Standards in Genomic Sciences (2011) 5:298-310 DOI:10.4056/sigs.2215005

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T)

David Schleheck1*, Michael Weiss1, Sam Pitluck2, David Bruce3, Miriam L. Land4, Shunsheng Han3, Elizabeth Saunders3, Roxanne Tapia3, Chris Detter3, Thomas Brettin4, James Han2, Tanja Woyke2, Lynne Goodwin3, Len Pennacchio2, Matt Nolan2, Alasdair M. Cook1, Staffan Kjelleberg5, Torsten Thomas5

1 Department of Biological Sciences and Research School Chemical Biology, University of Konstanz, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Centre for Marine Bio-Innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia

*Corresponding author: [email protected]

Keywords: Parvibaculum lavamentivorans DS-1, aerobic, Gram-negative, Rhodobiaceae, sur- factant biodegradation

Parvibaculum lavamentivorans DS-1T is the type of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Al- phaproteobacteria. Strain DS-1T is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that cata- lyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first com- pleted genome sequence of the genus Parvibaculum, and the first genome sequence of a rep- resentative of the family Rhodobiaceae.

Introduction Parvibaculum lavamentivorans strain DS-1T P. lavamentivorans DS-1T is therefore an example (DSM13023 = NCIMB13966) was isolated for its of a first tier member of a two-step process that ability to degrade linear alkylbenzenesulfonate mineralizes environmentally important surfac- (LAS), a major laundry surfactant with a world- tants. wide use of 2.5 million tons per annum [1]. Strain Other representatives of the novel genus Parviba- DS-1T was difficult to isolate, is difficult to culti- culum have been recently isolated. Parvibaculum vate, and represents a novel genus in the Alpha- sp. strain JP-57 was isolated from seawater [6] [2,3]. Strain DS-1 catalyzes not only and is also difficult to cultivate [3]. Parvibaculum the degradation of LAS, but also of 16 other com- indicum sp. nov. was also isolated from seawater, mercially important anionic and non-ionic surfac- via an enrichment culture that degraded polycyc- tants (hence the species name lavamentivorans = lic aromatic hydrocarbons (PAH) and crude oil [7]. consuming [chemicals] used for washing [3]). The Another Parvibaculum sp. strain was isolated from initial degradation as catalyzed by strain DS-1T a PAH-degrading enrichment culture, using river involves the activation and shortening of the alkyl- sediment as inoculum [8]. Parvibaculum species chain of the surfactant molecules, and the excre- were also reported in a study on marine alkane- tion of short-chain degradation intermediates. degrading [9]. Parvibaculum species are These intermediates are then completely utilized frequently detected by cultivation-independent by other bacteria in the community [4,5]. methods, predominantly in habitats or settings

The Genomic Standards Consortium Schleheck et al. with hydrocarbon degradation. These include a succinate, or alkanes, alkanols and alkanoates (C8 - bacterial community on marine rocks polluted C16); no sugars tested were utilized [3]. with diesel oil [10], a bacterial community from To allow for growth in liquid culture with most of diesel-contaminated soil [11], a p