Monthly Archives: October 2014

Article: Applied Microbiology and Biotechnology

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Occurrence of lignin degradation genotypes and phenotypes among prokaryotes

JH Tian, AM Pourcher, T Bouchez, E Gelhaye, P Peu
Applied Microbiology and Biotechnology, 1-18

Abstract

A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNAsequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.

Article: Molecular Plant-Microbe Interactions

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The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses

JM Plett, E Tisserant, A Brun, E Morin, IV Grigoriev, A Kuo, FM Martin, …

Molecular Plant-Microbe Interactions

Abstract
The coordinated transcriptomic responses of both mutualistic ectomycorrhizal (ECM) fungi and their hosts during the establishment of symbiosis are not well understood. This study characterizes the transcriptomic alterations of the ECM fungus Laccaria bicolor during different colonization stages on two hosts (Populus trichocarpa and Pseudotsuga menziesii) and compares this to the transcriptomic variations of P. trichocarpa across the same time-points. A large number of L. bicolor genes (>8,000) were significantly regulated at the transcriptional level in at least one stage of colonization. From our data we identify 1,249 genes that we hypothesize is the “core” gene regulon necessary for the mutualistic interaction between L. biolor and its host plants. We further identify a group of 1,210 genes that are regulated in a host-specific manner. This variable regulon encodes a number of genes coding for proteases and xenobiotic efflux transporters that we hypothesize act to counter chemical based defenses simultaneously activated at the transcriptomic level in P. trichocarpa. The transcriptional response of the host plant P. trichocarpa consisted of differential waves of gene regulation related to signaling perception and transduction, defense response and the induction of nutrient transfer in P. trichocarpa tissues. This study, therefore, gives fresh insight into the shifting transcriptomic landscape in both the colonizing fungus and their hosts and the different strategies employed by both partners in orchestrating a mutualistic

Newcomer: Emilie HOSCHEIT

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Name HOSCHEIT Emilie  Hosheit Emilie
Position and team BTS work-study contract, Ecology of forest pathogenic fungi team
Supervisor O. Caël
Subject Impact de l’agent pathogène invasif Chalara fraxinea. BTS gestion forestière
Period September, 2014 – September, 2016

Article: Frontiers in Microbiology

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Expanding Genomics of Mycorrhizal Symbiosis

A Kuo, A Kohler, FM Martin, IV Grigoriev – Microbial Symbioses, 2014
 

Abstract

The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant and soil health, and carbon and nutrient cycles. The symbiosis evolved repeatedly and independently as multiple morphological types (e.g. arbuscular [AM], ectomycorrhizal [ECM]) in multiple fungal clades (e.g. phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and culturability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first 3 mycorrhizal fungal genomes, representing 3 fungal phyla and 2 mycorrhizal types. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant-degrading enzymes (PDEs) and expansion of lineage-specific gene families, including short secreted protein (SSP) effectors and other symbiosis genes. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of gene families in contrast to Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other 2 fungi, the symbiosis can involve similar solutions as loss of PDEs and mycorrhiza-induced SSPs. The mycorrhizal community is building on these studies with 3 large-scale initiatives. The Mycorrhizal Genomics Initiative (MGI) is sequencing 35 genomes of multiple fungal clades and mycorrhizal types for phylogenomic and population analyses. 17 MGI species whose symbiosis is reconstitutable in vitro are targeted for comprehensive transcriptomics of mycorrhiza formation. MGI genomes are seeding a set of 50+ reference fungal genomes for annotating metatranscriptomes sampled from 7 diverse well-described soil sites. These 3 projects address fundamental questions about the nature and role of a vital mutualism.

Seminar: Wendish V.

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The  seminar of Pr. Volker Wendisch (Bielefeld University, Germany) entitled  « Production of diamines and carotenoids from alternative carbon sources by microbial cell factories » will be held Friday 10th October .
The seminar will start at 13.00 pm in the meeting room Bat B, 7th floor FST.

Seminar: Skrede I.

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The  seminar of Inger Skrede (Mirobial Evolution Research Group, University of Oslo, Norvège) entiteld « Speciation processes and comparative genomics in the brown rot fungus Serpula » will be held Friday 10th October (LGEF meeting room/visio UL).
The seminar will start at 11.00 am in the LGEF meeting room.

New Ph.D. student (CJS)

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Name LORRAIN Cécile  cecile-lorrain
Teams Ecogenomics of interactions/Stress response and redox regulation teams
Supervisors S. Duplessis/A. Hecker
Subject of thesis Functional analysis of poplar rust candidate effectors targeting chloroplasts
Period 10/2014-09/2017

Seminar: Sophie Mieskin

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The seminar of the week (Friday 3th October) will be given by Sophie Mieskin, lecturer who recently joined our unit. Sophie will present the work she performed during her PhD and Post-doc:
“Molecular diagnosis of the origin of faecal contaminations in coastal environment – Development of host-specific Bacteroidales markers”
Post-doc: “Does a bacterial biofilm influence the settlement and the adhesion strength of marine algae? »
The seminar will start at 1.30pm in the LGEF meeting room.