Draft Genome Sequence of the Plant Growth-Promoting Bacterium Bacillus siamensis KCTC 13613 ^T

Abstract

b Bacillus siamensis KCTC 13613T , a novel halophilic Bacillus species isolated from a salted Thai food, produced antimicrobial compounds against plant pathogens and promoted plant growth by volatile emission. We determined the 3.8-Mb genome sequence of B. siamensis KCTC 13613T to reveal the plant-beneficial effect at the genomic level.T he genus Bacillus includes ubiquitous Gram-positive endospore-forming bacteria that have a great impact on the environment, agriculture, biotechnology, and human health. Many Bacillus species have been used for their industrial enzymes (9) in the pharmaceutical (10) and food production (4, 7) industries. Another major application of Bacillus species is for enhancing growth of crop species (3,5). Here, during a systematic approach to screen Bacillus species that produce novel antibiotic compounds, we found that Bacillus siamensis KCTC 13613 T significantly inhibited mycelial growth of the plant-pathogenic fungi Rhizoctonia solani and Botrytis cinerea (data not shown). The KCTC 13613T strain also exhibited strong antibacterial activity against a Gram-positive bacterium, Micrococcus luteus. B. siamensis is a novel halophilic species that was isolated from a type of salted crab product (poo-khem) eaten in Thailand (11). Strain KCTC 13613T significantly increased seedling growth of Arabidopsis thaliana without physical contact in the I Plate, indicating that bacterial volatiles promoted plant growth (data not shown). These observations led us to decipher its genome sequence to investigate the genomic basis for the plant growth-promoting effect and biocontrol potential.The genome sequence of B. siamensis KCTC 13613 T was determined using a whole-genome shotgun strategy and an Illumina HiSeq 2000 instrument. Paired-end reads of 4.96 Gb (average read length of 96.1 bp) were produced from a 490-bp genomic library. Quality trimming and de novo assembly (word size, 64) were performed using CLC Genomics Workbench, version 4.8. The assembly contained 3,779,696 bp in 51 large contigs over 200 bp (N 50 , 589,476 bp) with 46.3% GϩC content. Maximum and average contig sizes were 965,626 bp and 74,112 bp, respectively. When Velvet, version 1.2.01, was used with various k-mers (55 to 75) (12), 38 scaffolds totaling 3,784,323 bp (N 50 , maximum scaffold size of 1,991,923 bp) were obtained. Not only were the two assembly results consistent with each other by direct comparison using MUMmer (6), but they were also the largest aligned blocks between two 100% identical results (593,857 bp), suggesting that the assembled sequences were accurate regardless of the assembly software. Automatic gene prediction and functional annotation of CLC assemblies were carried out using the RAST server (2). Among the 3,892 putative protein-coding genes, 47% were assigned to 446 subsystem categories. Average nucleotide identity analysis using completely sequenced Bacillus species showed that B. amyloliquefaciens was closely related to B. siamensis (Ͼ94% identity) (8). A polyketide synthase (PKS)/nonribosomal peptide sy...

Genomics-guided discovery and structure identification of cyclic lipopeptides from the Bacillus siamensis JFL15

“…Previous studies revealed that many Bacillus species can control pathogens[34]. However, few reports have presented that Bacillus siamensis has strong antimicrobial activities against pathogens[35]. Our work is the first to show that B .…”

“…So far, only two reports have presented that B . siamensis could secrete CLPs based on standard control[41] or whole-genome analyses[35]. However, CLPs purification and structural identification from the species of B .…”

Effect of Different Substrates on Soil Microbial Community Structure and the Mechanisms of Reductive Soil Disinfestation

“…Notably, during RSD treatment, the relative abundance of Desulfosporosinus reached a maximum of only 0.1% in the CK group, which could also explain why there was a lack of pathogen inhibition. After tomato planting, the relative abundances of genera with disease resistance, phosphorus solubilization, or nitrogen fixation ability, such as Bacillus (Ji et al, 2008;Jeong et al, 2012), Clostridium, Streptomyces (Watve et al, 2001), and Flavisolibacter (Mpanga et al, 2018), were significantly higher in the RSD treatment with 0.5% substrate addition than in the CK group, corresponding to the results of tomato plant biomass.…”

Diversity and functional characterization of bacterial endophytes dwelling in various rice (Oryza sativa L.) tissues, and their seed-borne dissemination into rhizosphere under gnotobiotic P-stress

“…Although, the PCR-DGGE profile of seed endospheres revealed predominance of Bacillus particularly restricted to TCN1 and TCS10, our culture-dependent analysis clearly showed prevalence of Bacillus strains in the rice cultivars planted at two contrasting soil-types. Interestingly, several endophytic Bacillus strains isolated in this study resembled the air-borne strains that were collected at high altitudes (Shivaji et al 2006), whereas others were related to plant-probiotic strains (Niu et al 2011;Jeong et al 2012;Lee et al 2012) and heavy metal resistant species (Suresh et al 2004). In addition, almost all (except for Bacillus safensis LS-066) endophytic Bacillus showed single or several plant-probiotic features.…”