Abstract:

A heterotrophic, gram-stain-negative, aerobic, sodium-requiring and motile bacterium was isolated from oil-contaminated surface water of the Gulf of Mexico during the Deepwater Horizon oil spill. Strain O3.65T showed highest 16S rRNA gene sequence similarity to Phaeobacter gallaeciensis BS107T and Phaeobacter inhibens T5T, both with 98.3 %, respectively. Based on complete genome analysis, highest similarity was observed to species of the genus Ruegeria. Phylogenetic, phylogenomic and phenotypic differences revealed that strain O3.65T represents a new species of a novel genus within the family Rhodobacteraceae, for which we propose the name Tritonibacter horizontis gen. nov., sp. nov. The type strain of the type species is O3.65T (=DSM 101689 T =LMG 29740 T). Repository UDI: The GenBank accession number for the genome sequence of Tritonibacter horizontis O3.65 is LPUY00000000.1. The locus_tag including the 16S rRNA gene sequence is TRIHO_RS00090. The sample was collected on June 1st, 2010 and the strain was isolated from the location close to the Macondo wellhead (28.732778°C -88.383222°C) in the Gulf of Mexico. This dataset supports the publication: Klotz, F., Brinkhoff, T., Freese, H. M., Wietz, M., Teske, A., Simon, M., & Giebel, H.-A. (2018). Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. International Journal of Systematic and Evolutionary Microbiology, 68(3), 736–744. doi:10.1099/ijsem.0.002573

Suggested Citation:

Andreas Teske. 2019. Dataset for: Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-abb9-6557

Publications:

Klotz, F., Brinkhoff, T., Freese, H. M., Wietz, M., Teske, A., Simon, M., & Giebel, H.-A. (2018). Tritonibacter horizontis gen. nov., sp. nov., a member of the Rhodobacteraceae, isolated from the Deepwater Horizon oil spill. International Journal of Systematic and Evolutionary Microbiology, 68(3), 736–744. doi:10.1099/ijsem.0.002573

Purpose:

Microbial species and genus description.

Data Parameters and Units:

The dataset contains 1 excel file that describes the characterization of the species in terms of bacteriochlorophyll a determination, temperature growth response, vitamin requirement, substrate utilization, antibiotic susceptibility, growth rate (µ) and doubling time (t d=ln2/µ) under the conditions of: 20 °C, pH 7.6, salinity 31 psu, and 104 r.p.m, and gram stain profile. Adenine [A], cytosine [C], guanine [G], thymine [T], and uracil [U]; note: thymine occurs only in DNA and uracil only in RNA. Nucleic acid information is given as a sequence of nucleic acid acronyms.

Methods:

Whole-genome DNA sequencing was performed using Illumina technology (Illumina, San Diego, CA, USA).

Instruments:

Genome analyzer IIx Sampling scales and rates: A total of 4.6 million paired-end reads were derived from sequencing and trimmed using Trimmomatic version 0.32 (Bolger et al. 2014). De novo assembly of all trimmed reads with SPAdes version 3.5.0 resulted in 125 contigs and 71.5-fold coverage (Bankevich et al. 2012). The strain is available from the German Collection of Microorganisms and Cell cultures [DSMZ].

Provenance and Historical References:

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114–2120. doi:10.1093/bioinformatics/btu170 Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., … Pevzner, P. A. (2012). SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 19(5), 455–477. doi:10.1089/cmb.2012.0021

Individual Files: