Genome Sequence of Microbacterium testaceum StLB037, an N-Acylhomoserine Lactone-Degrading Bacterium Isolated from Potato Leaves

Abstract

Microbacterium testaceum is an endophytic Gram-positive bacterium that resides within plant hosts. M. testaceum StLB037 was isolated from potato leaves and shows N-acylhomoserine lactone-degrading activity. Here, we present the 3.98-Mb complete genome sequence of StLB037, with an average GC content of 70.28%.The genus Microbacterium belongs to the class of high-GCcontent Actinobacteria. Microbacterium testaceum is an endophytic bacterium that resides within plant hosts without causing disease symptoms (12). In many Gram-negative bacterial species, N-acylhomoserine lactone (AHL) has been identified as a signal compound involved in the quorum-sensing system (2). Many Gram-negative plant pathogens produce AHLs and regulate their virulence by AHL-mediated quorum sensing (10). We have reported the isolation of AHL-degrading M. testaceum strains from the leaf surface of the potato (6). We also cloned the aiiM gene from the genomic library of StLB037, which has AHL-lactonase activity and shows high homology with the ␣/␤ hydrolase fold family from Actinobacteria (11). To our knowledge, the complete genome sequence of the genus Microbacterium has not been deposited in the DDBJ/EMBL/GenBank databases at this point in time. In this work, we determined the genome sequence of M. testaceum StLB037.Single-and paired-end whole-genome shotgun sequencing of StLB037 was performed using Roche genome sequencer FLX Titanium pyrosequencing technology (5) provided by Operon Biotechnologies (Tokyo, Japan). We produced 584,678 reads, with an average read length of 287 bases. The total number of sequenced bases is 167,947,725, representing a sequencing depth of 42ϫ. With the use of Celera Assembler version 5.3, these reads were assembled into one large scaffold including 29 large contigs (Ͼ1,000 bp). Gap closure was attempted using gap-spanning clones and PCR products. Prediction of putative coding sequences and gene annotation were done using the Microbial Genome Annotation Pipeline (http://migap.lifesciencedb.jp/). Briefly, protein-coding sequences (CDSs) were predicted by the combined use of MetaGeneAnnotator (7), RNAmmer (3), tRNAScan (4), and BLAST (1).The complete genomic information for M. testaceum StLB037 is contained on a single circular chromosome of 3,982,034 bp with an average GC content of 70.28%. The genome contains 3,676 protein-coding genes, two rRNA operons, and 45 tRNA genes.The aiiM gene, which has been identified from the genomic library of StLB037, was found as a single copy in the complete genome. Many AHL-degrading genes have been cloned and characterized from various bacterial species (8). We searched for the homologs of the reported AHL-degrading genes in the complete genome of StLB037. As a result, one predicted CDS (MTES_1124), which encoded 309 amino acids, showed 26.3% identity to the reported AHL-degrading enzyme, QsdA (9). QsdA is a phosphotriesterase-like AHL lactonase from Rhodococcus erythropolis W2, which belongs to the class of Actinobacteria as well as M. testaceum.In summary, the AHL-degrading activi...

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

“…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% GϩC content, measurements which are similar to the 3.98-Mb size and 70.28% average GϩC 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).…”

Bioremediation strategies for removal of residual atrazine in the boreal groundwater zone

“…In well 608, the most common clones were identified as Acinetobacter (24 %), which are known to be versatile degraders and efficient atrazine degraders in high concentration (Singh et al 2004). Other clones related to potential atrazine degraders included Microbacterium species (Morohoshi et al 2011), as well as Polaromonas (Devers et al 2007), Aminobacter (McDonald et al 2005), Rhodococcus (Behki et al 1995), Pseudomonas, and Arthrobacter, species extensively studied because of their atrazine-degrading capabilities. As the 16S rRNA gene used for constructing the clone library does not reflect the metabolic functions the bacteria carry out, it is a poor indication of atrazine degradation as such.…”

Genome sequences published outside of Standards in Genomic Sciences, January – June 2011

“…longum BBMN68, sequence accession CP002286 [131] Corynebacterium pseudotuberculosis I19, sequence accession CP002251 [132] Janibacter sp. HTCC2649, sequence accession AAMN00000000 [133] Microbacterium testaceum StLB037, sequence accession AP012052 [134] Mycobacterium bovis BCG, sequence accession later [135] Nocardioides sp. JS614, sequence accession CP000509, CP000508 [136] Saccharopolyspora spinosa NRRL 18395, sequence accession AEYC00000000 [137] Streptomyces griseoaurantiacus, sequence accession AEYX01000000 [138] Streptomyces griseus XyelbKG-1, sequence accession ADFC00000000 [139] Streptomyces sp.…”