Abstract
Achromobacter piechaudii strain HLE is a betaproteobacterium (previously known as Alcaligenes faecalis) that was an early isolate with arsenite oxidase activity. This draft genome of 6.89 Mb is the second available genome for this species in the opportunistic pathogen Alcaligenaceae family.
GENOME ANNOUNCEMENT
Achromobacter piechaudii strain HLE was reported 36 years ago as one of two arsenite-oxidizing Alcaligenes isolates (from the soil of the campus of Rensselaer Polytechnic Institute in 1974) (4, 5), about which no further research reports were published. Ehrlich (2) described unpublished thesis work in his recent memoir. This strain was not deposited in a culture collection previously and is available from L. T. Phung (who is in the process of depositing it at the ATCC).
A. piechaudii strain HLE was grown in the LB broth medium (7) at 30°C with shaking. Late-log-phase cells were harvested and lysed by EDTA, lysozyme, and detergent treatment, followed by proteinase K and RNase digestion. DNA isolation was by phenol-chloroform-isoamyl alcohol extraction and repeated isopropanol-ethanol precipitation (7). DNA purity was measured as an A260/A280 ratio. The genome was sequenced using the Illumina HiSeq 2000 sequencing platform, with a random subset of 4.5 million paired-end reads (132× coverage) used for assembly with MIRA v3.4 (1a) into 186 contigs that were submitted to GenBank, along with independent genome analysis on the RAST server (1). The draft genome of 6.89 Mb, with a G+C content of 65.1%, contains 6,431 recognized genes, including 6,360 coding sequences, 13 rRNAs, and 58 tRNAs.
Based on the 16S rRNA gene sequence (GenBank accession number ALJE01000119), strain HLE is renamed Achromobacter piechaudii, as the sequence is 99% identical (1,802 identities/1,828 matched positions) to that of A. piechaudii strain ATCC 43553 (GenBank accession number ADMS01000149). The 16S sequence from a PCR 16S product of strain HLE was previously deposited in GenBank (accession number AY027506) (8).
This is the second draft genome available for this common soil and opportunistic human pathogen after that of A. piechaudii strain ATCC 43553 (GenBank accession number ADMS00000000.1) from the Baylor College of Medicine. Strain A. piechaudii ATCC 43553 is reported to have a genome of 6.07 Mb with a G+C content of 64.75% and 5,817 genes. With the A. piechaudii HLE draft genome totaling 6.89 Mb, this is nearly twice the size of the genome of Alcaligenes faecalis (6), the species to which this strain was initially assigned (2, 4).
The deposited contigs ALJE01000001.1 and ALJE01000015.1 overlap at their 5′ ends by 175 bp, forming a larger contig of 282,049 bp. The overlap occurs within the aioA gene determining the Mo-pterin-containing subunit of arsenite oxidase within a 26-gene “arsenic gene island.” Arsenic gene islands are generally found with the genes for arsenite oxidase (3, 6, 9). The closest currently available match to the arsenic gene island of A. piechaudii HLE is the recently deposited genome of Achromobacter arsenitoxydans SY8 (3), for which 26 genes are in the same order in both genomes. The protein products for the two arsenite oxidase subunits are 94% (AioA) and 90% (AioB) identical between strains HLE and SY8, with lower percentages (50% to 80%) of identity for other arsenic gene island protein products.
Nucleotide sequence accession numbers.
The draft genome of A. piechaudii strain HLE was deposited under accession numbers ALJE01000001 through ALJE01000183 in GenBank (http://www.ncbi.nlm.nih.gov/projects/WGS/WGSprojectlist.cgi).
ACKNOWLEDGMENTS
We thank Henry L. Ehrlich for the bacterial strain and for information concerning its microbiology and arsenite oxidase activity.
This work was supported by funds from the U.S. Department of Energy.
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