High-quality reads were defined by a minimal length of 250 base pairs with an average quality value of phred 20. CrossRef Trends Microbiol 4: 495503. Alcanivorax was one of the types of bacteria that Todd and his group . The bacteria are widespread and are found in barely detectable concentrations wherever even a thin film of oil is present in the ocean, a common phenomenon resulting from natural oil deposits as. Bioinformatics 21, 853859 (2005). contributed to the annotation, A.G. contributed to the automatic and manual annotation and the coordination of software development for genome analysis, O.V.G. Citation in PubAg 50; Full Text 6; Journal. If feathers come into contact with oil, the seabird ingests the oil while trying to preen. Indeed, although many constituents in crude oil are biodegradable, the main limitation to their actual biodegradation is nutrient availability, particularly nitrogen and phosphorus3. et al. Yakimov, M.M. van Beilen, J.B. et al. Environ. In the case of Alcanivorax borkumensis, the reaction can erupt on the skin like MRSA infections. A cluster putatively specifying alginate biosynthesis is located elsewhere (432,500 to 448,500, Supplementary Results 2 online). Before the manual annotation of each predicted gene, an automatic annotation was computed based on different tool results as follows: similarity searches were performed against different databases including SWISS-PROT and TrEMBL, KEGG, Pfam, TIGRFAM and InterPro. Venter, J.C. et al. The COG database: an updated version includes eukaryotes. Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library. You are using a browser version with limited support for CSS. It belongs to the marine slow-growing hydrocarbonoclastic bacteria group. CIP 105606 DSM 11573 SK2. Cells grown with pyruvate were observed to be 2.0-3.0 micrometers in length and 0.4-07 micrometers in diameter, however, cells were shorter (1.0-1.5 micrometers in length) when cells were grown with n-alkanes as the carbon source (see Figure 1) [5]. BACCardIa tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. contributed to the gene prediction, F.M. Whole genome shotgun sequencing guided by bioinformatics pipelinesan optimized approach for an established technique. contributed to the annotation, F.K. Appl Environ Microbiol 72: 5965. Several recent field studies on bacterial community dynamics and hydrocarbon degradation in coastal systems have demonstrated the pivotal role of A. borkumensis in oil-spill bioremediation5,7. Oil-eating bacteria produce bio-films. 67, 19701974 (2001). J. Biol. Type IV pili-related natural transformation systems: DNA transport in mesophilic and thermophilic bacteria. Environ Microbiol 4: 141147. FEMS Microbiol Lett 203: 1121. The absence of a functional PEP-dependent sugar/phosphotransferase system or other types of sugar transporters, as well as the lack of several determinants for key enzymes of the glycolytic, pentose phosphate shunt and Entner-Doudoroff pathways (Supplementary Results 1 online), is consistent with the inability of A. borkumensis SK2 to utilize simple hexoses and other simple carbohydrates for growth. This wealth of scavenging abilities enables A. borkumensis SK2 to use its alkane-degrading potential to tackle quickly and effectively the sudden increase in carbon availability and consequent carbon/nutrient imbalance that results from typical oil spills. 4, 799808 (2002). Mohanty BK, Kushner SR (2003) Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. The microbes simply eat up contaminants such as oil and organic matter (e.g., waste food), convert them and then let off carbon dioxide and water. 7, 773779 (2005). Smits, T.H.M., Balada, S.B., Withold, B. . The microbes are used to remove organic wastes from the environment. Sabirova, J.S., Ferrer, M., Regenhardt, D., Timmis, K.N. Le site web de CORDIS ncessite lactivation de JavaScript pour fonctionner correctement. Environ. Syutsubo, K., Kishira, H. & Harayama, S. Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains. 37, 281286 (1992). masc./fem. "Blueprint of an Oil-eating Bacterium." Kasai, Y., Kishira, H., Syutsubo, K. & Harayama, S. Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Christopher R. Marks, Kathleen E. Duncan, Joseph M. Suflita, Luis Felipe Muriel-Milln, Sofa Milln-Lpez & Liliana Pardo-Lpez, Erika Boulant, Emmanuelle Cambon, Jean Michel Bolla, Keren Davidov, Evgenia Iankelevich-Kounio, Matan Oren, Nature Biotechnology Aby witryna CORDIS dziaaa poprawnie, obsuga JavaScript musi by wczona. J Mol Microbiol Biotechnol 1: 6370. Sabirova JS, Ferrer M, Regenhardt D, Timmis KN, Golyshin PN (2006a) Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization. Mutant thioesterases having enhanced medium chain substrate activity, polynucleotides encoding and configured to express the mutant thioesterases in a transformed host cell, host cells transformed to contain the polynucleotides, and methods of using same. This paucity of mobile elements may be explained by counterselection against variants with increased numbers of mobile elements, thus avoiding the detrimental effects of transposition events on the fitness of bacteria. This organism is found in the upper layers of freshwater and also in the marine environments. nov., a novel alkane-degrading bacterium isolated from sea water and deep-sea sediment. contributed to the processing of sequence reads and quality assessment, M.B. Bacteriol. This process is experimental and the keywords may be updated as the learning algorithm improves. -type alkane degrading bacteria . Reeves PR, Hobbs M, Valvano MA, Skurnik M, WhitfieldC, Coplin D, Kido N, Klena J, Maskell D, Raetz CRH, Rick PD (1996) Bacterial polysaccharide synthesis and gene nomenclature. The optimial conditions described for A.borkumensis growth include temperatures in the range of 20-30 degrees celsius, and a NaCl concentration of 3-10%. The A. borkumensis SK2 genome encodes six subunits of a Na+-dependent NADH-quinone dehydrogenase (nqrABCDEF, ABO_1032-1037), enabling it to use the sodium gradient as a source of energy for nutrient uptake. Lorenzo, Vctor De. van Beilen, J.B. et al. 3b), which catalyzes the terminal oxidation of alkanes22. (PDF 786 kb), Overview of the occurrence of AlkB homologuous proteins in marine bacteria (PDF 72 kb), Inventory of genes possibly involved into the genome stability, maintenance, DNA repair in A. borkumensis SK2 and chaperones. Microbe Descriptions - Read online for free. J. Mol. Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. Microbiology 144: 361373. ISSN 1546-1696 (online) 3a). Some of it seeps from natural oil fields, but the bulk of the discharge comes as a result of anthropogenic activities. Bruns A, Berthe-Corti L (1999) Fundibacter jadensis gen. nov., sp. FEMS Microbiol Lett 285: 8996. S2A and Alcanivorax borkumensis SK2. Nat Biotechnol 24, 9971004 (2006). Although barely detectable in unpolluted environments, A. borkumensis becomes the dominant microbe in oil-polluted waters. Microbiol. Int J Syst Evol Microbiol 57: 13311335. The two alkane-induced cytochromes of A. borkumensis SK2 are phylogenetically grouped in one branch with the P450 cytochrome of Acinetobacter sp. An integrated metagenomic and metabolite profiling study of hydrocarbon biodegradation and corrosion in navy ships, Biotechnological applications of marine bacteria in bioremediation of environments polluted with hydrocarbons and plastics, Tolerance engineering in Deinococcus geothermalis by heterologous efflux pumps, Polycyclic aromatic hydrocarbon and n-alkane pollution characteristics and structural and functional perturbations to the microbial community: a case-study of historically petroleum-contaminated soil, Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION, Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes, http://creativecommons.org/licenses/by-nc-sa/3.0/. Scientists at the University of Quebec have found that the bacterium, called Alcanivorax borkumensis, uses the key components that make up natural gas and petroleum to energize. II. "Description of Alcanivorax Venustensis sp. Alcanivorax borkumensis is a cosmopolitan marine bacterium that uses oil hydrocarbons as its exclusive source of carbon and energy. PubMed Biochimie 78, 364369 (1996). Alcanivorax was one of the types of bacteria . The A. borkumensis SK2 chromosome harbors 16 pil genes related to Type IV pili, which mediate the formation of biofilms and are involved in surface translocations27. 48, 339348 (1998). Alcanivorax borkumensis is a hydrocarbon degrading bacterium linked to oil degradation around oil spill sites. To deal with the damaging effects of UV light, A. borkumensis has a number of genes that reduce the damage. Error probabilities. Putative ribosomal binding sites and transfer RNA genes were identified with RBSFINDER42 and tRNAscan-SE43, respectively. Comparisons of chromosomal sequences were performed with GenDB. Anyone you share the following link with will be able to read this content: Sorry, a shareable link is not currently available for this article. %%EOF van Beilen JB, Smits THM, Roos FF, Brunner T, Balada SB, Rthlisberger M, Witholt B (2005) Identification of an amino acid position that determines the substrate range of integral membrane alkane hydroxylases. [5] Yakimov, Michail M., Peter N. Golyshin, Siegmund Lang, Edward R. B. Moore, Wolf-Rainer Abraham, Heinrich Lunsdorf, and Kenneth N. Timmis. 2015 Alcanivorax hongdengensis Wu et al. Res. CrossRef PubMed The ubiquity of A. borkumensis reflects its highly developed ability to adapt to the varying conditions it faces in different unpolluted and polluted marine environments. Alcanivorax, first described in 1998, is a Gram-negative, halophilic, aerobic, rod-shaped, oil-degrading marine bacterium that is found in low abundances in unpolluted environments in the upper layers of the ocean, but quickly becomes the predominant microbe in oil-contaminated open oceans and coastal waters when nitrogen and phosphorus are not limiting [2]. The genome also includes 11 genes coding for different lipases/esterases of unknown specificity. Here we report the amphiphilic amphibactin siderophores produced by the oil-associated bacteria, Vibrio sp. 4). A. borkumensis specifies as well a variety of chaperone-like activity proteins, many of which are commonly found in all bacterial genomes (Supplementary Results 2 online). J Bacteriol 181: 66796688. Google Scholar. et al. Cloning and functional analysis of alkB genes in Alcanivorax borkumensis SK2. No other carbohydrate transporters, such as ABC-type transport systems for ribose, xylose, arabinose and galactoside, that are usually present in other bacteria, were identified. Rling WFM, Milner MG, Jones DM, Fratepietro F, Swannell RPJ, Daniel F, Head IM (2004) Bacterial community dynamics and hydrocarbon degradation during a field-scale evaluation of bioremediation on a mudflat beach contaminated with buried oil. Reva ON, Hallin PF, Willenbrock H, Sicheritz-Ponten T, Tmmler B, Ussery DW (2008) Global features of the Alcanivorax borkumensis SK2 genome. Species [ edit] Alcanivorax comprises the following species: [1] Alcanivorax balearicus Rivas et al. Genome Res. Alcanivorax borkumensis Alcanivorax borkumensis is a helpful microbe that can eat oil and hydrocarbons in the presence of oxygen it is called an alkane degrader. Mol Microbiol 53: 857869. Kalscheuer R, Stveken T, Malkus U, Reichelt R, Golyshin PN, Sabirova JS, Ferrer M, Timmis KN, Steinbchel A (2007) Analysis of storage lipid accumulation in Alcanivorax borkumensis: evidence for alternative triacylglycerol biosynthesis routes in bacteria. J. Syst. It is aerobic, meaning it uses oxygen to gain energy, and it is halophilic, meaning it tends to live in environments that contain salt, such as salty ocean water. volume24,pages 9971004 (2006)Cite this article. Microbiology 147, 16211630 (2001). Rocchetta HL, Burrows LL, Lam JS (1999) Genetics of O-antigen biosynthesis in Pseudomonas aeruginosa. This framework will thus undoubtedly contribute to the development of new strategies for the bioremediation of petroleum-contaminated marine sites. Wcz obsug JavaScript. It has been detected worldwide in places such as the Mediterranean Sea, Pacific Ocean, and the Arctic Sea [4]. . Export or import of solutes is designated by the direction of the arrow through the transporter. This license does not permit commercial exploitation, and derivative works must be licensed under the same or similar license. The Gene Ontology (GO) database and informatics resource. While sequencing the A. borkumensis genome, we had to readjust the estimated genome size of 2.1 Mbp (as measured by pulse field gel electrophoresis) to a real size of 3.1 Mbp35. & Golyshin, P.N. Yanisch-Perron, C., Vieira, J. Share this article: This article uses material from the Wikipedia article Alcanivorax borkumensis, and is written by contributors. 6, 191197 (2004). tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. A search for alkB genes in sequenced marine organisms and the only marine metagenomic database available19 revealed that only a comparatively small number of bacteria harbor alkB homologs and even fewer have multiple copies (Supplementary Fig. To make things a little scarier, some of the oil-eating bacteria have been genetically modified, or otherwise bioengineered, to better eat the oil -- including Alcanivorax borkumensis and some of the Pseudomonas. The A. borkumensis SK2 genome encodes diverse and alternative systems for the uptake of both dissolved organic and inorganic nitrogen28.