PXD011160

PXD011160 is an original dataset announced via ProteomeXchange.

Title	Grazing-resistance, antibiotic production and internal carbon cycling are characteristics for bacteria that prevail in long-term enclosure experiments
Description	Enclosure experiments are frequently used to investigate the impact of changing environmental conditions on microbial assemblages. Yet, the question how individual members of bacterial communities respond to challenges posed by the incubation itself remained unanswered. We used metaproteomic profiling, 16S rRNA gene analysis and high nucleic acid content analysis to monitor bacterial communities during long-term incubations (55 days) under marine (M1), mesohaline (M2) and oligohaline (M3) conditions with and without the addition of terrestrial dissolved organic matter. Our results showed that early in the experiment (after one week, T2), bacterial communities were highly diverse and their composition differed significantly between marine, mesohaline and oligohaline conditions. Controls (BS) and tDOM-treated samples (FKB) showed notable differences at this stage. In contrast, in the late phase of the experiment (after 55 days, T6), bacterial communities in both, manipulated and untreated marine and mesohaline enclosures were quite similar to each other and were dominated by gammaproteobacterial Spongiibacter. In the oligohaline enclosure, the actinobacterial hgc-I clade was very abundant in this phase. Our findings suggest that individual capacities, e.g. grazing-resistance, antibiotics production, and the ability to access alternative carbon sources may enable Spongiibacter and hgc-I clade members to successfully prevail during long-term incubations. Bacterial community composition in enclosure experiments thus seems to be strongly influenced by the individual inherent bacterial strategies to cope with the incubation as such. Researchers intending to investigate the effects of manipulation on complex microbial communities may therefore want to use short incubation periods or sophisticated systems that avoid these unspecific effects of long-term experiments.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:14:26.666.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011160
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Frank Unfried
SpeciesList	scientific name: Eukaryota (eucaryotes); NCBI TaxID: 2759; scientific name: Viruses; NCBI TaxID: 10239; scientific name: Bacteria; NCBI TaxID: 2;
ModificationList	Oxidation
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-23 23:42:29	ID requested
1	2019-07-10 08:55:53	announced
⏵ 2	2024-10-22 04:14:27	announced	2024-10-22: Updated project metadata.

10.1128/aem.00825-19;

10.6019/PXD011160;

Herlemann DPR, Markert S, Meeske C, Andersson AF, de Bruijn I, Hentschker C, Unfried F, Becher D, J, ü, rgens K, Schweder T, Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations. Appl Environ Microbiol, 85(15):(2019) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: LC-MSMS, metaproteome, Baltic Sea,Enclosure experiments

Stephanie Markert
contact affiliation	Universität Greifswald Institut für Pharmazie, AG Pharmazeutische Biotechnologie Greifswald, Germany
contact email	stephanie.markert@uni-greifswald.de
lab head
Frank Unfried
contact affiliation	University of Greifswald
contact email	fu072203@uni-greifswald.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2019/07/PXD011160

PRIDE project URI

• PRIDE
  1. PXD011160
     1. Label: PRIDE project
     2. Name: Grazing-resistance, antibiotic production and internal carbon cycling are characteristics for bacteria that prevail in long-term enclosure experiments