Paraburkholderia terrae strain:COX
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ABSTRACT:
PROVIDER: PRJNA1001293 | ENA |
REPOSITORIES: ENA
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Project description:Paraburkholderia terrae strain KU-15 has been investigated for its ability to degrade 2-nitrobenzoate. Here, we report the complete 10,422,345-bp genome of this microorganism, which consists of six circular replicons containing 9,483 protein-coding sequences. The genome carries genes that are potentially responsible for 2-nitrobenzoate and 4-nitirobenzoate degradation.
| S-EPMC9302171 | biostudies-literature
Project description:Bacteriophages constitute key gene transfer agents in many bacteria. Specifically, they may confer gene mobility to Paraburkholderia spp. that dwells in soil and the mycosphere. In this study, we first screened mycosphere and bulk soils for phages able to produce plaques, however found these to be below detection. Then, prophage identification methods were applied to the genome sequences of the mycosphere-derived Paraburkholderia terrae strains BS001, BS007, BS110 and BS437, next to P. phytofirmans strains BS455, BIFAS53, J1U5 and PsJN. These analyses revealed all bacterial genomes to contain considerable amounts [up to 13.3%] of prophage-like sequences. One sequence predicted to encode a complete phage was found in the genome of P. terrae BS437. Using the inducing agent mitomycin C, we produced high-titered phage suspensions. These indeed encompassed the progeny of the identified prophage (denoted ɸ437), as evidenced using phage major capsid gene molecular detection. We obtained the full sequence of phage ɸ437, which, remarkably, had undergone a reshuffling of two large gene blocks. One predicted moron gene was found, and it is currently analyzed to understand the extent of its ecological significance for the host.
| S-EPMC5567305 | biostudies-literature
Project description:Here, we report the draft genome sequences of three fungal-interactive 10.1601/nm.27008 strains, denoted BS110, BS007 and BS437. Phylogenetic analyses showed that the three strains belong to clade II of the genus 10.1601/nm.1619, which was recently renamed 10.1601/nm.26956. This novel genus primarily contains environmental species, encompassing non-pathogenic plant- as well as fungal-interactive species. The genome of strain BS007 consists of 11,025,273 bp, whereas those of strains BS110 and BS437 have 11,178,081 and 11,303,071 bp, respectively. Analyses of the three annotated genomes revealed the presence of (1) a large suite of substrate capture systems, and (2) a suite of genetic systems required for adaptation to microenvironments in soil and the mycosphere. Thus, genes encoding traits that potentially confer fungal interactivity were found, such as type 4 pili, type 1, 2, 3, 4 and 6 secretion systems, and biofilm formation (PGA, alginate and pel) and glycerol uptake systems. Furthermore, the three genomes also revealed the presence of a highly conserved five-gene cluster that had previously been shown to be upregulated upon contact with fungal hyphae. Moreover, a considerable number of prophage-like and CRISPR spacer sequences was found, next to genetic systems responsible for secondary metabolite production. Overall, the three 10.1601/nm.27008 strains possess the genetic repertoire necessary for adaptation to diverse soil niches, including those influenced by soil fungi.
| S-EPMC5735546 | biostudies-literature
Project description:The movement of bacterial cells along with fungal hyphae in soil (the mycosphere) has been reported in several previous studies. However, how local soil conditions affect bacterial migration direction in the mycosphere has not been extensively studied. Here, we investigated the influence of two soil parameters, pH and soil moisture content, on the migration, and survival, of Paraburkholderia terrae BS001 in the mycosphere of Lyophyllum sp. strain Karsten in microcosms containing a loamy sand soil. The data showed that bacterial movement along the hyphal networks took place in both the "forward" and the "backward" directions. Low soil pH strongly restricted bacterial survival, as well as dispersal in both directions, in the mycosphere. The backward movement was weakly correlated with the amount of fungal tissue formed in the old mycelial network. The initial soil moisture content, set at 12 versus 17% (corresponding to 42 and 60% of the soil water holding capacity), also significantly affected the bacterial dispersal along the fungal hyphae. Overall, the presence of fungal hyphae was found to increase the soil pH (under conditions of acidity), which possibly exerted protective effects on the bacterial cells. Finally, we provide a refined model that describes the bacterial migration patterns with fungal hyphae based on the new findings in this study.
| S-EPMC6061471 | biostudies-literature
Project description:Fungal-associated Paraburkholderia terrae strains in soil have been extensively studied, but their sensing strategies to locate fungi in soil have remained largely elusive. In this study, we investigated the behavior of five mycosphere-isolated P. terrae strains [including the type-3 secretion system negative mutant BS001-ΔsctD and the type strain DSM 17804T] with respect to their fungal-sensing strategies. The putative role of oxalic acid as a signaling molecule in the chemotaxis toward soil fungi, as well as a potential carbon source, was assessed. First, all P. terrae strains, including the type strain, were found to sense, and show a chemotactic response toward, the different levels of oxalic acid (0.1, 0.5, and 0.8%) applied at a distance. The chemotactic responses were faster and stronger at lower concentrations (0.1%) than at higher ones. We then tested the chemotactic responses of all strains toward exudates of the soil fungi Lyophyllum sp. strain Karsten and Trichoderma asperellum 302 used in different dilutions (undiluted, 1:10, 1:100 diluted) versus the control. All P. terrae strains showed significant directed chemotactic behavior toward the exudate source, with full-strength exudates inciting the strongest responses. In a separate experiment, strain BS001 was shown to be able to grow on oxalate-amended (0.1 and 0.5%) mineral medium M9. Chemical analyses of the fungal secretomes using proton nuclear magnetic resonance (1H NMR), next to high-performance liquid chromatography (HPLC), indeed revealed the presence of oxalic acid (next to glycerol, acetic acid, formic acid, and fumaric acid) in the supernatants of both fungi. In addition, citric acid was found in the Lyophyllum sp. strain Karsten exudates. Given the fact that, next to oxalic acid, the other compounds can also serve as C and energy sources for P. terrae, the two fungi clearly offer ecological benefits to this bacterium. The oxalic acid released by the two fungi may have primarily acted as a signaling molecule, and, as a "second option," a carbon source for P. terrae strains like BS001.
| S-EPMC5986945 | biostudies-literature
Project description:Burkholderia terrae KU-15
| PRJDB10639 | ENA
Project description:Paraburkholderia terrae KU-46
| PRJDB17035 | ENA
Project description:Paraburkholderia terrae KU-64
| PRJDB11943 | ENA
Project description:Burkholderia terrae NBRC 100964 genome sequencing project
| PRJDB257 | ENA