Genome Sequence of the Marine Bacterium Marinobacter hydrocarbonoclasticus SP17, Which Forms Biofilms on Hydrophobic Organic Compounds

Abstract

f Marinobacter hydrocarbonoclasticus SP17 forms biofilms specifically at the interface between water and hydrophobic organic compounds (HOCs) that are used as carbon and energy sources. Biofilm formation at the HOC-water interface has been recognized as a strategy to overcome the low availability of these nearly water-insoluble substrates. Here, we present the genome sequence of SP17, which could provide further insights into the mechanisms of enhancement of HOCs assimilation through biofilm formation.H ydrophobic organic compounds (HOCs) encompassing lipids, hydrocarbons, and some organic pollutants are widely distributed in the environment but are weakly soluble in water and as a consequence poorly available for assimilation by heterotrophic bacteria. Biofilm formation at the HOC-water interface is a strategy employed by Marinobacter hydrocarbonoclasticus SP17 (ATCC 49840) to overcome the low bioavailability of HOCs. SP17 was isolated from chronically oil-contaminated sediment for its ability to use alkanes as the sole carbon and energy source (5). M. hydrocarbonoclasticus is a Gram-negative, aerobic, motile, nonspore-forming, and rod-shaped bacterium (5). It exhibits extreme halotolerance (0.08 to 3.5 M NaCl) and synthesizes ectoine as an osmoprotectant (2, 3).SP17 adheres and forms biofilms on alkanes and produces an extracellular-surface-active compound (2, 6). Physiological and proteomic studies revealed that biofilm formation is an efficient strategy to colonize hydrophobic interfaces (1,11,12). SP17 forms biofilms at the interface between aqueous-phase and HOC substrates like n-alkanes, fatty alcohols, or apolar lipids, such as wax esters and triacylglycerols. In contrast, biofilms were not observed on the nonmetabolizable compounds (n-C 32 alkanes, pristane, and heptamethylnonane) and glass or plastics (7). The discrimination between metabolizable and nonmetabolizable compounds indicates that at some level, biofilm formation is controlled by the presence of a nutritive interface. Adhesion and biofilm formation could be a behavioral strategy to acquire carbon and energy from HOCs contained in marine aggregates.The sequencing of the M. hydrocarbonoclasticus SP17 genome was obtained using a conventional whole-genome shotgun strategy with three libraries (3-, 10-, and 25-kb fragments) on ABI3730 sequencers. Assembly was done using the Phred/Phrap/Consed software package (www.phrap.org) with primer walking, PCR, and in vitro transposition technology (Template generation system II kit; Finnzyme, Espoo, Finland) as finishing steps, yielding a single contig molecule without gaps. Automatic genome annotation was performed using the MAGE annotation server (9, 10) followed by manual annotation. The genome of SP17 encompasses a unique chromosome with a similar GϩC content (57.43%) to but a smaller size (3989,480 bases) than that of the other Marinobacter genomes (ranging between 4,333 and 4,894 kb) (4, 8, 13). The SP17 genome contains 3 rRNA operons, 50 tRNA genes, and 3807 protein-coding sequences (CDSs) (967.89-b...

Substrates specialization in lipid compounds and hydrocarbons of Marinobacter genus

“…Comparison of physiological and genomic approaches focusing on transporters was evaluated by comparison of patterns obtained from M. hydrocarbonoclasticus strain17. From its genome fully annotated (Grimaud et al 2012), no EnzIIC of sugar could be detected in congruence with results of physiological study. The inability to use carbohydrates or to degrade the polysaccharides has been reported previously for some Marinobacter strains (Bowman and McMeekin 2005).…”

Draft Genome Sequence of a Novel Marinobacter sp. Strain from Honolulu Harbor, Hawai‘i

“…X15-166B T can switch between flagellum-mediated swimming and pili-mediated twitching. Unlike in the genome of Marinobacter aquaeolei VT8 (a heterotypic synonym for Marinobacter hydrocarbonoclasticus SP17) (13, 14), in which 18 proteins were predicted to be involved in the siderophore subsystem, no such biosynthesis subsystem was identified in the genome of X15-166B T . However, siderophore-dependent iron acquisition ABC transporters, including FhuB, FhuC, and FhuX, and the siderophore-independent ferric uptake system, FbpABC (15), were predicted in X15-166B T by BLASTP ( E < 1e −10 ), suggesting that X15-166B T may have lost the siderophore biosynthesis pathway and be a “cheater” that takes up others’ siderophores (16).…”

Genome Sequence of Hydrothermal Arsenic-Respiring Bacterium Marinobacter santoriniensis NKSG1 T

“…Analyses of genome sequences may improve our understanding of this genus and its role in biogeochemical cycling in the marine environment. Currently there are 9 other publically available genomes for characterized Marinobacter species and a further 5 for uncharacterized members (3, 7–9). …”