Bacteria associated with Spirulina biomass during the biogas producation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA822084 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18962935_1.fastq.gz | Fastqsanger.gz | |||
| SRR18962935_2.fastq.gz | Fastqsanger.gz | |||
| SRR18962936_1.fastq.gz | Fastqsanger.gz | |||
| SRR18962936_2.fastq.gz | Fastqsanger.gz | |||
| SRR18962937_1.fastq.gz | Fastqsanger.gz |
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Project description:Mitigation of N2O-emissions from soils is needed to reduce climate forcing by food production. Inoculating soils with N2O-reducing bacteria would be effective, but costly and impractical as a standalone operation. Here we demonstrate that digestates obtained after biogas production may provide a low-cost and widely applicable solution. Firstly, we show that indigenous N2O-reducing bacteria in digestates grow to high levels during anaerobic enrichment under N2O. Gas kinetics and meta-omic analysis show that the N2O respiring organisms, recovered as metagenome-assembled genomes (MAGs) grow by harvesting fermentation intermediates of the methanogenic consortium. Three digestate-derived denitrifying bacteria were obtained through isolation, one of which matched the recovered MAG of a dominant Dechloromonas-affiliated N2O reducer. While the identified N2O-reducers encoded genes required for a full denitrification pathway and could thus both produce and sequester N2O, their regulatory traits predicted that they act as N2O-sinks in the current system. Secondly, moving towards practical application, we show that these isolates grow by aerobic respiration in digestates, and that fertilization with these enriched digestates reduces N2O emissions. This shows that the ongoing implementation of biogas production in agriculture opens a new avenue for cheap and effective reduction of N2O emissions from food production.
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Project description:Biogas plants (BGPs) produce methane and carbon dioxide through the anaerobic digestion of agricultural waste. Identification of strategies for more stable biogas plant operation and increased biogas yields require better knowledge about the individual degradation steps and the interactions within the microbial communities. The metaprotein profiles of ten agricultural BGPs and one laboratory reactor were investigated using a metaproteomics pipeline. Fractionation of samples using SDS-PAGE was combined with a high resolution Orbitrap mass spectrometer, metagenome sequences specific for BGPs, and the MetaProteomeAnalyzer software. This enabled us to achieve a high coverage of the metaproteome of the BGP microbial communities. The investigation revealed approx. 17,000 protein groups (metaproteins), covering the majority of the expected metabolic networks of the biogas process such as hydrolysis, transport, fermentation processes, amino acid metabolism, methanogenesis and bacterial C1-metabolism. Biological functions could be linked with the taxonomic composition. Two different types of BGPs were classified by the abundance of the acetoclastic methanogenesis and by abundance of enzymes implicating syntrophic acetate oxidation. Linking of the identified metaproteins with the process steps of the Anaerobic Digestion Model 1 proved the main model assumptions but indicated also some improvements such as considering syntrophic acetate oxidation. Beside the syntrophic interactions, the microbial communities in BGPs are also shaped by competition for substrates and host-phage interactions causing cell lysis. In particular, larger amounts of Bacteriophages for the bacterial families Bacillaceae, Enterobacteriaceae and Clostridiaceae, exceeding the cell number of the Bacteria by approximately four-fold. In contrast, less Bacteriophages were found for Archaea, but more CRISPR proteins were detected. On the one hand, the virus induced turnover of biomass might cause slow degradation of complex biomass in BGP. On the other hand, the lysis of bacterial cells allows cycling of essential nutrients.
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Project description:Current developments have led to a reconsidering of energy policy in many countries with the aim of increasing the share of renewable energies in the energy supply, where the anaerobic digestion (AD) of biomass to produce methane also plays an important role. To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies became more important. By applying combined metagenome and metaproteome, as well as metagenomically assembled genome (MAG)-centric analyses, it is possible to determine not only the functional potential but also the expressed functions of the entire microbial community and also individual MAGs. This approach was used in this study for the production-scale biogas plant 35 (BP35) consisting of three digesters which were operated differently regarding process temperatures, feedstocks and other process parameters. Different process conditions were hypothesized to result in specific microbiome adaptations and differentially abundant metabolic functions in the digesters. Based on metagenomic single-read analyses, several taxa residing in the three digesters of BP35 were shown to correlate with the corresponding substrates and temperatures. In particular, the genus Defluviitoga showed the strongest correlation to the process temperature and the genus Acetomicrobium featured a direct correlation to the concentartions of different acids including acetic acid. Analysis of the functional potential and expressed functions of the entire microbial community of the three digesters revealed that the genes and key enzymes relevant for the biogas process were present and also expressed. Differences between the abundances of certain genes and expressed enzymes could be related to the specific parameters of the corresponding digesters. Regarding the biogas related metabolic pathways, MAG-centric metagenomics and metaproteomics indicated the functional potential and the actual expressed metabolic functions of certain MAGs that are differentially abundant in the three digesters. These MAGs, belonging to the phylum Firmicutes, the class Bacilli and the orders Caldicoprobacterales and Bacteroidales showed a specific metabolic activity within the three digesters and have important roles in the hydrolysis, acidogenesis or acetogenesis of the anaerobic digestion process. An archaeal MAG assigned to the species Methanothermobacter wolfeii was the most abundant and highly active hydrogenotrophic methanogen in digester 3 featuring an operation temperature of 54 °C. Beside the MAGs that were differentially abundant in the three digesters, also MAGs which were more evenly distributed were analyzed. The most abundant and highly active MAG in all digesters belongs to the class Limnochordia and was shown to be ubiquitous in all three digesters and exhibit activity in a variety of pathways representing hydrolysis as well as the acido- and acetogenesis steps of the biogas process. Other MAGs assigned to the phylum Firmicutes, genus Acetomicrobium and the hydrogenotrophic species Methanoculleus thermohydrogenotrophicum were also shown to be more evenly distributed and active in the three digesters. Corresponding taxa appeared to be more resilient to the different process parameters of the three digesters, and therefore, may support a stable biogas process. Overall, the combined metagenome and metaproteome analysis of biogas digesters helps to gain deeper insights into the composition of the whole microbial community, biogas related pathways and their expression, which could contribute to an improved microbiome-based process management in the future.
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