An improved method compatible with metagenomic analyses to extract genomic DNA from soils in Tuber melanosporum orchards.

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, optimization 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 re-extraction is recommended to obtain high-quality gDNA from calcareous soils of T. melanosporum orchards. SIGNIFICANCE AND IMPACT OF THE STUDY: The method recommended here significantly improves gDNA quality obtained from T. melanosporum orchards to make it acceptable for highly sensitive methods such as microarray.

Effect of poplar genotypes on mycorrhizal infection and secreted enzyme activities in mycorrhizal and non-mycorrhizal roots.

The impact of ectomycorrhiza formation on the secretion of exoenzymes by the host plant and the symbiont is unknown. Thirty-eight F(1) individuals from an interspecific Populus deltoides (Bartr.)×Populus trichocarpa (Torr. & A. Gray) controlled cross were inoculated with the ectomycorrhizal fungus Laccaria bicolor. The colonization of poplar roots by L. bicolor dramatically modified their ability to secrete enzymes involved in organic matter breakdown or organic phosphorus mobilization, such as N-acetylglucosaminidase, ß-glucuronidase, cellobiohydrolase, ß-glucosidase, ß-xylosidase, laccase, and acid phosphatase. The expression of genes coding for laccase, N-acetylglucosaminidase, and acid phosphatase was studied in mycorrhizal and non-mycorrhizal root tips. Depending on the genes, their expression was regulated upon symbiosis development. Moreover, it appears that poplar laccases or phosphatases contribute poorly to ectomycorrhiza metabolic activity. Enzymes secreted by poplar roots were added to or substituted by enzymes secreted by L. bicolor. The enzymatic activities expressed in mycorrhizal roots differed significantly between the two parents, while it did not differ in non-mycorrhizal roots. Significant differences were found between poplar genotypes for all enzymatic activities measured on ectomycorrhizas except for laccases activity. In contrast, no significant differences were found between poplar genotypes for enzymatic activities of non-mycorrhizal root tips except for acid phosphatase activity. The level of enzymes secreted by the ectomycorrhizal root tips is under the genetic control of the host. Moreover, poplar heterosis was expressed through the enzymatic activities of the fungal partner.

A genetic linkage map for the ectomycorrhizal fungus Laccaria bicolor and its alignment to the whole-genome sequence assemblies.

A genetic linkage map for the ectomycorrhizal basidiomycete Laccaria bicolor was constructed from 45 sib-homokaryotic haploid mycelial lines derived from the parental S238N strain progeny. For map construction, 294 simple sequence repeats (SSRs), single-nucleotide polymorphisms (SNPs), amplified fragment length polymorphisms (AFLPs) and random amplified polymorphic DNA (RAPD) markers were employed to identify and assay loci that segregated in backcross configuration. Using SNP, RAPD and SSR sequences, the L. bicolor whole-genome sequence (WGS) assemblies were aligned onto the linkage groups. A total of 37.36 Mbp of the assembled sequences was aligned to 13 linkage groups. Most mapped genetic markers used in alignment were colinear with the sequence assemblies, indicating that both the genetic map and sequence assemblies achieved high fidelity. The resulting matrix of recombination rates between all pairs of loci was used to construct an integrated linkage map using JoinMap. The final map consisted of 13 linkage groups spanning 812 centiMorgans (cM) at an average distance of 2.76 cM between markers (range 1.9-17 cM). The WGS and the present linkage map represent an initial step towards the identification and cloning of quantitative trait loci associated with development and functioning of the ectomycorrhizal symbiosis.

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.

Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.

Spatial and temporal variability of foliar mineral concentration in beech (Fagus sylvatica) stands in northeastern France.

Foliar mineral concentration may provide a basis for monitoring the consequences of long-term environmental changes, such as eutrophication and acidification of soils, or increase in atmospheric CO(2) concentration. However, analytical drifts and inter-tree and year-to-year variations may confound environmental effects on long-term changes in foliar mineral concentration. We have characterized the relative effects of these potentially confounding factors on foliar carbon, nitrogen, phosphorus, calcium, potassium, magnesium and manganese concentrations in 118 pure beech (Fagus sylvatica L.) stands, sampled in 1969-71 and 1996-97. Interannual fluctuations of these elements were quantified in a subset of six beech stands monitored for 5 years. Intercalibration between the methods used at each sampling period for nitrogen and phosphorus analyses showed significant, but low, relative differences (0.8 and 3.3% for N and P, respectively). Based on inter-tree variability, elements could be arranged in four groups: C (constant), N and P (low variability), K and Ca (medium variability), Mn and Mg (high variability). Inter-tree coefficients of variation were 2, 6, 8, 15, 18, 22 and 27%, respectively. Year-to-year fluctuations increased in the order N, P, Mg, K, Ca, and Mn coefficients of variation of 4, 4, 7, 9, 11, 15 and 29%, respectively). Between the two sampling periods, foliar N concentration increased 12%, whereas decreases were observed for P (-23%), Mg (-38%) and Ca (-16%). Ratios of N/P, N/K and N/Mg increased by 42, 19 and 77%, respectively. These changes were larger than the interannual variations for P, Mg, N/P, N/Mg and Mg/Ca. Decreasing concentrations of P and cations were particularly marked for trees growing on acidic soils, whereas the positive N trend did not depend on soil type. Both increasing atmospheric CO(2) concentrations and acidification of forest soils could contribute to decreasing P and cation concentrations in foliage. The increase in foliar N concentration with time suggests a nitrogen deposition effect. Whatever the causes of these changes, the large shift in element ratios indicates an accelerating imbalance between nitrogen and cation status.

Structure and dynamics of experimentally introduced and naturally occurring laccaria sp. Discrete genotypes in a douglas fir plantation

Ectomycorrhizal fungi have been introduced in forest nurseries to improve seedling growth. Outplanting of inoculated seedlings to forest plantations raises the questions about inoculant persistence and its effects on indigenous fungal populations. We previously showed (M.-A. Selosse et al. Mol. Ecol. 7:561-573, 1998) that the American strain Laccaria bicolor S238N persisted 10 years after outplanting in a French Douglas fir plantation, without introgression or selfing and without fruiting on uninoculated adjacent plots. In the present study, the relevance of those results to sympatric strains was assessed for another part of the plantation, planted in 1985 with seedlings inoculated with the French strain L. bicolor 81306 or left uninoculated. About 720 Laccaria sp. sporophores, collected from 1994 to 1997, were typed by using randomly amplified polymorphic DNA markers and PCR amplification of the mitochondrial and nuclear ribosomal DNAs. All plots were colonized by small spontaneous discrete genotypes (genets). The inoculant strain 81306 abundantly fruited beneath inoculated trees, with possible introgression in indigenous Laccaria populations but without selfing. In contrast to our previous survey of L. bicolor S238N, L. bicolor 81306 colonized a plot of uninoculated trees. Meiotic segregation analysis verified that the invading genet was strain 81306 (P < 0.00058), implying a vegetative growth of 1.1 m. year-1. This plot was also invaded in 1998 by strain S238N used to inoculate other trees of the plantation. Five other uninoculated plots were free of these inoculant strains. The fate of inoculant strains thus depends less on their geographic origin than on unknown local factors.

The land flora: a phototroph-fungus partnership?

Numerous mutualistic associations between phototrophs and fungi exist in the extant land biota. Some are widespread, such as lichens and mycorrhizae, but some are less well known or restricted to special ecological conditions, such as endophytes in plants and algae. Recent molecular data and fossils suggest that associations arose repeatedly and that some of them are ancient, and even ancestral in the case of land plants. Mutualism, that provides various adaptations to terrestrial constraints, may have played a crucial role during terrestrialization and evolution of land phototrophs.

The auxin transport inhibitor 2,3,5-triiodobenzoic acid (TIBA) inhibits the stimulation of in vitro lateral root formation and the colonization of the tap-root cortex of Norway spruce (Picea abies) seedlings by the ectomycorrhizal fungus Laccaria bicolor.

Norway spruce (Picea abies (L.) Karst.) seedlings were inoculated with the ectomycorrhizal fungus Laccaria bicolor ((Marie) Orton), strain S238 N, in axenic conditions. The presence of the fungus slowed tap-root elongation by 26% during the first 15 d after inoculation and then stimulated it by 136%. In addition, it multiplied in vitro lateral root formation by 4.3, the epicotyl growth of the seedlings by 8.4 and the number of needles by 2. These effects were maintained when the fungus was separated from the roots by a cellophane membrane preventing symbiosis establishment, thus suggesting that the fungus acted by non-nutritional effects. We tested the hypothesis that IAA produced by L. bicolor S238 N would be responsible for the stimulation of fungal induced rhizogenesis. We showed in previous work that L. bicolor S238 N can synthesize IAA in pure culture. Exogenous IAA supplies (100 and 500 µm) reproduced the stimulating effect of the fungus on root branching but inhibited root elongation. The presence of 2,3,5-triiodobenzoic acid (TIBA) in the culture medium significantly depressed lateral root formation of inoculated seedlings. As TIBA had no significant effect on IAA released in the medium by L. bicolor S238 N, but counteracted the stimulation of lateral rhizogenesis induced by an exogenous supply of IAA, we suggest that TIBA inhibited the transport of fungal IAA in the root. Furthermore TIBA blocked the colonization of the main root cortex by L. bicolor S238 N and the formation of the Hartig net. These results specified the role of fungal IAA in the stimulation of lateral rhizogenesis and in ectomycorrhizal symbiosis establishment.

In vitro effects of Laccaria bicolor S238 N and Pseudomonas fluorescens strain BBc6 on rooting of de-rooted shoot hypocotyls of Norway spruce.

The ectomycorrhizal fungus Laccaria bicolor S238 N and the bacterium Pseudomonas fluorescens BBc6 were used separately and in combination to induce in vitro rooting of de-rooted shoot hypocotyls of Norway spruce (Picea abies (L.) Karst.). When the culture medium was supplemented with tryptophan, a precursor of indole-3-acetic acid (IAA) synthesis, the presence of the ectomycorrhizal fungus increased the percentage of hypocotyls forming roots; furthermore, both the fungal and bacterial inoculations enhanced the number of roots formed per rooted hypocotyl. Similar results were obtained by adding exogenous IAA (5 and 10 &mgr;M) to the rooting medium. After the rooting phase, the fungal inoculation enhanced adventitious root elongation and branching as well as the aerial growth of the cuttings. Pseudomonas fluorescens BBc6 had no effect on these parameters. The production of IAA by pure cultures of L. bicolor S238 N and P. fluorescens BBc6 was estimated by immunochemical analysis using specific anti-IAA antibodies. Both L. bicolor S238 N and P. fluorescens BBc6 synthesized IAA in pure culture and synthesis was stimulated in the presence of tryptophan. Thus, the effect of the fungus in stimulating adventitious root formation and subsequent elongation and branching can be attributed, at least partially, to the synthesis of IAA by the fungus. The finding that P. fluorescens BBc6 had no effect on root elongation and branching although it produced IAA suggests that either IAA was not the only parameter involved in the stimulation of these processes by L. bicolor S238 N or the bacterium produced other compounds that counteracted the stimulatory effects of IAA on root elongation and branching.

Glutamate dehydrogenases in ectomycorrhizas of spruce (Picea excelsa L.) and beech (Fagus sylvatica L.).

The ammonia assimilation enzyme glutamate dehydrogenase as studied in extracts of spruce (Picea excelsa L.) roots, mycelium of a mycorrhizal fungus (Hebeloma sp.) and associated ectomycorrhizas. Evidence from enzyme reactions in crude extracts, electrophoretic patterns and immunological tests Using antibodies raised against purified NADP-GDH of Cenococcum geophilum Fr. consistently showed that Hebeloma NADP-dependent GDH was active in spruce ectomycorrhizas. Histochemical studies associated some NADP-GDH activity with the Hartig net. By contrast, the NADP-GDH fungal pathway was strongly suppressed in beech (Fagus sylvatica L.) associations with Hebeloma crustuliniforme (Bull. ex St Amans) Quél. and Paxillus involutus (Batsch ex Fr.) Fr.

ASSIMILATION OF 15 NH4 + BY BEECH (FAGUS SYLVATICA L.) ECTOMYCORRHIZAS.

Ammonia assimilation has been followed in ectomycorrhizal roots of Fagus sylvatica. The absorption of ammonium ions was associated with a rapid synthesis of free amino acids in mycorrhizal tissues, glutamine being the most prominent. In the presence of [15 N]ammonium, glutamate, glutamine and alanine became the most strongly labelled metabolites of ectomycor-rhizas. Nitrogen-15 nuclear magnetic resonance spectroscopy demonstrated that the glutamine amide-N was the most highly enriched component of the extracts. Methionine sulphoximine and albizine, inhibitors of glutamine synthetase and glutamate synthase, almost completely blocked the incorporation of 15 N label into amino acids and induced an accumulation of NH4 + . These observations suggest that in the ammonia-fed beech ectomycorrhizas, ammonia assimilation occurs mainly via the glutamine synthetase/glutamate synthase pathway, and that glutamate dehydrogenase plays little, if any, part in this process. Alternative models for the nitrogen assimilation pathways in fungal and host tissues are presented.

IMPROVED HYPHAL GROWTH OF TWO SPECIES OF VESICULAR-ARBUSCULAR MYCORRHIZAL FUNGI IN THE PRESENCE OF SUSPENSION-CULTURED PLANT CELLS.

Conditions required for the combined culture of either Glomus caledonium (Nicol. &Gerd.) Trappe &Gerdemann or Glomus mosseae (Nicol. &Gerd.) Gerdemann &Trappe with suspension-cultured plant cells have been investigated. Sucrose levels (0.05 to 0.5%, w/v) lower than those used for growth of plant cells were optimal for hyphal growth of both G. caledonium and G. mosseae. In vitro hyphal growth from chlamydospores of G. caledonium was stimulated by addition of cells of wheat (Triticum aestivum L. cv. Maris Butler), lucerne (Medicago sativa L. cv. Europ) and potato (Solanum tuberosum L. cv. Maris Piper). The presence of wheat cells similarly stimulated hyphal growth from chlamydospores of G. mosseae. Further tests on the effect of lucerne cells on G. caledonium indicated that a volatile substance was involved in the improvement of hyphal growth.