Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain JS

Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.     

Genome sequence of the leaf-colonizing Bacterium Bacillus sp. strain 5B6, isolated from a cherry tree

Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 5B6, which was isolated from the leaf of a cherry tree. The 3.9-Mb genome uncovers its potential for understanding the nature of leaf colonization as well as antibiosis against plant pathogens.     

Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus species

Bacillus sphaericus strain C3-41 is an aerobic, mesophilic, spore-forming bacterium that has been used with great success in mosquito control programs worldwide. Genome sequencing revealed that the complete genome of this entomopathogenic bacterium is composed of a chromosomal replicon of 4,639,821 bp and a plasmid replicon of 177,642 bp, containing 4,786 and 186 potential protein-coding sequences, respectively. Comparison of the genome with other published sequences indicated that the B. sphaericus C3-41 chromosome is most similar to that of Bacillus sp. strain NRRL B-14905, a marine species that, like B. sphaericus, is unable to metabolize polysaccharides. The lack of key enzymes and sugar transport systems in the two bacteria appears to be the main reason for this inability, and the abundance of proteolytic enzymes and transport systems may endow these bacteria with exclusive metabolic pathways for a wide variety of organic compounds and amino acids. The genes shared between B. sphaericus C3-41 and Bacillus sp. strain NRRL B-14905, including mobile genetic elements, membrane-associated proteins, and transport systems, demonstrated that these two species are a biologically and phylogenetically divergent group. Knowledge of the genome sequence of B. sphaericus C3-41 thus increases our understanding of the bacilli and may also offer prospects for future genetic improvement of this important biological control agent.     

Molecular identification of alkaliphilic and halotolerant strain<Emphasis Type="Italic"> Bacillus</Emphasis> sp. FTU as<Emphasis Type="Italic"> Bacillus pseudofirmus</Emphasis> FTU

The systematic position of the alkaliphilic and halotolerant strain Bacillus sp. FTU was refined in view of the comprehensive taxonomic revision of the group of alkaliphilic and alkalitolerant Bacillus strains. Sequence analysis of almost the entire 16S rRNA gene of Bacillus sp. FTU revealed 99.8% homology with two Bacillus pseudofirmus strains. Subsequent DNA-DNA hybridization analysis confirmed the close relationship of Bacillus sp. FTU with the type strain of B. pseudofirmus (the level of homology reached 86%). Results of physiological and biochemical characterizations relevant for the group clearly underlined the positioning of strain FTU within this species. It is therefore concluded that Bacillus sp. FTU represents a strain of the alkaliphilic species B. pseudofirmus and is to be renamed as B. pseudofirmus FTU. The phylogeny of different Bacillus species is discussed using N-terminal sequence homologies of some caa (3)-type oxidase subunits.     

Genes encoding the N-acyl homoserine lactone-degrading enzyme are widespread in many subspecies of Bacillus thuringiensis

Gram-negative bacteria can communicate with each other by N-acyl homoserine lactones (AHLs), which are quorum-sensing autoinducers. Recently, the aiiA gene (encoding an enzyme catalyzing the degradation of AHL) has been cloned from Bacillus sp. strain 240B1. During investigations in the course of the ongoing Bacillus thuringiensis subsp. morrisoni genome project, an aiiA homologue gene in the genome sequence was found. These results led to consideration of the possibility of the widespread existence of the gene in B. thuringiensis. aiiA homologue genes were found in 16 subspecies of B. thuringiensis, and their sequences were determined. Comparison of the Bacillus sp. strain 240B1 aiiA gene with the B. thuringiensis aiiA homologue genes showed high homologies of 89 to 95% and 90 to 96% in the nucleotide sequence and deduced amino acid sequence, respectively. Among the subspecies of B. thuringiensis having an aiiA gene, the subspecies aizawai, galleriae, kurstaki, kyushuensis, ostriniae, and subtoxicus were shown to degrade AHL. It was observed that recombinant Escherichia coli producing AiiA proteins also had AHL-degrading activity and could also attenuate the plant pathogenicity of Erwinia carotovora. These results indicate that insecticidal B. thuringiensis strains might have potential to compete with gram-negative bacteria in natural ecosystems by autoinducer-degrading activity.     

Endophytic bacillus sp. isolated from the interior of balloon flower root

A bacterial strain, designated CY22, was isolated from the interior of balloon flower (Platycodon grandiflorum) root in the Republic of Korea. The isolate coproduced an iturin-like antifungal compound and a surfactin-like potent biosurfactant. Analysis of the 16S-rDNA of strain CY22 showed that the isolate was a member of Bacillus. High similarities were observed between strain CY22 and Bacillus sp. TKSP 24, and between strain CY22 and B. subtilis 168. Phylogenetic analysis based on 16S-rDNA sequences showed that strain CY22 was closely related to Bacillus sp. The main whole-cell fatty acids were anteiso-C15:0 (37%), C17:0 (5.1%), and iso-C15:0 (27.7%). DNA G+C content was 54 mol%. Based on phylogenetic inference, phenotypic and chemotaxonomic characteristics, this endophytic strain Bacillus sp. CY22 was assigned to the genus Bacillus.     

Thermogenesis of mesophilic, thermotolerant and thermophilic strains of microorganisms--producers of fungal cell wall--destroying enzymes]

Investigations were carried out to clarify the relationship between thermogenesis and production of yeast wall lyzing enzymes by the mesophilic strain of Bacillus subtilis, thermotolerant strain of Actinomyces sp. II and thermophilic strain of Actinomyces sp. 10. The enzymic lyzing activity was measured in the culture liquid filtrate of those microorganisms. The thermophilic strain of Actinomyces sp. 10 showed the highest enzymic activity. The thermogenetic curves of the cultures had several inflections. The mesophilic culture of Bacillus subtilis whose enzymic lyzing activity was the lowest displayed the highest heat release.     

产纳豆激酶菌株Bacillus sp.ZLK08的分离及酶纯化

获得稳定产纳豆激酶菌株,为高酶活纳豆激酶产生菌的改造奠定基础.取各来源纳豆,用平板梯度稀释法分离菌株,测定菌株酶活,利用16S rDNA鉴定产酶菌株,凝胶过滤法纯化纳豆激酶并SDS-PAGE检测分析.成功获得稳定产酶芽胞杆菌Bacillus sp.ZLK08,16S rDNA分析表明其与GenBank中序列同源率达到99％,液体发酵表明酶活达到2.5 FU/mL,经纯化,SDS-PAGE表明纳豆激酶分子量为28.46 ku.分离出的Bacillus sp.ZLK08菌株能稳定产纳豆激酶且具有较高酶活.     

芽孢杆菌Bacillus sp. S-1壳聚糖酶基因的克隆与序列分析

从连云港海滩晒虾蟹壳的泥土里筛选出一株产壳聚糖酶能力较高的菌株S-1,根据其形态特征、生理生化以及16S rDNA鉴定,初步认定该菌为芽孢杆菌属（Bacillus）。利用NCBI数据库中已经报道的Bacillus壳聚糖酶序列设计兼并引物,以菌株Bacillus sp. S-1的基因组DNA为模板进行聚合酶链式反应（PCR）,克隆到壳聚糖酶基因的部分序列;利用Clontech公司Universal GenomeWalker试剂盒构建该菌株的基因组步移文库,根据已测定的序列信息设计特异性引物,结合两步法PCR技术分别克隆两端未知序列,拼接获得壳聚糖酶基因的全长序列（该基因全长1362 bp编码453个氨基酸,注册号：EU924147）,并对该序列进行了生物信息学方面的分析。     

Molecular cloning and expression of the xylanase gene of alkalophilic Bacillus sp. strain C-125 in Escherichia coli.

The gene for xylanase A of alkalophilic Bacillus sp. strain C-125 was cloned in Escherichia coli with pBR322. The plasmid pCX311 contained 2.6- and 2.0-kilobase-pair HindIII fragments. The characteristics of the purified pCX311-encoded xylanase were the same as those of purified xylanase A from alkalophilic Bacillus sp. strain C-125.     

Expression of small RNAs by Bacillus sp. strain PS3 and B. subtilis cells during sporulation

A small RNA sequence identified in an rRNA-tRNA cluster from the thermophilic Bacillus sp. strain PS3 was examined. An oligonucleotide probe specific for the RNA bound to multiple restriction fragments in Bacillus sp. strain PS3 DNA, thus several copies of this sequence occur in its genome. Similar findings were observed using DNA from B. subtilis, B. stearothermophilus, Escherichia coli, Staphylococcus aureus, Haemophilus influenzae and Thermus thermophilus. This sequence apparently is widespread in the eubacteria. Northern analysis of RNA from sporulating Bacillus sp. strain PS3 and B. subtilis cells revealed RNA species homologous to the probe in both bacteria. Expression of the small RNA in B. subtilis depended on σ^H.     

Biological control agent of common scab disease by antagonistic strain Bacillus sp. sunhua

AIMS: To identify an antagonistic strain against Streptomyces scabiei and to characterize the antibiotic agent. The efficacy of the isolated strain in controlling common scab disease was also evaluated. METHODS AND RESULTS: A bacterial strain antagonistic against S. scabiei was isolated from the soil of a potato-cultivating area. This bacterium was identified as a Bacillus species by 16S rRNA gene sequence analysis and was designated Bacillus sp. sunhua. Antibiotics produced by this strain were proven to be stable within a broad pH range and at high temperatures. The culture broth was extracted with ethyl acetate, and then the crude extract was applied to HPLC. Two compounds were isolated and identified as iturin A and macrolactin A by 1H-NMR, 13C-NMR, HMBC, HMQC and mass spectrometer. The culture broth of Bacillus sp. sunhua had a suppressive effect on common scab disease in a pot assay, decreasing the infection rate from 75 to 35%. This strain also suppressed Fusarium oxysporum, the pathogen of potato dry rot disease. CONCLUSIONS: Bacillus sp. sunhua was shown to inhibit S. scabiei effectively. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report demonstrating that macrolactin A and iturin A inhibit S. scabiei. This study demonstrated the possibility of controlling potato scab disease using Bacillus sp. sunhua.     

Newly isolated bacterial strains belonging to Bacillaceae (Bacillus sp.) and Micrococcaceae accelerate death of the honey bee mite, Varroa destructor (V. jacobsoni), in laboratory assays

Newly isolated bacterial strains belonging to Bacillaceae (Bacillus sp.), Micrococcaceae and three unidentified strains were tested for their pathogenicity against the mite, Varroa destructor. The Bacillus sp. strain and two of the strains belonging to the Micrococcaceae family significantly decreased the time for 50% mortality of the mite population (up to 57%) and hence may be potential control agents. In in vitro bioassay whole cells, extracellular broth and cellular extract of the Bacillus sp. strain effectively killed the mites, suggesting that both endotoxins and exotoxins contributed to the killing.     

Genome Sequence of the Aerobic Bacterium Bacillus sp. Strain FJAT-13831

Bacillus sp. strain FJAT-13831 was isolated from the no. 1 pit soil of Emperor Qin''s Terracotta Warriors in Xi''an City, People''s Republic of China. The isolate showed a close relationship to the Bacillus cereus group. The draft genome sequence of Bacillus sp. FJAT-13831 was 4,425,198 bp in size and consisted of 5,567 genes (protein-coding sequences [CDS]) with an average length of 782 bp and a G+C value of 36.36%.     

耐盐菌Staphylococcus sp. YZ-1和Bacillus cereus CC-1的Cr(VI)脱毒特性与机理

[背景]高盐含铬废水的去除过程中,Cr(Ⅵ)还原菌是研究者关注的重点,但目前对耐盐菌株的Cr(Ⅵ)脱毒特性及机理的分析仍较少。[目的]比较两株耐盐菌株的Cr(Ⅵ)移除特性,并区分Cr(Ⅵ)耐受机制的差异;通过基因组测序分析,从基因层面推测铬耐受相关基因;构建铬还原菌的混菌体系,考察两者对去除污染物的协同作用。[方法]从青海茶卡盐湖分离耐盐菌Staphylococcus sp.YZ-1,与Bacillus cereus CC-1进行基础特性和Cr(Ⅵ)去除性能的比较,并通过全基因组序列的分析验证特性测试的结果。[结果]两株菌都具有铬移除特性,但CC-1的铬移除效率更高,在初始Cr(Ⅵ)浓度为0.1 mmol/L情况下,CC-1能在12h内移除95.3%的Cr(Ⅵ),而YZ-1只能移除40.1%。在进一步实验中发现YZ-1只能对Cr(Ⅵ)进行还原,将其转化为可溶的有机态Cr(Ⅲ),而CC-1能同时对Cr(Ⅵ)进行还原和吸附。全基因组分析发现YZ-1具有编码外排泵蛋白的基因和编码NAD(P)H氧化还原酶的基因,而CC-1具有编码铬转运蛋白ChrA和细胞色素C氧化还原酶的基因。两株菌的混菌体系在处理含Cr(Ⅵ)、Te(Ⅳ)的废水时,菌群能将还原产物聚集成团并沉淀到底部。[结论]菌株YZ-1和CC-1均为耐盐铬还原菌,但YZ-1中的铬还原酶为诱导型酶,CC-1则为组成型酶。基因组数据分析鉴别出两者可能同时存在多种铬耐受机制相关编码基因。混合菌群可以结合YZ-1的自絮凝特性和两者均有的Te(Ⅳ)/Cr(Ⅵ)还原活性,具有潜在的实用价值。     

Complete Genome Sequence of Bacillus subtilis Strain QB928, a Strain Widely Used in B. subtilis Genetic Studies

The complete genome sequence of Bacillus subtilis strain QB928 was constructed to facilitate studies in the evolution of the genetic code. With a widespread use of the strain in Bacillus subtilis genetics studies, its complete genome sequence would facilitate deeper understanding of Bacillus subtilis genetics.     

Extracellular hydrolases of strain Bacillus sp. 739 and their involvement in the lysis of micromycete cell walls

The mycolytic bacterial strain Bacillus sp. 739 produces extracellular enzymes which degrade in vitro the cell walls of a number of phytopathogenic and saprophytic fungi. When Bacillus sp. 739 was cultivated with Bipolaris sorokiniana, a cereal root-rot pathogen, the fungus degradation process correlated with the levels of the beta-1,3-glucanase and protease activity. The comparative characteristic of Bacillus sp. 739 enzymatic preparations showed that efficient hydrolysis of the fungus cell walls was the result of the action of the complex of enzymes produced by the strain when grown on chitin-containing media. Among the enzymes of this complex, chitinases and beta-1,3-glucanases hydrolyzed most actively the disintegrated cell walls of B. sorokiniana. However, only beta-1,3-glucanases were able to degrade the cell walls of native fungal mycelium in the absence of other hydrolases, which is indicative of their key role in the mycolytic activity of Bacillus sp. 739.     

Isolation and characterization of Bacillus sp. producing broad-spectrum antibiotics against human and plant pathogenic fungi

A strain of bacterium producing antifungal antibiotic was isolated and identification of the strain was attempted. We could identify the bacterium as being a Bacillus sp., based on morphological observation, physiological characteristics, and 16S rDNA sequence analysis, thus leading us to designate the strain as Bacillus sp. AH-E-1. The strain showed potent antibiotic activity against phytopathogenic and human pathogenic fungi by inducing mycelial distortion and swelling and inhibiting spore germination. The antibiotic metabolite produced by the strain demonstrated excellent thermal and pH (2-11) stability, but was labile to autoclaving. From these results, we could find a broader antifungal activity of Bacillus genus. Isolation and characterization of the active agent produced by the strain are under progress.     

Highly repetitive DNA sequences in cyanobacterial genomes.

We characterized three distinct families of repeated sequences in the genome of the cyanobacterium Calothrix sp. strain PCC 7601. These repeated sequences were present at a level of about 100 copies per Calothrix genome and consisted of tandemly amplified heptanucleotides. These elements were named short tandemly repeated repetitive (STRR) sequences. We used the three different Calothrix STRR sequences as probes to perform Southern hybridization experiments with DNAs extracted from various cyanobacterial strains, Bacillus subtilis, and Escherichia coli. The three different STRR sequences were found as repetitive genomic DNA components specific to the heterocystous strains tested. The role of the STRR sequences, as well as their possible use in taxonomic studies, is discussed.     

Transfer of Tn916 and Tn916ΔE into Clostridium difficile: demonstration of a hot-spot for these elements in the C. difficile genome

The conjugative transposon Tn916 and a derivative Tn916 delta E was transferred from Bacillus subtilis into Clostridium difficile CD37 by filter mating. All the C. difficile transconjugants appeared to contain one copy of the transposon integrated into the same position in the genome. Transposition from the original site of integration was not observed. Like Tn916 the transferable tetracycline resistance determinant (Tc-CD) of C. difficile has a preferred site of integration in C. difficile and is homologous with Tn916 along the whole length of Tn916. However comparisons of the distribution of TaqI and Sau3AI sites in the homologous regions of the two elements did not demonstrate any hybridizing fragments in common.