Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

Summary1. Upon facing biotic stresses, plants orchestrate defence mechanisms via internal and external mechanisms that are mediated by signalling molecules such as salicylic acid, jasmonic acid, ethylene and various other volatile compounds. Although pathogen-and chemical-induced plant resistance has been studied extensively within the same plant compartment, the effects of above-ground (AG) insect-elicited plant defence on the resistance expression in roots and the below-ground (BG) microbial community are not well understood. 2. We assessed the effect of AG whitefly (Bemisia tabaci) attack on the elicitation of induced resistance against a leaf pathogen, Xanthomonas axonopodis pv. vesicatoria, a soil-borne pathogen, Ralstonia solanacearum, and on BG modifications of the rhizosphere microflora in peppers (Capsicum annuum). 3. Symptom development caused by the two bacterial pathogens on leaves and roots was significantly reduced in whitefly-exposed plants as compared to controls. A combined treatment with benzothiadiazole (BTH) and whitefly caused an additive effect on induced resistance, indicating that whitefly-induced plant defence can utilize salicylic acid (SA)-dependent signalling. To obtain further genetic evidence of this phenomenon, we evaluated the gene expression of Capsicum annuum pathogenesis-related protein (CaPR) 1, CaPR4, CaPR10 and Ca protease inhibitor II, and observed increased expression after BTH and ⁄ or whitefly treatment indicating that AG whitefly infestation elicited SA and jasmonic acid signalling in AG and BG. Since the expression pattern of PR genes in the roots differed, we assessed microbial diversity in plants treated with BTH and ⁄ or whitefly. 4. In addition to eliciting BG defence responses, a whitefly infestation of the leaves augmented the population of root-associated Gram-positive bacteria and fungi, which may have positively affected plant growth and induced systemic resistance. Whitefly feeding reduced plant size, which usually occurs as a consequence of the high costs of direct resistance induction. 5. Synthesis. Our results demonstrate that whitefly-induced resistance against bacterial pathogens can cross the AG-BG border and may cause further indirect benefits on future plant development, because it can positively affect the association or plant roots with putatively beneficial microorganisms.Key-words: above-ground, below-ground, plant growth-promoting rhizobacteria, plant-herbivore interactions, Ralstonia solanacearum, whitefly, Xanthomonas axonopodis *Correspondence author. E-mail: cmryu@kribb.re.kr † These authors contributed equally to this study.

Volatile compounds, such as short chain alcohols, acetoin, and 2,3-butanediol, produced by certain strains of root-associated bacteria (rhizobacteria) elicit induced systemic resistance in plants. The effects of bacterial volatile compounds (BVCs) on plant and fungal growth have been extensively studied; however, the impact of bacterial BVCs on bacterial growth remains poorly understood. In this study the effects of a well-characterized bacterial volatile, 2,3-butanediol, produced by the rhizobacterium Bacillus subtilis, were examined in the rhizosphere. The nature of 2,3-butanediol on bacterial cells was assessed, and the effect of the molecule on root colonization was also determined. Pepper roots were inoculated with three B. subtilis strains: the wild type, a 2,3-butanediol overexpressor, and a 2,3-butanediol null mutant. The B. subtilis null strain was the first to be eliminated in the rhizosphere, followed by the wild-type strain. The overexpressor mutant was maintained at roots for the duration of the experiment. Rhizosphere colonization by a saprophytic fungus declined from 14 days post-inoculation in roots treated with the B. subtilis overexpressor strain. Next, exudates from roots exposed to 2,3-butanediol were assessed for their impact on fungal and bacterial growth in vitro. Exudates from plant roots pre-treated with the 2,3-butanediol overexpressor were used to challenge various microorganisms. Growth was inhibited in a saprophytic fungus (Trichoderma sp.), the 2,3-butanediol null B. subtilis strain, and a soil-borne pathogen, Ralstonia solanacearum. Direct application of 2,3-butanediol to pepper roots, followed by exposure to R. solanacearum, induced expression of Pathogenesis-Related (PR) genes such as CaPR2, CaSAR8.2, and CaPAL. These results indicate that 2,3-butanediol triggers the secretion of root exudates that modulate soil fungi and rhizosphere bacteria. These data broaden our knowledge regarding bacterial volatiles in the rhizosphere and their roles in bacterial fitness and as important inducers of plant defenses.

Paenibacillus polymyxa E681, a spore-forming, low-G؉C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes.

A 3-kb DNA segment of the Bacillus caldolyticus genome including the 5' end end of the pyr cluster has been cloned and sequenced. The sequence revealed the presence of two open reading frames, pyrR and pyrP, located immediately upstream of the previously sequenced pyrB gene encoding the pyrimidine biosynthesis enzyme aspartate transcarbamoylase. The pyrR and pyrP genes encoded polypeptides with calculated molecular masses of 19.9 and 45.2 kDa, respectively. Expression of these ORFs was confirmed by analysis of plasmid-encoded polypeptides in minicells. Sequence alignment and complementation analyses identified the pyrR gene product as a uracil phosphoribosyltransferase and the pyrP gene product as a membrane-bound uracil permease. By using promoter expression vectors, a 650-bp EcoRI-HincII fragment, including the 5' end of pyrR and its upstream region, was found to contain the pyr operon promoter. The transcriptional start point was located by primer extension at a position 153 bp upstream of the pyrR translation initiation codon, 7 bp 3' of a sequence resembling a sigma A-dependent Bacillus subtilis promoter. This established the following organization of the ten cistrons within the pyr operon: promoter-pyrR-pyrP-pyrB-pyrC-pyrAa-pyrA b-orf2-pyrD-pyrF-pyrE. The nucleotide sequences of the region upstream of pyrR and of the pyrR-pyrP and pyrP-pyrB intercistronic regions indicated that the transcript may form two mutually exclusive secondary structures within each of these regions. One of these structures resembled a rho-independent transcriptional terminator. The possible implication of these structures for pyrimidine regulation of the operon is discussed.