Phytophthora on Alnus spp.(alders)
B Marçais, C Husson
JKI Data sheets-Plant Diseases and Diagnosis, English

Mycorrhizas and New Phytologist: une vraie histoire d’amour
C MA Selosse, F Martin
New Phytologist

Keywords

arbuscular mycorrhizas; ectomycorrhizas; Ian Dickie; Maarja Öpik; mycorrhizas; New Phytologist ; New Phytologist symposia

A short-term mineral amendment impacts the mineral weathering bacterial communities in an acidic forest soil
C Lepleux, S Uroz, C Collignon, JL Churin, MP Turpault, P Frey-Klett
Research in microbiology

Abstract

Mineral amendment (i.e. calcium, phosphorous, potassium and/or magnesium) is a management practice used in forestry to improve nutrient availability and recover soil fertility, especially in nutrient-poor forest ecosystems. However, whether this amendment can lead to modifications of the soil characteristics and an improvement in tree growth, and its impact on the soil bacterial communities, especially the mineral weathering bacterial communities, remains poorly documented. In this study, we investigated the short-term impact of a mineral amendment on the taxonomic and functional structure of the mineral weathering bacterial communities. To do this, a plantation of four-year old oak (Quercus petraea) trees amended with or without dolomite [CaMg(CO₃)₂] was established in the experimental forest site of Breuil-Chenue, which is characterized by an acidic soil and a low availability of calcium and magnesium. Three years after amendment, soil samples were used to isolate bacteria as well as to determine the soil characteristics and the metabolic potentials of these soil microbial communities. Based on a bioassay for quantifying the solubilisation of inorganic phosphorous, we demonstrate that the bacterial isolates coming from the non-amended bulk soil were significantly more efficient than those from the amended bulk soil. No difference was observed between the bacterial isolates coming from the amended and non-amended rhizospheres. Notably, the taxonomic analyses revealed a dominance of bacterial isolates belonging to the Burkholderia genus in both samples. Overall, our results suggest that the bioavailability of nutritive cations into soil impacts the distribution and the efficacy of mineral weathering bacterial communities coming from the soil but not those coming from the rhizosphere.

Keywords

• Acidic forest soil;
• Bacterial communities;
• Cultivation-dependent approach;
• Mineral amendment;
• Mineral weathering;
• Oak plantation

Black truffle‐associated bacterial communities during the development and maturation of Tuber melanosporum ascocarps and putative functional roles
S Antony‐Babu, A Deveau, JD Van Nostrand, J Zhou, F Le Tacon, C Robin, P …
Environmental Microbiology

Abstract

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus A Patyshakuliyeva, E Jurak, A Kohler, A Baker,E  Battaglia, de Bruijn W,… BMC Genomics 2013, 14:663

Abstract (provisional)

Background

Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present.

Results

In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies.

Conclusions

The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples.

Effects of the use of biocontrol agent (< i> Phlebiopsis gigantea</i>) on fungal communities on the surface of Picea abies  stumps
E Terhonen, H Sun, M Buée, R Kasanen, L Paulin, FO Asiegbu
Forest Ecology and Management 310, 428-433

Abstract

One of the main objectives of sustainable forestry policies is to phase out, if possible, the use of chemical agents in forestry. The saprotrophic fungus Phlebiopsis gigantea has for several years been used as a biocontrol agent against the pathogen Heterobasidion annosum sensu lato. This pathogen is the major cause of root rot disease in conifers that results in economic losses estimated at 50 million euros to Finnish forestry industry annually. A major problem is that, although the effectiveness of P. gigantea as a bio-control agent has empirically been shown, the long term biological effect of this fungus on conifer trees as well as on other wood microflora has not been empirically proven. We investigated the impact of P. gigantea treatment on stump mycobiota using 454-pyrosequencing approach as this has not done before. Samples from forest sites pre-treated with P. gigantea for 1, 6 and 13 years ago were collected, DNA was isolated and the ITS regions were pyrosequenced. Similarly samples were also collected from untreated stumps within the same forest site over the same period of time. A total of 53,117 fungal sequences were generated by 454-pyrosequencing from 18 wood samples. After data cleaning we had 26,127 sequences representing 49% of the original sequences. Possible impact of the treatment on fungal communities in different study sites was analyzed using Principal Component Analysis (PCA). Also diversity indexes and similarity indexes between controls and treated stumps were calculated. Biocontrol P. gigantea represented 0.43% of all fungal sequences and was found only from stumps after one year post-treatment. The pathogen H. annosum s.l. was not observed in this study. Numbers of different OTUs were always higher in the control stumps. However there was no statistical difference noted between treated and non-treated stumps. Based on our results we can conclude that stump treatment should continue as there is no obvious adverse effect on the other stump mycobiota.

Keywords

• Stump treatment;
• Biocontrol;
• Phlebiopsis gigantea;
• 454-Pyrosequencing

Extreme diversification of the mating type–high‐mobility group (MATA‐HMG) gene family in a plant‐associated arbuscular mycorrhizal fungus
R Riley, P Charron, A Idnurm, L Farinelli, Y Dalpé, F Martin, N Corradi
New Phytologist

Summary

Arabidopsis thaliana Nfu2 accommodates [2Fe-2S] or [4Fe-4S] clusters and is competent for in vitro maturation of chloroplast [2Fe-2S] and [4Fe-4S] cluster-containing proteins
H Gao, S Subramanian, J Couturier, SG Naik, SK Kim, T Leustek, DB Knaff, HC …
Biochemistry

Abstract

Nfu-type proteins are essential in the biogenesis of iron-sulfur (Fe-S) clusters in numerous organisms. A number of phenotypes including low levels of Fe-S cluster incorporation are associated with deletion of the gene encoding a chloroplast-specific Nfu-type protein, Nfu2 from Arabidopsis thaliana (AtNfu2). Here we report that recombinant AtNfu2 is able to assemble both [2Fe-2S] and [4Fe-4S] clusters. Analytical data and gel filtration studies support cluster/protein stoichiometries of one [2Fe-2S] cluster/homotetramer and one [4Fe-4S] cluster/homodimer. The combination of UV-visible absorption and circular dichroism, resonance Raman and Mössbauer spectroscopies has been employed to investigate the nature, properties and transfer of the clusters assembled on Nfu2. The results are consistent with subunit-bridging [2Fe-2S]²⁺ and [4Fe-4S]²⁺ clusters coordinated by the cysteines in the conserved CXXC motif. The results also provided insight into the specificity of Nfu2 for maturation of chloroplastic Fe-S proteins via intact, rapid and quantitative cluster transfer. [2Fe-2S] cluster-bound Nfu2 is shown to be an effective [2Fe-2S]²⁺ cluster donor for glutaredoxin S16, but not glutaredoxin S14. Moreover, [4Fe-4S] cluster-bound Nfu2 is shown to be a very rapid and efficient [4Fe-4S]²⁺ cluster donor for adenosine 5’-phosphosulfate reductase (APR1) and yeast two-hybrid studies indicate that APR1 forms a complex with Nfu2, but not with Nfu1 and Nfu3, the two other chloroplastic Nfu proteins. This cluster transfer is likely to be physiologically relevant and is particularly significant for plant metabolism as APR1 catalyzes the second step in reductive sulfur assimilation which ultimately results in the biosynthesis of cysteine, methionine, glutathione, and Fe-S clusters.

Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification
L Perrochia, D Guetta, A Hecker, P Forterre, T Basta
Nucleic Acids Research

Abstract

N⁶-threonylcarbamoyladenosine (t⁶A) is a universal tRNA modification essential for normal cell growth and accurate translation. In Archaea and Eukarya, the universal protein Sua5 and the conserved KEOPS/EKC complex together catalyze t⁶A biosynthesis. The KEOPS/EKC complex is composed of Kae1, a universal metalloprotein belonging to the ASHKA superfamily of ATPases; Bud32, an atypical protein kinase and two small proteins, Cgi121 and Pcc1. In this study, we investigated the requirement and functional role of KEOPS/EKC subunits for biosynthesis of t⁶A. We demonstrated that Pcc1, Kae1 and Bud32 form a minimal functional unit, whereas Cgi121 acts as an allosteric regulator. We confirmed that Pcc1 promotes dimerization of the KEOPS/EKC complex and uncovered that together with Kae1, it forms the tRNA binding core of the complex. Kae1 binds L-threonyl-carbamoyl-AMP intermediate in a metal-dependent fashion and transfers the L-threonyl-carbamoyl moiety to substrate tRNA. Surprisingly, we found that Bud32 is regulated by Kae1 and does not function as a protein kinase but as a P-loop ATPase possibly involved in tRNA dissociation. Overall, our data support a mechanistic model in which the final step in the biosynthesis of t⁶A relies on a strictly catalytic component, Kae1, and three partner proteins necessary for dimerization, tRNA binding and regulation.