PXD042980-1

PXD042980 is an original dataset announced via ProteomeXchange.

Title	Metaproteogenomics resolution of a high-CO2 aquifer community suggests a predatory lifestyle of groundwater Gracilibacteria
Description	Background. Bacteria of the Candidate Phyla Radiation (CPR), constituting about 25% of the bacterial biodiversity, are characterized by small cell size and patchy genomes without complete key metabolic pathways suggesting symbiotic life styles. Gracilibacteria (BD1-5) are part of the CPR branch, they possess alternate coded genomes and have two cultivated members that were shown to be microbial predators. However, besides genomic sampling, little is known about the lifestyle of Gracilibacteria, their temporal dynamics, and activity in natural ecosystems, and particularly groundwater where they have initially been genomically resolved. The current study was set out with the aim of investigating the metaproteogenome of Gracilibacteria as a function of time in the cold-water geyser Wallender Born in the Volcanic Eifel region in Germany, to estimate their activity in situ and discern expressed genes involved in their lifestyle. Results. We coupled genome-resolved metagenomics and metaproteomics to investigate a microbial community enriched in Gracilibacteria across a 12-day time-series. Groundwater was collected and sequentially filtered onto 0.2-μm and 0.1-μm filters to fraction CPR and other bacteria. Based on 670 Gbps of metagenomic data, 1129 different ribosomal protein S3 marker genes and 751 high-quality genomes (123 population genomes after dereplication), we identified dominant bacteria belonging to Galionellales and Gracilibacteria along with keystone microbes, low in genomic abundance but substantially contributing to proteomic abundance. Seven high-quality Gracilibacteria genomes showed typical limitations in their central metabolism but no co-occurrence to potential hosts. Their genomes encoded for a high number of proteins related to a predatory lifestyle, whose expression was detected in the proteome and included subunits related to type IV and type II secretion systems, as well as features related to cell-cell interactions and cell motility. Conclusion. We present a highly resolved analysis coupling metagenomics to metaproteomics for elucidating microbial dynamics of Gracilibacteria in groundwater. We posit that Gracilibacteria are successful microbial predators in this ecosystem potentially aiding in population control of this highly disturbed microbial community from the deep biosphere.
HostingRepository	PRIDE
AnnounceDate	2024-08-08
AnnouncementXML	Submission_2024-08-08_03:55:24.151.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sandra Maass
SpeciesList	scientific name: environmental samples
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-14 05:57:51	ID requested
⏵ 1	2024-08-08 03:55:24	announced

10.1186/S40168-024-01889-8;

submitter keyword: Gracilibacteria, predatory bacteria, proteomics, genome-resolved metagenomics, metaproteogenomics,CPR bacteria, BD1-5, groundwater

Dörte Becher
contact affiliation	Microbial Proteomics, Institute of Microbiology, University of Greifswald, 17489 Greifswald, Germany
contact email	dbecher@uni-greifswald.de
lab head
Sandra Maass
contact affiliation	University of Greifswald, Department for Microbial Proteomics
contact email	sandra.maass@uni-greifswald.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD042980
     1. Label: PRIDE project
     2. Name: Metaproteogenomics resolution of a high-CO2 aquifer community suggests a predatory lifestyle of groundwater Gracilibacteria