PXD050137

PXD050137 is an original dataset announced via ProteomeXchange.

Title	Microbial consortia driving lignocellulose transformation in agricultural woodchip bioreactors
Description	Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers often utilize denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen-gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well-described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci. However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to highlight microbial drivers for lignocellulose transformation in woodchip bioreactors with the aim to provide an in-depth characterization of the indigenous microorganisms and their active enzymes. Our findings highlight a microbial community enriched for lignocellulose-degrading denitrifiers with key players from Giesbergeria, Cellulomonas, Azonexus, and UBA5070, including polysaccharide utilization loci from Bacteroidetes. A wide substrate specificity is observed among the many expressed carbohydrate active enzymes (CAZymes), evidencing a swift degradation of lignocellulose, including even enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.
HostingRepository	PRIDE
AnnounceDate	2024-10-21
AnnouncementXML	Submission_2024-10-21_05:23:09.218.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Magnus Arntzen
SpeciesList	scientific name: Archaea; NCBI TaxID: 2157; scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-26 01:43:00	ID requested
⏵ 1	2024-10-21 05:23:09	announced

Dataset with its publication pending

submitter keyword: metaproteomics, lignocellulose, anaerobe

Magnus Øverlie Arntzen
contact affiliation	Norwegian University of Life Sciences
contact email	magnus.arntzen@nmbu.no
lab head
Magnus Arntzen
contact affiliation	Norwegian University of Life Sciences
contact email	magnus.arntzen@nmbu.no
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD050137
     1. Label: PRIDE project
     2. Name: Microbial consortia driving lignocellulose transformation in agricultural woodchip bioreactors