Biology subjects

Matteoli, F. P.

Publications and source records attributed to Matteoli, F. P..

5 recordsLinked to original sources

bioRxiv2021

Genome sequencing of the vermicompost strain Stenotrophomonas maltophilia UENF-4GII and population structure analysis of the S. maltophilia Sm3 genogroup

The Stenotrophomonas maltophilia complex (Smc) is a cosmopolitan bacterial group that has been proposed an emergent multidrug-resistant pathogen. Taxonomic studies support the genomic heterogeneity of Smc, which comprises genogroups exhibiting a range of phenotypically distinct strains from different sources. Here, we report the genome sequencing and in-depth analysis of S. maltophilia UENF-4GII, isolated from vermicompost. This genome harbors a unique region encoding a penicillin-binding protein (pbpX) that was carried by a transposon, as well as horizontally-transferred genomic islands involved in anti-phage defense via DNA modification, and pili glycosylation. We also analyzed all available Smc genomes to investigate genes associated with resistance and virulence, niche occupation, and population structure. S. maltophilia UENF-4GII belongs to genogroup 3 (Sm3), which comprises three phylogenetic clusters (PC). Pan-GWAS analysis uncovered 471 environment-associated and 791 PC-associated genes, including antimicrobial resistance (e.g. blaL1 and blaR1) and virulence determinants (e.g. treS and katG) that provide insights on the resistance and virulence potential of Sm3 strains. Together, the results presented here provide the grounds for more detailed clinical and ecological investigations of S. maltophilia.

microbiology↗

bioRxiv2021

Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter, as well as root dry matter, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.

microbiology↗

bioRxiv2019

Population structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. Here, we report the genome of a non-clinical E. bugandensis strain. We used this and other several publicly available E. bugandensis genomes to obtain the species pangenome, investigate the conservation of important genes, and elucidate general population structure features of the species. Core- and whole-genome multilocus sequence typing (cgMLST and wgMLST, respectively) allowed the detection of five E. bugandensis phylogroups (PG-A to E). We found important antimicrobial resistance and virulence determinants associated with specific PGs, notably PG-A and PG-E. IncFII was the most prevalent plasmid replicon type in this species. We uncovered several extended-spectrum {beta}-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the resemblance of this plasmid with other IncX plasmids isolated from other bacteria from the same country. Further, three distinctive siderophore producing operons were found in the E. bugandensis pangenome: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). The latter operon is conserved in all PG-E isolates. Collectively, our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.

genomics↗

bioRxiv2018

Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost

Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a Gram-negative species found in a wide range of environments, including soil. Here we describe the genome sequencing and assessment of plant-growth promoting abilities of S. marcescens UENF-22GI (SMU), a strain isolated from mature cattle manure vermicompost. In vitro, SMU is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with SMU remarkably increased seedling growth and biomass under greenhouse conditions. The SMU genome has 5 Mb, assembled in 17 scaffolds comprising 4,662 genes (4,528 are protein-coding). No plasmids were identified. SMU is phylogenetically placed within a clade comprised almost exclusively of environmental strains. We were able to find the genes and operons that are likely responsible for all the interesting plant-growth promoting features that were experimentally described. Genes involved other interesting properties that were not experimentally tested (e.g. tolerance against metal contamination) were also identified. The SMU genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to the SMU competitiveness against other bacteria. Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for Agriculture.

microbiology↗

bioRxiv2017

A Duplication Lost In Sugarcane Hybrids Revealed By Chloroplast Genome Assembly Of Wild Species Saccharum officinarum

Sugarcane is a crop of paramount importance for sustainable energy. Modern sugarcane cultivars are derived from interspecific crosses between the two wild species Saccharum officinarum and Saccharum spontaneum and this event occurred very early in the sugarcane domestication history. This hybridization allowed the generation of cultivars with complex aneuploidy genomes containing 100-130 chromosomes that are unequally inherited - ~80% from S. officinarum, ~10% from S. spontaneum and ~10% from inter-specific crosses. Several studies have highlighted the importance of chloroplast genomes (cpDNA) to investigate hybridization events in plant lineages. Few sugarcane cpDNAs have been assembled and published, including those from sugarcane hybrids. However, cpDNAs of wild Saccharum species remains unexplored. In the present study, we used whole-genome sequencing data to survey the chloroplast genome of the wild sugarcane species S. officinarum. Illumina sequencing technology was used for assembly 142,234 bp of S.officinarum cpDNA with 2,065,893 reads and 1043x of coverage. The analysis of the S. officinarum cpDNA revealed a notable difference in the LSC region of wild and cultivated sugarcanes. Chloroplasts of sugarcane cultivars showed a loss of a duplicated fragment with 1,031 bp in the beginning of the LSC region, which decreased the chloroplast gene content in hybrids. Based on these results, we propose the comparative analysis of organelle genomes as a very important tool for deciphering and understanding hybrid Saccharum lineages.

genomics↗