Andreoni, V.

Cavalca, L.

Corsini, A.

Muyzer, G.

English

Here, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a 4.15-Mb chromosome and contains different genes that are involved in arsenic transformations

International Migration, Integration and Social Cohesion online publications

UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl)UvA-DARE (Digital Academic Repository)Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW,isolated from arsenic-contaminated groundwaterCavalca, L.; Corsini, A.; Andreoni, V.; Muyzer, G.DOI10.1128/genomeA.01072-13Publication date2013Document VersionFinal published versionPublished inGenome AnnouncementsLink to publicationCitation for published version (APA):Cavalca, L., Corsini, A., Andreoni, V., & Muyzer, G. (2013). Draft genome sequence of thearsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminatedgroundwater. Genome Announcements, 1(6), e1072-13.https://doi.org/10.1128/genomeA.01072-13General rightsIt is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s)and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an opencontent license (like Creative Commons).Disclaimer/Complaints regulationsIf you believe that digital publication of certain material infringes any of your rights or (privacy) interests, pleaselet the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the materialinaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letterto: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. Youwill be contacted as soon as possible.Download date:09 Mar 2023Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoefleasp. 2WW, Isolated from Arsenic-Contaminated GroundwaterLucia Cavalca,a Anna Corsini,a Vincenza Andreoni,a Gerard Muyzera,bDipartimento di Scienze per gli Alimenti, la Nutrizione e l’Ambiente (DEFENS), Università degli Studi di Milano, Milan, Italya; Institute for Biodiversity and EcosystemDynamics, University of Amsterdam, Amsterdam, The NetherlandsbHere, we report the draft genome sequence of the arsenite-oxidizing bacterium Aliihoeflea sp. strain 2WW, which consists of a4.15-Mb chromosome and contains different genes that are involved in arsenic transformations.Received 12 November 2013 Accepted 26 November 2013 Published 19 December 2013Citation Cavalca L, Corsini A, Andreoni V, Muyzer G. 2013. Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminatedgroundwater. Genome Announc. 1(6):e01072-13. doi:10.1128/genomeA.01072-13.Copyright © 2013 Cavalca et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Gerard Muyzer, g.muijzer@uva.nl.Aliihoeflea sp. strain 2WW was isolated from a biofilter treatingarsenic-contaminated groundwater in the city of Cremona(Lombardia, Italy). It is a strictly aerobic, mobile, and rod-shapedGram-negative bacterium. Phylogenetic analysis of the 16S rRNAgene sequence showed that the strain is closely (98.7%) affiliatedwith Aliihoeflea aestuarii N8T (1) within the family Phyllobacteri-aceae in the class Alphaproteobacteria. Strain 2WW is highly arse-nic resistant, with MIC values of 200 mM and 5 mM for arsenate[As(V)] and arsenite [As(III)], respectively. Under heterotrophicconditions, it can oxidize As(III) to As(V), with specific growthrates (h-1) of 0.23, 0.13, and 0.006 at 30°C, 15°C, and 5°C, re-spectively. In growth experiments, As(III) was always oxidized toAs(V) in the early exponential growth phase and the oxidation wascomplete within 24 h at 30°C, 96 h at 15°C, and 350 h at 5°C.Complete As(III) oxidation occurred in the pH range 5.0 to 8.0.The resting cells of an As(III)-induced culture of strain 2WW wereable to oxidize completely 200 g liter-1 of As(III) in 8 h, whilenoninduced cells oxidized As(III) in 24 h.The genome sequence of Aliihoeflea sp. strain 2WW was ob-tained by Illumina sequencing (Illumina, Inc., San Diego, CA),producing paired-end and mate-pair sequence reads of ~50 bp,with insert sizes of ~300 bp and ~4,000 bp, respectively. CLCGenomics Workbench version 5.5.1 (CLC bio, Aarhus, Denmark)was used to assemble the quality-filtered paired-end reads into 273contigs. Subsequently, SSPACE Premium scaffolder version 2.0(2) and GapFiller version 1.11 (3) were used to place the contigsinto 10 gap-closed scaffolds with an average sequence size of415,210 bp. This resulted in a draft genome of 4,152,101 bp and aGC content of 64.4%. IMG/ER (4) and RAST (5) were used toannotate the draft genome. The genome contains 4,140 genes,including 65 RNA genes. It possesses two different arsenic islands,one including 4 genes of the ars operon for arsenic resistance [arsRfor regulatory protein, acr3 for arsenite efflux pump, arsC for ar-senate reductase, and arsH for protein conferring high resistanceto As(V)], and the second containing an arsenite oxidase, aioBA.Phylogenetic analysis of aioA confirmed the phylogenetic affilia-tion with the Alphaproteobacteria and showed close affiliationwith members of the family Phyllobacteriaceae, although 2WW isnot chemoautotrophic. Although 2WW possesses arsC, normallyretrieved in the ars operon of As(V)-resistant strains, it was notable to reduce As(V) to As(III). In addition, many genes encodingputative metal (lead, cadmium, zinc, mercury, copper, and chro-mium) transporters and cobalt-zinc-cadmium resistance protein(CzcD) were also identified on the genome.Nucleotide sequence accession number. The draft genome se-quence of Aliihoeflea sp. strain 2WW has been deposited in Gen-Bank under the accession no. AYOD00000000.ACKNOWLEDGMENTThis work was supported by a grant from the Cariplo Foundation, projectno. 2010-2221.REFERENCES1. Roh SW, Kim KH, Nam YD, Chang HW, Kim MS, Shin KS, Yoon JH,Oh HM, Bae JW. 2008. Aliihoeflea aestuarii gen. nov., sp. nov., a novelbacterium isolated from tidal flat sediment. J. Microbiol. 46:594 –598.2. Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W. 2011. Scaf-folding pre-assembled contigs using SSPACE. Bioinformatics 27:578 –579.3. Boetzer M, Pirovano W. 2012. Toward almost closed genomes with Gap-Filler. Genome Biol. 13:R56. doi:10.1186/gb-2012-13-6-r56.4. Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y,Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I,Mavromatis K, Ivanova NN, Kyrpides NC. 2012. IMG: the integratedmicrobial genomes database and comparative analysis system. Nucleic Ac-ids Res. 40:D115–D122. doi:10.1093/nar/gkr1044.5. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, FormsmaK, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, OstermanAL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, PuschGD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.2008. The RAST server: Rapid Annotations using Subsystems Technology.BMC Genomics 9:75. doi:10.1186/1471-2164-9-75.Genome AnnouncementsNovember/December 2013 Volume 1 Issue 6 e01072-13 genomea.asm.org 1

Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminated groundwater

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Draft genome sequence of the arsenite-oxidizing strain Aliihoeflea sp. 2WW, isolated from arsenic-contaminated groundwater

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