PXD049428

PXD049428 is an original dataset announced via ProteomeXchange.

Title	Unraveling the Molecular Mechanism of Biofilm Formation by Rhodanobacter under Environmental Stressors
Description	Bacteria are known to adhere to surfaces via self-produced extracellular polymeric substances organized as biofilms. In subsurface areas with low oxygen, limited nutrients, and toxic contaminants, biofilms are crucial for microbial survival and persistence. However, the relationship between biofilm formation and survival in such environments is not well-documented. At the Oak Ridge Reservation Field Research Center (ORRFRC), we observed a high abundance of Rhodanobacter species in conditions with elevated nitrate, metals, organics, and nitric acid. This study investigated the role of biofilm formation in their survival and the underlying molecular mechanisms in diverse geochemical niches. We examined sixteen phylogenetically diverse Rhodanobacter strains for biofilm formation under varying nutrient, pH, and nitrate conditions. Our findings indicate that biofilm formation is a strain-specific phenotype, correlating with environmental stresses, especially in low pH and nitrate conditions. Comparative genomic analysis revealed unique traits in the high biofilm-forming FW021-MT20 strain, such as the absence of flagella and chemotaxis genes and the presence of unique secretion system VI genes, as supported by pangenomic results. Additional tests on biofilm formation in response to field-relevant metals highlighted increased biofilm formation under aluminum stress in strains typically exhibiting weaker biofilm capabilities. Further investigation using RB-Tnseq, proteomics, and TEM indicated flagellar loss under aluminum stress, linked to increased cyclic AMP and di-GMP levels. Our results shed light on the adaptive strategies of Rhodanobacter strains in subsurface environments, suggesting genetic factors linked to biofilm formation and metal stress tolerance, thereby enhancing our understanding of microbial survival under environmental stress.
HostingRepository	PRIDE
AnnounceDate	2025-03-08
AnnouncementXML	Submission_2025-03-07_19:56:27.097.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Rhodanobacter sp.; NCBI TaxID: 1883446;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-16 10:38:35	ID requested
⏵ 1	2025-03-07 19:56:28	announced

10.1093/ismejo/wrae151;

Chen M, Trotter VV, Walian PJ, Chen Y, Lopez R, Lui LM, Nielsen TN, Malana RG, Thorgersen MP, Hendrickson AJ, Carion H, Deutschbauer AM, Petzold CJ, Smith HJ, Arkin AP, Adams MWW, Fields MW, Chakraborty R, Molecular mechanisms and environmental adaptations of flagellar loss and biofilm growth of Rhodanobacter under environmental stress. ISME J, 18(1):(2024) [pubmed]

submitter keyword: stress response,Biofilm, Rhodanobacter

Christopher Petzold
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD049428
     1. Label: PRIDE project
     2. Name: Unraveling the Molecular Mechanism of Biofilm Formation by Rhodanobacter under Environmental Stressors