The draft genomes of the nitrate-dependent iron-oxidizing bacteria Acidovorax sp. strain BoFeN1 and Paracoccus pantotrophus strain KS1 are presented. These genomes supply supporting data to investigations of the mechanisms underlying this anaerobic form of microbial biogeochemical iron cycling

Macey, M. C.

Miot, J.

Olsson-Francis, K.

Price, A.

English

Open Research Online (The Open University)

Open Research OnlineThe Open University’s repository of research publicationsand other research outputsDraft Genome Sequences of the Nitrate-DependentIron-Oxidizing Proteobacteria Acidovorax sp. StrainBoFeN1 and Paracoccus pantotrophus Strain KS1Journal ItemHow to cite:Price, A.; Macey, M. C.; Miot, J. and Olsson-Francis, K. (2018). Draft Genome Sequences of the Nitrate-Dependent Iron-Oxidizing Proteobacteria Acidovorax sp. Strain BoFeN1 and Paracoccus pantotrophus Strain KS1.Microbiology Resource Announcements, 7(10), article no. e01050-18.For guidance on citations see FAQs.c© 2018 The AuthorsVersion: Version of RecordLink(s) to article on publisher’s website:http://dx.doi.org/doi:10.1128/MRA.01050-18Copyright and Moral Rights for the articles on this site are retained by the individual authors and/or other copyrightowners. For more information on Open Research Online’s data policy on reuse of materials please consult the policiespage.oro.open.ac.ukDraft Genome Sequences of the Nitrate-Dependent Iron-Oxidizing Proteobacteria Acidovorax sp. Strain BoFeN1 andParacoccus pantotrophus Strain KS1A. Price,a M. C. Macey,a J. Miot,b K. Olsson-FrancisaaFaculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes, UnitedKingdombInstitut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Muséum National d’HistoireNaturelle, Université Pierre et Marie Curie–Sorbonne Universités, CNRS UMR 7590, IRD 206, Paris, FranceABSTRACT The draft genomes of the nitrate-dependent iron-oxidizing bacteria Aci-dovorax sp. strain BoFeN1 and Paracoccus pantotrophus strain KS1 are presented.These genomes supply supporting data to investigations of the mechanisms under-lying this anaerobic form of microbial biogeochemical iron cycling.Acidovorax sp. strain BoFeN1 and Paracoccus pantotrophus strain KS1 have bothdemonstrated the capability to perform nitrate-dependent Fe2 oxidation (NDFO),whereby Fe3 precipitates are formed during microbial nitrate reduction (1, 2). NDFOis a geomicrobiological process which has been recognized for the past 2 decades (3)and is responsible for the production of Fe3-bearing minerals in anaerobic, circum-neutral, reducing environments under conditions similar to those that were prevalenton the early Earth and ancient Mars (1, 4–6). Despite this potential importance in theearly history of life, the putative underlying mechanisms are largely unconﬁrmedexperimentally (7), despite some advances (8, 9).Acidovorax sp. strain BoFeN1 is a Gram-negative, rod-shaped bacterium belongingto the family Comamonadaceae in the order Burkholderiales of the class Betaproteobac-teria. Acidovorax sp. strain BoFeN1 was isolated from littoral sediments of Lake Con-stance on the Germany-Switzerland border and assigned to the genus Acidovoraxbased on 16S rRNA gene sequence analysis (1). This isolate was donated by JennyferMiot of the Mineralogy, Material Physics and Cosmochemistry Institute (IMPMC) in Paris,France.Paracoccus pantotrophus strain KS1 is a Gram-negative, motile coccoid bacteriumbelonging to the family Rhodobacteraceae in the order Rhodobacterales, in the classAlphaproteobacteria. Paracoccus pantotrophus strain KS1 was isolated from soil at KewGardens in the United Kingdom and was originally reported as a member of the genusThiobacillus but was later reclassiﬁed to the genus Paracoccus based on the 16S rRNAgene sequence (10, 11). This strain was purchased as a live culture (DSM 11072) fromthe German Collection of Microorganisms and Cell Cultures (DSMZ) in Leibniz,Germany.The two strains were maintained in pure culture in aerobic nutrient medium (5.0 gliter1 peptone and 3.0 g liter1 meat extract) at 30°C prior to DNA extraction andgenome sequencing, which was performed by MicrobesNG (https://microbesng.uk/)using the Illumina MiSeq platform with 2  250-bp paired-end reads. Trimmed readswere produced using Trimmomatic version 0.30 (http://www.usadellab.org/cms/?pagetrimmomatic) with a sliding window quality cutoff of Q15, and de novo assembly wasperformed using SPAdes version 3.7 (http://cab.spbu.ru/software/spades/) (12, 13).Coverage of 30 was achieved during sequencing, and genome annotation wasReceived 30 July 2018 Accepted 15 August2018 Published 13 September 2018Citation Price A, Macey MC, Miot J, Olsson-Francis K. 2018. Draft genome sequences of thenitrate-dependent iron-oxidizingproteobacteria Acidovorax sp. strain BoFeN1and Paracoccus pantotrophus strain KS1.Microbiol Resour Announc 7:e01050-18.https://doi.org/10.1128/MRA.01050-18.Editor J. Cameron Thrash, Louisiana StateUniversityCopyright © 2018 Price et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to A. Price,alex.price@open.ac.uk.GENOME SEQUENCEScrossmVolume 7 Issue 10 e01050-18 mra.asm.org 1 on October 18, 2018 by guesthttp://mra.asm.org/Downloaded from performed using the RAST annotation server version 2.0 (http://rast.nmpdr.org/rast.cgi)via the classic RAST pipeline (14). The draft genome of strain Acidovorax sp. strainBoFeN1 consisted of 4.06 Mb in 184 contigs (N50 37,384), with a GC content of63.77%. A total of 3,794 protein-coding sequences were predicted from the annotatedgenome, with 50 tRNAs identiﬁed using the ARAGORN version 1.1 tRNA detectionprogram (http://mbio-serv2.mbioekol.lu.se/ARAGORN/) (15). The closest match for the16S rRNA gene was identiﬁed in the GenBank database, by using the BLASTN program(https://blast.ncbi.nlm.nih.gov/Blast.cgi), as Acidovorax deﬂuvii strain BSB411 (99% sim-ilarity; GenBank accession number NR_026506). The draft genome of Paracoccus pan-totrophus strain KS1 consisted of 4.16 Mb in 227 contigs (N50 36,889), with a GCcontent of 67.69%. A total of 3,941 protein-coding sequences and 54 tRNAs werepredicted from the annotated genome. The nearest 16S rRNA gene sequence wasidentiﬁed using BLASTN, with a best match as Paracoccus pantotrophus (100%; acces-sion number AB098590).Neither genome contained a dedicated ferroxidase, suggesting that NDFO in thesestrains is not a direct enzymatic process to acquire electrons. Full denitriﬁcationpathways were conﬁrmed in both strains by the presence of nitrogen species reductasegenes (nar, nir, nor, and nos), with additional genes for a periplasmic nitrate reductase(Nap) in the Paracoccus pantotrophus strain KS1 genome.Data availability. DDBJ/ENA/GenBank accession numbers have been assignedfor Acidovorax sp. strain BoFeN1 (QOZT00000000) and Paracoccus pantotrophus strainKS1 (QOZU00000000). Raw sequencing reads for Acidovorax sp. strain BoFeN1(SRP157586) and Paracoccus pantotrophus strain KS1 (SRP157588) are available in theNCBI Sequence Read Archive.ACKNOWLEDGMENTSGenome sequencing was provided by MicrobesNG (http://www.microbesng.uk),which is supported by the BBSRC (grant number BB/L024209/1).This work was supported by STFC training grant ST/N50421X/1.REFERENCES1. Kappler A, Schink B, Newman DK. 2005. Fe(III) mineral formation and cellencrustation by the nitrate-dependent Fe(II)-oxidizer strain BoFeN1. Geo-biology 3:235–245. https://doi.org/10.1111/j.1472-4669.2006.00056.x.2. Kumaraswamy R, Sjollema K, Kuenen G, Van Loosdrecht M, Muyzer G.2006. Nitrate-dependent [Fe(II)EDTA]2 oxidation by Paracoccus ferrooxi-dans sp. nov., isolated from a denitrifying bioreactor. Syst Appl Microbiol29:276–286. https://doi.org/10.1016/j.syapm.2005.08.001.3. Straub KL, Benz M, Schink B, Widdel F. 1996. Anaerobic, nitrate-dependent microbial oxidation of ferrous iron. Appl Environ Microbiol62:1458–1460.4. Miot J, Etique M. 2016. Formation and transformation of iron-bearingminerals by iron (II)-oxidizing and iron (III)-reducing bacteria, p. 53–98. InFaivre D (ed), Iron oxides: from nature to applications. Wiley-VCH,Weinheim, Germany.5. Ilbert M, Bonnefoy V. 2013. Insight into the evolution of the iron oxida-tion pathways. Biochim Biophys Acta 1827:161–175. https://doi.org/10.1016/j.bbabio.2012.10.001.6. Price A, Pearson VK, Schwenzer SP, Miot J, Olsson-Francis K. 2018. Nitrate-dependent iron oxidation: a potential mars metabolism. Front Microbiol9:513. https://doi.org/10.3389/fmicb.2018.00513.7. Carlson H, Clark I, Melnyk R, Coates J. 2012. Toward a mechanisticunderstanding of anaerobic nitrate-dependent iron oxidation: balancingelectron uptake and detoxiﬁcation. Front Microbiol 3:57. https://doi.org/10.3389/fmicb.2012.00057.8. Carlson HK, Clark IC, Blazewicz SJ, Iavarone AT, Coates JD. 2013. Fe(II)oxidation is an innate capability of nitrate-reducing bacteria that in-volves abiotic and biotic reactions. J Bacteriol 195:3260–3268. https://doi.org/10.1128/JB.00058-13.9. Miot J, Remusat L, Duprat E, Gonzalez A, Pont S, Poinsot M. 2015. Febiomineralization mirrors individual metabolic activity in a nitrate-dependent FeII-oxidizer. Front Microbiol 6:879. https://doi.org/10.3389/fmicb.2015.00879.10. Jordan SL, Kraczkiewicz-Dowjat AJ, Kelly DP, Wood AP. 1995. Novel eubac-teria able to grow on carbon disulﬁde. Arch Microbiol 163:131–137.11. Jordan SL, McDonald IR, Kraczkiewicz-Dowjat AJ, Kelly DP, Rainey FA,Murrell JC, Wood AP. 1997. Autotrophic growth on carbon disulﬁde is aproperty of novel strains of Paracoccus denitriﬁcans. Arch Microbiol168:225–236. https://doi.org/10.1007/s002030050492.12. Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a ﬂexible trimmer forIllumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170.13. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS,Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV,Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a newgenome assembly algorithm and its applications to single-cell sequenc-ing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021.14. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K,Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL,Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD,Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008.The RAST server: Rapid Annotations using Subsystems Technology. BMCGenomics 9:75. https://doi.org/10.1186/1471-2164-9-75.15. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genesand tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16.https://doi.org/10.1093/nar/gkh152.Price et al.Volume 7 Issue 10 e01050-18 mra.asm.org 2 on October 18, 2018 by guesthttp://mra.asm.org/Downloaded from 

Draft Genome Sequences of the Nitrate-Dependent Iron-Oxidizing Proteobacteria <i>Acidovorax</i> sp. Strain BoFeN1 and <i>Paracoccus pantotrophus</i> Strain KS1

http://oro.open.ac.uk/58418/1/Price%20et%20al%202018%20Draft%20Genome%20Sequences%20NDFO%20Proteobacteria%20Acidovorax%20BoFeN1%20Paracoccus%20pantotrophus%20KS1.pdf

Draft Genome Sequences of the Nitrate-Dependent Iron-Oxidizing Proteobacteria <i>Acidovorax</i> sp. Strain BoFeN1 and <i>Paracoccus pantotrophus</i> Strain KS1

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