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186 results on '"Concheri, G"'

19. Pangenomics of the symbiotic Rhizobiales. Core and accessory functions across a group endowed with high levels of genomic plasticity

Author

Rosselli, R., La Porta, N., Muresu, R., Stevanato, P., Concheri, G., Squartini, A., Rosselli, R., La Porta, N., Muresu, R., Stevanato, P., Concheri, G., and Squartini, A.

Abstract

Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N2 into ammonia (nitrogen-fixation). The pangenome of 12 nitrogen-fixing plant symbionts of the Rhizobiales was analyzed yielding total 37,364 loci, with a core genome constituting 700 genes. The percentage of core genes averaged 10.2% over single genomes, and between 5% to 7% were found to be plasmid-associated. The comparison between a representative reference genome and the core genome subset, showed the core genome highly enriched in genes for macromolecule metabolism, ribosomal constituents and overall translation machinery, while membrane/periplasm-associated genes, and transport domains resulted under-represented. The analysis of protein functions revealed that between 1.7% and 4.9% of core proteins could putatively have different functions.

Published
2021

21. The hidden layers of microbial community structure: Extracting the concealed diversity dimensions from our sequencing data

Author

Fasolo, A., Treu, L., Stevanato, P., Concheri, G., Campanaro, S., and Squartini, A.

Subjects
DNA, Bacterial, Relation (database), OTU Success Index, Microbiology, 16S sequencing, 03 medical and health sciences, 0302 clinical medicine, RNA, Ribosomal, 16S, OTU-centered Rank Power, Genetics, OSI, Cluster analysis, Molecular Biology, Bacterial metabarcoding, Ecosystem, Soil Microbiology, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Bacteria, OTUs abundance, Phylum, Microbiota, Bacterial diversity, 16S sequencing, OTU-centered Rank Power, Abundance-centered Rank Power, OTU Success Index, OSI, Biodiversity, Sequence Analysis, DNA, Geography, Taxon, Habitat, Microbial population biology, Bacterial diversity, Evolutionary biology, Abundance-centered Rank Power, 030217 neurology & neurosurgery, Diversity (business)
Abstract

Microbial metabarcoding is the standard approach to assess communities’ diversity. However reports are often limited to simple OTU abundances for each phylum, giving rather one-dimensional views of microbial assemblages, overlooking other accessible aspects. The first is masked by databases incompleteness; OTU picking involves clustering at 97% (near-species) sequence identity, but different OTUs regularly end up under a same taxon name. When expressing diversity as number of obtained taxonomical names, a large portion of the real diversity lying within the data remains underestimated. Using the 16S sequencing results of an environmental transect across a gradient of 17 coastal habitats we first extracted the number of OTUs hidden under the same name. Further, we observed which was the deepest rank yielded by annotation, revealing for which microbial groups are we missing most knowledge. Data were then used to infer an evolutionary aspect: what is, in each phylum the success of the present time individuals (abundances for each OTU) in relation to their prior evolutionary success in differentiation (number of OTUs). This information reveals whether the past speciation/diversification force is matched by the present competitiveness in reproduction/persistence. The final layer explored is functional diversity, i.e. abundances of groups involved in specific environmental processes.

Published
2020

43. Root morphological and molecular responses induced by microalgae extracts in sugar beet (Beta vulgaris L.)

Author

Barone, V., primary, Baglieri, A., additional, Stevanato, Piergiorgio, additional, Broccanello, C., additional, Bertoldo, G., additional, Bertaggia, M., additional, Cagnin, M., additional, Pizzeghello, D., additional, Moliterni, V. M. C., additional, Mandolino, G., additional, Fornasier, F., additional, Squartini, A., additional, Nardi, S., additional, and Concheri, G., additional

Published
2017
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