Category Archives: Academic productions

Article: J. Appl. Microbio.

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An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards
S Antony‐Babu, C Murat, A Deveau, F Tacon, P Frey‐Klett, S Uroz
Journal of Applied Microbiology

Keywords:

DNA extraction; Soil; Tuber melanosporum ; Calcareous soil

Abstract

Aims

The development of high-throughput methods such as pyrosequencing and microarrays has greatly improved our understanding of the microbial diversity in complex environments such as soils. Nevertheless, albeit advancements in such techniques, the first major step is to obtain high quantity and good quality genomic DNA (gDNA). The work presented here aims to present an inherent problem with 260:230 nm ratio of extracted gDNA from calcareous soils of Tuber melanosporum orchards and a protocol to overcome this problem.

Methods and Results

Using two commercial gDNA extraction kits on spatially distant truffle orchards, we demonstrated that the 260:230 nm ratio was very low, consequentially yielding gDNA incompatible with microarray analyses. In order to solve this problem, optimisation steps were tested including several wash steps performed before and/or after lysis. These washes significantly improved the gDNA quality (Ratio 260:230 nm >1.7) without modification of the structure of the bacterial communities as stated by temporal temperature gradient gel electrophoresis analysis. A final re-extraction with phenol:chloroform was required for one of the soil samples.

Conclusions

A combination of wash-steps included into the extraction protocol followed by phenol: chloroform reextraction is recommended to obtain high quality gDNA from calcareous soils of T. melanosporum orchards.

Significance and impact

The method recommended here significantly improves gDNA quality obtained from T. melanosporum orchards to make it acceptable for highly sensitive methods such as microarray.

Article: Mycorrhiza

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Biotrophic transportome in mutualistic plant–fungal interactions
L Casieri, NA Lahmidi, J Doidy, C Veneault-Fourrey, A Migeon, L Bonneau, PE …
Mycorrhiza, 1-29

Abstract

Understanding the mechanisms that underlie nutrient use efficiency and carbon allocation along with mycorrhizal interactions is critical for managing croplands and forests soundly. Indeed, nutrient availability, uptake and exchange in biotrophic interactions drive plant growth and modulate biomass allocation. These parameters are crucial for plant yield, a major issue in the context of high biomass production. Transport processes across the polarized membrane interfaces are of major importance in the functioning of the established mycorrhizal association as the symbiotic relationship is based on a ‘fair trade’ between the fungus and the host plant. Nutrient and/or metabolite uptake and exchanges, at biotrophic interfaces, are controlled by membrane transporters whose regulation patterns are essential for determining the outcome of plant–fungus interactions and adapting to changes in soil nutrient quantity and/or quality. In the present review, we summarize the current state of the art regarding transport systems in the two major forms of mycorrhiza, namely ecto- and arbuscular mycorrhiza.

Article: New Phytologist

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Fine‐scale spatial genetic structure of the black truffle (Tuber melanosporum) investigated with neutral microsatellites and functional mating type genes
C Murat, A Rubini, C Riccioni, H la Varga, E Akroume, B Belfiori, M Guaragno …
New Phytologist

Keywords:

  • ectomycorrhizas;
  • genets;
  • genetic structure;
  • intraspecific competition;
  • sexual reproduction;
  • truffle

Summary

  • The genetic structure of ectomycorrhizal (ECM) fungal populations results from both vegetative and sexual propagation. In this study, we have analysed the spatial genetic structure of Tuber melanosporum populations, a heterothallic ascomycete that produces edible fruit bodies.
  • Ectomycorrhizas from oaks and hazels from two orchards were mapped and genotyped using simple sequence repeat markers and the mating type locus. The distribution of the two T. melanosporum mating types was also monitored in the soil. In one orchard, the genetic profiles of the ascocarps were compared with those of the underlying mycorrhizas.
  • A pronounced spatial genetic structure was found. The maximum genet sizes were 2.35 and 4.70 m in the two orchards, with most manifesting a size < 1 m. Few genets persisted throughout two seasons. A nonrandom distribution pattern of the T. melanosporumwas observed, resulting in field patches colonized by genets that shared the same mating types.
  • Our findings suggest that competition occurs between genets and provide basic information on T. melanosporum propagation patterns that are relevant for the management of productive truffle orchards.

Article: Frontiers in Plant Proteomics

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Cysteine-based redox regulation and signalling in plants J. Couturier, K. Chibani, JP Jacquot Jacquot and N. Rouhier. Frontiers in Plant Proteomics

Living organisms are subjected to oxidative stress conditions which are characterized by the production of reactive oxygen (ROS), nitrogen (RNS) and sulfur (RSS) species. In plants as in other organisms, many of these compounds have a dual function as they damage different types of macromolecules but they also likely fulfil an important role as secondary messengers. Owing to the reactivity of their thiol groups, some protein cysteine residues are particularly prone to oxidation by these molecules. In the past years, besides their recognized catalytic and regulatory functions, the modification of cysteine thiol group was increasingly viewed as either protective or redox signalling mechanisms. The most physiologically relevant reversible redox post-translational modifications (PTMs) are disulfide bonds, sulfenic acids, S-glutathionylated adducts, S-nitrosothiols and to a lesser extent S-sulfenylamides, thiosulfinates and S-persulfides. These redox PTMs are mostly controlled by two oxidoreductase families, thioredoxins and glutaredoxins. This review focuses on recent advances highlighting the variety and physiological roles of these PTMs and the proteomic strategies used for their detection.

New paper

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Microbe-independent entry of oomycete RxLR effectors and fungal RxLR-like effectors into plant and animal cells is specific and reproducible
BM Tyler, SD Kale, Q Wang, K Tao, HR Clark, K Drews, V Antignani, A Rumore …
Molecular Plant-Microbe Interactions

Abstract:
A wide diversity of pathogens and mutualists of plant and animal hosts, including oomycetes and fungi, produce effector proteins that enter the cytoplasm of host cells. A major question has been whether or not entry by these effectors can occur independently of the microbe or requires machinery provided by the microbe. Numerous publications have documented that oomycete RxLR effectors and fungal RxLR-like effectors can enter plant and animal cells independent of the microbe. A recent re-examination of whether the RxLR domain of oomycete RxLR effectors is sufficient for microbe-independent entry into host cells, concluded that the RxLR domains of P. infestans Avr3a and of P. sojae Avr1b alone are NOT sufficient to enable microbe-independent entry of proteins into host and non-host plant and animal cells. Here we present new, more detailed data that unambiguously demonstrate that the RxLR domain of Avr1b does show efficient and specific entry into soybean root cells, and also into wheat leaf cells, at levels well above background non-specific entry. We also summarize host cell entry experiments with a wide diversity of oomycete and fungal effectors with RxLR or RxLR-like motifs that have been independently carried out by the six different labs that co-authored this letter. Finally we discuss possible technical reasons why specific cell entry may have been not detected.

New paper

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Who is Controlling whom within the Ectomycorrhizal Symbiosis: Insights from Genomic and Functional Analyses
C Veneault‐Fourrey, JM Plett, F Martin
Molecular Microbial Ecology of the Rhizosphere: Volume 1 & 2, 501-512

Keywords:

  • ectomycorrhiza;
  • eukaryotic symbiosis;
  • effectors;
  • genomics;
  • nutrient exchanges

Summary

During a lifetime that can span several hundred years, a tree will be challenged by generations of parasites and will encounter a host of different limitations related to nutrition that will affect its growth and health. Concurrently, in different soil horizons, thousands of fungi vie with each other for a limited nutrient pool. In order to avoid competition, a wide range of plants and fungi have evolved the ability to form a mutualistic relationship – a niche market where the fungus provides nutrients not normally bioavailable to the plant in exchange for plant photosynthate. One class of mutualistic fungi is the ectomycorrhizal (ECM) fungi. This group of fungi, thought to have evolved from saprotrophic fungi, grows into the apoplast of the host root without disturbing plant cell integrity or the host defense response. In this review, we will focus our attention on the evolutionary history of ECM fungi, how their genomes differ from their saprotrophic cousins, and how unique aspects of their genomic repertoire allow them to colonize the niche of the plant root. A better understanding of the biology of ECM fungi will be important in the future to inform models of sustainable forest management and to improve the productivity of tree plantations in marginal soils.

Scientific papers

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New articles

Laser microdissection and microarray analysis of Tuber melanosporum ectomycorrhizas reveal functional heterogeneity between mantle and Hartig net compartments (Stéphane Hacquard, Emilie Tisserant, Annick Brun, Valérie Legué, Francis Martin, Annegret Kohler) has been accepted in Environmental Microbiology

Xenomic networks variability and adaptation traits in wood decaying fungi (Mélanie Morel, Edgar Meux, Yann Mathieu, Anne Thuillier, Kamel Chibani, Luc Harvengt, Jean‐Pierre Jacquot, Eric Gelhaye) has been accepted in Microbial Biotechnology

Monothiol glutaredoxins and A-type proteins: partners in Fe–S cluster trafficking ( Daphne T Mapolelo, Bo Zhang, Sajini Randeniya, Angela-Nadia Albetel, Haoran Li, Jérémy Couturier, Caryn E Outten, Nicolas Rouhier, Michael K Johnson) has been published in Dalton Transactions