Pseudogulbenkiania ferrooxidans strain 2002 was isolated as a lithoautotrophic, Fe(II)-oxidizing, nitrate-reducing bacterium. Phylogenetically, it is in a clade within the family Neisseriaceae in the order Nessieriales of the class Betaproteobacteria. It is anticipated that comparative genomic analysis of this strain with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in the elucidation of the genetics and biochemistry underlying this critically important geochemical metabolism

Byrne-Bailey, Kathryne G.

Coates, John D.

Weber, Karrie A.

English

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University of Nebraska - Lincoln 
DigitalCommons@University of Nebraska - Lincoln 
Faculty Publications in the Biological Sciences Papers in the Biological Sciences 
2012 
Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, 
Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans 
Strain 2002 
Kathryne G. Byrne-Bailey 
University of California, Berkeley 
Karrie A. Weber 
University of Nebraska-Lincoln, kweber@unl.edu 
John D. Coates 
University of California, Berkeley, jdcoates@berkeley.edu 
Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub 
 Part of the Life Sciences Commons 
Byrne-Bailey, Kathryne G.; Weber, Karrie A.; and Coates, John D., "Draft Genome Sequence of the 
Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002" 
(2012). Faculty Publications in the Biological Sciences. 194. 
https://digitalcommons.unl.edu/bioscifacpub/194 
This Article is brought to you for free and open access by the Papers in the Biological Sciences at 
DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the 
Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. 
Draft Genome Sequence of the Anaerobic, Nitrate-Dependent,
Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans
Strain 2002
Kathryne G. Byrne-Bailey,a Karrie A. Weber,a,b and John D. Coatesa
Department of Plant and Microbial Biology, University of California, Berkeley, California, USA,a and School of Biological Sciences, University of Nebraska, Lincoln,
Nebraska, USAb
Pseudogulbenkiania ferrooxidans strain 2002 was isolated as a lithoautotrophic, Fe(II)-oxidizing, nitrate-reducing bacterium.
Phylogenetically, it is in a clade within the familyNeisseriaceae in the orderNessieriales of the class Betaproteobacteria. It is an-
ticipated that comparative genomic analysis of this strain with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in the
elucidation of the genetics and biochemistry underlying this critically important geochemical metabolism.
Pseudogulbenkiania ferrooxidans strain 2002 (formerly Lutiellanitroferrum strain 2002) is a non-spore-forming, Gram-nega-
tive, motile rod belonging to the family Neisseriaceae in the order
Nessieriales of the class Betaproteobacteria (13). Strain 2002 was
isolated as part of a study of nitrate-dependent Fe(II) oxidation in
freshwater lake sediments and characterized as the first meso-
philic, nitrate-dependent, lithoautotrophic Fe(II) oxidizer (13).
The 16S rRNA gene sequence had 99.3% similarity to the type
species Pseudogulbenkiania subflava (10), whose genomic se-
quence is not publically available, and 99.8% similarity to Pseu-
dogulbenkiania sp. strain NH8B, whose complete genomic se-
quence is available (8). The latter nitrate-reducing strain was
isolated from agricultural paddy rice and soybean fields in Japan
(12). It is anticipated that comparative genomics of P. ferrooxidans
strain 2002 with other nitrate-dependent, Fe(II)-oxidizing bacte-
ria will aid in the elucidation of the genetics underlying this glob-
ally important metabolism.
The draft genome of strain 2002 consisted of 4.2 Mb in 20
contigs with an average GC content of 64.66%. A total of 3,927
protein-encoding genes were predicted. Sequencing performed at
the Joint Genome Institute (JGI) included Sanger sequencing and
454 pyrosequencing to a depth of 20 coverage. All JGI library
construction and sequencing techniques can be found at http:
//www.jgi.doe.gov/. Sequence assembly, quality assessment, and
annotation were performed using the Phred/Phrap/Consed
(CodonCode Corporation, Dedham,MA) (4, 5), Dupfinisher (6),
PRODIGAL (7), and GENERATION software and the JGI Inte-
grated Microbial Genomes site (11).
Early comparative genomics revealed little synteny between
strain 2002 and the genome of Acidovorax ebreus strain TPSY, the
first nitrate-dependent iron oxidizer for which there is a publically
available genome sequence (2; K. G. Byrne-Bailey et al., unpub-
lished data). In addition, preliminary annotation did not reveal a
known carbon fixation pathway that would allow strain 2002 to
survive by a lithoautotrophic lifestyle.
Type c cytochromes have been implicated in themechanism of
nitrate-dependent Fe(II) oxidation (3), with further biophysical
evidence for strain 2002 (13) and A. ebreus strain TPSY (Byrne-
Bailey et al., unpublished). Automated annotation of the genome
of strain 2002 identified 41 genes predicted to encode c-type cyto-
chromes, only 1 ofwhichwas a diheme,with nopredicted proteins
containing multiple heme domains. This is equivalent to both the
predicted number of cytochrome proteins in A. ebreus strain TPSY
and other organisms known to metabolize iron (Byrne-Bailey et al.,
unpublished). However,manual curation of the genome identified a
number of low-similarity homologues to pio genes and MtrA pro-
teins which have defined multiple heme domains, none of which
were clustered in strain 2002. Iron oxidation in the phototrophRho-
dopseudomonas palustris TIE-1 was shown to involve a number of
proteins encoded by the pio genes (9), whereas iron reduction by
Shewanella spp. involves theMtr proteins (1). It is hoped that further
investigationof these andother geneswill aid in theunderstandingof
nitrate-dependent iron oxidation in neutrophilic bacteria.
Nucleotide sequence accession number. The genomic se-
quence of P. ferrooxidans strain 2002 reported here has been
deposited in the GenBank database under accession number
NZ_ACIS01000000.
ACKNOWLEDGMENTS
We thank Lynne Goodwin for her management of the sequencing project
at the JGI.
The sequencing work was performed through Community Sequenc-
ing Project 2008 for the JGI under the auspices of the U.S. Department of
EnergyOffice of Science Biological and Environmental Research Program
and by the University of California Lawrence Berkeley National Labora-
tory under contract DE-AC02-05CH11231, the Lawrence Livermore Na-
tional Laboratory under contract DE-AC52-07NA27344, and the Los
Alamos National Laboratory under contract DE AC02-06NA25396. Re-
search in the lab of J.D.C. on nitrate-dependent Fe(II) oxidation is funded
by the Energy Biosciences Institute, Berkeley, CA.
REFERENCES
1. Beliaev AS, Saffarini DA. 1998. Shewanella putrefaciens mtrB encodes an
outer membrane protein required for Fe(III) and Mn(IV) reduction. J.
Bacteriol. 180:6292–6297.
2. Byrne-Bailey KG, et al. 2010. Completed genome sequence of the anaer-
Received 10 February 2012 Accepted 20 February 2012
Address correspondence to John D. Coates, jdcoates@berkeley.edu.
Copyright © 2012, American Society for Microbiology. All Rights Reserved.
doi:10.1128/JB.00214-12
GENOME ANNOUNCEMENT
2400 jb.asm.org 0021-9193/12/$12.00 Journal of Bacteriology p. 2400–2401
 
 
obic iron-oxidizing bacteriumAcidovorax ebreus strain TPSY. J. Bacteriol.
192:1475–1476.
3. Chaudhuri SK, Lack JG, Coates JD. 2001. Biogenic magnetite formation
through anaerobic biooxidation of Fe(II). Appl. Environ. Microbiol. 67:
2844–2848.
4. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using
phred. II. Error probabilities. Genome Res. 8:186–194.
5. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated
sequencer traces using phred. I. Accuracy assessment.GenomeRes. 8:175–185.
6. Han CS, Chain P. 2006. Finishing repeat regions automatically with
Dupfinisher, p 141–146. InArabnia HR, Valafar H (ed), Proceeding of the
2006 International Conference on Bioinformatics & Computational Biol-
ogy. CSREA Press, Las Vegas, NV.
7. Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and transla-
tion initiation site identification. BMC Bioinformatics 11:119.
8. Ishii S, et al. 2011. Complete genome sequence of the denitrifying and
N(2)O-reducing bacterium Pseudogulbenkiania sp. strain NH8B. J. Bacte-
riol. 193:6395–6396.
9. Jiao Y, Newman DK. 2007. The pio operon is essential for phototrophic
Fe(II) oxidation in Rhodopseudomonas palustris TIE-1. J. Bacteriol. 189:
1765–1773.
10. Lin MC, Chou JH, Arun AB, Young CC, Chen WM. 2008. Pseudogul-
benkiania subflava gen. nov., sp. nov., isolated from a cold spring. Int J.
Syst Evol Microbiol. 58:2384–2388.
11. Markowitz VM, et al. 2008. The integrated microbial genomes (IMG)
system in 2007: data content and analysis tool extensions. Nucleic Acids
Res. 36:D528–D533.
12. Tago K, Ishii S, Nishizawa T, Otsuka S, Senoo K. 2011. Phylogenetic
and functional diversity of denitrifying bacteria isolated from various
rice paddy and rice-soybean rotation fields. Microbes Environ. 26:
30 –35.
13. Weber KA, et al. 2009. Physiological and taxonomic description of the
novel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp.
strain 2002. Appl. Microbiol. Biotechnol. 83:555–565.
Genome Announcement
May 2012 Volume 194 Number 9 jb.asm.org 2401
 ?


Draft Genome Sequence of the Anaerobic, Nitrate-Dependent,
Fe(II)-Oxidizing Bacterium \u3ci\u3ePseudogulbenkiania ferrooxidans\u3c/i\u3e Strain 2002

DigitalCommons@University of Nebraska

University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications in the Biological Sciences Papers in the Biological Sciences 2012 Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002 Kathryne G. Byrne-Bailey University of California, Berkeley Karrie A. Weber University of Nebraska-Lincoln, kweber@unl.edu John D. Coates University of California, Berkeley, jdcoates@berkeley.edu Follow this and additional works at: https://digitalcommons.unl.edu/bioscifacpub  Part of the Life Sciences Commons Byrne-Bailey, Kathryne G.; Weber, Karrie A.; and Coates, John D., "Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidans Strain 2002" (2012). Faculty Publications in the Biological Sciences. 194. https://digitalcommons.unl.edu/bioscifacpub/194 This Article is brought to you for free and open access by the Papers in the Biological Sciences at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications in the Biological Sciences by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Draft Genome Sequence of the Anaerobic, Nitrate-Dependent,Fe(II)-Oxidizing Bacterium Pseudogulbenkiania ferrooxidansStrain 2002Kathryne G. Byrne-Bailey,a Karrie A. Weber,a,b and John D. CoatesaDepartment of Plant and Microbial Biology, University of California, Berkeley, California, USA,a and School of Biological Sciences, University of Nebraska, Lincoln,Nebraska, USAbPseudogulbenkiania ferrooxidans strain 2002 was isolated as a lithoautotrophic, Fe(II)-oxidizing, nitrate-reducing bacterium.Phylogenetically, it is in a clade within the familyNeisseriaceae in the orderNessieriales of the class Betaproteobacteria. It is an-ticipated that comparative genomic analysis of this strain with other nitrate-dependent, Fe(II)-oxidizing bacteria will aid in theelucidation of the genetics and biochemistry underlying this critically important geochemical metabolism.Pseudogulbenkiania ferrooxidans strain 2002 (formerly Lutiellanitroferrum strain 2002) is a non-spore-forming, Gram-nega-tive, motile rod belonging to the family Neisseriaceae in the orderNessieriales of the class Betaproteobacteria (13). Strain 2002 wasisolated as part of a study of nitrate-dependent Fe(II) oxidation infreshwater lake sediments and characterized as the first meso-philic, nitrate-dependent, lithoautotrophic Fe(II) oxidizer (13).The 16S rRNA gene sequence had 99.3% similarity to the typespecies Pseudogulbenkiania subflava (10), whose genomic se-quence is not publically available, and 99.8% similarity to Pseu-dogulbenkiania sp. strain NH8B, whose complete genomic se-quence is available (8). The latter nitrate-reducing strain wasisolated from agricultural paddy rice and soybean fields in Japan(12). It is anticipated that comparative genomics of P. ferrooxidansstrain 2002 with other nitrate-dependent, Fe(II)-oxidizing bacte-ria will aid in the elucidation of the genetics underlying this glob-ally important metabolism.The draft genome of strain 2002 consisted of 4.2 Mb in 20contigs with an average GC content of 64.66%. A total of 3,927protein-encoding genes were predicted. Sequencing performed atthe Joint Genome Institute (JGI) included Sanger sequencing and454 pyrosequencing to a depth of 20 coverage. All JGI libraryconstruction and sequencing techniques can be found at http://www.jgi.doe.gov/. Sequence assembly, quality assessment, andannotation were performed using the Phred/Phrap/Consed(CodonCode Corporation, Dedham,MA) (4, 5), Dupfinisher (6),PRODIGAL (7), and GENERATION software and the JGI Inte-grated Microbial Genomes site (11).Early comparative genomics revealed little synteny betweenstrain 2002 and the genome of Acidovorax ebreus strain TPSY, thefirst nitrate-dependent iron oxidizer for which there is a publicallyavailable genome sequence (2; K. G. Byrne-Bailey et al., unpub-lished data). In addition, preliminary annotation did not reveal aknown carbon fixation pathway that would allow strain 2002 tosurvive by a lithoautotrophic lifestyle.Type c cytochromes have been implicated in themechanism ofnitrate-dependent Fe(II) oxidation (3), with further biophysicalevidence for strain 2002 (13) and A. ebreus strain TPSY (Byrne-Bailey et al., unpublished). Automated annotation of the genomeof strain 2002 identified 41 genes predicted to encode c-type cyto-chromes, only 1 ofwhichwas a diheme,with nopredicted proteinscontaining multiple heme domains. This is equivalent to both thepredicted number of cytochrome proteins in A. ebreus strain TPSYand other organisms known to metabolize iron (Byrne-Bailey et al.,unpublished). However,manual curation of the genome identified anumber of low-similarity homologues to pio genes and MtrA pro-teins which have defined multiple heme domains, none of whichwere clustered in strain 2002. Iron oxidation in the phototrophRho-dopseudomonas palustris TIE-1 was shown to involve a number ofproteins encoded by the pio genes (9), whereas iron reduction byShewanella spp. involves theMtr proteins (1). It is hoped that furtherinvestigationof these andother geneswill aid in theunderstandingofnitrate-dependent iron oxidation in neutrophilic bacteria.Nucleotide sequence accession number. The genomic se-quence of P. ferrooxidans strain 2002 reported here has beendeposited in the GenBank database under accession numberNZ_ACIS01000000.ACKNOWLEDGMENTSWe thank Lynne Goodwin for her management of the sequencing projectat the JGI.The sequencing work was performed through Community Sequenc-ing Project 2008 for the JGI under the auspices of the U.S. Department ofEnergyOffice of Science Biological and Environmental Research Programand by the University of California Lawrence Berkeley National Labora-tory under contract DE-AC02-05CH11231, the Lawrence Livermore Na-tional Laboratory under contract DE-AC52-07NA27344, and the LosAlamos National Laboratory under contract DE AC02-06NA25396. Re-search in the lab of J.D.C. on nitrate-dependent Fe(II) oxidation is fundedby the Energy Biosciences Institute, Berkeley, CA.REFERENCES1. Beliaev AS, Saffarini DA. 1998. Shewanella putrefaciens mtrB encodes anouter membrane protein required for Fe(III) and Mn(IV) reduction. J.Bacteriol. 180:6292–6297.2. Byrne-Bailey KG, et al. 2010. Completed genome sequence of the anaer-Received 10 February 2012 Accepted 20 February 2012Address correspondence to John D. Coates, jdcoates@berkeley.edu.Copyright © 2012, American Society for Microbiology. All Rights Reserved.doi:10.1128/JB.00214-12GENOME ANNOUNCEMENT2400 jb.asm.org 0021-9193/12/$12.00 Journal of Bacteriology p. 2400–2401  obic iron-oxidizing bacteriumAcidovorax ebreus strain TPSY. J. Bacteriol.192:1475–1476.3. Chaudhuri SK, Lack JG, Coates JD. 2001. Biogenic magnetite formationthrough anaerobic biooxidation of Fe(II). Appl. Environ. Microbiol. 67:2844–2848.4. Ewing B, Green P. 1998. Base-calling of automated sequencer traces usingphred. II. Error probabilities. Genome Res. 8:186–194.5. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automatedsequencer traces using phred. I. Accuracy assessment.GenomeRes. 8:175–185.6. Han CS, Chain P. 2006. Finishing repeat regions automatically withDupfinisher, p 141–146. InArabnia HR, Valafar H (ed), Proceeding of the2006 International Conference on Bioinformatics & Computational Biol-ogy. CSREA Press, Las Vegas, NV.7. Hyatt D, et al. 2010. Prodigal: prokaryotic gene recognition and transla-tion initiation site identification. BMC Bioinformatics 11:119.8. Ishii S, et al. 2011. Complete genome sequence of the denitrifying andN(2)O-reducing bacterium Pseudogulbenkiania sp. strain NH8B. J. Bacte-riol. 193:6395–6396.9. Jiao Y, Newman DK. 2007. The pio operon is essential for phototrophicFe(II) oxidation in Rhodopseudomonas palustris TIE-1. J. Bacteriol. 189:1765–1773.10. Lin MC, Chou JH, Arun AB, Young CC, Chen WM. 2008. Pseudogul-benkiania subflava gen. nov., sp. nov., isolated from a cold spring. Int J.Syst Evol Microbiol. 58:2384–2388.11. Markowitz VM, et al. 2008. The integrated microbial genomes (IMG)system in 2007: data content and analysis tool extensions. Nucleic AcidsRes. 36:D528–D533.12. Tago K, Ishii S, Nishizawa T, Otsuka S, Senoo K. 2011. Phylogeneticand functional diversity of denitrifying bacteria isolated from variousrice paddy and rice-soybean rotation fields. Microbes Environ. 26:30 –35.13. Weber KA, et al. 2009. Physiological and taxonomic description of thenovel autotrophic, metal oxidizing bacterium, Pseudogulbenkiania sp.strain 2002. Appl. Microbiol. Biotechnol. 83:555–565.Genome AnnouncementMay 2012 Volume 194 Number 9 jb.asm.org 2401 

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Draft Genome Sequence of the Anaerobic, Nitrate-Dependent, Fe(II)-Oxidizing Bacterium \u3ci\u3ePseudogulbenkiania ferrooxidans\u3c/i\u3e Strain 2002

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