Alcanivorax pacificus

Last updated

Alcanivorax pacificus
Scientific classification Red Pencil Icon.png
Domain: Bacteria
Phylum: Pseudomonadota
Class: Gammaproteobacteria
Order: Oceanospirillales
Family: Alcanivoracaceae
Genus: Alcanivorax
Species:
A. pacificus
Binomial name
Alcanivorax pacificus
Lai et al. 2011

Alcanivorax pacificus is a pyrene-degrading marine gammaproteobacterium. [1] It is of the genus Alcanivorax , a group of marine bacteria known for degrading hydrocarbons. [2] When originally proposed, the genus Alcanivorax comprised six distinguishable species. [1] However, A. pacificus, a seventh strain, was isolated from deep sea sediments in the West Pacific Ocean by Shanghai Majorbio Bio-pharm Technology Co., Ltd. in 2011. [1] A. pacificus’s ability to degrade hydrocarbons can be employed for cleaning up oil-contaminated oceans through bioremediation. The genomic differences present in this strain of Alcanivorax that distinguish it from the original consortium are important to understand to better utilize this bacteria for bioremediation. [1]

Contents

Characteristics

A. pacificus is a non-motile, Gram-negative bacillus. [1] It is oxidase- and catalase-positive. It forms light grey colonies that are between 1 and 2 millimeters in diameter when grown on 216L marine agar medium containing seawater, sodium acetate, tryptone, yeast extract, ammonium nitrate, and sodium citrate. [1] A. pacificus is mesophilic and moderately halophilic, growing best in an environment between 10-42 degrees Celsius that contains 0.5-12% NaCl. [1]

Genome

Shanghai Majorbio Bio-pharm Technology Co., Ltd. sequenced a total of 5,855,964 paired ends of A. pacificus using Solexa paired-end sequencing technology. The obtained type strain of A. pacificus is W11-5T (=MCCC 1A00474T =CCTCC AB 208236T =LMG 25514T). [3] The GC-content of strain W11-5 T is 62.62%. [4] Strain W11-5T is made of 42 contigs (N90 = 19) of 4,137,438 bp. [5]

Results from automatic gene annotation, which was completed by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline (PGAAP), revealed that the genome of strain W11-5T contains 3,762 candidate protein-encoding genes. [5] Out of these genes, 2,870 proteins were assigned to orthologous groups. Additionally identified were 41 tRNA genes for 19 amino acids and one 16S-23S-5S rRNA operon. [5]

Particularly close attention was paid to genes that potentially coded for alkane degradation. [5] Found were genes encoding for four integral-membrane alkane monooxygenases, three cytochrome P450 enzymes, and four genes encoding flavin-binding family monooxygenases. [5] These monooxygenases are especially important, as they account for long-chain n-alkane hydroxylation. [5]

Diversity

A. Pacificus is closely related to other strains in the genus Alcanivorax. It shares 16S rRNA gene sequence similarities of 93.9, 93.1, 93.1, 93.0, 93.0 and 92.9% with neighboring strains A.dieselolei B-5 T, A. balearicus MACL04 T, A. hongdengensis A-11-3 T, A. venustensis ISO4 T, A. borkumensis SK2 T and A. jadensis T9 T respectively. [1] However, as the gene sequence of A. Pacificus diverges more than 3% from all other strains, it is different enough to represent a novel bacterial strain. [6] Part of this difference results from a 549 nucleotide fragment of the alkane hydroxylase gene alkB, which was amplified from the strand W11-5T. [1] The gene alkB is a protein that is produced by A. pacificus and other strains in the genus Alcanivorax that reverses the damage of alkylation, the process by which an alkane missing one hydrogen is transferred from one molecule to another. The amino acid sequences deduced from this fragment show that there is not a clear grouping between the species of Alcanivorax, as some strains within this genus contain multiple alkB sequences, which places them on different branches of the phylogenetic tree. [1]

Related Research Articles

Thermus thermophilus is a Gram-negative bacterium used in a range of biotechnological applications, including as a model organism for genetic manipulation, structural genomics, and systems biology. The bacterium is extremely thermophilic, with an optimal growth temperature of about 65 °C (149 °F). Thermus thermophilus was originally isolated from a thermal vent within a hot spring in Izu, Japan by Tairo Oshima and Kazutomo Imahori. The organism has also been found to be important in the degradation of organic materials in the thermogenic phase of composting. T. thermophilus is classified into several strains, of which HB8 and HB27 are the most commonly used in laboratory environments. Genome analyses of these strains were independently completed in 2004.

Pseudomonas citronellolis is a Gram-negative, bacillus bacterium that is used to study the mechanisms of pyruvate carboxylase. It was first isolated from forest soil, under pine trees, in northern Virginia, United States.

Pseudomonas mendocina is a Gram-negative environmental bacterium that can cause opportunistic infections, such as infective endocarditis and spondylodiscitis, although cases are very rare. It has potential use in bioremediation as it is able to degrade toluene. Based on 16S rRNA analysis, P. mendocina has been placed in the P. aeruginosa group.

<i>Pseudomonas stutzeri</i> Species of bacterium

Pseudomonas stutzeri is a Gram-negative soil bacterium that is motile, has a single polar flagellum, and is classified as bacillus, or rod-shaped. While this bacterium was first isolated from human spinal fluid, it has since been found in many different environments due to its various characteristics and metabolic capabilities. P. stutzeri is an opportunistic pathogen in clinical settings, although infections are rare. Based on 16S rRNA analysis, this bacterium has been placed in the P. stutzeri group, to which it lends its name.

Marinobacter hydrocarbonoclasticus is a species of bacteria found in sea water which are able to degrade hydrocarbons. The cells are rod-shaped and motile by means of a single polar flagellum.

"Aromatoleum" is a genus of bacteria capable of microbial biodegradation of organic pollutants. It has one single described species member, A. aromaticum, for which the only strain is strain EbN1.

<i>Alcanivorax</i> Genus of bacteria

Alcanivorax is a genus of alkane-degrading marine bacteria.

Alcanivorax borkumensis is an alkane-degrading marine bacterium which naturally propagates and becomes predominant in crude-oil-containing seawater when nitrogen and phosphorus nutrients are supplemented.

Gallaecimonas is a recently described genus of bacteria. The first described species of this genus was Gallaecimonas pentaromativorans gen. nov., sp. nov. isolated by Rodríguez Blanco et al. in 2010 from intertidal sediments of the ria of Corcubión. It is a Gram-negative, rod-shaped, halotolerant bacterium in the class Gammaproteobacteria. It can degrade high molecular mass polycyclic aromatic hydrocarbons of 4 and 5 rings. The 16S rRNA gene sequences of the type strain CEE_131(T) proved to be distantly related to those of Rheinheimera and Serratia. Its G+C content was 41.7 mol%.

Alcanivorax dieselolei is a species of alkane-degrading bacteria. Its genome has been sequenced. It is halophilic, aerobic, Gram-negative, non-spore-forming, catalase- and oxidase-positive, motile and rod-shaped. Its type strain is B-5T.

Novosphingobium pentaromativorans is a species of high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium. It is Gram-negative, yellow-pigmented and halophilic. With type strain US6-1T. Its genome has been sequenced.

Thermoanaerobacterium aotearoense is a slightly acidophilic, anaerobic, thermophile first isolated from hot springs in New Zealand, hence its name. It is Gram-negative, peritrichously flagellated, rod-shaped forming oval terminal endospores. Strain JW/SL-NZ613T is its type strain. Its genome has been sequenced.

Brevibacillus borstelensis is a Gram-positive, aerobic, rod-shaped, endospore-forming bacterium of the genus Brevibacillus. The genome of several B. borstelensis strains have been sequenced.

Gordonia alkanivorans is a bacterium from the genus of Gordonia which has been isolated from soil which was contaminated with tar and phenol in Rositz in Germany. Gordonia alkanivorans has the ability to metabolize hexadecane. The strain RIPI90A of Gordonia alkanivorans can desulfurize dibenzothiophene.

Bowmanella is a bacteria genus from the family of Alteromonadaceae.

Olivibacter is a genus from the family of Sphingobacteriaceae.

Hydrocarboniphaga is a genus of bacteria from the family of Sinobacteraceae.

Alcanivorax mobilis is a Gram-negative, hydrocarbon-degrading and motile bacterium from the genus of Alcanivorax which has been isolated from deep-sea sediments from the Indian Ocean.

Akkermansia glycanphila is a species of intestinal mucin-degrading bacterium. It was first isolated from reticulated python feces in 2016.

Sphingobacterium olei is a Gram-stain-negative, rod-shaped, and non-motile bacterium. It was first isolated from oil-contaminated soil in Daqing oil field, China. S. olei has been found to be able to degrade herbicides quizalofop-p-ethyl and diclofop-methyl. Before a name was given, S. olei was designated as strain HAL-9T. The species name olei means "of oil" in Latin.

References

  1. 1 2 3 4 5 6 7 8 9 10 Lai Q, Wang L, Liu Y, Fu Y, Zhong H, Wang B, Chen L, Wang J, Sun F, Shao Z (June 2011). "Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 6): 1370–4. doi: 10.1099/ijs.0.022368-0 . PMID   20584816.
  2. ↑ Yakimov MM, Golyshin PN, Lang S, Moore ER, Abraham WR, Lünsdorf H, Timmis KN (April 1998). "Alcanivorax borkumensis gen. nov., sp. nov., a new, hydrocarbon-degrading and surfactant-producing marine bacterium". International Journal of Systematic Bacteriology. 48 Pt 2 (2): 339–48. doi: 10.1099/00207713-48-2-339 . PMID   9731272.
  3. ↑ Lai Q, Wang L, Liu Y, Fu Y, Zhong H, Wang B, Chen L, Wang J, Sun F, Shao Z (June 2011). "Alcanivorax pacificus sp. nov., isolated from a deep-sea pyrene-degrading consortium". International Journal of Systematic and Evolutionary Microbiology. 61 (Pt 6): 1370–4. doi: 10.1099/ijs.0.022368-0 . PMID   20584816.
  4. ↑ Lai Q, Shao Z (December 2012). "Genome sequence of an alkane-degrading bacterium, Alcanivorax pacificus type strain W11-5, isolated from deep sea sediment". Journal of Bacteriology. 194 (24): 6936. doi:10.1128/JB.01845-12. PMC   3510602 . PMID   23209202.
  5. 1 2 3 4 5 6 Lai, Qiliang; Shao, Zongze (2012-12-15). "Genome Sequence of an Alkane-Degrading Bacterium, Alcanivorax pacificus Type Strain W11-5, Isolated from Deep Sea Sediment". Journal of Bacteriology. 194 (24): 6936. doi:10.1128/JB.01845-12. ISSN   0021-9193. PMC   3510602 . PMID   23209202.
  6. ↑ Stackenbrandt E, Goebel BM (1994). "Taxonomic Note: A Place for DNA-DNA Reassociation and 16S rRNA Sequence Analysis in the Present Species Definition in Bacteriology". International Journal of Systematic and Evolutionary Microbiology. 44 (4): 846–849. doi: 10.1099/00207713-44-4-846 .

Further reading

This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.