Metadata and Data for https://doi.org/10.1128/mSystems.00124-16

2017-01-12T08:40:05Z (GMT) by Shane Hogle
<b>Citation:</b><div>Hogle SL, Brahamsha B, Barbeau KA. Direct heme uptake by phytoplankton-associated <i>Roseobacter</i> bacteria. <i>mSystems</i>. 2016. 2(1):e00124-16. DOI: 10.1128/mSystems.00124-16<br></div><div><br></div><div><b>Data availability:</b></div><div>Raw sequence data for reproducing all analyses can be obtained from JGI IMG Integrated Microbial Genomes & Microbiomes database (also see Dataset S1 for accession numebrs) and the NCBI Gene Expression Omnibus (GEO accession GSE65189 and see Dataset S2). For user convenience R scripts for reproducing the transcriptomes processing analysis are available here.</div><div><br></div><div><b>Description:</b></div><div><div>In this study we investigated the molecular basis of heme transport, an organic iron acquisition pathway, in phytoplankton-associated <i>Roseobacter</i> bacteria and explored the potential role of bacterial heme uptake in the marine environment. We searched 153 <i>Roseobacter</i> genomes and found that nearly half contained putative complete heme transport systems with near identical synteny. We also examined a publicly available co-culture transcriptome and found that the <i>Roseobacter</i> strain, <i>Sulfitobacter</i> sp. SA11, strongly downregulated a putative heme transport gene cluster during mutualistic growth with a marine diatom suggesting that the regulation of heme transport might be influenced by host cues. We generated a mutant of the phytoplankton-associated <i>Roseobacter</i> strain <i>Ruegeria</i> sp. TM1040 by insertionally inactivating its homolog of the TonB-dependent heme transporter <i>hmuR</i> and confirmed the role of this gene in the uptake of heme and hemoproteins. We performed competition experiments between iron-limited wild type and mutant TM1040 strains and found that the wild type maintains a growth advantage when competing with the mutant for iron compounds derived solely from lysed diatom cells. Heme transport systems were largely absent from public marine metagenomes and metatranscriptomes, suggesting that marine bacteria with the potential for heme transport likely have small standing populations in the free-living bacterioplankton. Heme transport is likely a useful strategy for phytoplankton-associated bacteria because it provides direct access to components of the host intracellular iron pool after lysis. </div></div>