Biology subjects

Decorosi, F.

Publications and source records attributed to Decorosi, F..

5 recordsLinked to original sources

bioRxiv2024

Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi.

We present the description of the new species, Rhodococcus (Prescottella) parequi, found during phylogenomic investigations of a global collection of strains identified as Rhodococcus (Prescottella) equi. Strain PAM 2766 was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from R. equi based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766 in the same Rhodococcus sublineage as R. equi, together with Rhodococcus agglutinans, Rhodococcus defluvii, Rhodococcus soli, Rhodococcus subtropicus, Rhodococcus spongiicola and Rhodococcus xishaensis. PAM 2766 is most closely related to, but sufficiently distinct from R. equi DSM 20307T to be considered as a separate species. Average Nucleotide Identity (ANI) and Average Amino Acid Identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766 draft genome is [~]5.3 Mb in size with 68.98% G+C mol content. PAM 2766T is aerobic, non-motile, and produces smooth creamy to buff-coloured colonies very similar to those of R. equi. It phenotypically differs from the latter by the ability to grow at 5{degrees}C, a strongly positive urease test at 24 h, and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766 belongs to a novel species, for which the name Rhodococcus parequi sp. nov. is proposed. R. parequi was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766T (=CETC 30995T = NCTC 14987T).

microbiology↗

bioRxiv2020

Competitiveness prediction for nodule colonization in Sinorhizobium meliloti through combined in vitro tagged strain characterization and genome-wide association analysis

Associations between leguminous plants and symbiotic nitrogen fixing bacteria (rhizobia) are a classical example of mutualism between a eukaryotic host and a specific group of prokaryotic microbes. Though being in part species-specific, different strains may colonize the same plant symbiotic structure (nodule). It is known that some rhizobial strains are better competitor than others, but detailed analyses aimed to predict from the rhizobial genome its competitive abilities are still scarce. Here we performed a bacterial genome wide association (GWAS) analysis to define the genomic determinants related to the competitive capabilities in the model rhizobial species Sinorhizobium meliloti. Thirteen tester strains were GFP-tagged and assayed against three reference competitor strains RFP-tagged (Rm1021, AK83 and BL225C) in a Medicago sativa nodule occupancy test. Competition data in combination with strains genomic sequences were used to build-up a model for GWAS based on k-mers. The model was then trained and applied for competition capabilities prediction. The model was able to well predict the competition abilities against two partners, BL225C, Rm1021 with coefficient of determination of 0.96 and 0.84, respectively. Four strains showing the highest competition phenotypes (> 60% single strain nodule occupancy; GR4, KH35c, KH46 and SM11) versus BL225C were used to identify k-mers associated with competition. The k-mers with highest scores mapped on the symbiosis-related megaplasmid pSymA and on genes coding for transporters, proteins involved in the biosynthesis of cofactors and proteins related to metabolism (i.e. glycerol, fatty acids) suggesting that competition abilities reside in multiple genetic determinants comprising several cellular components. IMPORTANCEDecoding the competitive pattern that occurs in the rhizosphere is challenging in the study of bacterial social interaction strategies. To date, single-gene approach has been mainly used to uncover the bases of nodulation, but there is still a gap about the main features that a priori turn out rhizobial strains able to outcompete indigenous rhizobia. Therefore, tracking down which traits make different rhizobial strains able to win the competition for plant infection over other indigenous rhizobia will allow ameliorating strain selection and consequently plant yield in sustainable agricultural production systems. We have proven that a k-mer based GWAS approach can effectively predict the competition abilities of a panel of strains, which were analyzed for their plant tissue occupancy by using double fluorescent labeling. The reported strategy could be used for detailed studies on the genomic aspects of the evolution of bacterial symbiosis and for an extensive evaluation of rhizobial inoculants.

microbiology↗

bioRxiv2020

Symbiotic and non-symbiotic members of the genus Ensifer (syn. Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping

Rhizobium - legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF emerged several times within the genus Ensifer, likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the "symbiotic" and "non-symbiotic" clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of ten Ensifer strains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.

microbiology↗

bioRxiv2018

Creation and multi-omics characterization of a genomically hybrid strain in the nitrogen-fixing symbiotic bacterium Sinorhizobium meliloti

Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbour a multipartite genome composed by more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extra-cellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modelling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.

synthetic biology↗

bioRxiv2018

Metabolic modeling of Pectobacterium parmentieri SCC3193 provides insights into metabolic pathways of plant pathogenic bacteria

Understanding the plant-microbe interactions are crucial for improving plant productivity and plant protection. The latter aspect is particularly relevant for sustainable agriculture and development of new preventive strategies against the spread of plant diseases. Constraint-based metabolic modeling is providing one of the possible ways to investigate the adaptation to different ecological niches and may give insights into the metabolic versatility of plant pathogenic bacteria. In this study, we present a curated metabolic model of the emerging plant pathogenic bacterium Pectobacterium parmentieri SCC3193. Using flux balance analysis (FBA), we predict the metabolic adaptation to two different ecological niches, relevant for the persistence and the plant colonization by this bacterium: soil and rhizosphere. We performed in silico gene deletions to predict the set of core essential genes for this bacterium to grow in such environments. We anticipate that our metabolic model will be a valuable element for defining a set of metabolic targets to control infection and spreading of this plant pathogen and a scaffold to interpret future -omics datasets for this bacterium.

systems biology↗