Pseudomonas wadenswilerensis CCOS 864T was isolated in 2014 from forest soil. The organism belongs taxonomically to the Pseudomonas putida group, members of which have been well studied for their potential in biotechnological applications. We present here the draft genome sequence of P. wadenswilerensis CCOS 864T

Blom, Jochen

Frasson, David

Pothier, Joël

Rezzonico, Fabio

Rutz, Dominik

Sievers, Martin

Smits, Theo

ZHAW digitalcollection

High-Quality Draft Genome Sequence of Pseudomonaswadenswilerensis CCOS 864TDominik Rutz,a,b David Frasson,b Martin Sievers,b Jochen Blom,c Fabio Rezzonico,a Joël F. Pothier,a Theo H. M. SmitsaaEnvironmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, ZurichUniversity of Applied Sciences (ZHAW), Wädenswil, SwitzerlandbMicrobiology and Molecular Biology Research Group, Institute of Chemistry and Biotechnology, ZurichUniversity of Applied Sciences (ZHAW), Wädenswil, SwitzerlandcBioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, GermanyABSTRACT Pseudomonas wadenswilerensis CCOS 864T was isolated in 2014 fromforest soil. The organism belongs taxonomically to the Pseudomonas putida group,members of which have been well studied for their potential in biotechnological ap-plications. We present here the draft genome sequence of P. wadenswilerensis CCOS864T.The genus Pseudomonas belongs to the gamma subclass of Proteobacteria and formsa large taxonomic grouping of species (1, 2). Members of this genus appear as Gramnegative and are involved in a highly diverse range of activities (2). Pseudomonads canbe isolated from many different environmental sources, including soil, water, plants,animals, and air (3). Over the years, members of the Pseudomonas putida group werestudied because of their usage as an efﬁcient cell factory in industrial biotechnologicalapplications (4). Nowadays, Pseudomonas spp. are used for the production of bio-basedpolymers, small-molecular-weight chiral compounds, heterologous proteins, biosurfac-tants, and several biotechnologically important enzymes (lipases, proteases, and amy-lases) (3–5). In 2014, a new species of Pseudomonas was isolated during the search fornovel biocatalysts. The isolate, identiﬁed as Pseudomonas wadenswilerensis CCOS 864T,was obtained from soil samples collected in the Riedholz Forest in Richterswil, Swit-zerland (6).Genomic DNA of P. wadenswilerensis CCOS 864T, grown overnight at 28°C in LBmedium, was isolated using the NucleoSpin tissue kit (Macherey-Nagel, Düren, Ger-many) and fragmented using the Covaris E220 ultrasonicator (average target size,550 bp). Library preparation was done using the Illumina NeoPrep library systemaccording to the manufacturer’s instructions. Genome sequencing was done at ZurichUniversity of Applied Sciences (ZHAW) using an Illumina MiSeq instrument (2 300-bpreads) with a total output of 1,960,890 reads (6). For de novo assembly, the SeqManNGen software version 12.1.0 (DNASTAR, Madison, WI) with standard settings was used.After several assembly steps, a ﬁnal 18 contigs and an N50 value of 532,738 bp wereobtained. The ﬁnal assembly had a total length of 5,966,942 bp and a GC content of63.39%. After annotation in GenDB (7), comparative genomics to related pseudomon-ads was performed in EDGAR version 2.3 (8).By determination of the genome-to-genome distances values (GGDC) based on insilico DNA-DNA hybridization (DDH) (9) and calculation of average nucleotide identities(ANIb) with JSpeciesWS version 3.0.20 (10), we conﬁrmed the species delineationagainst other species of the P. putida group. An average ANIb result of 92.39% 0.03%and GGDC of 51.2%  0.1% DDH were obtained with three genomes from the speciesPseudomonas donghuensis (11, 12), while all other members of the P. putida group hadlower ANIb and GGDC values. Therefore, the genome sequence conﬁrms that P.Received 13 August 2018 Accepted 1October 2018 Published 25 October 2018Citation Rutz D, Frasson D, Sievers M, Blom J,Rezzonico F, Pothier JF, Smits THM. 2018. High-quality draft genome sequence ofPseudomonas wadenswilerensis CCOS 864T.Microbiol Resour Announc 7:e01059-18.https://doi.org/10.1128/MRA.01059-18.Editor John J. Dennehy, Queens CollegeCopyright © 2018 Rutz et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Joël F. Pothier,joel.pothier@zhaw.ch.GENOME SEQUENCEScrossmVolume 7 Issue 16 e01059-18 mra.asm.org 1 on October 25, 2018 by guesthttp://mra.asm.org/Downloaded from wadenswilerensis CCOS 864T constitutes a separate species distinguishable from othermembers of the P. putida group. The analysis of the genome content will still show theunique properties of this strain.Data availability. The draft genome sequence of P. wadenswilerensis CCOS 864T hasbeen deposited in DDBJ/EMBL/GenBank under the BioProject number PRJEB27830 andthe sequence accession number UIDD00000000. The version described in this paper isversion UIDD01000000. Raw sequence reads (Illumina) have been deposited in theSequence Read Archive under the accession number ERR2814815.ACKNOWLEDGMENTThis study was supported by the Department of Life Sciences and Facility Manage-ment of the Zurich University of Applied Sciences (ZHAW) in Wädenswil, Switzerland.REFERENCES1. Palleroni NJ. 2015. Genus I. Pseudomonas, p 323–379. In Brenner DJ,Krieg NR, Staley JT, Garrity GM (ed), Bergey’s manual of systematics ofarchaea and bacteria. John Wiley & Sons, Chichester, United Kingdom.2. Timmis KN. 2002. Pseudomonas putida: a cosmopolitan opportunist parexcellence. Environ Microbiol 4:779–781. https://doi.org/10.1046/j.1462-2920.2002.00365.x.3. Peix A, Ramírez-Bahena M-H, Velázquez E. 2018. The current status onthe taxonomy of Pseudomonas revisited: an update. Infect Genet Evol57:106–116. https://doi.org/10.1016/j.meegid.2017.10.026.4. Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. 2012.Industrial biotechnology of Pseudomonas putida and related species.Appl Microbiol Biotechnol 93:2279–2290. https://doi.org/10.1007/s00253-012-3928-0.5. Kahlon RS. 2016. Pseudomonas for industrial biotechnology, p 282–327.In Kahlon RS (ed), Pseudomonas: molecular and applied biology.Springer, New York, NY.6. Frasson D, Opoku M, Picozzi T, Torossi T, Balada S, Smits THM, Hilber U.2017. Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidhol-zensis sp. nov., two novel species within the Pseudomonas putida groupisolated from forest soil. Int J Syst Evol Microbiol 67:2853–2861. https://doi.org/10.1099/ijsem.0.002035.7. Meyer F, Goesmann A, McHardy A, Bartels D, Bekel T, Clausen J, Kali-nowski J, Linke B, Rupp O, Giegerich R, Pühler A. 2003. GenDB—an opensource genome annotation system for prokaryote genomes. NucleicAcids Res 31:2187–2195. https://doi.org/10.1093/nar/gkg312.8. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A. 2016.EDGAR 2.0: an enhanced software platform for comparative gene con-tent analyses. Nucleic Acids Res 44:W22–W28. https://doi.org/10.1093/nar/gkw255.9. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. 2013. Genomesequence-based species delimitation with conﬁdence intervals and im-proved distance functions. BMC Bioinformatics 14:60. https://doi.org/10.1186/1471-2105-14-60.10. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. 2016.JSpeciesWS: a Web server for prokaryotic species circumscription basedon pairwise genome comparison. Bioinformatics 32:929–931. https://doi.org/10.1093/bioinformatics/btv681.11. Gao J, Xie G, Peng F, Xie Z. 2015. Pseudomonas donghuensis sp. nov.,exhibiting high-yields of siderophore. Antonie Van Leeuwenhoek 107:83–94. https://doi.org/10.1007/s10482-014-0306-1.12. Krzyzanowska DM, Ossowicki A, Jafra S. 2014. Genome sequence ofPseudomonas sp. strain P482, a tomato rhizosphere isolate with broad-spectrum antimicrobial activity. Genome Announc 2:e00394-14. https://doi.org/10.1128/genomeA.00394-14.Rutz et al.Volume 7 Issue 16 e01059-18 mra.asm.org 2 on October 25, 2018 by guesthttp://mra.asm.org/Downloaded from 

High-quality draft genome sequence of pseudomonas wadenswilerensis CCOS 864T

ZHAW Zürcher Hochschule für Angewandte Wissenschaften

High-Quality Draft Genome Sequence of Pseudomonas
wadenswilerensis CCOS 864T
Dominik Rutz,a,b David Frasson,b Martin Sievers,b Jochen Blom,c Fabio Rezzonico,a Joël F. Pothier,a Theo H. M. Smitsa
aEnvironmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences, Zurich
University of Applied Sciences (ZHAW), Wädenswil, Switzerland
bMicrobiology and Molecular Biology Research Group, Institute of Chemistry and Biotechnology, Zurich
University of Applied Sciences (ZHAW), Wädenswil, Switzerland
cBioinformatics and Systems Biology, Justus-Liebig-Universität, Giessen, Germany
ABSTRACT Pseudomonas wadenswilerensis CCOS 864T was isolated in 2014 from
forest soil. The organism belongs taxonomically to the Pseudomonas putida group,
members of which have been well studied for their potential in biotechnological ap-
plications. We present here the draft genome sequence of P. wadenswilerensis CCOS
864T.
The genus Pseudomonas belongs to the gamma subclass of Proteobacteria and formsa large taxonomic grouping of species (1, 2). Members of this genus appear as Gram
negative and are involved in a highly diverse range of activities (2). Pseudomonads can
be isolated from many different environmental sources, including soil, water, plants,
animals, and air (3). Over the years, members of the Pseudomonas putida group were
studied because of their usage as an efficient cell factory in industrial biotechnological
applications (4). Nowadays, Pseudomonas spp. are used for the production of bio-based
polymers, small-molecular-weight chiral compounds, heterologous proteins, biosurfac-
tants, and several biotechnologically important enzymes (lipases, proteases, and amy-
lases) (3–5). In 2014, a new species of Pseudomonas was isolated during the search for
novel biocatalysts. The isolate, identified as Pseudomonas wadenswilerensis CCOS 864T,
was obtained from soil samples collected in the Riedholz Forest in Richterswil, Swit-
zerland (6).
Genomic DNA of P. wadenswilerensis CCOS 864T, grown overnight at 28°C in LB
medium, was isolated using the NucleoSpin tissue kit (Macherey-Nagel, Düren, Ger-
many) and fragmented using the Covaris E220 ultrasonicator (average target size,
550 bp). Library preparation was done using the Illumina NeoPrep library system
according to the manufacturer’s instructions. Genome sequencing was done at Zurich
University of Applied Sciences (ZHAW) using an Illumina MiSeq instrument (2  300-bp
reads) with a total output of 1,960,890 reads (6). For de novo assembly, the SeqMan
NGen software version 12.1.0 (DNASTAR, Madison, WI) with standard settings was used.
After several assembly steps, a final 18 contigs and an N50 value of 532,738 bp were
obtained. The final assembly had a total length of 5,966,942 bp and a GC content of
63.39%. After annotation in GenDB (7), comparative genomics to related pseudomon-
ads was performed in EDGAR version 2.3 (8).
By determination of the genome-to-genome distances values (GGDC) based on in
silico DNA-DNA hybridization (DDH) (9) and calculation of average nucleotide identities
(ANIb) with JSpeciesWS version 3.0.20 (10), we confirmed the species delineation
against other species of the P. putida group. An average ANIb result of 92.39%  0.03%
and GGDC of 51.2%  0.1% DDH were obtained with three genomes from the species
Pseudomonas donghuensis (11, 12), while all other members of the P. putida group had
lower ANIb and GGDC values. Therefore, the genome sequence confirms that P.
Received 13 August 2018 Accepted 1
October 2018 Published 25 October 2018
Citation Rutz D, Frasson D, Sievers M, Blom J,
Rezzonico F, Pothier JF, Smits THM. 2018. High-
quality draft genome sequence of
Pseudomonas wadenswilerensis CCOS 864T.
Microbiol Resour Announc 7:e01059-18.
https://doi.org/10.1128/MRA.01059-18.
Editor John J. Dennehy, Queens College
Copyright © 2018 Rutz et al. This is an open-
access article distributed under the terms of
the Creative Commons Attribution 4.0
International license.
Address correspondence to Joël F. Pothier,
joel.pothier@zhaw.ch.
GENOME SEQUENCES
crossm
Volume 7 Issue 16 e01059-18 mra.asm.org 1
 on O
ctober 25, 2018 by guest
http://m
ra.asm
.org/
D
ow
nloaded from
 
wadenswilerensis CCOS 864T constitutes a separate species distinguishable from other
members of the P. putida group. The analysis of the genome content will still show the
unique properties of this strain.
Data availability. The draft genome sequence of P. wadenswilerensis CCOS 864T has
been deposited in DDBJ/EMBL/GenBank under the BioProject number PRJEB27830 and
the sequence accession number UIDD00000000. The version described in this paper is
version UIDD01000000. Raw sequence reads (Illumina) have been deposited in the
Sequence Read Archive under the accession number ERR2814815.
ACKNOWLEDGMENT
This study was supported by the Department of Life Sciences and Facility Manage-
ment of the Zurich University of Applied Sciences (ZHAW) in Wädenswil, Switzerland.
REFERENCES
1. Palleroni NJ. 2015. Genus I. Pseudomonas, p 323–379. In Brenner DJ,
Krieg NR, Staley JT, Garrity GM (ed), Bergey’s manual of systematics of
archaea and bacteria. John Wiley & Sons, Chichester, United Kingdom.
2. Timmis KN. 2002. Pseudomonas putida: a cosmopolitan opportunist par
excellence. Environ Microbiol 4:779 –781. https://doi.org/10.1046/j.1462
-2920.2002.00365.x.
3. Peix A, Ramírez-Bahena M-H, Velázquez E. 2018. The current status on
the taxonomy of Pseudomonas revisited: an update. Infect Genet Evol
57:106 –116. https://doi.org/10.1016/j.meegid.2017.10.026.
4. Poblete-Castro I, Becker J, Dohnt K, dos Santos VM, Wittmann C. 2012.
Industrial biotechnology of Pseudomonas putida and related species.
Appl Microbiol Biotechnol 93:2279 –2290. https://doi.org/10.1007/
s00253-012-3928-0.
5. Kahlon RS. 2016. Pseudomonas for industrial biotechnology, p 282–327.
In Kahlon RS (ed), Pseudomonas: molecular and applied biology.
Springer, New York, NY.
6. Frasson D, Opoku M, Picozzi T, Torossi T, Balada S, Smits THM, Hilber U.
2017. Pseudomonas wadenswilerensis sp. nov. and Pseudomonas reidhol-
zensis sp. nov., two novel species within the Pseudomonas putida group
isolated from forest soil. Int J Syst Evol Microbiol 67:2853–2861. https://
doi.org/10.1099/ijsem.0.002035.
7. Meyer F, Goesmann A, McHardy A, Bartels D, Bekel T, Clausen J, Kali-
nowski J, Linke B, Rupp O, Giegerich R, Pühler A. 2003. GenDB—an open
source genome annotation system for prokaryote genomes. Nucleic
Acids Res 31:2187–2195. https://doi.org/10.1093/nar/gkg312.
8. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A. 2016.
EDGAR 2.0: an enhanced software platform for comparative gene con-
tent analyses. Nucleic Acids Res 44:W22–W28. https://doi.org/10.1093/
nar/gkw255.
9. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. 2013. Genome
sequence-based species delimitation with confidence intervals and im-
proved distance functions. BMC Bioinformatics 14:60. https://doi.org/10
.1186/1471-2105-14-60.
10. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. 2016.
JSpeciesWS: a Web server for prokaryotic species circumscription based
on pairwise genome comparison. Bioinformatics 32:929 –931. https://doi
.org/10.1093/bioinformatics/btv681.
11. Gao J, Xie G, Peng F, Xie Z. 2015. Pseudomonas donghuensis sp. nov.,
exhibiting high-yields of siderophore. Antonie Van Leeuwenhoek 107:
83–94. https://doi.org/10.1007/s10482-014-0306-1.
12. Krzyzanowska DM, Ossowicki A, Jafra S. 2014. Genome sequence of
Pseudomonas sp. strain P482, a tomato rhizosphere isolate with broad-
spectrum antimicrobial activity. Genome Announc 2:e00394-14. https://
doi.org/10.1128/genomeA.00394-14.
Rutz et al.
Volume 7 Issue 16 e01059-18 mra.asm.org 2
 on O
ctober 25, 2018 by guest
http://m
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.org/
D
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nloaded from
 


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High-quality draft genome sequence of pseudomonas wadenswilerensis CCOS 864T

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