PXD044571-1

PXD044571 is an original dataset announced via ProteomeXchange.

Title	Microbiome adaptations and the role of abundant metagenomically assembled genomes (MAGs) from a production-scale biogas plant consisting of three independent digesters as revealed by MAG-centric metagenomics and metaproteomics
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.
HostingRepository	PRIDE
AnnounceDate	2024-01-26
AnnouncementXML	Submission_2024-01-26_07:23:03.951.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Patrick Hellwig
SpeciesList	scientific name: anaerobic digester metagenome; NCBI TaxID: 1263854;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-14 13:11:18	ID requested
⏵ 1	2024-01-26 07:23:04	announced

10.3390/microorganisms11102412;

Hassa J, Tubbesing TJ, Maus I, Heyer R, Benndorf D, Effenberger M, Henke C, Osterholz B, Beckstette M, P, ü, hler A, Sczyrba A, Schl, ü, ter A, Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics. Microorganisms, 11(10):(2023) [pubmed]

submitter keyword: anaerobic digestion, metagenome analyses,Biogas microbiome, metagenomic binning, metaproteome analyses, biogas process chain

Robert Heyer
contact affiliation	ISAS Bunsen-Kirchhoff-Str. 11 44139 Dortmund Germany
contact email	robert.heyer@isas.de
lab head
Patrick Hellwig
contact affiliation	Otto-von-Guericke-University Universitätsplatz 2 39106 Magdeburg Germany
contact email	hellwig@mpi-magdeburg.mpg.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044571
     1. Label: PRIDE project
     2. Name: Microbiome adaptations and the role of abundant metagenomically assembled genomes (MAGs) from a production-scale biogas plant consisting of three independent digesters as revealed by MAG-centric metagenomics and metaproteomics