PXD015067

PXD015067 is an original dataset announced via ProteomeXchange.

Title	Meta-genomic and –proteomic insights into photoautotrophic and heterotrophic interactions in a Synechococcus culture
Description	Microbial photoautotroph-heterotroph interactions underlie marine food webs and shape ecosystem diversity and structure in upper ocean environments. However, the high complexity of in situ ecosystems renders it difficult to study these interactions. Two-member co-culture systems of picocyanobacteria and single heterotrophic bacterial strains have been thoroughly investigated. However, in situ interactions comprise far more diverse heterotrophic bacterial associations with single photoautotrophic organisms. Here, bacterial community composition, lifestyle preference, and genomic- and proteomic-level metabolic characteristics were investigated for an open ocean Synechococcus ecotype and its associated heterotrophs over 91 days of co-cultivation. The associated heterotrophic bacterial assembly mostly constituted five classes including Flavobacteria, Bacteroidetes, Phycisphaerae, Gammaproteobacteria, and Alphaproteobacteria. The seven most abundant taxa/genera comprised >90% of the total heterotrophic bacterial community, and five of these displayed distinct lifestyle preferences (free-living or attached) and responses to Synechococcus growth phases. Six high-quality genomes from the co-culture system were reconstructed inclusive of Synechococcus and the five dominant heterotrophic bacterial populations. The only primary producer of the co-culture system, Synechococcus, displayed metabolic processes primarily involved in inorganic nutrient uptake, photosynthesis, and organic matter biosynthesis and release. Two of the flavobacterial populations, Muricauda and Winogradskyella, and an SM1A02 population, displayed preferences for initial degradation of complex compounds and biopolymers, as evinced by high abundances of TBDT, glycoside hydrolase, and peptidases proteins. In contrast, the alphaproteobacterium Oricola sp. population mainly utilized low molecular weight DOM, including Flavobacteria metabolism byproducts, through ABC, TRAP, and TTT transport systems. Polysaccharide-utilization loci present in the flavobacterial genomes encoded similar trans-membrane protein complexes as Sus/cellulosome and may influence their lifestyle preferences and close associations with phytoplankton. The heterotrophic bacterial populations exhibited complementary mechanisms for degrading Synechococcus-derived organic matter and driving nutrient cycling. In addition to nutrient exchange, removal of reactive oxygen species and vitamin trafficking also contributed to the maintenance of the Synechococcus / heterotroph co-culture system and the interactions shaping the system.
HostingRepository	PRIDE
AnnounceDate	2020-05-26
AnnouncementXML	Submission_2020-05-26_15:03:44.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yu Wang
SpeciesList	scientific name: Synechococcus sp. YX04-3; NCBI TaxID: 1979153;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive Plus

Revision	Datetime	Status	ChangeLog Entry
0	2019-08-19 00:51:29	ID requested
⏵ 1	2020-05-26 15:03:45	announced

Zheng Q, Wang Y, Lu J, Lin W, Chen F, Jiao N, Culture. mBio, 11(1):(2020) [pubmed]

submitter keyword: Synechococcus culture

Exoproteome

Metaproteome

Qiang Zheng
contact affiliation	Xiamen University
contact email	zhengqiang@xmu.edu.cn
lab head
Yu Wang
contact affiliation	Xiamen University
contact email	wangyu@xmu.edu.cn
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/2020/05/PXD015067

PRIDE project URI

• PRIDE
  1. PXD015067
     1. Label: PRIDE project
     2. Name: Meta-genomic and –proteomic insights into photoautotrophic and heterotrophic interactions in a Synechococcus culture