PXD031173

PXD031173 is an original dataset announced via ProteomeXchange.

Title	Bacterial necromass is rapidly metabolized by heterotrophic bacteria and supports multiple trophic levels of the groundwater microbiome
Description	Pristine groundwater is a highly stable environment with microbes adapted to dark, oligotrophic conditions. Input events like heavy rainfalls can introduce excess particulate organic matter including surface-derived microbes into the groundwater, hereby creating a disturbance to the groundwater microbiome. Some of the translocated bacteria are not able to thrive in groundwater and will form necromass. Here, we investigated the effects of necromass addition to the microbial community in fractured bedrock groundwater, using groundwater mesocosms as model systems. We followed the uptake of 13C-labeled necromass by the bacterial and eukaryotic groundwater community quantitatively and over time by employing a combined protein and DNA stable isotope probing approach. Necromass was rapidly depleted in the mesocosms within four days, accompanied by a strong decrease of Shannon diversity and an increase of bacterial 16S rRNA gene copy numbers by one order of magnitude. Species of Flavobacterium, Massilia, Rheinheimera, Rhodoferax and Undibacterium dominated the microbial community within two days and were identified as key players in necromass degradation, based on a 13C incorporation of > 90% in their peptides. Their proteomes showed various uptake and transport related proteins, and many proteins involved in metabolizing amino acids. After four and eight days of incubation, autotrophic and mixotrophic groundwater species of Nitrosomonas, Limnohabitans, Paucibacter and Acidovorax increased in abundance, with a 13C incorporation between 0.5 and 23%. Our data point towards a very fast and exclusive uptake of labeled necromass by a few specialists followed by a concerted action of groundwater microorganisms, including autotrophs presumably fueled by released, reduced nitrogen and sulfur compounds generated during necromass degradation.
HostingRepository	PRIDE
AnnounceDate	2022-05-31
AnnouncementXML	Submission_2022-05-31_01:57:04.550.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-22 09:51:29	ID requested
⏵ 1	2022-05-31 01:57:04	announced

Dataset with its publication pending

submitter keyword: groundwater, necromass, surface input, stable isotope probing, metaproteomics, subsurface, AquaDiva

Nico Jehmlich
contact affiliation	Helmholtz Centre for Environmental Research – UFZ GmbH Department of Molecular Systems Biology Permoserstrasse 15 04316 Leipzig, Germany
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD031173
     1. Label: PRIDE project
     2. Name: Bacterial necromass is rapidly metabolized by heterotrophic bacteria and supports multiple trophic levels of the groundwater microbiome