|
|
||||||||
1 Istituto per l'Ambiente Marino Costiero, CNR Consiglio Nazionale Ricerche, Spianata San Raineri 86, 98122 Messina, Italy
2 Division of Microbiology, GBF National Research Centre for Biotechnology, Mascheroder Weg 1, 38124 Braunschweig, Germany
Correspondence
Michail M. Yakimov
iakimov{at}ist.me.cnr.it
| ABSTRACT |
|---|
|
|
|---|
-Proteobacteria and has about 94·4 % sequence similarity to Oceanobacter kriegii (the closest bacterial species with a validly published name). The deduced protein sequence of the putative alkane hydrolase, AlkB, of strain MIL-1T is related to the corresponding enzymes of Alcanivorax borkumensis and Pseudomonas oleovorans (81 and 80 % similarity, respectively). On the basis of the analyses performed, Thalassolituus oleivorans gen. nov., sp. nov. is described. Strain MIL-1T (=DSM 14913T=LMG 21420T) is the type and only strain of T. oleivorans.
Published online ahead of print on 11 July 2003 as DOI 10.1099/ijs.0.02424-0.
The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA and putative alkane hydroxylase gene sequences of strain MIL-1T are AJ431699 and AJ431700, respectively.
| INTRODUCTION |
|---|
|
|
|---|
-subclass of the Proteobacteria; however, they are separate and distinct from other bacteria of this group and represent the genera Alcanivorax (Yakimov et al., 1998
During studies on the diversity of hydrocarbonoclastic marine bacteria that occur naturally in coastal ecosystems that have been chronically exposed to oil hydrocarbon pollution, a heterotrophic
-proteobacterium that was obligate for hydrocarbon utilization was isolated. In this work, the phenotypic characterization of strain MIL-1T, its phylogenetic assignment and DNA base and lipid compositions are presented. The isolate constitutes a species within a novel genus for which, by considering its origin, morphology and metabolism, the name Thalassolituus oleivorans gen. nov., sp. nov. is proposed. Strain MIL-1T (=DSM 14913T=LMG 21420T) is designated as the type strain.
| METHODS |
|---|
|
|
|---|
Growth conditions and phenotypic analysis.
The isolate was cultivated aerobically in ONR7a medium that was supplemented with 0·2 % (v/v) n-tetradecane. Bacto agar (Difco) (15 g l-1) was added for the preparation of solid medium. For all phenotypic tests, cultures were pre-grown in ONR7a medium that was supplemented with n-hexadecane. Growth under anaerobic conditions and utilization of carbon sources were determined and routine tests were carried out as described previously (Golyshin et al., 2002
).
The effects of hydrocarbons, salinity and temperature on growth were also examined. The capacity of various aliphatic hydrocarbons to serve as the sole source of carbon and energy was determined at 20 °C in liquid ONR7a medium. Substrates were sterilized separately and added aseptically at 0·2 % (v/v). To determine the salinity range for growth, ONR7a medium that contained no sodium ions and was supplemented with n-tetradecane was prepared by adjustment with appropriate concentrations of NaCl [0·012·0 M, i.e. 0·0612 % (w/v)]. Temperature range for growth was determined by incubation of cultures in the same medium at 4, 10, 15, 20, 25 and 30 °C. In all experiments, growth was scored by measuring OD600. Five replicates of test cultures of each strain were analysed after three serial transfers under identical conditions.
Electron microscopy.
The isolate was cultivated aerobically in ONR7a medium that was supplemented with 0·2 % (v/v) n-tetradecane; cells in mid-exponential growth phase were sedimented and fixed in 5 % glutaraldehyde that was buffered with 50 mM PBS, pH 7·1. Negative-staining, shadow-casting, embedding and ultra-thin sectioning were done according to methods described previously (Yakimov et al., 1998
; Golyshina et al., 2000
).
Cellular fatty acid analysis.
Lipids were extracted from mid-exponential cells that had been grown in ONR7a/tetradecane medium by using a modified BlighDyer procedure (Bligh & Dyer, 1959
). Later on, fatty acid methyl esters were generated and analysed by GC as described previously (Vancanneyt et al., 1996
).
Phospholipid analysis.
Lipids of cells that had been harvested in the mid-exponential phase were extracted and polar lipids were separated by flash chromatography, as described previously (Abraham et al., 1997
). The polar lipid fraction was analysed by using electrospray ionization in the negative mode in a quadrupol-time-of-flight mass spectrometer. Abundant molecular ions were separated and the parent ions then underwent collision-induced dissociations (CID); resulting fragments were finally detected in the time-of-flight part of the instrument.
G+C content and genome format.
The DNA G+C content of strain MIL-1T was determined by using an HPLC method that was described previously (Mesbah et al., 1989
; Tamaoka & Komagata, 1984
). Purified non-methylated
-phage DNA (Sigma) was used as a control. PFGE separation of the DNA digests by endonucleases AscI, PacI, PmeI, SwaI and SfiI (New England Biolabs) was performed by using a Gene Navigator Electrophoresis device (Pharmacia) with switch times that ramped between 2 and 64 s at 6 V cm-1. In order to obtain plasmids, cells of MIL-1T were extracted with a Large Construct kit (Qiagen). The extracted DNA was later analysed by gel electrophoresis.
16S rRNA gene sequence analysis.
To investigate the phylogenetic relationships of strain MIL-1T, isolation of genomic DNA, PCR amplification, determination of the sequence of the 16S rRNA gene and its subsequent phylogenetic affiliation were performed according to previously described protocols (Golyshin et al., 2002
).
Cloning of the putative alkB gene.
Chromosomal DNA of strain MIL-1T was amplified by using oligonucleotides and conditions described by Smits et al. (1999)
and the deduced putative AlkB protein sequence from MIL-1T was aligned manually by using the Se-Al sequence alignment editor, version 1.0
1 (Rambaut, 1996
). Maximum-likelihood evolutionary distances of the proteins were calculated by using the PROTDIST program and a dendrogram depicting phylogenetic relationships was derived by using the fitchmargoliash method (FITCH version 3.572c) with random-order input of sequences and using the global rearrangement option (Felsenstein, 1993
).
| RESULTS AND DISCUSSION |
|---|
|
|
|---|
|
Physiology and biochemical characteristics
Consistent with its phylogenetic placement, strain MIL-1T shares many phenotypic properties with Oceanospirillum and related genera. However, there are some crucial phenotypic differences that suggest that the new strain does not belong to any previously described genus. Isolate MIL-1T was oxidase-positive and did not catabolize any substrate tested except for acetate, aliphatic hydrocarbons with a carbon chain length between C7 and C20 and their oxidized derivatives. Poor growth was observed in ONR7a medium that was supplemented with L-arabinose and psicose. During growth on Tweens 20, 40 and 80, production of extracellular lipase was detected. Neither nitrate reduction nor denitrifying activity was detected. The reaction for catalase was positive. Biochemical and physiological characteristics that differentiate isolate MIL-1T from related genera are summarized in Table 1
. In contrast with the genera Marinobacter, Marinomonas and Oceanobacter, which are characterized by nutritional versatility, uptake by isolate MIL-1T is almost restricted to aliphatic hydrocarbons. Such a narrow spectrum of substrates that support growth of MIL-1T is a typical physiological feature for marine, obligately alkane-degrading
-proteobacteria that belong to the recently described genera Alcanivorax, Oleiphilus and Oleispira (Yakimov et al., 1998
, 2002; Golyshin et al., 2002
).
|
|
|
Molecular phylogenetic analysis
An almost-complete 16S rDNA sequence (1366 bp) was determined for isolate MIL-1T. Preliminary sequence comparison against the 16S rRNA sequences held in GenBank and the Ribosomal Database Project database (Altschul et al., 1997
; Maidak et al., 1997
) indicated that the organism belongs to the
-subclass of the Proteobacteria. The sequence was aligned manually against representatives of the
-Proteobacteria by using the secondary structure model of bacterial 16S rRNA (Gutell, 1994
). On the basis of 16S rDNA similarity, strain MIL-1T showed an apparent relationship with bacteria that belonged to the Marinomonas assemblage, within a heterogeneous group that also contained the genus Oceanospirillum. The closest relatives are Oceanobacter kriegii ATCC 27133T (94·4 % 16S rDNA sequence similarity), Oleispira antarctica LMG 21398T (92·5 %), Marinobacterium georgiense IAM 1419 (91·6 %), Oceanospirillum multiglobuliferum NBRC 13614T (91·5 %), Marinomonas mediterranea ATCC 700492T (91·2 %) and Oceanospirillum linum ATCC 11336T (90·9 %). According to the method of analysis (Satomi et al., 2002
), strain MIL-1T formed a stable phyletic group with Oceanobacter kriegii and Oleispira antarctica and was evidently placed in the Marinomonas assemblage. The branching point of MIL-1T was stable, as the corresponding bootstrap values were very high (100, 71 and 78 %, respectively; Fig. 2
). A very similar tree topology was reconstructed by using the JukesCantor treeing algorithm (data not shown).
|
|
Description of Thalassolituus gen. nov.
Thalassolituus (Tha.las.so.li.tu'us. Gr. fem. n. thalassa the sea; L. masc. n. lituus a curved rod, crook; N.L. masc. n. Thalassolituus a marine, curve-shaped organism).
Gram-negative, vibrioid to spiral, motile cells, 1·23·5 µm long by 0·6 µm wide. Strictly halophilic: Na+ ions are required for growth. Chemoorganoheterotrophic; strictly aerobic; unable to grow under anaerobic conditions by fermentation, nitrate reduction or phototrophically. Oxidase-positive. Ammonia and nitrate may serve as nitrogen sources. Indole-, arginine dihydrolase- and gelatinase-negative. Acetate, C7C20 aliphatic hydrocarbons and their oxidized derivatives are the only carbon sources that are used for growth. Principal cellular fatty acids are laurate, palmitate and octadecenoate. According to 16S rRNA gene sequence analysis, the genus belongs to the
-subgroup of the Proteobacteria, namely to the Oceanospirillum/Marinomonas/Marinobacterium assemblage. The type and only species (to date) of the genus is Thalassolituus oleivorans.
Description of Thalassolituus oleivorans sp. nov.
Thalassolituus oleivorans (o.le.i.vo'rans. L. n. oleum oil; L. part. adj. vorans devouring; N.L. adj. oleivorans oil-devouring).
Polymorphic bacteria that are motile by means of one to four polar flagella. Genome size is about 2·2 Mbp. Marine; requires at least 25 % sea water salinity for growth. Na+ ions are required; growth occurs at NaCl concentrations of 0·55·7 % (w/v), with optimum growth at 2·3 % NaCl. Growth occurs at 430 °C, with optimum growth at 2025 °C. pH range for growth is 7·59·0, with optimum growth at pH 8·0. Tweens 20, 40 and 80 are degraded, whereas agarase, amylase, arginine dihydrolase, ornithine decarboxylase, lysine decarboxylase, gelatinase and aesculinase activities are not detected. Nitrate is not reduced to nitrite. Acetate, aliphatic hydrocarbons with a chain-length between C7 and C20 and their oxidized derivatives are the only substrates that support growth. The principal fatty acids in total TLFA, PLFA and GLFA profiles are C12 : 0, C16 : 0 and C18 : 1. The TLFA and PLFA profiles are characterized by an almost equal presence of saturated and monounsaturated fatty acids, with a strong predominance of C14 : 0, C16 : 1, C16 : 0 and C18 : 1. Phospholipids are represented by the PE and PG types. DNA G+C content is 53·2 mol%. According to analysis of the 16S rRNA gene sequence, this bacterium belongs to the
-subclass of the Proteobacteria and forms a stable phyletic group with Oceanobacter kriegii.
The type and only strain to date, MIL-1T (=DSM 14913T=LMG 21420T), was isolated after serial dilutions from an enrichment culture that was established from sea water/sediment samples collected in the harbour of Milazzo, Sicily, Italy, by addition of n-tetradecane as the sole carbon source.
| ACKNOWLEDGEMENTS |
|---|
| REFERENCES |
|---|
|
|
|---|
Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 33893402.
Bligh, E. G. & Dyer, W. J. (1959). A rapid method for total lipid extraction and purification. Can J Biochem Physiol 37, 911917.
Bowditch, R. D., Baumann, L. & Baumann, P. (1984). Description of Oceanospirillum kriegii sp. nov. and O. jannaschii sp. nov. and assignment of two species of Alteromonas to this genus as O. commune comb. nov. and O. vagum comb. nov. Curr Microbiol 10, 221230.[CrossRef]
Button, D. K., Robertson, B. R., Lepp, P. W. & Schmidt, T. M. (1998). A small, dilute-cytoplasm, high-affinity, novel bacterium isolated by extinction culture and having kinetic constants compatible with growth at ambient concentrations of dissolved nutrients in seawater. Appl Environ Microbiol 64, 44674476.
Dutta, T. K. & Harayama, S. (2001). Biodegradation of n-alkylcycloalkanes and n-alkylbenzenes via new pathways in Alcanivorax sp. strain MBIC 4326. Appl Environ Microbiol 67, 19701974.
Dyksterhouse, S. E., Gray, J. P., Herwig, R. P., Lara, J. C. & Staley, J. T. (1995). Cycloclasticus pugetii gen. nov., sp. nov., an aromatic hydrocarbon-degrading bacterium from marine sediments. Int J Syst Bacteriol 45, 116123.
Fang, J., Barcelona, M. J., Nogi, Y. & Kato, C. (2000). Biochemical implications and geochemical significance of novel phospholipids of the extremely barophilic bacteria from the Mariana Trench at 11,000 m. Deep-Sea Res Part I Oceanogr Res Pap 47, 11731182.[CrossRef]
Felsenstein, J. (1993). PHYLIP (phylogeny inference package), version 3.5c. Department of Genetics, University of Washington, Seattle, USA.
Gauthier, M. J., Lafay, B., Christen, R., Fernandez, L., Acquaviva, M., Bonin, P. & Bertrand, J.-C. (1992). Marinobacter hydrocarbonoclasticus gen nov., sp. nov., a new, extremely halotolerant, hydrocarbon-degrading marine bacterium. Int J Syst Bacteriol 42, 568576.
Golyshin, P. N., Chernikova, T. N., Abraham, W.-R., Lünsdorf, H., Timmis, K. N. & Yakimov, M. M. (2002). Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. Int J Syst Evol Microbiol 52, 901911.[Abstract]
Golyshina, O. V., Pivovarova, T. A., Karavaiko, G. I. & 7 other authors (2000). Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea. Int J Syst Evol Microbiol 50, 9971006.[Abstract]
González, J. M. & Whitman, W. B. (2001). Oceanospirillum and related genera. In The Prokaryotes (available at http://link.springer-ny.com/link/service/books/10125/tocs.htm).
Gutell, R. R. (1994). Collection of small subunit (16S- and 16S-like) ribosomal RNA structures: 1994. Nucleic Acids Res 22, 35023507.
Harayama, S., Kishira, H., Kasai, Y. & Shutsubo, K. (1999). Petroleum biodegradation in marine environments. J Mol Microbiol Biotechnol 1, 6370.[CrossRef][Medline]
Hedlund, B. P., Geiselbrecht, A. D., Bair, T. J. & Staley, J. T. (1999). Polycyclic aromatic hydrocarbon degradation by a new marine bacterium, Neptunomonas naphthovorans gen. nov., sp. nov. Appl Environ Microbiol 65, 251259.
Kasai, Y., Kishira, H., Syutsubo, K. & Harayama, S. (2001). Molecular detection of marine bacterial populations on beaches contaminated by the Nakhodka tanker oil-spill accident. Environ Microbiol 3, 246255.[CrossRef][Medline]
Krieg, N. R. (1984). Genus Oceanospirillum Hylemon, Wells, Krieg and Jannasch 1973, 361AL. In Bergey's Manual of Systematic Bacteriology, vol. 1, pp. 104110. Edited by N. R. Krieg & J. G. Holt. Baltimore: Williams & Wilkins.
Lechevalier, M. P. (1977). Lipids in bacterial taxonomy a taxonomist's view. Crit Rev Microbiol 5, 109210.[CrossRef]
Maidak, B. L., Olsen, G. J., Larsen, N., Overbeek, R., McCaughey, M. J. & Woese, C. R. (1997). The RDP (Ribosomal Database Project). Nucleic Acids Res 25, 109111.
Mesbah, M., Premachandran, U. & Whitman, W. B. (1989). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39, 159167.
Murphy, R. C. & Harrison, K. A. (1994). Fast atom bombardment mass spectrometry of phospholipids. Mass Spectrom Rev 13, 5775.[CrossRef]
Pot, B., Gillis, M. & De Ley, J. (1992). The genus Oceanospirillum. In The Prokaryotes. A Handbook on the Biology of Bacteria: Ecophysiology, Isolation, Identification, Applications, 2nd edn, vol. 4., pp. 32303236. Edited by A. Balows, H. G. Trüper, M. Dworkin, W. Harder & K.-H. Schleifer. New York: Springer.
Rambaut, A. (1996). Se-Al (Sequence Alignment Editor), version 1.0
1. Distributed by the author and available via http://evolve.zoo.ox.ac.uk/software.html?id=seal. Department of Zoology, University of Oxford, UK.
Satomi, M., Kimura, B., Hayashi, M., Shouzen, Y., Okuzumi, M. & Fujii, T. (1998). Marinospirillum gen. nov., with descriptions of Marinospirillum megaterium sp. nov., isolated from kusaya gravy, and transfer of Oceanospirillum minutulum to Marinospirillum minutulum comb. nov. Int J Syst Bacteriol 48, 13411348.
Satomi, M., Kimura, B., Hamada, T., Harayama, S. & Fujii, T. (2002). Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol 52, 739747.[Abstract]
Smits, T. H. M., Röthlisberger, M., Witholt, B. & van Beilen, J. B. (1999). Molecular screening for alkane hydroxylase genes in Gram-negative and Gram-positive strains. Environ Microbiol 1, 307317.[CrossRef][Medline]
Syutsubo, K., Kishira, H. & Harayama, S. (2001). Development of specific oligonucleotide probes for the identification and in situ detection of hydrocarbon-degrading Alcanivorax strains. Environ Microbiol 3, 371379.[CrossRef][Medline]
Tamaoka, J. & Komagata, K. (1984). Determination of DNA base composition by reverse-phase high-performance liquid chromatography. FEMS Microbiol Lett 25, 125128.
Vancanneyt, M., Witt, S., Abraham, W.-R., Kersters, K. & Fredrickson, H. L. (1996). Fatty acid content in whole-cell hydrolysates and phospholipid fractions of pseudomonads: a taxonomic evaluation. Syst Appl Microbiol 19, 528540.
Wang, Y., Lau, P. C. K. & Button, D. K. (1996). A marine oligobacterium harboring genes known to be part of aromatic hydrocarbon degradation pathways of soil pseudomonads. Appl Environ Microbiol 62, 21692173.[Abstract]
Yakimov, M. M., Golyshin, P. N., Lang, S., Moore, E. R. B., Abraham, W.-R., Lünsdorf, H. & Timmis, K. N. (1998). Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium. Int J Syst Bacteriol 48, 339348.
Yakimov, M. M., Giuliano, L., Gentile, G., Crisafi, E., Chernikova, T. N., Abraham, W.-R., Lünsdorf, H., Timmis, K. N. & Golyshin, P. N. (2003). Oleispira antarctica gen. nov., sp. nov., a novel hydrocarbonoclastic marine bacterium isolated from Antarctic coastal sea water. Int J Syst Evol Microbiol 53, 779785.
This article has been cited by other articles:
![]() |
R. Kalscheuer, T. Stoveken, U. Malkus, R. Reichelt, P. N. Golyshin, J. S. Sabirova, M. Ferrer, K. N. Timmis, and A. Steinbuchel Analysis of Storage Lipid Accumulation in Alcanivorax borkumensis: Evidence for Alternative Triacylglycerol Biosynthesis Routes in Bacteria J. Bacteriol., February 1, 2007; 189(3): 918 - 928. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. V. Vasilyeva, M. V. Omelchenko, Y. Y. Berestovskaya, A. M. Lysenko, W.-R. Abraham, S. N. Dedysh, and G. A. Zavarzin Asticcacaulis benevestitus sp. nov., a psychrotolerant, dimorphic, prosthecate bacterium from tundra wetland soil. Int J Syst Evol Microbiol, September 1, 2006; 56(Pt 9): 2083 - 2088. [Abstract] [Full Text] [PDF] |
||||
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| INT J SYST EVOL MICROBIOL | MICROBIOLOGY | J GEN VIROL |
| J MED MICROBIOL | ALL SGM JOURNALS | |