Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity…
We report here the improved draft genome sequence of Bacillus sp. strain YF23, a bacterium originally isolated from switchgrass (Panicum virgatum) plants and shown to exhibit plant growth-promoting activity. The genome comprised 5.82 Mbp, containing 5,933 genes, with 193 as RNA genes, and a GC content of 35.10%.Copyright © 2019 Xia et al.
We report here the improved draft genome sequence of Pseudomonas poae strain A2-S9, a bacterium that was originally isolated from switchgrass plants and exhibited the capacity for plant growth promotion. Its genome has a size of 6.68 Mbp and a GC content of 61.3%. The genome encodes 6,022 predicted protein-coding genes. Copyright © 2019 Xia et al.
Achromobacter spanius UQ283 is a soilborne bacterium found to exhibit plant growth-promoting and disease-suppressing attributes in several plant species. Accordingly, we used long-read sequencing to determine its complete genome sequence. The assembled genome will aid in understanding the multifaceted interactions between plant growth-promoting rhizobacteria, pathogens, and plants. Copyright © 2019 Wass et al.
Bacillus velezensis DSYZ is a plant growth-promoting rhizobacterium with the capacity to control fungal pathogens. It was isolated from the rhizosphere soil of garlic. Here, we present the complete genome sequence of B. velezensis DSYZ. Several gene clusters that are related to the biosynthesis of antimicrobial compounds were predicted.
Caulobacter flavus RHGG3T, a novel type species in the genus Caulobacter, originally isolated from rhizosphere soil of watermelon (Citrullus lanatus), has the ability to improve the growth of watermelon seedling and tolerate heavy metals. In vitro, C. flavus RHGG3T was able to solubilize phosphate (80.56 mg L-1), produce indole-3-acetic acid (IAA) (11.58 mg L-1) and was resistant to multiple heavy metals (copper, zinc, cadmium, cobalt and lead). Inoculating watermelon with this strain increased shoot and root length by 22.1% and 43.7%, respectively, and the total number of lateral roots by 55.9% compared to non-inoculated watermelon. In this study, we present the complete…
This article reports the full genome sequence of Sphingomonas panacis DCY99T (=KCTC 42347T =JCM30806T), which is a Gram-negative rod-shaped, non-spore forming, motile bacterium isolated from rusty ginseng root in South Korea. A draft genome of S. panacis DCY99T and a single circular plasmid were generated using the PacBio platform. Antagonistic activity experiment showed S. panacis DCY99T has the plant growth promoting effect. Thus, the genome sequence of S. panacis DCY99T may contribute to biotechnological application of the genus Sphingomonas in agriculture.
Peanut suffer from a number of fungal and bacterial pathogens, while plant endophytes were considered excellent candidates as biocontrol agents. In this study, the peanut endophytic bacterium LDO2 was evaluated for the potential of peanut pathogens inhibition and growth-promotion, and the genetic mechanisms were explored by genome mining. Strain LDO2 significantly inhibited the growth of peanut pathogenic fungi and pathogenic bacteria, and specifically, it showed pronounced inhibition on mycelia growth of Aspergillus flavus mycelia and caused mycelial deformity. Gene clusters responsible for antifungal metabolites (fengycin, surfactin, bacilysin) and antibacterial metabolites (butirosin, bacillaene, difficidin, macrolactin, surfactin, bacilysin) were identified. Strain LDO2…
Arabidopsis thaliana has a diverse but consistent root microbiome, recruited in part by the release of fixed carbon in root exudates. Here we focussed on the recruitment of Streptomyces bacteria, which are well established plant-growth-promoting rhizobacteria and which have been proposed to be recruited to A. thaliana roots by the release of salicylic acid. We generated high quality genome sequences for eight Streptomyces endophyte strains and showed that although some strains do enhance plant growth, they are not attracted to, and do not feed on, salicyclic acid. We used 13CO2 DNA-stable isotope probing to determine which bacteria are fed by…
A gram-negative bacterium GXGL-4A was originally isolated from maize roots. It displayed nitrogen-fixing (NF) ability under nitrogen-free culture condition, and had a significant promotion effect on cucumber growth in the pot inoculation test. The preliminary physiological and biochemical traits of GXGL-4A were characterized. Furthermore, a phylogenetic tree was constructed based on 16S ribosomal DNA (rDNA) sequences of genetically related species. To determine the taxonomic status of GXGL-4A and further utilize its nitrogen-fixing potential, genome sequence was obtained using PacBio RS II technology. The analyses of average nucleotide identity based on BLAST+ (ANIb) and correlation indexes of tetra-nucleotide signatures (Tetra) showed…
Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome…
Microbe-assisted phytoremediation has great potential for practical applications. Plant growth-promoting bacteria (PGPB) with heavy metal (HM) resistance are important for the implementation of PGPB-assisted phytoremediation of HM-contaminated environments. Arthrobacter sp. PGP41 is a Cd(II)-resistant bacterium isolated from the rhizosphere soils of a Cd(II) hyperaccumulator plant, Solanum nigrum. Strain PGP41 can significantly improve plant seedling and root growth under Cd(II) stress conditions. This bacterium exhibited the ability to produce high levels of indole-3-acetic acid (IAA), as well as the ability to fix nitrogen and solubilize phosphate, and it possessed 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity. Here, we present the complete genome sequence of…
Disease-suppressive soils are ecosystems in which plants suffer less from root infections due to the activities of specific microbial consortia. The characteristics of soils suppressive to specific fungal root pathogens are comparable to those of adaptive immunity in animals, as reported by Raaijmakers and Mazzola (Science 352:1392-3, 2016), but the mechanisms and microbial species involved in the soil suppressiveness are largely unknown. Previous taxonomic and metatranscriptome analyses of a soil suppressive to the fungal root pathogen Rhizoctonia solani revealed that members of the Burkholderiaceae family were more abundant and more active in suppressive than in non-suppressive soils. Here, isolation, phylogeny,…
The recent worldwide discovery of plant growth-promoting (PGP) Kosakonia radicincitans in a large variety of crop plants suggests that this species confers significant influence on plants, both in terms of yield increase and product quality improvement. We provide a comparative genome analysis which helps to unravel the genetic basis for K. radicincitans' motility, competitiveness and plant growth-promoting capacities. We discovered that K. radicincitans carries multiple copies of complex gene clusters, among them two flagellar systems and three type VI secretion systems (T6SSs). We speculate that host invasion may be facilitated by different flagella, and bacterial competitor suppression by effector proteins…
Variovorax is a metabolically diverse genus of plant growth-promoting rhizobacteria (PGPR) that engages in mutually beneficial interactions between plants and microbes. Unlike most PGPR, Variovorax cannot synthesize the phytohormone indole-3-acetic acid (IAA) via tryptophan. However, we found that V. boronicumulans strain CGMCC 4969 could produce IAA using indole-3-acetonitrile (IAN) as the precursor. Thus, in the present study, the IAA synthesis mechanism of V. boronicumulans CGMCC 4969 was investigated. V. boronicumulans CGMCC 4969 metabolized IAN to IAA through both a nitrilase-dependent pathway and a nitrile hydratase (NHase) and amidase-dependent pathway. Cobalt enhanced the metabolic flux via the NHase/amidase, by which IAN…