Insight in the quorum sensing-driven lifestyle of the non-pathogenic Agrobacterium tumefaciens 6N2 and the interactions with the yeast Meyerozyma guilliermondii

Agrobacterium tumefaciens is considered a prominent phytopathogen, though most isolates are nonpathogenic. Agrobacteria can inhabit plant tissues interacting with other microorganisms. Yeasts are likewise part of these communities. We analyzed the quorum sensing (QS) systems of A. tumefaciens strain 6N2, and its relevance for the interaction with the yeast Meyerozyma guilliermondii, both sugarcane endophytes. We show that strain 6N2 is nonpathogenic, produces OHC8-HSL, OHC10-HSL, OC12-HSL and OHC12-HSL as QS signals, and possesses a complex QS architecture, with one truncated, two complete systems, and three additional QS-signal receptors. A proteomic approach showed differences in QS-regulated proteins between pure (64 proteins) and dual (33 proteins) cultures. Seven proteins were consistently regulated by quorum sensing in pure and dual cultures. M. guilliermondii proteins influenced by QS activity were also evaluated. Several up- and down- regulated proteins differed depending on the bacterial QS. These results show the importance of the QS regulation in the bacteria-yeast interactions.Fil: Bertini, Elisa Violeta. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Torres, Mariela Analía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Leger, Thibaut. Institut Jacues Monod; FranciaFil: Garcia, Camille. Institut Jacques Monod; FranciaFil: KarWai, Hong. University Of Malaya; MalasiaFil: Teik Min, Chong. University Of Malaya; MalasiaFil: Castellanos, Lucia Ines. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: KokGan, Chan. University Of Malaya; MalasiaFil: Dessaux, Yves. Universite Paris-sud; FranciaFil: Camadro, Jean Michel. Institut Jacques Monod; FranciaFil: Nieto Peñalver, Carlos Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; Argentin

Identification of IncA/C plasmid replication and maintenance genes and development of a plasmid multilocus sequence typing scheme

Plasmids of incompatibility group A/C (IncA/C) are becoming increasingly prevalent within pathogenic Enterobacteriaceae. They are associated with the dissemination of multiple clinically relevant resistance genes, including blaCMY and blaNDM. Current typing methods for IncA/C plasmids offer limited resolution. In this study, we present the complete sequence of a blaNDM-1-positive IncA/C plasmid, pMS6198A, isolated from a multidrug-resistant uropathogenic Escherichia coli strain. Hypersaturated transposon mutagenesis, coupled with transposon-directed insertion site sequencing (TraDIS), was employed to identify conserved genetic elements required for replication and maintenance of pMS6198A. Our analysis of TraDIS data identified roles for the replicon, including repA, a toxin-antitoxin system; two putative partitioning genes, parAB; and a putative gene, 053. Construction of mini-IncA/C plasmids and examination of their stability within E. coli confirmed that the region encompassing 053 contributes to the stable maintenance of IncA/C plasmids. Subsequently, the four major maintenance genes (repA, parAB, and 053) were used to construct a new plasmid multilocus sequence typing (PMLST) scheme for IncA/C plasmids. Application of this scheme to a database of 82 IncA/C plasmids identified 11 unique sequence types (STs), with two dominant STs. The majority of blaNDM-positive plasmids examined (15/17; 88%) fall into ST1, suggesting acquisition and subsequent expansion of this blaNDM-containing plasmid lineage. The IncA/C PMLST scheme represents a standardized tool to identify, track, and analyze the dissemination of important IncA/C plasmid lineages, particularly in the context of epidemiological studies

Characterization of Quorum Sensing and Quorum Quenching Soil Bacteria Isolated from Malaysian Tropical Montane Forest

We report the production and degradation of quorum sensing N-acyl-homoserine lactones by bacteria isolated from Malaysian montane forest soil. Phylogenetic analysis indicated that these isolates clustered closely to the genera of Arthrobacter, Bacillus and Pseudomonas. Quorum quenching activity was detected in six isolates of these three genera by using a series of bioassays and rapid resolution liquid chromatography analysis. Biosensor screening and high resolution liquid chromatography-mass spectrometry analysis revealed the production of N-dodecanoyl-L-homoserine lactone (C12-HSL) by Pseudomonas frederiksbergensis (isolate BT9). In addition to degradation of a wide range of N-acyl-homoserine lactones, Arthrobacter and Pseudomonas spp. also degraded p-coumaroyl-homoserine lactone. To the best of our knowledge, this is the first documentation of Arthrobacter and Pseudomonas spp. capable of degrading p-coumaroyl-homoserine lactone and the production of C12-HSL by P. frederiksbergensis

Adaptive features of two copper-resistant Pseudomonas strains isolated from a French vineyard soil / Chong Teik Min

Trace metals are required in many cellular processes in bacteria but could also be tenacious and cause toxicity when present in excess. Vitis vinifera (grapevine) is a non-rotating crop that has been routinely treated with copper sulphate over the years in order to control fungal diseases. Consequently, such anthropogenic accumulation of copper ions in the vineyard soil causes selection that favours the prevalence of copper resistant microorganisms. Thus it would be of interest to investigate the microbiota inhabiting these soils. DNA methylation is one of the common epigenetic markers found widespread in prokaryotes and often regulates gene expressions under the influence of external factors. Hence, exploring the genetic determinants for metal resistance as well as the methylation patterns could also provide insights on adaptability of these soil inhabitants in the presence of metal induced stress. A bacterial isolation attempt on a French vineyard soil sample has resulted in identification of Pseudomonas strains, shown to confer resistance to copper ions. Phenotypic microarray analysis also showed that two strains namely P. mendocina strain S5.2 and P. putida strain S13.1.2 were highly capable of tolerating other heavy metals including nickel, cobalt, cadmium, zinc and arsenic. Subsequently, complete genome analysis was conducted using Single Molecule, Real Time (SMRT) sequencing followed by genome assembly and annotation procedures to elucidate the genetic determinants involved in metal resistance of these strains. Methylome study in terms of genome-wide methylation patterns and presence of DNA methyltransferases in both strains were also conducted. Genome assembly has resulted in complete genome of P. mendocina strain S5.2 consisted in a 5.1 Mb circular chromosome with one linear plasmid, pPME5, at the size of approximately 250 kb. The linearity of this large plasmid was further verified using S1 nuclease treatment followed by pulse field gel electrophoresis. Besides, the complete iv genome of P. putida strain S13.1.2 comprised of one circular chromosome at the size of 6.6 Mb. A series of operons and gene clusters such as cop, cus, czc, nik, and asc systems were present, reflecting the observed metal resistance phenotypes. The features in terms of specificity and arrangements of these genetic determinants were also highlighted in the study. Methylome analysis revealed the presence of Type I and Type II DNA methyltransferases recognizing CGCANNNNNNGGG and GACGAG motifs, respectively in P. mendocina strain S5.2. For P. putida strain S13.1.2, one type II DNA methyltransferase recognizing GTTCCG motifs were also identified. Further analysis also showed that these genes were methylated indicating the possibility that these genes were regulated by DNA methylation. In addition, unique traits of P. mendocina strain S5.2 such as twitching motility and DNA methylation contributed by the presence of plasmid pPME5 were lost following plasmid curing of the strain. Such observations have demonstrated probable roles of the plasmid for fitness of the strain in native vineyard soil environments. In conclusion, the comprehensive genomic and phenotypic profiling of heavy metal resistance and methylome analysis have demonstrated the adaptation of Pseudomonas strains to the grapevine soils enriched with copper and perhaps other metals

Characterisation of quorum sensing and quorum quenching soil bacteria isolated from Malaysian tropical montane forest / Chong Teik Min

Quorum sensing (QS) describes bacterial cell density dependent signaling mechanisms through autoinducers that are involved in mediation of bioluminescence, biofilm development, antibiotic production and virulence factor expressions. Attenuation of quorum sensing signals termed as quorum quenching (QQ) have been identified in a range of living organisms, including bacteria and eukaryotes. The production and degradation of QS compound N-acyl homoserine lactones (AHL) by bacteria isolated from Malaysian montane forest soil were assessed in this study. Phylogenetic analysis indicated that these isolates were distinct members of genera of Arthrobacter, Bacillus and Pseudomonas. Biosensor screening and liquid chromatography mass spectrometry analysis have revealed the production of N-dodecanoyl-L-homoserine lactone (C12-HSL) by Pseudomonas frederiksbergensis (isolate BT9). Strong QQ activity with broad substrate specificity against various AHLs has been detected among Arthrobacter, Bacillus and Pseudomonas isolates using whole-cell AHL inactivation assay and rapid resolution liquid chromatography analysis (RRLC). In addition, degradation of p-coumaroyl-homoserine lactone by Arthrobacter and Pseudomonas spp. was documented first in this study. Further studies involving whole genome sequencing of these isolates for the purpose of assessing regulation of QS and QQ genes is currently being carried out

Complete chromosome and plasmid sequences of two plant pathogens, Dickeya solani strains D s0432-1 and PPO 9019

Dickeya solani species are emerging bacterial pathogens of Solanum tuberosum. Here, we announce the complete genome sequences of two strains, Dickeya solani D s0432-1 and PPO 9019. Strain PPO 9019 represents the first described member of the genus Dickeya with an extrachromosomal genetic element

Complete genome anatomy of the emerging potato pathogen Dickeya solani type strain IPO 2222(T).

International audienceSeveral species of the genus Dickeya provoke soft rot and blackleg diseases on a wide range of plants and crops. Dickeya solani has been identified as the causative agent of diseases outbreaks on potato culture in Europe for the last decade. Here, we report the complete genome of the D. solani IPO 2222(T). Using PacBio and Illumina technologies, a unique circular chromosome of 4,919,833 bp was assembled. The G + C content reaches 56% and the genomic sequence contains 4,059 predicted proteins. The ANI values calculated for D. solani IPO 2222(T) vs. other available D. solani genomes was over 99.9% indicating a high genetic homogeneity within D. solani species

Complete Genome Sequences of the Plant Pathogens Dickeya solani RNS 08.23.3.1.A and Dickeya dianthicola RNS04.9

Dickeya spp. are bacterial pathogens causing soft- rot and blackleg diseases on a wide range of ornamental plants and crops. In this paper, we announce the PacBio complete genome sequences of the plant pathogens Dickeya solani RNS 08.23.3.1. A (PRI3337) and Dickeya dianthicola RNS04.9

Core genome and plasmidome of the quorum-quenching bacterium Rhodococcus erythropolis.

International audienceRhodococcus erythropolis is a worldwide-distributed actinobacterium that exhibits a remarkable metabolic versatility illustrated by its ability to degrade complex compounds, such as quorum-sensing signals N-acylhomoserine lactones (NAHLs), phenols, sterols and fuel derivatives. Because of its catabolic properties, R. erythropolis strains are proposed as anti-biofouling agents against NAHL-dependent biofilms, biocontrol agents against NAHL-emitting plant pathogens, and bioremediation agents in contaminated waters and soils. Here, we used the PacBio technology to resolve the complete genome sequence of the biocontrol strain R. erythropolis R138. Its genome consisted in a circular chromosome (6,236,862 bp), a linear plasmid pLRE138 (477,915 bp) and a circular plasmid pCRE138 (91,729 bp). In addition, draft genomes of five R. erythropolis strains were determined by Illumina technology and compared with the other five R. erythropolis genomes that are available in public databases: 5,825 common CDSs were present in all of the eleven analyzed genomes and represented up to 87 % of those identified in R. erythropolis R138. This study highlighted the high proportion of core-genome genes in R. erythropolis, but a high variability of the plasmid content. Key-metabolic pathways which are involved in the degradation of complex molecules, such as NAHLs and phenol, catechol and sterol derivatives are coded by the R. erythropolis core-genome