |||
| ERR1074711.fastq.gz | Fastqsanger.gz | |||
| ERR1074721.fastq.gz | Fastqsanger.gz |
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Project description:BackgroundBiogas is a renewable energy carrier which is used for heat and power production or, in the form of purified methane, as a vehicle fuel. The formation of methane from organic materials is carried out by a mixed microbial community under anaerobic conditions. However, details about the microbes involved and their function are limited. In this study we compare the metagenomes of four parallel biogas reactors digesting a protein-rich substrate, relate microbiology to biogas performance, and observe differences in these reactors' microbial communities compared to the original inoculum culture.ResultsThe biogas process performance during the startup phase of four parallel continuous stirred tank reactors (designated R1, R2, R3, and R4) co-digesting fish waste and cow manure was studied. The microbial composition of the inoculum (day 0) and the four reactors at day 59 was studied and compared using 454 FLX Titanium pyrosequencing. In the inoculum and the reactor samples, the Bacteria Clostridium and Syntrophomonas were highly abundant, and the dominating methanogen was the hydrogenotrophic Methanoculleus. Syntrophic prokaryotes frequently found in biogas reactors with high concentrations of ammonium and volatile fatty acids were detected in all samples. The species Candidatus Cloacimonas acidaminovorans of the candidate phylum Cloacimonetes (WWE1) increased in all reactors and was the dominating bacterium at day 59. In particular, this bacterium showed a very high abundance in R1, which distinguished this reactor significantly from the other reactors in terms of microbial composition. Methane production and the reactor slurry characteristics were monitored in the digestion period. Generally all four reactors operated stably and showed rather similar characteristics. The average methane production in the reactors varied between 0.278 and 0.296 L gVS(-1), with the lowest production in R1.ConclusionsThis study showed that four parallel reactors co-digesting manure and fish waste silage operated stably during a startup phase. Several important Archaea and Bacteria degrading the protein-rich substrate were identified. In particular, microorganisms involved in syntrophic methane production seemed to be important. The detailed characterization of the microbial communities presented in this work may be useful for the operation of biogas plants degrading substrates with high concentrations of proteins.
| S-EPMC4200192 | biostudies-literature
Project description:Understanding microbial community diversity is thought to be crucial for improving process functioning and stabilities of wastewater treatment systems. However, current studies largely focus on taxonomic groups based on 16S rRNA, which are not necessarily linked to functioning, or a few selected functional genes. Here we launched a study to profile the overall functional genes of microbial communities in three full-scale wastewater treatment systems. Triplicate activated sludge samples from each system were analyzed using a high-throughput metagenomics tool named GeoChip 4.2, resulting in the detection of 38,507 to 40,647 functional genes. A high similarity of 75.5% to 79.7% shared genes was noted among the nine samples. Moreover, correlation analyses showed that the abundances of a wide array of functional genes were associated with system performances. For example, the abundances of overall nitrogen cycling genes had a strong correlation to total nitrogen (TN) removal rates (r = 0.7647, P < 0.01). The abundances of overall carbon cycling genes were moderately correlated with COD removal rates (r = 0.6515, P < 0.01). Lastly, we found that influent chemical oxygen demand (COD inf) and total phosphorus concentrations (TP inf), and dissolved oxygen (DO) concentrations were key environmental factors shaping the overall functional genes. Together, the results revealed vast functional gene diversity and some links between the functional gene compositions and microbe-mediated processes.
2014-12-31 | GSE53744 | GEO
Project description:Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops
| PRJEB7413 | ENA
Project description:BackgroundBiogas production with anaerobic digestion (AD) is one of the most promising solutions for both renewable energy production and resolving the environmental problem caused by the worldwide increase in organic waste. However, the complex structure of the microbiome in AD is poorly understood.FindingsIn this study, we constructed a microbial gene catalog of AD (22,840,185 genes) based on 1,817 Gb metagenomic data derived from digestate samples of 56 full-scale biogas plants fed with diverse feedstocks. Among the gene catalog, 73.63% and 2.32% of genes were taxonomically annotated to Bacteria and Archaea, respectively, and 57.07% of genes were functionally annotated with KEGG orthologous groups. Our results confirmed the existence of core microbiome in AD and showed that the type of feedstock (cattle, chicken, and pig manure) has a great influence on carbohydrate hydrolysis and methanogenesis. In addition, 2,426 metagenome-assembled genomes were recovered from all digestate samples, and all genomes were estimated to be ?80% complete with ?10% contamination.ConclusionsThis study deepens our understanding of the microbial composition and function in the AD process and also provides a huge number of reference genome and gene resources for analysis of anaerobic microbiota.
| S-EPMC7842101 | biostudies-literature
Project description:BACKGROUND:In recent years biogas plants in Germany have been supposed to be involved in amplification and dissemination of pathogenic bacteria causing severe infections in humans and animals. In particular, biogas plants are discussed to contribute to the spreading of Escherichia coli infections in humans or chronic botulism in cattle caused by Clostridium botulinum. Metagenome datasets of microbial communities from an agricultural biogas plant as well as from anaerobic lab-scale digesters operating at different temperatures and conditions were analyzed for the presence of putative pathogenic bacteria and virulence determinants by various bioinformatic approaches. RESULTS:All datasets featured a low abundance of reads that were taxonomically assigned to the genus Escherichia or further selected genera comprising pathogenic species. Higher numbers of reads were taxonomically assigned to the genus Clostridium. However, only very few sequences were predicted to originate from pathogenic clostridial species. Moreover, mapping of metagenome reads to complete genome sequences of selected pathogenic bacteria revealed that not the pathogenic species itself, but only species that are more or less related to pathogenic ones are present in the fermentation samples analyzed. Likewise, known virulence determinants could hardly be detected. Only a marginal number of reads showed similarity to sequences described in the Microbial Virulence Database MvirDB such as those encoding protein toxins, virulence proteins or antibiotic resistance determinants. CONCLUSIONS:Findings of this first study of metagenomic sequence reads of biogas producing microbial communities suggest that the risk of dissemination of pathogenic bacteria by application of digestates from biogas fermentations as fertilizers is low, because obtained results do not indicate the presence of putative pathogenic microorganisms in the samples analyzed.
| S-EPMC3639179 | biostudies-literature
Project description:Numerous observations indicate a high flexibility of microbial communities in different biogas reactors during anaerobic digestion. Here, we describe the functional redundancy and structural changes of involved microbial communities in four lab-scale continuously stirred tank reactors (CSTRs, 39°C, 12 L volume) supplied with different mixtures of maize silage (MS) and sugar beet silage (SBS) over 80 days. Continuously stirred tank reactors were fed with mixtures of MS and SBS in volatile solid ratios of 1:0 (Continuous Fermenter (CF) 1), 6:1 (CF2), 3:1 (CF3), 1:3 (CF4) with equal organic loading rates (OLR 1.25 kgVS m(-3) d(-1) ) and showed similar biogas production rates in all reactors. The compositions of bacterial and archaeal communities were analysed by 454 amplicon sequencing approach based on 16S rRNA genes. Both bacterial and archaeal communities shifted with increasing amounts of SBS. Especially pronounced were changes in the archaeal composition towards Methanosarcina with increasing proportion of SBS, while Methanosaeta declined simultaneously. Compositional shifts within the microbial communities did not influence the respective biogas production rates indicating that these communities adapted to environmental conditions induced by different feedstock mixtures. The diverse microbial communities optimized their metabolism in a way that ensured efficient biogas production.
| S-EPMC4554470 | biostudies-literature
Project description:BACKGROUND:Decomposition of biomass for biogas production can be practiced under wet and dry fermentation conditions. In contrast to the dry fermentation technology, wet fermentation is characterized by a high liquid content and a relatively low total solid content. In this study, the composition and functional potential of a biogas-producing microbial community in an agricultural biogas reactor operating under wet fermentation conditions was analyzed by a metagenomic approach applying 454-pyrosequencing. The obtained metagenomic dataset and corresponding 16S rRNA gene amplicon sequences were compared to the previously sequenced comparable metagenome from a dry fermentation process, meeting explicitly identical boundary conditions regarding sample and community DNA preparation, sequencing technology, processing of sequence reads and data analyses by bioinformatics tools. RESULTS:High-throughput metagenome sequencing of community DNA from the wet fermentation process applying the pyrosequencing approach resulted in 1,532,780 reads, with an average read length of 397 bp, accounting for approximately 594 million bases of sequence information in total. Taxonomic comparison of the communities from wet and dry fermentation revealed similar microbial profiles with Bacteria being the predominant superkingdom, while the superkingdom Archaea was less abundant. In both biogas plants, the bacterial phyla Firmicutes, Bacteroidetes, Spirochaetes and Proteobacteria were identified with descending frequencies. Within the archaeal superkingdom, the phylum Euryarchaeota was most abundant with the dominant class Methanomicrobia. Functional profiles of the communities revealed that environmental gene tags representing methanogenesis enzymes were present in both biogas plants in comparable frequencies. 16S rRNA gene amplicon high-throughput sequencing disclosed differences in the sub-communities comprising methanogenic Archaea between both processes. Fragment recruitments of metagenomic reads to the reference genome of the archaeon Methanoculleus bourgensis MS2(T) revealed that dominant methanogens within the dry fermentation process were highly related to the reference. CONCLUSIONS:Although process parameters, substrates and technology differ between the wet and dry biogas fermentations analyzed in this study, community profiles are very similar at least at higher taxonomic ranks, illustrating that core community taxa perform key functions in biomass decomposition and methane synthesis. Regarding methanogenesis, Archaea highly related to the type strain M. bourgensis MS2(T) dominate the dry fermentation process, suggesting the adaptation of members belonging to this species to specific fermentation process parameters.
| S-EPMC4329661 | biostudies-literature
Project description:21 independent full-scale biogas digesters with manures as materials
| PRJEB6969 | ENA
Project description:Functional redundant and similar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage
| PRJEB7938 | ENA
Project description:The use of wildflower species as biogas feedstock carries the risk that their seeds survive anaerobic digestion (AD) and cause weed problems if spread with the digestate. Risk factors for seed survival in AD include low temperature, short exposure and hardseededness (HS). However, it is not possible to predict how AD will affect seed viability of previously unstudied species. In laboratory-scale reactors, we exposed seeds of eight species from a mixture of flowering wild plants intended as biogas feedstock and three reference species to AD at two mesophilic temperatures. Half of the species were HS, the other was non-HS (NHS). Viability was determined using a combination of tetrazolium and germination tests. Viability and germinability were modeled as functions of exposure time using a dose-response approach. Responses to AD varied considerably among species, and none of the considered influencing factors (time, temperature, HS) had a consistent effect. Seed lots of a species differed in inactivation times and seed-killing efficacy. The HS species Melilotus officinalis, Melilotus albus, and Malva sylvestris were particularly AD-resistant. They were the only ones that exhibited biphasic viability curves and tended to survive and germinate more at 42°C than at 35°C. Viability of the remaining species declined in a sigmoidal curve. Most NHS species were inactivated within a few days (Cichorium intybus, Daucus carota, Echium vulgare, and Verbascum thapsus), while HS species survived longer (Malva alcea). AD stimulated germination in the HS species A. theophrasti and its AD-resistance overlapped with that of the most resistant NHS species, C. album and tomato. In all seed lots, germinability was lost faster than viability, implying that mainly dormant seeds survived. After the maximum exposure time of 36 days, seeds of HS species and Chenopodium album were still viable. We concluded that viability responses to mesophilic AD were determined by the interplay of AD-conditions and species- and seed-lot-specific traits, of which HS was an important but only one factor. For the use of wildflowers as biogas feedstock, we recommended long retention times and special care with regard to HS species.
| S-EPMC9337220 | biostudies-literature