Publications by authors named "Barbara Pivato"

10 Publications

  • Page 1 of 1

Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping.

Front Microbiol 2021 28;12:674556. Epub 2021 May 28.

Agroécologie, AgroSup Dijon, INRAE, Université de Bourgogne - Université de Bourgogne Franche-Comté, Dijon, France.

Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.
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http://dx.doi.org/10.3389/fmicb.2021.674556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8195745PMC
May 2021

Pseudomonas fluorescens C7R12 type III secretion system impacts mycorrhization of Medicago truncatula and associated microbial communities.

Mycorrhiza 2017 Jan 22;27(1):23-33. Epub 2016 Aug 22.

Agroécologie, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 21000, Dijon, France.

Type three secretion systems (T3SSs) mediate cell-to-cell interactions between Gram-negative bacteria and eukaryotes. We hypothesized that fluorescent pseudomonads harboring T3SS (T3SS+) would be beneficial to arbuscular mycorrhizal symbiosis because non-pathogenic fluorescent pseudomonads have been previously shown to be much more abundant in mycorrhizal than in non-mycorrhizal roots. We tested this hypothesis by comparing mycorrhization and the associated rhizosphere microbial communities of Medicago truncatula grown in a non-sterile soil inoculated with either the T3SS+ mycorrhiza helper bacterium Pseudomonas fluorescens (C7R12) or a T3SS- mutant of the strain. Results showed that the bacterial secretion system was responsible for the promotion of mycorrhization because root colonization by arbuscular mycorrhizal fungi was not promoted by the T3SS- mutant. The observed T3SS-mediated promotion of mycorrhization was associated with changes in the rhizosphere bacterial communities and the increased occurrence of Claroidoglomeraceae within the intraradical arbuscular mycorrhizal fungi. Furthermore, both pseudomonad strains promoted the host-free growth of a model arbuscular mycorrhizal fungus in vitro, suggesting that T3SS-mediated promotion of mycorrhization occurs during plant-fungal interactions rather than during the pre-symbiotic phase of fungal growth. Taken together, these data provide evidence for the involvement of T3SS in promoting arbuscular mycorrhization by a model fluorescent pseudomonad and suggest the implication of interactions between the bacterium and mycorrhizas.
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http://dx.doi.org/10.1007/s00572-016-0730-3DOI Listing
January 2017

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation.

Plant Methods 2016 7;12:31. Epub 2016 Jun 7.

UMR 1347 Agroécologie AgroSup/INRA/uB, 17 Rue Sully, BP 86510, 21065 Dijon Cedex, France.

Background: In order to maintain high yields while saving water and preserving non-renewable resources and thus limiting the use of chemical fertilizer, it is crucial to select plants with more efficient root systems. This could be achieved through an optimization of both root architecture and root uptake ability and/or through the improvement of positive plant interactions with microorganisms in the rhizosphere. The development of devices suitable for high-throughput phenotyping of root structures remains a major bottleneck.

Results: Rhizotrons suitable for plant growth in controlled conditions and non-invasive image acquisition of plant shoot and root systems (RhizoTubes) are described. These RhizoTubes allow growing one to six plants simultaneously, having a maximum height of 1.1 m, up to 8 weeks, depending on plant species. Both shoot and root compartment can be imaged automatically and non-destructively throughout the experiment thanks to an imaging cabin (RhizoCab). RhizoCab contains robots and imaging equipment for obtaining high-resolution pictures of plant roots. Using this versatile experimental setup, we illustrate how some morphometric root traits can be determined for various species including model (Medicago truncatula), crops (Pisum sativum, Brassica napus, Vitis vinifera, Triticum aestivum) and weed (Vulpia myuros) species grown under non-limiting conditions or submitted to various abiotic and biotic constraints. The measurement of the root phenotypic traits using this system was compared to that obtained using "classic" growth conditions in pots.

Conclusions: This integrated system, to include 1200 Rhizotubes, will allow high-throughput phenotyping of plant shoots and roots under various abiotic and biotic environmental conditions. Our system allows an easy visualization or extraction of roots and measurement of root traits for high-throughput or kinetic analyses. The utility of this system for studying root system architecture will greatly facilitate the identification of genetic and environmental determinants of key root traits involved in crop responses to stresses, including interactions with soil microorganisms.
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http://dx.doi.org/10.1186/s13007-016-0131-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4897935PMC
June 2016

Plant traits related to nitrogen uptake influence plant-microbe competition.

Ecology 2015 Aug;96(8):2300-10

Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more relevant for understanding plant-microbe interactions than composite traits, such as nitrophily, which are related to a number of ecophysiological processes.
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http://dx.doi.org/10.1890/14-1761.1DOI Listing
August 2015

Changes in gene expression during adaptation of Listeria monocytogenes to the soil environment.

PLoS One 2011 23;6(9):e24881. Epub 2011 Sep 23.

Université de Bourgogne, UMR 1229, Dijon, France.

Listeria monocytogenes is a ubiquitous opportunistic pathogen responsible for listeriosis. In order to study the processes underlying its ability to adapt to the soil environment, whole-genome arrays were used to analyse transcriptome modifications 15 minutes, 30 minutes and 18 h after inoculation of L. monocytogenes EGD-e in soil extracts. Growth was observed within the first day of incubation and large numbers were still detected in soil extract and soil microcosms one year after the start of the experiment. Major transcriptional reprofiling was observed. Nutrient acquisition mechanisms (phosphoenolpyruvate-dependent phosphotransferase systems and ABC transporters) and enzymes involved in catabolism of specific carbohydrates (β-glucosidases; chitinases) were prevalent. This is consistent with the overrepresentation of the CodY regulon that suggests that in a nutrient depleted environment, L. monocytogenes recruits its extensive repertoire of transporters to acquire a range of substrates for energy production.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0024881PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179493PMC
March 2012

Effects of Pseudomonas putida S1Pf1Rif against chrysanthemum yellows phytoplasma infection.

Phytopathology 2010 Aug;100(8):805-13

Università del Piemonte Orientale "Amedeo Avogadro", Dipartimento di Scienze dell'Ambiente e della Vita, Viale Teresa Michel 11, Alessandria, 15121, Italy.

Phytoplasmas cause damage on a number of plant species leading to relevant economical loss. Up to now, strategies to limit their spread led to only partial success. In this context, the use of plant-beneficial bacteria to control phytoplasmas has never been explored. The aim of this work was to assess the effect of Pseudomonas putida S1Pf1Rif against chrysanthemum yellows phytoplasma (CYP) infection of daisy. Plant biomass, root architecture, symptom severity, phytoplasma titer, and viability were evaluated in inoculated and control plants. CYP reduced plant growth and root development. Although the phytoplasma titer in young apical leaves was not affected by inoculation with S1Pf1Rif, the pseudomonad improved plant growth of CYP-infected plants. Whereas CYP titer increased over time in uninoculated plants, its viability decreased, regardless of the presence of P. putida S1Pf1Rif. Finally, phytoplasma cells in fully developed leaves of CYP-infected plants inoculated with S1Pf1Rif often appeared degenerated. Overall, our results indicate that P. putida S1Pf1Rif is able to alleviate the disease, although it does not affect the presence of viable phytoplasmas in young, developing leaves of the infected plants.
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http://dx.doi.org/10.1094/PHYTO-100-8-0805DOI Listing
August 2010

Colonization of adventitious roots of Medicago truncatula by Pseudomonas fluorescens C7R12 as affected by arbuscular mycorrhiza.

FEMS Microbiol Lett 2008 Dec 29;289(2):173-80. Epub 2008 Oct 29.

Dipartimento di Scienze dell'Ambiente e della Vita, Università del Piemonte Orientale 'Amedeo Avogadro', Alessandria, Italy.

Pseudomonas fluorescens C7R12 was previously shown to promote colonization of Medicago truncatula roots by Glomus mosseae BEG12. To gain more insight into the interaction between C7R12 and BEG12, the cell organization of C7R12 was characterized on adventitious roots mycorrhized or not with BEG12 and on extraradical hyphae. Bacterial cell observations were made using the immuno-fluorescence technique and confocal laser scanning microscopy. Five types of cell organization, so-called organization types (OT), were identified: small or large single cells, cells by pair and cells in microcolonies or in strings. The frequencies of each OT on the roots were expressed as the percentage of observations in which these OTs were represented. The OT frequencies on mycorrhizal and nonmycorrhizal roots differed significantly. Bacterial cells were more frequently single on mycorrhizal than on nonmycorrhizal roots, and in microcolonies and strings on nonmycorrhizal roots. Furthermore, the root area covered by bacterial cells, as assessed by image analysis, appeared to be significantly lower on mycorrhizal than on nonmycorrhizal roots. C7R12 cells were abundant on extraradical hyphae and organized both as single cells and microcolonies. Taken together, these results suggest that P. fluorescens C7R12 cells were less active and less abundant on mycorrhizal than on nonmycorrhizal roots.
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http://dx.doi.org/10.1111/j.1574-6968.2008.01391.xDOI Listing
December 2008

Bacterial effects on arbuscular mycorrhizal fungi and mycorrhiza development as influenced by the bacteria, fungi, and host plant.

Mycorrhiza 2009 Feb 22;19(2):81-90. Epub 2008 Oct 22.

Università del Piemonte Orientale 'Amedeo Avogadro', I-15100, Alessandria, Italy.

Bacterial strains from mycorrhizal roots (three belonging to Comamonadaceae and one to Oxalobacteraceae) and from non-mycorrhizal roots (two belonging to Comamonadaceae) of Medicago truncatula and two reference strains (Collimonas fungivorans Ter331 and Pseudomonas fluorescens C7R12) were tested for their effect on the in vitro saprophytic growth of Glomus mosseae BEG12 and on its colonization of M. truncatula roots. Only the Oxalobacteraceae strain, isolated from barrel medic mycorrhizal roots, and the reference strain P. fluorescens C7R12 promoted both the saprophytic growth and root colonization of G. mosseae BEG12, indicating that they acted as mycorrhiza helper bacteria. Greatest effects were achieved by P. fluorescens C7R12 and its influence on the saprophytic growth of G. mosseae was compared to that on Gigaspora rosea BEG9 to determine if the bacterial stimulation was fungal specific. This fungal specificity, together with plant specificity, was finally evaluated by comparing bacterial effects on arbuscular mycorrhizal symbiosis when each of the fungal species was inoculated to two different plant species (M. truncatula and Lycopersicon esculentum). The results obtained showed that promotion of saprophytic growth by P. fluorescens C7R12 was expressed in vitro towards G. mosseae but not towards G. rosea. Bacterial promotion of mycorhization was also expressed towards G. mosseae, but not G. rosea, in roots of M. truncatula and L. esculentum. Taken together, results indicated that enhancement of arbuscular mycorrhiza development was only induced by a limited number of bacteria, promotion by the most efficient bacterial strain being fungal and not plant specific.
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http://dx.doi.org/10.1007/s00572-008-0205-2DOI Listing
February 2009

Microdiversity of Burkholderiales associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula.

FEMS Microbiol Ecol 2008 Aug 28;65(2):180-92. Epub 2008 May 28.

INRA, Université de Bourgogne, UMR1229 Microbiologie du Sol et de l'Environnement, CMSE, BP, Dijon, France.

The genetic diversity of bacterial communities associated with mycorrhizal and nonmycorrhizal roots of Medicago truncatula was characterized by two approaches. Firstly, phylogenetic analysis was performed on 164 partial 16S rRNA gene-intergenic spacer (IGS) sequences from operational taxonomic units previously shown to be preferentially associated with mycorrhizal roots. These sequences were distributed into three branches corresponding to Comamonadaceae, Oxalobacteraceae and Rubrivivax subgroups. Most sequences were obtained from mycorrhizal roots, indicating the preferential association of the corresponding families with mycorrhizal roots. A second phylogenetic analysis was performed on the partial 16S rRNA gene-IGS sequences of 173 isolates among a large collection of isolates, from mycorrhizal and nonmycorrhizal roots, belonging to Comamonadaceae and Oxalobacteraceae on the basis of their positive hybridization with a partial 16S rRNA gene-IGS probe obtained in this study. Sequence analysis confirmed the affiliation of 166 isolates to Comamonadaceae and seven to Oxalobacteraceae. Oxalobacteraceae isolates were more abundant in mycorrhizal (five) than in nonmycorrhizal (two) roots, whereas Comamonadaceae isolates were more abundant in nonmycorrhizal (109) than mycorrhizal roots (57). Further analysis of Comamonadaceae isolates by BOX-PCR showed that the genetic structure of culturable populations belonging to this family differed significantly in mycorrhizal and nonmycorrhizal roots, as indicated by distributions in different BOX types, differences being significantly explained by BOX types only including isolates from mycorrhizal roots. These data are discussed in an ecological context.
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http://dx.doi.org/10.1111/j.1574-6941.2008.00504.xDOI Listing
August 2008

Colonization of tomato root seedling by Pseudomonas fluorescens 92 rkG5: spatio-temporal dynamics, localization, organization, viability, and culturability.

Microb Ecol 2005 Aug 13;50(2):289-97. Epub 2005 Oct 13.

Dipartimento di Scienze dell'Ambiente e della Vita, Università del Piemonte Orientale "Amedeo Avogadro", Via Bellini 25/G, 15100 Alessandria, Italy.

The localization, viability, and culturability of Pseudomonas fluorescens 92 rkG5 were analyzed on three morphological root zones (root tip + elongation, root hair, and collar) of 3-, 5-, and 7-day-old tomato plants. Qualitative information about the localization and viability was collected by confocal laser scanning microscopy. Quantitative data concerning the distribution, viability, and culturability were obtained through combined dilution plating and flow cytometry. Colonization by P. fluorescens affected root development in a complex way, causing a general increase in the length of the collar and early stimulation of the primary root growth (3rd day), followed by a reduction in length (7th day). The three root zones showed different distribution, organization, and viability of the bacterial cells, but the distribution pattern within each zone did not change with time. Root tips were always devoid of bacteria, whereas with increasing distance from the apex, microcolonies or strings of cells became more and more prominent. Viability was high in the elongation zone, but it declined in the older parts of the roots. The so-called viable but not culturable cells were observed on the root, and their proportion in the distal (root tip + elongation) zone dramatically increased with time. These results suggest the existence of a specific temporal and spatial pattern of root colonization, related to cell viability and culturability, expressed by the plant-beneficial strain P. fluorescens 92 rkG5.
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http://dx.doi.org/10.1007/s00248-004-0149-9DOI Listing
August 2005