Publications by authors named "Marie-Lara Bouffaud"

12 Publications

  • Page 1 of 1

Soil Texture, Sampling Depth and Root Hairs Shape the Structure of ACC Deaminase Bacterial Community Composition in Maize Rhizosphere.

Front Microbiol 2021 4;12:616828. Epub 2021 Feb 4.

Helmholtz Centre for Environmental Research, Halle, Germany.

Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the gene. We stated the hypothesis that the relative phylogenetic distribution of carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective mutant in the substrates loam and sand, and harvest was implemented from three depths. Most sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. , and sequences dominated in loam, whereas and were more abundant in sand. Soil depth caused strong variations in sequence distribution, with differential levels in the relative abundances of sequences affiliated to , and in loam, but , , and in sand. Maize genotype influenced the distribution of sequences mainly in loam and only in the uppermost depth. Variovorax sequences were more abundant in WT, but , and in rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on carrying bacterial populations.
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http://dx.doi.org/10.3389/fmicb.2021.616828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7891401PMC
February 2021

Oak displays common local but specific distant gene regulation responses to different mycorrhizal fungi.

BMC Genomics 2020 Jun 12;21(1):399. Epub 2020 Jun 12.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, D-04103, Leipzig, Germany.

Background: Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct impacts of different fungi on gene expression in local and distant plant organs. Using a large scale transcriptome sequencing approach, we compared the impact of three ectomycorrhizal (EMF) and one orchid mycorrhizal fungi (OMF) on gene regulation in colonized roots (local), non-colonized roots (short distance) and leaves (long distance) of the Quercus robur clone DF159 with reference to the recently published oak genome. Since different mycorrhizal fungi form symbiosis in a different time span and variable extents of apposition structure development, we sampled inoculated but non-mycorrhizal plants, for which however markedly symbiotic effects have been reported. Local root colonization by the fungi was assessed by fungal transcript analysis.

Results: The EMF induced marked and species specific effects on plant development in the analysed association stage, but the OMF did not. At local level, a common set of plant differentially expressed genes (DEG) was identified with similar patterns of responses to the three EMF, but not to the OMF. Most of these core DEG were down-regulated and correspond to already described but also new functions related to establishment of EMF symbiosis. Analysis of the fungal transcripts of two EMF in highly colonized roots also revealed onset of a symbiosis establishment. In contrast, in the OMF, the DEG were mainly related to plant defence. Already at short distances, high specificities in transcriptomic responses to the four fungi were detected, which were further enhanced at long distance in leaves, where almost no common DEG were found between the treatments. Notably, no correlation between phylogeny of the EMF and gene expression patterns was observed.

Conclusions: Use of clonal oaks allowed us to identify a core transcriptional program in roots colonized by three different EMF, supporting the existence of a common EMF symbiotic pathway. Conversely, the specific responses in non-colonized organs were more closely related to the specific impacts of the different of EMF on plant performance.
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http://dx.doi.org/10.1186/s12864-020-06806-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7291512PMC
June 2020

Co-occurrence of rhizobacteria with nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities in the maize rhizosphere.

FEMS Microbiol Ecol 2020 05;96(5)

Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France.

The plant microbiota may differ depending on soil type, but these microbiota probably share the same functions necessary for holobiont fitness. Thus, we tested the hypothesis that phytostimulatory microbial functional groups are likely to co-occur in the rhizosphere, using groups corresponding to nitrogen fixation (nifH) and 1-aminocyclopropane-1-carboxylate deamination (acdS), i.e. two key modes of action in plant-beneficial rhizobacteria. The analysis of three maize fields in two consecutive years showed that quantitative PCR numbers of nifH and of acdS alleles differed according to field site, but a positive correlation was found overall when comparing nifH and acdS numbers. Metabarcoding analyses in the second year indicated that the diversity level of acdS but not nifH rhizobacteria in the rhizosphere differed across fields. Furthermore, between-class analysis showed that the three sites differed from one another based on nifH or acdS sequence data (or rrs data), and the bacterial genera contributing most to field differentiation were not the same for the three bacterial groups. However, co-inertia analysis indicated that the genetic structures of both functional groups and of the whole bacterial community were similar across the three fields. Therefore, results point to co-selection of rhizobacteria harboring nitrogen fixation and/or 1-aminocyclopropane-1-carboxylate deamination abilities.
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http://dx.doi.org/10.1093/femsec/fiaa062DOI Listing
May 2020

1-Aminocyclopropane-1-carboxylate deaminase producers associated to maize and other Poaceae species.

Microbiome 2018 06 20;6(1):114. Epub 2018 Jun 20.

Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRA, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622, Villeurbanne, France.

Background: Complex plant-microbe interactions have been established throughout evolutionary time, many of them with beneficial effects on the host in terms of plant growth, nutrition, or health. Some of the corresponding modes of action involve a modulation of plant hormonal balance, such as the deamination of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC). Despite its ecological importance, our understanding of ACC deamination is impaired by a lack of direct molecular tools. Here, we developed PCR primers to quantify the ACC deaminase gene acdS and its mRNA in soil communities and assessed acdS microorganisms colonizing maize and other Poaceae species.

Results: Effective acdS primers suitable for soil microbial communities were obtained, enabling recovery of bona fida acdS genes and transcripts of diverse genetic backgrounds. High numbers of acdS genes and transcripts were evidenced in the rhizosphere of Poaceae, and numbers fluctuated according to plant genotype. Illumina sequencing revealed taxonomic specificities of acdS microorganisms according to plant host. The phylogenetic distance between Poaceae genotypes correlated with acdS transcript numbers, but not with acdS gene numbers or the genetic distance between acdS functional groups.

Conclusion: The development of acdS primers enabled the first direct analysis of ACC deaminase functional group in soil and showed that plant ability to interact with soil-inhabiting acdS microorganisms could also involve particular plant traits unrelated to the evolutionary history of Poaceae species.
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http://dx.doi.org/10.1186/s40168-018-0503-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6011333PMC
June 2018

Oak genome reveals facets of long lifespan.

Nat Plants 2018 07 18;4(7):440-452. Epub 2018 Jun 18.

Commissariat à l'Energie Atomique (CEA), Genoscope, Institut de Biologie François-Jacob, Evry, France.

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times. With 450 species spread throughout Asia, Europe and America, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical and modelling approaches have shown that intra-organismal genetic heterogeneity can be selected for and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.
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http://dx.doi.org/10.1038/s41477-018-0172-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6086335PMC
July 2018

Soil networks become more connected and take up more carbon as nature restoration progresses.

Nat Commun 2017 02 8;8:14349. Epub 2017 Feb 8.

NIOO-KNAW, Microbial Ecology, Droevendaalsesteeg 10, Wageningen 6708 PB, The Netherlands.

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid- and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.
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http://dx.doi.org/10.1038/ncomms14349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309817PMC
February 2017

Is plant evolutionary history impacting recruitment of diazotrophs and nifH expression in the rhizosphere?

Sci Rep 2016 Feb 23;6:21690. Epub 2016 Feb 23.

Université de Lyon, F-69622, Lyon, France.

Plant evolutionary history influences the taxonomic composition of the root-associated bacterial community, but whether it can also modulate its functioning is unknown. Here, we tested the hypothesis that crop diversification is a significant factor determining the ecology of the functional group of nitrogen-fixing bacteria the rhizosphere of Poaceae. A greenhouse experiment was carried out using a range of Poaceae, i.e. four Zea mays varieties (from two genetic groups) and teosinte (representing maize's ancestor), sorghum (from the same Panicoideae subfamily), and wheat (from neighboring Pooideae subfamily), as well as the dicot tomato as external reference. Diazotroph rhizosphere community was characterized at 21 days in terms of size (quantitative PCR of nifH genes), composition (T-RFLP and partial sequencing of nifH alleles) and functioning (quantitative RT-PCR, T-RFLP and partial sequencing of nifH transcripts). Plant species and varieties had a significant effect on diazotroph community size and the number of nifH transcripts per root system. Contrarily to expectations, however, there was no relation between Poaceae evolutionary history and the size, diversity or expression of the rhizosphere diazotroph community. These results suggest a constant selection of this functional group through evolution for optimization of nitrogen fixation in the rhizosphere.
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http://dx.doi.org/10.1038/srep21690DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763242PMC
February 2016

The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field.

PLoS One 2014 2;9(9):e107783. Epub 2014 Oct 2.

Université de Bourgogne, UMR1347 Agroécologie, Dijon, France.

Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107783PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4183475PMC
June 2015

Root microbiome relates to plant host evolution in maize and other Poaceae.

Environ Microbiol 2014 Sep 7;16(9):2804-14. Epub 2014 Apr 7.

Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, Villeurbanne, France.

Prokaryote-eukaryote interactions are primordial, but host selection of its bacterial community remains poorly understood. Because eukaryote evolution affects numerous traits shaping the ecology of their microbiome, we can expect that many evolutionary changes in the former will have the potential to impact on the composition of the latter. Consequently, the more phylogenetically distant the eukaryotic hosts, the more distinct their associated bacterial communities should be. We tested this with plants, by comparing the bacterial communities associated with maize genotypes or other Poaceae. 16S rRNA taxonomic microarray analysis showed that the genetic distance between rhizobacterial communities correlated significantly with the phylogenetic distance (derived from chloroplastic sequences) between Poaceae genotypes. This correlation was also significant when considering specific bacterial populations from all main bacterial divisions, instead of the whole rhizobacterial community. These results indicate that eukaryotic host's evolutionary history can be a significant factor shaping directly the assembly and composition of its associated bacterial compartment.
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http://dx.doi.org/10.1111/1462-2920.12442DOI Listing
September 2014

Cell culturability of Pseudomonas protegens CHA0 depends on soil pH.

FEMS Microbiol Ecol 2014 Feb 14;87(2):441-50. Epub 2013 Nov 14.

Plant Pathology, Institute of Integrative Biology, Swiss Federal Institute of Technology, Zürich, Switzerland; Agroscope Changins-Wädenswil research station ACW, Nyon, Switzerland.

Pseudomonas inoculants may lose colony-forming ability in soil, but soil properties involved are poorly documented. Here, we tested the hypothesis that soil acidity could reduce persistence and cell culturability of Pseudomonas protegens CHA0. At 1 week in vitro, strain CHA0 was found as culturable cells at pH 7, whereas most cells at pH 4 and all cells at pH 3 were noncultured. In 21 natural soils of contrasted pH, cell culturability loss of P. protegens CHA0 took place in all six very acidic soils (pH < 5.0) and in three of five acidic soils (5.0 < pH < 6.5), whereas it was negligible in the neutral and alkaline soils at 2 weeks and 2 months. No correlation was found between total cell counts of P. protegens CHA0 and soil composition data, whereas colony counts of the strain correlated with soil pH. Maintenance of cell culturability in soils coincided with a reduction in inoculant cell size. Some of the noncultured CHA0 cells were nutrient responsive in Kogure's viability test, both in vitro and in soil. Thus, this shows for the first time that the sole intrinsic soil composition factor triggering cell culturability loss in P. protegens CHA0 is soil acidity.
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http://dx.doi.org/10.1111/1574-6941.12234DOI Listing
February 2014

Plant growth-promoting rhizobacteria and root system functioning.

Front Plant Sci 2013 Sep 17;4:356. Epub 2013 Sep 17.

Université de Lyon Lyon, France ; Université Claude Bernard Lyon 1 Villeurbanne, France ; Centre National de la Recherche Scientifique, UMR 5557, Ecologie Microbienne, Université Lyon 1 Villeurbanne, France.

The rhizosphere supports the development and activity of a huge and diversified microbial community, including microorganisms capable to promote plant growth. Among the latter, plant growth-promoting rhizobacteria (PGPR) colonize roots of monocots and dicots, and enhance plant growth by direct and indirect mechanisms. Modification of root system architecture by PGPR implicates the production of phytohormones and other signals that lead, mostly, to enhanced lateral root branching and development of root hairs. PGPR also modify root functioning, improve plant nutrition and influence the physiology of the whole plant. Recent results provided first clues as to how PGPR signals could trigger these plant responses. Whether local and/or systemic, the plant molecular pathways involved remain often unknown. From an ecological point of view, it emerged that PGPR form coherent functional groups, whose rhizosphere ecology is influenced by a myriad of abiotic and biotic factors in natural and agricultural soils, and these factors can in turn modulate PGPR effects on roots. In this paper, we address novel knowledge and gaps on PGPR modes of action and signals, and highlight recent progress on the links between plant morphological and physiological effects induced by PGPR. We also show the importance of taking into account the size, diversity, and gene expression patterns of PGPR assemblages in the rhizosphere to better understand their impact on plant growth and functioning. Integrating mechanistic and ecological knowledge on PGPR populations in soil will be a prerequisite to develop novel management strategies for sustainable agriculture.
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http://dx.doi.org/10.3389/fpls.2013.00356DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3775148PMC
September 2013

Is diversification history of maize influencing selection of soil bacteria by roots?

Mol Ecol 2012 Jan 29;21(1):195-206. Epub 2011 Nov 29.

Université de Lyon, F-69622, Lyon, France.

A wide range of plant lines has been propagated by farmers during crop selection and dissemination, but consequences of this crop diversification on plant-microbe interactions have been neglected. Our hypothesis was that crop evolutionary history shaped the way the resulting lines interact with soil bacteria in their rhizospheres. Here, the significance of maize diversification as a factor influencing selection of soil bacteria by seedling roots was assessed by comparing rhizobacterial community composition of inbred lines representing the five main genetic groups of maize, cultivated in a same European soil. Rhizobacterial community composition of 21-day-old seedlings was analysed using a 16S rRNA taxonomic microarray targeting 19 bacterial phyla. Rhizobacterial community composition of inbred lines depended on the maize genetic group. Differences were largely due to the prevalence of certain Betaproteobacteria and especially Burkholderia, as confirmed by quantitative PCR and cloning/sequencing. However, these differences in bacterial root colonization did not correlate with plant microsatellite genetic distances between maize genetic groups or individual lines. Therefore, the genetic structure of maize that arose during crop diversification (resulting in five main groups), but not the extent of maize diversification itself (as determined by maize genetic distances), was a significant factor shaping rhizobacterial community composition of seedlings.
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http://dx.doi.org/10.1111/j.1365-294X.2011.05359.xDOI Listing
January 2012