Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand

Sumpavapol, Punnanee; Tongyonk, Linna; Tanasupawat, Somboon; Chokesajjawatee, Nipa; Luxananil, Plearnpis; Visessanguan, Wonnop

doi:10.1099/ijs.0.018879-0

Cited by 80 publications

(60 citation statements)

References 37 publications

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“…The strain used in this work was selected by Barquero () on the basis of a combination of high IAA production and ACC deaminase activity. From the taxonomic viewpoint, Bacillus siamensis ( Sumpavapol et al, ) belongs to the Bacillus amyloliquefaciens group, which includes several strains known as biocontrollers but also strains with growth‐promoting activity by mechanisms other than biocontrol ( Wu et al, ; Chung et al, ), as was observed in our study.…”

Section: Resultssupporting

confidence: 71%

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis: Field testing on sweet pepper

Pastor-Bueis

Mulas

Gómez

et al. 2017

J. Plant Nutr. Soil Sci.

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A biofertilizer (BF) based on the plant growth promoting rhizobacterium (PGPR) Bacillus siamensis was produced using anaerobic digestate (AD) as the main ingredient of the growth medium, alongside a carbon source from residual origin. The use of residues for the growth of PGPR reduces the production costs of biofertilizers, but makes an assessment of the possible toxicity of residues for the bacteria or plants necessary. Therefore, the growth medium of PGPR was first optimized using the response surface methodology (RSM), followed by phytotoxicity tests and a field trial of the BF in a sweet pepper (Capsicum annuum L.) crop at two different locations. AD at 50% dilution, supplemented with 2.3% sugar beet molasses, was the optimum growth medium for producing the BF, with a bacterial concentration of 109 cfu mL−1. In the field trial, the treatments inoculated with BF and fertilized with decreased mineral N (80%) produced significantly better yields per ha than the controls with decreased N (80%) and full N (100%) without BF. This indicates improved efficiency of N use by the crop, as a consequence of the use of BF.

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Section: Resultssupporting

confidence: 71%

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis: Field testing on sweet pepper

Pastor-Bueis

Mulas

Gómez

et al. 2017

J. Plant Nutr. Soil Sci.

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“…Its separation was based mainly on the significantly low DNA relatedness values experimentally determined by DDH, and their different fatty acid profiles (Priest et al, 1987). Besides the “original members” B. subtilis, B. licheniformis , and B. pumilus , early described by Gordon et al (1973), many novel species belonging to the B. subtilis species complex have been described in last decades: B amyloliquefaciens (Priest et al, 1987), Bacillus atrophaeus (Nakamura, 1989), Bacillus mojavensis (Roberts et al, 1994), Bacillus vallismortis (Roberts et al, 1996), Bacillus sonorensis (Palmisano et al, 2001), Bacillus velezensis (Ruiz-García et al, 2005a), Bacillus axarquiensis (Ruiz-García et al, 2005b), Bacillus tequilensis (Gatson et al, 2006), Bacillus aerius, Bacillus aerophilus, Bacillus stratosphericus, Bacillus altitudinis (Shivaji et al, 2006), Bacillus safensis (Satomi et al, 2006), Bacillus methylotrophicus (Madhaiyan et al, 2010), Bacillus siamensis (Sumpavapol et al, 2010), Bacillus xiamenensis (Lai et al, 2014), Bacillus vanillea (Chen et al, 2014), Bacillus paralicheniformis (Dunlap C. et al, 2015), Bacillus glycinifermentas (Kim et al, 2015), Bacillus oryzicola (Chung et al, 2015), Bacillus gobiensis (Liu et al, 2016), and Bacillus nakamurai (Dunlap C. A. et al, 2016). B. vanillea, B. oryzicola , and B. methylotrophicus could not be corroborated as valid species and were identified as later heterotypic synonyms of either B. siamensis (Dunlap, 2015), or B. velezensis (Dunlap C. et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis Species Complex

et al. 2017

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The plant growth promoting model bacterium FZB42T was proposed as the type strain of Bacillus amyloliquefaciens subsp. plantarum (Borriss et al., 2011), but has been recently recognized as being synonymous to Bacillus velezensis due to phylogenomic analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as “B. amyloliquefaciens.” Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7T, the type strain of B. amyloliquefaciens. We identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7T. Dendrograms based on complete rpoB nucleotide sequences and on core genome sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1) B. amyloliquefaciens, (2) Bacillus siamensis, and (3) a conspecific group containing the type strains of B. velezensis, Bacillus methylotrophicus, and B. amyloliquefaciens subsp. plantarum. The three monophyletic clades shared a common mutation rate of 0.01 substitutions per nucleotide position, but were distantly related to Bacillus subtilis (0.1 substitutions per nucleotide position). The tight relatedness of the three clusters was corroborated by TETRA, dDDH, ANI, and AAI analysis of the core genomes, but dDDH and ANI values were found slightly below species level thresholds when B. amyloliquefaciens DSM7T genome sequence was used as query sequence. Due to these results, we propose that the B. amyloliquefaciens clade should be considered as a taxonomic unit above of species level, designated here as “operational group B. amyloliquefaciens” consisting of the soil borne B. amyloliquefaciens, and plant associated B. siamensis and B. velezensis, whose members are closely related and allow identifying changes on the genomic level due to developing the plant-associated life-style.

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“…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 13613…”

mentioning

confidence: 99%

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

Jeong

Kim

et al. 2012

J Bacteriol

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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...

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Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand

Cited by 80 publications

References 37 publications

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis: Field testing on sweet pepper

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis: Field testing on sweet pepper

Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis Species Complex

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

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Bacillus siamensis sp. nov., isolated from salted crab (poo-khem) in Thailand

Cited by 80 publications

References 37 publications

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis: Field testing on sweet pepper

Innovative liquid formulation of digestates for producing a biofertilizer based on Bacillus siamensis: Field testing on sweet pepper

Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an “Operational Group B. amyloliquefaciens” within the B. subtilis Species Complex

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

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