Abstract
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.
GENOME ANNOUNCEMENT
Pseudogulbenkiania ferrooxidans strain 2002 (formerly Lutiella nitroferrum strain 2002) is a non-spore-forming, Gram-negative, 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 mesophilic, 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 sequence is not publically available, and 99.8% similarity to Pseudogulbenkiania sp. strain NH8B, whose complete genomic sequence 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 bacteria will aid in the elucidation of the genetics underlying this globally important metabolism.
The draft genome of strain 2002 consisted of 4.2 Mb in 20 contigs with an average G+C 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 Integrated 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iron oxidizer for which there is a publically available genome sequence (2; K. G. Byrne-Bailey et al., unpublished data).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 the mechanism 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 cytochromes, only 1 of which was a diheme, with no predicted 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 proteins which have defined multiple heme domains, none of which were clustered in strain 2002. Iron oxidation in the phototroph Rhodopseudomonas palustris TIE-1 was shown to involve a number of proteins encoded by the pio genes (9), whereas iron reduction by Shewanella spp. involves the Mtr proteins (1). It is hoped that further investigation of these and other genes will aid in the understanding of nitrate-dependent iron oxidation in neutrophilic bacteria.
Nucleotide sequence accession number.
The genomic sequence 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 Sequencing Project 2008 for the JGI under the auspices of the U.S. Department of Energy Office of Science Biological and Environmental Research Program and by the University of California Lawrence Berkeley National Laboratory under contract DE-AC02-05CH11231, the Lawrence Livermore National Laboratory under contract DE-AC52-07NA27344, and the Los Alamos National Laboratory under contract DE AC02-06NA25396. Research in the lab of J.D.C. on nitrate-dependent Fe(II) oxidation is funded by the Energy Biosciences Institute, Berkeley, CA.
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