Draft Genome Sequence for Microbacterium laevaniformans Strain OR221, a Bacterium Tolerant to Metals, Nitrate, and Low pH

Abstract

Microbacterium laevaniformans strain OR221 was isolated from subsurface sediments obtained from the Field Research Center (FRC) in Oak Ridge, TN. It was characterized as a bacterium tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. We present its draft genome sequence.

GENOME ANNOUNCEMENT

The U.S. Department of Energy (DOE) has begun to remediate many contaminated former nuclear weapon production sites (9). Due to the high cost and low efficiency of physical and chemical cleaning methods, in situ bioremediation is being considered as a promising and cost-effective approach. An improved fundamental understanding of biogeochemical processes may facilitate bioremediation in the future. Many environmental microorganisms are known only from studies of 16S rRNA genes (5, 6, 11), and while important insights can be gained (e.g., see reference 4), often the assessment of their roles in the community can be difficult. New cultivation and molecular approaches, such as metagenomics, proteogenomics, and other functional approaches, have been used to examine potential functional roles and capabilities recently (e.g., see references 7, 12, and 13).

Microbacterium laevaniformans strain OR221 was isolated as part of a study that used in situ diffusion chamber-based and conventional cultivation approaches to isolate novel species from the Field Research Center (FRC) in Oak Ridge, TN (3). A number of isolates reported in that study were tolerant to heavy metals, such as uranium, nickel, cobalt, and cadmium, as well as nitrate and low pH. Strain OR221 was notable, as it was not inhibited by stressor concentrations above the ranges found at the study sites. We generated a draft genome sequence for M. laevaniformans strain OR221 to gain insights into its physiology.

Draft genome data for strain OR221 were generated using an Illumina (2) HiSeq2000 next-generation DNA sequencer derived from a 500-bp paired-end library. The DNA library was prepared using the standard TruSeq DNA sample preparation kit (Illumina), and a version 3 flow cell was used to run the TruSeq chemistry in a 2- by 100-bp configuration on the sequencing instrument. After trimming and filtering Illumina data (CLC Genomics Workbench, version 4.9), there were 13,474,667,042 bp of sequence data from 163,660,760 reads, with an average length of 82 bp. Trimmed Illumina reads were assembled into 548 contigs (CLC Genomics Workbench), with 55 found to be larger than 500 bp, and the largest contig was 462,042 bp. The OR221 draft genome size was approximately 3.4 Mb and had a 68% G+C content, measurements which are similar to the 3.98-Mb size and 70.28% average G+C content for the Microbacterium testaceum StLB037 complete genome (10). DNA contigs were annotated using an automated annotation pipeline based on the Prodigal gene prediction algorithm (8). The sequence data for the DNA contigs, coding and translation models, annotations, and metabolic reconstructions are available at http://genome.ornl.gov/microbial/guest/OR221_CLC/. A number of ABC-type transporters, heavy-metal-translocating P-type ATPases, and heavy-metal transport/detoxification proteins were predicted.

The Microbacterium testaceum genome (10) and the OR221 genome are the only ones that we are presently aware of for this genus. A complete genome for the Microbacterium nematophilum phage Min1 has been reported (1). The OR221 genome sequence will facilitate further studies with this genus and aid in the identification of genes that contribute to tolerance of metals, nitrate, and low pH.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AJGR00000000. The version described in this paper is the first version, AJGR01000000. The entire data set has been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA049910).