This is the final version of the article. Available from American Society for Microbiology via the DOI in this record.A variety of bacteria associate with the hydrocarbon-producing microalga Botryococcus braunii, some of which may influence its growth. We report here the genome sequences for Achromobacter piechaudii GCS2, Agrobacterium sp. strain SUL3, Microbacterium sp. strain GCS4, and Shinella sp. strains GWS1 and SUS2, isolated from a laboratory culture of B. braunii, race B, strain Guadeloupe.K.J.J. was funded by a Ph.D. studentship from the Biotechnology and
Biologaical Sciences Research Council (BBSRC) LoLa award BB/
K003240/2. The Exeter Sequencing Service was supported by the Wellcome
Trust Institutional Strategic Support Fund (WT097835MF), a Wellcome
Trust Multi User Equipment Award (WT101650MA), and a BBSRC
LoLa award (BB/K003240/2).
We gratefully acknowledge the Exeter Sequencing Service and computational
core facilities at the University of Exete

Aves, SJ

Jones, KJ

Love, J

Moore, K

Sambles, C

Studholme, DJ

Genome Announcements

PubMed

ABSTRACT
 
 A variety of bacteria associate with the hydrocarbon-producing microalga
 Botryococcus braunii
 , some of which may influence its growth. We report here the genome sequences for
 Achromobacter piechaudii
 GCS2,
 Agrobacterium
 sp. strain SUL3,
 Microbacterium
 sp. strain GCS4, and
 Shinella
 sp. strains GWS1 and SUS2, isolated from a laboratory culture of
 B. braunii
 , race B, strain Guadeloupe.
 </jats:p

Katy J. Jones

Karen Moore

Christine Sambles

John Love

David J. Studholme

Stephen J. Aves

Crossref

Draft Genome Sequences of Achromobacter piechaudii GCS2,
 Agrobacterium
 sp. Strain SUL3,
 Microbacterium
 sp. Strain GCS4,
 Shinella
 sp. Strain GWS1, and
 Shinella
 sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga
 Botryococcus braunii

A variety of bacteria associate with the hydrocarbon-producing microalga Botryococcus braunii, some of which may influence its growth. We report here the genome sequences for Achromobacter piechaudiiGCS2, Agrobacterium sp. strain SUL3,Microbacte-rium sp. strain GCS4, and Shinella sp. strains GWS1 and SUS2, isolated from a laboratory culture of B. braunii, race B, strain Guadeloupe

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Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus brauni

This is the final version of the article. Available from the American Society for Microbiology via the DOI in this record.A variety of bacteria associate with the hydrocarbon-producing microalga Botryococcus braunii, some of which may influence its growth. We report here the genome sequences for Achromobacter piechaudii GCS2, Agrobacterium sp. strain SUL3, Microbacterium sp. strain GCS4, and Shinella sp. strains GWS1 and SUS2, isolated from a laboratory culture of B. braunii, race B, strain Guadeloupe.K.J.J. was funded by a Ph.D. studentship from the Biotechnology and
Biologaical Sciences Research Council (BBSRC) LoLa award BB/
K003240/2. The Exeter Sequencing Service was supported by the Wellcome
Trust Institutional Strategic Support Fund (WT097835MF), a Wellcome
Trust Multi User Equipment Award (WT101650MA), and a BBSRC
LoLa award (BB/K003240/2).
We gratefully acknowledge the Exeter Sequencing Service and computational
core facilities at the University of Exete

Open Research Exeter

Draft Genome Sequences of Achromobacter piechaudii GCS2,Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4,Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated fromConsortium with the Hydrocarbon-Producing Alga BotryococcusbrauniiKaty J. Jones, Karen Moore, Christine Sambles, John Love, David J. Studholme, Stephen J. AvesDepartment of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United KingdomA variety of bacteria associate with the hydrocarbon-producing microalga Botryococcus braunii, some of which may influence itsgrowth. We report here the genome sequences for Achromobacter piechaudiiGCS2, Agrobacterium sp. strain SUL3,Microbacte-rium sp. strain GCS4, and Shinella sp. strains GWS1 and SUS2, isolated from a laboratory culture of B. braunii, race B, strainGuadeloupe.Received 6 November 2015 Accepted 9 November 2015 Published 14 January 2016Citation Jones KJ, Moore K, Sambles C, Love J, Studholme DJ, Aves SJ. 2016. Draft genome sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. strain SUL3,Microbacterium sp. strain GCS4, Shinella sp. strain GWS1, and Shinella sp. strain SUS2 isolated from consortium with the hydrocarbon-producing alga Botryococcus braunii.Genome Announc 4(1):e01527-15. doi:10.1128/genomeA.01527-15.Copyright © 2016 Jones et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Stephen J. Aves, s.j.aves@exeter.ac.uk.Botryococcus braunii is a greenmicroalga that is able to produceand accumulate high levels of hydrocarbons (up to 60% of itsdry weight, depending on the strain), which can be converted intoliquid fuels (1, 2). Strains of B. braunii are typically not axenic butconsist of a single algal strain accompanied by a variety of micro-organisms associated as both a biofilm and planktonic populationin the water column, which may greatly influence B. brauniigrowth and hydrocarbon production (3–6).Five bacterial strains (GCS2, SUL3, GCS4, GWS1, and SUS2)were isolated from a long-term laboratory culture of B. brauniistrain Guadeloupe (race B) (7), and the colonies were grown onLB plates. Genomic DNA fragmented by sonication was concen-trated and purified using a QIAquick column (Qiagen), andgenomic libraries were prepared using the NEBNext DNA LibraryPrep Master Mix Set for Illumina (New England BioLabs). Onehundred fifty-base pair paired-end sequencing, with a custom barcode, was carried out on an IlluminaMiSeq, and de novo assemblyof the sequence data was carried out using SPAdes version 3.5.0(8). The number of contigs, coverage, N50, and total sequencelength were, respectively, 20, 41, 626,645, and 6,180,134 bp forAchromobacter piechaudii GCS2; 72, 52, 358,737, and6,013,863 bp for Agrobacterium sp. strain SUL3; 7, 73, 944,354,and 3,652,908 bp for Microbacterium sp. strain GCS4; 141, 44,176,944, and 6,989,725 bp for Shinella sp. strain GWS1; and 112,32, 264,748, and 7,005,767 bp for Shinella sp. strain SUS2. Thegenomes were annotated using the NCBI Prokaryotic GenomeAnnotation Pipeline (PGAP), which predicted 5,433, 5,585, 3,325,6,636, and 6,361 coding sequences (CDSs), respectively, for thefive strains. The GC contents varied between 59.2% (Agrobacte-rium sp. SUL3) and 69.5% (Microbacterium sp. GCS4). The 16SrRNA gene sequences were extracted using RNAmmer (9).Phylogenetic analysis of 16S rRNA gene sequence, atpD, recA,rpoB, and tyrB suggested that GCS2 belongs to the species A.piechaudii; its genome shares 98.4% average nucleotide identity(ANI) with that of A. piechaudii strain ATCC 43553. Phylogeneticanalysis of 16S rRNA gene sequence, gyrB, ppk, recA, and rpoBsuggested that GCS4 belongs to the genusMicrobacterium. Phylo-genetic analysis of 16S rRNA gene sequence, atpD, and recA sug-gested thatGWS1 and SUS2both belong to the genus Shinella, andSUL3 belongs to the genus Agrobacterium.None of these five bacteria were previously reported in associ-ation with B. braunii, except for Shinella sp. GWS1 and SUS2,which, on the basis of partial 16S rRNA gene sequence, are indis-tinguishable froma biofilm isolate found to enhance the growth ofa laboratory-maintained monoculture of B. braunii (4) (reportedas Rhizobium sp. M14). Many species of algae are auxotrophic forvitamin B1 (thiamine), vitamin B7 (biotin), and vitamin B12 (co-balamin) (10). We identified genes encoding pathways for thia-mine synthesis in all five genomes; cobalamin is likely to be syn-thesized by Agrobacterium sp. SUL3 and Shinella spp. GWS1 andSUS2, while biotin is likely to be synthesized by A. piechaudiiGCS2 and Agrobacterium sp. SUL3. No evidence of nitrogen fixa-tion genes was found in any of the bacterial genomes, based ontBLASTn and BLASTn searches.Nucleotide sequence accession numbers. These genome se-quences have been deposited at GenBank under the following ac-cession numbers: A. piechaudii GCS2, LGYD00000000; Agrobac-terium sp. SUL3, LGZB00000000; Microbacterium sp. GCS4,LGYE00000000; Shinella sp. GWS1, LGYF00000000; and Shinellasp. SUS2, LGYG00000000. Theversionsdescribedinthispaperare thefirst versions: LGYD01000000, LGZB01000000, LGYE01000000,LGYF01000000, and LGYG01000000.crossmarkGenome AnnouncementsJanuary/February 2016 Volume 4 Issue 1 e01527-15 genomea.asm.org 1 on January 18, 2016 by UNIVERSITY OF EXETERhttp://genomea.asm.org/Downloaded from ACKNOWLEDGMENTSK.J.J. was funded by a Ph.D. studentship from the Biotechnology andBiologaical Sciences Research Council (BBSRC) LoLa award BB/K003240/2. The Exeter Sequencing Service was supported by the Well-comeTrust Institutional Strategic Support Fund (WT097835MF), aWell-comeTrustMulti User Equipment Award (WT101650MA), and a BBSRCLoLa award (BB/K003240/2).We gratefully acknowledge the Exeter Sequencing Service and com-putational core facilities at the University of Exeter.FUNDING INFORMATIONTheWellcomeTrust provided funding toKarenMoore under grant num-bers WT097835MF and WT101650MA. The Biotechnology and Biologi-cal Sciences Research Council (BBSRC) provided funding to Katy J. Jonesand Karen Moore under grant number BB/K003240/2.The funders had no role in study design, data collection and interpreta-tion, or the decision to submit the work for publication.REFERENCES1. Banerjee A, Sharma R, Chisti Y, Banerjee UC. 2002. Botryococcusbraunii: a renewable source of hydrocarbons andother chemicals. Crit RevBiotechnol 22:245–279. http://dx.doi.org/10.1080/07388550290789513.2. Metzger P, Largeau C. 2005. Botryococcus braunii: a rich source for hy-drocarbons and related ether lipids. Appl Microbiol Biotechnol 66:486–496. http://dx.doi.org/10.1007/s00253-004-1779-z.3. Chirac C, Casadevall E, Largeau C, Metzger P. 1985. Bacterial influenceupon growth and hydrocarbon production of the green alga Botryococcusbraunii. J Phycol 21:380–387.4. Rivas MO, Vargas P, Riquelme CE. 2010. Interactions of Botryococcusbraunii cultures with bacterial biofilms. Microb Ecol 60:628–635. http://dx.doi.org/10.1007/s00248-010-9686-6.5. Tanabe Y, Kato S, Matsuura H, Watanabe MM. 2012. A Botryococcusstrain with bacterial ectosymbionts grows fast and produces high amountof hydrocarbons. Procedia Environ Sci 15:22–26. http://dx.doi.org/10.1016/j.proenv.2012.05.005.6. Tanabe Y, Okazaki Y, Yoshida M, Matsuura H, Kai A, Shiratori T,Ishida K, Nakano S, Watanabe MM. 2015. A novel alphaproteobacterialectosymbiont promotes the growth of the hydrocarbon-rich green algaBotryococcus braunii. Sci Rep 5:10467. http://dx.doi.org/10.1038/srep10467.7. Metzger P, Berkaloff C, Casadevall E, Coute A. 1985. Alkadiene- andbotryococcene-producing races of wild strains of Botryococcus braunii.Phytochemistry 24:2305–2312. http://dx.doi.org/10.1016/S0031-9422(00)83032-0.8. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, KulikovAS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV,Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. http://dx.doi.org/10.1089/cmb.2012.0021.9. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T, UsseryDW. 2007. RNAmmer: consistent and rapid annotation of ribosomalRNA genes. Nucleic Acids Res 35:3100–3108. http://dx.doi.org/10.1093/nar/gkm160.10. Croft MT, Warren MJ, Smith AG. 2006. Algae need their vitamins.Eukaryot Cell 5:1175–1183. http://dx.doi.org/10.1128/EC.00097-06.Jones et al.Genome Announcements2 genomea.asm.org January/February 2016 Volume 4 Issue 1 e01527-15 on January 18, 2016 by UNIVERSITY OF EXETERhttp://genomea.asm.org/Downloaded from 

Draft genome sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii

ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/e8/9c/e01527-15.PMC4714109.pdf

Draft genome sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii.

Draft genome sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii.

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