Gordonia amicalis strain CCMA-559 was isolated from an oil-contaminated mangrove swamp and shown to produce biosurfactants. This strain is a strict aerobe that readily degrades an array of carbon sources, including N-acetylglucosamine, cellobiose, Tween 80, and 4-hydroxybenzoic acid, and, like other G. amicalis strains, likely desulfurizes dibenzothiophene.

Dellagnezze, Bruna M

Domingos, Daniela F

Greenfield, Paul

Melo, Itamar S

Midgley, David J

Oliveira, Valéria M

Reyes, Luciana R

Genome Announcements

English

Repositorio da Producao Cientifica e Intelectual da Unicamp

Draft Genome Sequence of the Biosurfactant-Producing Bacterium
Gordonia amicalis Strain CCMA-559, Isolated from Petroleum-
Impacted Sediment
Daniela F. Domingos,a,d Bruna M. Dellagnezze,a Paul Greenfield,b Luciana R. Reyes,c Itamar S. Melo,c David J. Midgley,d
Valéria M. Oliveiraa
Microbial Resources Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), Campinas University (UNICAMP), Campinas, São Paulo, Brazila; CSIRO
Mathematics, Informatics and Statistics, North Ryde, NSW, Australiab; Laboratory of Environmental Microbiology, EMBRAPA Environment, Jaguariúna, São Paulo, Brazilc;
CSIRO Animal Food and Health Sciences, North Ryde, NSW, Australiad
Gordonia amicalis strain CCMA-559 was isolated from an oil-contaminated mangrove swamp and shown to produce biosurfac-
tants. This strain is a strict aerobe that readily degrades an array of carbon sources, includingN-acetylglucosamine, cellobiose,
Tween 80, and 4-hydroxybenzoic acid, and, like other G. amicalis strains, likely desulfurizes dibenzothiophene.
Received 25 September 2013 Accepted 30 September 2013 Published 31 October 2013
Citation Domingos DF, Dellagnezze BM, Greenfield P, Reyes LR, Melo IS, Midgley DJ, Oliveira VM. 2013. Draft genome sequence of the biosurfactant-producing bacterium
Gordonia amicalis strain CCMA-559, isolated from petroleum-impacted sediment. Genome Announc. 1(6):e00894-13. doi:10.1128/genomeA.00894-13.
Copyright © 2013 Domingos et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.
Address correspondence to Daniela F. Domingos, dfdomingos@uol.com.br.
Gordonia amicalis strain CCMA-559 was obtained from man-grove swamp sediment contaminated with crude oil and was
isolated as described in Domingos et al. (1). The strain was shown
to produce industrially important biosurfactants and bioemulsi-
fiers and was thus subjected to genomic sequencing.
The shotgun sequencing of theG. amicalisCCMA-559 genome
was performed using IlluminaHiSeq 2000 technology. The result-
ing 100-bp paired-end sequences were corrected with Blue (http:
//www.bioinformatics.csiro.au/blue) and assembled by using Vel-
vet 1.2.07 (k  57) (2). The draft genome, as submitted to
GenBank, was 5,179,574 bp in length and comprised 117 contigs
(200 bp in size), with a mean contig size of 44,269 bp, a median
size of 5,879 bp, and maximum length of 380,987 bp. The mean
GC content of the genome was 65.09%, and genome coverage
depth was approximately 1,000. Fifty-six short contigs (each
200 bp, totaling 8,819 bp) were excluded from the GenBank
submission; however, these short sequences are available in the
annotation at the Integrated Microbial Genomes Expert Re-
view (IMG ER) website (https://img.jgi.doe.gov/er/). Annota-
tion was performed using the IMG ER pipeline (3), which pre-
dicted a total of 4,736 protein-coding genes and 63 structural
RNAs. Based on comparison of the 16S rRNA gene, G. amicalis
CCMA-559 was 100% identical (over 1,400 bp) with G. amica-
lis IEGM, the type strain for the species, isolated from garden
soil in Russia (4).
In terms of physiology, the IEGM and CCMA-559 strains of
G. amicalis are broadly similar. Both have genes for the desulfu-
rization of dibenzothiophene anduse some similar carbon sources
for growth. For example, both strains are capable of growth on
starch and polyols, such as glycerol. There are, however, some
notable differences between the strains.G. amicalis IEGMwas not
capable of growth on N-acetyl-D-glucosamine, cellobiose, and
Tween 80 (4). In contrast, Biolog EcoPlate data for G. amicalis
CCMA-559 indicate growth on N-acetylglucosamine, cellobiose,
andTween 80. To better understand themechanisms for observed
growth, genes fromG. amicalis CCMA-559 were submitted to the
dbCAN pipeline (5) for the classification of carbohydrate active
genes. In combination with the annotation at IMG ER, data from
dbCAN revealed the presence of at least one cellobiase (-
glucosidase) and numerous lipases/esterases in the genome of
G. amicalis CCMA-559 (from carboxylesterase [CE] families 1, 3,
5, 6, 10, and 14), which likely facilitate growth on cellobiose and
Tween 80, respectively. Growth on N-acetylglucosamine is pre-
sumably facilitated by the activity of acetylglucosaminidases in the
genome of G. amicalis CCMA-559. We were unable to locate this
gene in the annotation or dbCAN data; however, acetylgluco-
saminidases have been previously described for Gordonia bron-
chialis. In addition, growth on the monoaromatic compound
4-hydroxybenzoic acid was observed for G. amicalis CCMA-559
and is presumably facilitated by genes in the draft assembly that
encode dioxygenases. Investigation of the genomes of this and
other Gordonia species may yield further insights into their con-
siderable metabolic potential.
Nucleotide sequence accession numbers. This whole-
genome shotgun project has been deposited at DDBJ/EMBL/
GenBankunder the accession number AWTB00000000. The ver-
sion described in this paper is version AWTB01000000.
ACKNOWLEDGMENTS
We acknowledge the São Paulo Research Foundation—FAPESP for fi-
nancial support (Process 2010/15519-3).Genome sequencing, correction,
and assembly were funded by CSIRO Animal, Food and Health Sciences.
We are grateful to Philip Hendry for his intellectual input to this project.
REFERENCES
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Genome AnnouncementsNovember/December 2013 Volume 1 Issue 6 e00894-13 genomea.asm.org 1
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Domingos et al.
Genome Announcements2 genomea.asm.org November/December 2013 Volume 1 Issue 6 e00894-13


Draft Genome Sequence Of The Biosurfactant-producing Bacterium Gordonia Amicalis Strain Ccma-559, Isolated From Petroleum-impacted Sediment.

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Draft Genome Sequence Of The Biosurfactant-producing Bacterium Gordonia Amicalis Strain Ccma-559, Isolated From Petroleum-impacted Sediment.

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