The Complete Genome of Bacillus amyloliquefaciens subsp. plantarum CAU B946 Contains a Gene Cluster for Nonribosomal Synthesis of Iturin A

Abstract

The genome of the rhizobacterium Bacillus amyloliquefaciens subsp. plantarum CAU B946 was 4.02 Mb in size and harbored 3,823 genes (coding sequences [CDS]). Nine giant gene clusters were dedicated to nonribosomal synthesis of antimicrobial compounds. Remarkably, strain CAU B946 possessed a gene cluster involved in synthesis of iturin A.

GENOME ANNOUNCEMENT

Plant growth-promoting rhizobacteria (PGPR) have been applied as environmentally friendly alternatives of agrochemicals to improve crop yield and quality (10). The rhizobacterial strains belonging to Bacillus amyloliquefaciens subsp. plantarum (2) are known for their ability to promote plant growth by producing indole-3-acetic acid (IAA) (8) and volatile compounds (1). B. amyloliquefaciens FZB42 was shown to produce an array of secondary metabolites (3, 5, 11, 15, 16) which are important in controlling plant pathogens. Due to these properties, B. amyloliquefaciens subsp. plantarum is increasingly used as biofertilizer and as a biocontrol agent in agriculture (1). Recently, several representatives of industrially important B. amyloliquefaciens subsp. amyloliquefaciens, including the strain DSM7^T, have been completely sequenced (7, 14, 17, 18). However, from the plant-associated B. amyloliquefaciens subsp. plantarum group, only FZB42^T has been completely sequenced (4). Here, we report the genome sequence of the plant-associated strain CAU B946.

Strain CAU B946, isolated from the rice rhizosphere, was identified by 16S rRNA gene and gyrA gene sequencing and by physiological and biochemical analysis as being Bacillus amyloliquefaciens subsp. plantarum (2). Due to its capability to produce antibiotics, some products developed from strain CAU B946 have already been applied as biofungicides to control several plant diseases, such as tobacco black shank, rice sheath blight, cotton fusarium wilt, cotton verticillium wilt, and wheat scab (Q. Wang, unpublished data).

Genomic DNA prepared from strain CAU B946 was used for construction of a 3-kb-long paired-end library with a GS FLX library preparation kit in combination with GS FLX paired-end adaptors (both Roche, Mannheim, Germany) according to the manufacturer's protocol. The reads were assembled using the GS de novo assembler, and the resulting scaffolds were oriented based on the occurrence of unique single nucleotide polymorphisms (SNPs) in the repetitive rRNA gene clusters. Utilization of the paired-end information allowed scaffolding of the contigs larger than 500 bp. Gap closure was done by long-range PCR (using Phusion polymerase; New England BioLabs, Frankfurt am Main, Germany) and subsequent Sanger sequencing (IIT Biotech, Bielefeld, Germany). Prediction of protein-encoding sequences was initially accomplished with REGANOR (12). Manual and automatic annotations were done using the annotation software GenDB 2.4 (13).

The complete genome sequence of strain CAU B946 consisted of a circular 4,019,861-bp chromosome with a G+C value of 46.51%. The genome was slightly larger than that of strain FZB42 and was characterized by many phage-derived genes not present in the FZB42 genome. The chromosome consisted of 3,823 genes (coding sequences [CDS]), 10 rRNA operons, and 95 tRNAs.

Strain CAU B946 possessed a unique type I restriction modification system. Nine gene clusters involved in nonribosomal synthesis of lipopeptides, polyketides, and bacilysin were identified. Similar to the genome of FZB42 (6), about 8.5% of the whole CAU B-946 genome was involved in nonribosomal synthesis of antimicrobial compounds and siderophores. In addition, the complete gene cluster for synthesis and modification of the highly modified microcin plantazolicin (9), recently detected in strain FZB42 (16), was present in the genome of CAU B946.

Nucleotide sequence accession number.

The complete sequence of the CAU B-946 genome has been deposited in EMBL (accession number HE617159).