Dataset Information

Novel syntrophic populations dominate an ammonia-tolerant methanogenic microbiome

ABSTRACT: Metaproteomics was used to identify proteins from a mized community in a biogas reactor.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Clostridia

SUBMITTER: Magnus Arntzen

LAB HEAD: Vincent Eijsink

PROVIDER: PXD004512 | Pride | 2016-08-19

REPOSITORIES: Pride

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Publications

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

Frank J A JA Arntzen M Ø MØ Sun L L Hagen L H LH McHardy A C AC Horn S J SJ Eijsink V G H VG Schnürer A A Pope P B PB

mSystems 20160913 5

Biogas reactors operating with protein-rich substrates have high methane potential and industrial value; however, they are highly susceptible to process failure because of the accumulation of ammonia. High ammonia levels cause a decline in acetate-utilizing methanogens and instead promote the conversion of acetate via a two-step mechanism involving syntrophic acetate oxidation (SAO) to H<sub>2</sub> and CO<sub>2</sub>, followed by hydrogenotrophic methanogenesis. Despite the key role of syntroph ...[more]

PMID: 27822555

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Project description:Two-stage two-phase biogas reactor systems consisting each of one batch downflow hydrolysis reactor (HR, vol. 10 L), one process fluid storage tank (vol. 10 L), and one downstream upflow anaerobic filter reactor (AF, vol. 10 L), were operated at mesophilic (M, 37 °C) and thermophilic (T, 55 °C) temperatures and over a period of > 750 d (Figure 1, Additional file 1). For each reactor system and for each process temperature, two replicates were conducted in parallel, denominated further as biological replicates. Further process details were as previously published. Start-up of all fermenters were performed using liquid fermenter material from a biogas plant converting cattle manure in co-digestion with grass and maize silage and other biomass at varying concentrations and at mesophilic temperatures. Silage of perennial ryegrass (Lolium perenne L.) was digested as sole substrate in batches of varying amounts with retention times of 28 d (storage of bale silage at -20 °C, cutting length 3 cm, volatile substances (VS) 32 % of fresh mass (FM), total Kjeldahl nitrogen 7.6 g kgFM-1, NH4+-N 0.7 g kgFM-1, acetic acid 2.6 g kgFM-1, propionic acid < 0.04 g kgFM-1, lactic acid 2.6 g kgFM-1, ethanol 2.2 g kgFM-1, C/N ratio 19.3, chemical oxygen demand (COD) 357.7 g kgFM-1, analysis of chemical properties according to [6]. No spoilage was observed in the silage. Biogas yields were calculated as liters normalized to 0 °C and 1013 hPa (LN) per kilogram volatile substances (kgVS). For chemical analysis, samples were taken from the effluents of HR and AF. For sequencing of 16S rRNA gene amplicon libraries, microbial metagenomes, and microbial metatranscriptomes, samples were taken from the silage digestate in the HR digested for 2 d. At this time point, high AD rates were detected as indicated by the fast increase of volatile fatty acids (VFA), e.g., acetic acid. Sampling was performed at two different organic loading rates (OLR), i.e., batch-fermentation of 500 g (denominated as “low OLR”, samples MOLR500 and TOLR500) and 1,500 g silage (denominated as “increased OLR”, samples MOLR1500 and TOLR1500).

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.

Project description:Background: Methane yield and biogas productivity of biogas plants depend on microbial community structure and functionality, substrate supply, and general process parameters. Little is known, however, about the correlations between microbial community function and the process parameters. To close this knowledge gap the microbial community of 40 industrial biogas plants was evaluated by a metaproteomics approach in this study. Results: Liquid chromatography coupled to tandem mass spectrometry (Elite Hybrid Ion Trap Orbitrap) enabled the identification of 3138 metaproteins belonging to 162 biological processes and 75 different taxonomic orders. Therefore, database searches were performed against UniProtKB/Swiss-Prot and several metagenome databases. Subsequent clustering and principal component analysis of these data allowed to identify four main clusters associated to mesophilic and thermophilic process conditions, upflow anaerobic sludge blanket reactors and sewage sludge as substrate. Observations confirm a previous phylogenetic study of the same biogas plant samples that was based on 16S-rRNA gene by De Vrieze et al. (2015) (De Vrieze, Saunders et al. 2015). Both studies described similar microbial key players of the biogas process, namely Bacillales, Enterobacteriales, Bacteriodales, Clostridiales, Rhizobiales and Thermoanaerobacteriales as well as Methanobacteriales, Methanosarcinales and Methanococcales. In addition, a correlation study and a Gephi graph network based on the correlations between the taxonomic orders and process parameters suggested the presence of various trophic interactions, e.g. syntrophic hydrogen transfer between Thermoanaerobacteriales and Methanomicrobiales. For the elucidation of the main biomass degradation pathways the most abundant 1% of metaproteins were assigned to the KEGG map 1200 representing the central carbon metabolism. Additionally, the effect of the process parameters (i) temperature, (ii) organic loading rate (OLR), (iii) total ammonia nitrogen (TAN) and (iv) sludge retention time (SRT) on these pathways was investigated. For example high TAN correlated with hydrogenotrophic methanogens and bacterial one-carbon metabolism, indicating syntrophic acetate oxidation. Conclusion: This study shows the benefit of large-scale proteotyping of biogas plants, enabling the identification of general correlations between the process parameters and the microbial community structure and function. Changes in the level of microbial key functions or even in the microbial community type represent a valuable hint for process problems and disturbances.

Dataset Information

Novel syntrophic populations dominate an ammonia-tolerant methanogenic microbiome

Publications

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome.

Similar Datasets

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