Identification of genes differentially expressed in ectomycorrhizal roots during the Pinus pinaster-Laccaria bicolor interaction

Morphological and Transcriptional Characteristics of the Symbiotic Interaction between Pinus massoniana and Suillus bovinus

Ectomycorrhiza (ECM) function has been well studied; however, there is little detailed information regarding the establishment of ECM symbioses. We investigated the morphological and transcriptional changes that occur during the establishment of the Pinus massoniana-Suillus bovinus ECM. S. bovinus promoted the growth of P. massoniana via the release of volatile organic compounds and exudates during the pre-symbiotic stage. Exudate-induced effects showed host plant specificity. At seven days post-inoculation (dpi), the mycelium started to penetrate P. massoniana roots. At 28 dpi, the Hartig net and mantle formed. At the pre-symbiotic stage, most differentially expressed genes in P. massoniana roots were mapped to the biosynthesis of secondary metabolites, signal transduction, and carbohydrate metabolism. At the symbiotic stage, S. bovinus colonization induced the reprogramming of pathways involved in genetic information processing in P. massoniana, particularly at the Hartig net and mantle formation stage. Phenylpropanoid biosynthesis was present at all stages and was regulated via S. bovinus colonization. Enzyme inhibitor tests suggested that hydroxycinnamoyl-CoA shikimate/quinate transferase is involved in the development of the Hartig net. Our findings outline the mechanism involved in the P. massoniana-S. bovinus ECM. Further studies are needed to clarify the role of phenylpropanoid biosynthesis in ECM formation.

Identification and characterization of eight metallothionein genes involved in heavy metal tolerance from the ectomycorrhizal fungus Laccaria bicolor

Metallothioneins (MTs) are small, cysteine-rich, heavy metal-binding proteins involved in metal homeostasis and detoxification. The increasing numbers of available genomic sequences of ectomycorrhizal (ECM) fungi enable deeper insights into the characteristics of MT genes in these fungi that form the most important symbiosis with the host trees in forest ecosystems. The aim of this study was to establish a comprehensive, genome-wide inventory of MT genes from the ECM fungus Laccaria bicolor. Eight MT genes in L. bicolor were cloned, and the expression patterns of their transcripts at various developmental stages based on expressed sequence tag (EST) counts were analyzed. The expression levels of four MTs were significantly increased during symbiosis stages. Quantitative real-time PCR (qRT-PCR) analysis revealed that transcripts of LbMT1 were dominant in free-living mycelia and strongly induced by excessive copper (Cu), cadmium (Cd), and hydrogen peroxide (H2O2). To determine whether these eight MTs functioned as metal chelators, we expressed them in the Cu- and Cd-sensitive yeast mutants, cup1∆ and yap1∆, respectively. All LbMT proteins provided similar levels of Cu(II) or Cd(II) tolerance, but did not affect by H2O2. Our findings provide novel data on the evolution and diversification of fungal MT gene duplicates, a valuable resource for understanding the vast array of biological processes in which these proteins are involved.

New insights into HcPTR2A and HcPTR2B, two high-affinity peptide transporters from the ectomycorrhizal model fungus Hebeloma cylindrosporum

While plants mainly rely on the use of inorganic nitrogen sources like ammonium and nitrate, soil-borne microorganisms like the ectomycorrhizal fungus Hebeloma cylindrosporum can also take up soil organic N in the form of amino acids and peptides that they use as nitrogen and carbon sources. Following the previous identification and functional expression in yeast of two PTR-like peptide transporters, the present study details the functions and substrates of HcPTR2A and HcPTR2B by analysing their transport kinetics in Xenopus laevis oocytes. While both transporters mediated high-affinity di- and tripeptide transport, HcPTR2A also showed low-affinity transport of several amino acids-mostly hydrophobic ones with large side chains.

The complete mitochondrial genomes of two model ectomycorrhizal fungi (Laccaria): features, intron dynamics and phylogenetic implications

Laccaria amethystine and L. bicolor have served as model species for studying the life history and genetics of ectomycorrhizal fungi. However, the characterizations and variations of their mitogenomes are still unknown. In the present study, the mitogenomes of the two Laccaria species were assembled, annotated, and compared. The two mitogenomes of L. amethystine and L. bicolor comprised circular DNA molecules, with the sizes of 65,156 bp and 95,304 bp, respectively. Genome collinearity analysis revealed large-scale gene rearrangements between the two Laccaria species. Comparative mitogenome analysis indicated the introns of cox1 genes in Agaricales experienced frequent lost/gain eveants, which promoted the organization and size variations in Agaricales mitogenomes. Evolutionary analysis indicated the core protein-coding genes in the two mitogenomes were subject to strong pressure of purifying selection. Phylogenetic analysis using the Bayesian inference (BI) and Maximum likelihood (ML) methods based on a combined mitochondrial gene set resulted in identical and well-supported tree topologies, wherein the two Laccaria species were most closely related to Coprinopsis cinerea. This study severed as the first study on the mitogenomes of Laccaria species, which promoted a comprehensive understanding of the genetics and evolution of the model ectomycorrhizal fungi.

Molecular fundamentals of nitrogen uptake and transport in trees

Nitrogen (N) is frequently a limiting factor for tree growth and development. Because N availability is extremely low in forest soils, trees have evolved mechanisms to acquire and transport this essential nutrient along with biotic interactions to guarantee its strict economy. Here we review recent advances in the molecular basis of tree N nutrition. The molecular characteristics, regulation, and biological significance of membrane proteins involved in the uptake and transport of N are addressed. The regulation of N uptake and transport in mycorrhized roots and transcriptome-wide studies of N nutrition are also outlined. Finally, several areas of future research are suggested.

Oak protein profile alterations upon root colonization by an ectomycorrhizal fungus

An increased knowledge on the real impacts of ectomycorrhizal symbiosis in forest species is needed to optimize forest sustainable productivity and thus to improve forest services and their capacity to act as carbon sinks. In this study, we investigated the response of an oak species to ectomycorrhizae formation using a proteomics approach complemented by biochemical analysis of carbohydrate levels. Comparative proteome analysis between mycorrhizal and nonmycorrhizal cork oak plants revealed no differences at the foliar level. However, the protein profile of 34 unique oak proteins was altered in the roots. Consistent with the results of the biochemical analysis, the proteome analysis of the mycorrhizal roots suggests a decreasing utilization of sucrose for the metabolic activity of mycorrhizal roots which is consistent with an increased allocation of carbohydrates from the plant to the fungus in order to sustain the symbiosis. In addition, a promotion of protein unfolding mechanisms, attenuation of defense reactions, increased nutrient mobilization from the plant-fungus interface (N and P), as well as cytoskeleton rearrangements and induction of plant cell wall loosening for fungal root accommodation in colonized roots are also suggested by the results. The suggested improvement in root capacity to take up nutrients accompanied by an increase of root biomass without apparent changes in aboveground biomass strongly re-enforces the potential of mycorrhizal inoculation to improve cork oak forest resistance capacity to cope with coming climate change.

Deciphering the molecular basis of ammonium uptake and transport in maritime pine

Ammonium is the predominant form of inorganic nitrogen in the soil of coniferous forests. Despite the ecological and economic importance of conifers, the molecular basis of ammonium uptake and transport in this group of gymnosperms is largely unknown. In this study, we describe the functional characterization of members of the AMT gene family in Pinus pinaster: PpAMT1.1, PpAMT1.2 and PpAMT1.3 (subfamily 1) and PpAMT2.1 and PpAMT2.3 (subfamily 2). Our phylogenetic analysis indicates that in conifers, all members of the AMT1 subfamily evolved from a common ancestor that is evolutionarily related to the ancient PpAMT1.2 gene. Individual AMT genes are developmentally and nutritionally regulated, and their transcripts are specifically distributed in different organs. PpAMT1.3 was predominantly expressed in the roots, particularly during N starvation and mycorrhizal interaction, whereas PpAMT2.3 was preferentially expressed in lateral roots. Immunolocalization studies of roots with varied nitrogen availability revealed that PpAMT1 and PpAMT2 proteins play complementary roles in the uptake of external ammonium. Heterologous expression in yeast and Xenopus oocytes revealed that the AMT genes encode functional transporters with different kinetics and with different capacities for ammonium transport. Our results provide new insights on how nitrogen is acquired and transported in conifers.

Deep sequencing-based comparative transcriptional profiles of Cymbidium hybridum roots in response to mycorrhizal and non-mycorrhizal beneficial fungi

Background

The Orchidaceae is one of the largest families in the plant kingdom and orchid mycorrhizae (OM) are indispensable in the life cycle of all orchids under natural conditions. In spite of this, little is known concerning the mechanisms underlying orchid- mycorrhizal fungi interactions. Our previous work demonstrated that the non-mycorrhizal fungus Umbelopsis nana ZH3A-3 could improve the symbiotic effects of orchid mycorrhizal fungus Epulorhiza repens ML01 by co-cultivation with Cymbidium hybridum plantlets. Thus, we investigated the C. hybridum transcript profile associated with different beneficial fungi.

Results

More than 54,993,972 clean reads were obtained from un-normalized cDNA library prepared from fungal- and mock- treated Cymbidium roots at four time points using RNA-seq technology. These reads were assembled into 16,798 unique transcripts, with a mean length of 1127 bp. A total of 10,971 (65.31%) sequences were annotated based on BLASTX results and over ninety percent of which were assigned to plant origin. The digital gene expression profiles in Cymbidium root at 15 days post inoculation revealed that 1674, 845 and 1743 genes were sigificantly regulated in response to ML01, ZH3A-3 and ML01+ ZH3A-3 treatments, respectively. Twenty-six genes in different regulation patterns were validated using quantitative RT-PCR. Our analysis showed that general defense responses were co- induced by three treatments, including cell wall modification, reactive oxygen species detoxification, secondary biosynthesis and hormone balance. Genes involved in phosphate transport and root morphogenesis were also detected to be up-regulated collectively. Among the OM specifically induced transcripts, genes related to signaling, protein metabolism and processing, defense, transport and auxin response were identifed. Aside from these orchid transcripts, some putative fungal genes were also identified in symbiotic roots related to plant cell wall degradation, remodeling the fungal cell wall and nutrient transport.

Conclusion

The orchid root transcriptome will facilitate our understanding of orchid - associated biological mechanism. The comparative expression profiling revealed that the transcriptional reprogramming by OM symbiosis generally overlapped that of arbuscular mycorrhizas and ectomycorrhizas. The molecular basis of OM formation and function will improve our knowledge of plant- mycorrhzial fungi interactions, and their effects on plant and fungal growth, development and differentiation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-747) contains supplementary material, which is available to authorized users.

Oak root response to ectomycorrhizal symbiosis establishment: RNA-Seq derived transcript identification and expression profiling

Ectomycorrhizal symbiosis is essential for the life and health of trees in temperate and boreal forests where it plays a major role in nutrient cycling and in functioning of the forest ecosystem. Trees with ectomycorrhizal root tips are more tolerant to environmental stresses, such as drought, and biotic stresses such as root pathogens. Detailed information on these molecular processes is essential for the understanding of symbiotic tissue development in order to optimize the benefits of this natural phenomenon. Next generation sequencing tools allow the analysis of non model ectomycorrhizal plant-fungal interactions that can contribute to find the "symbiosis toolkits" and better define the role of each partner in the mutualistic interaction. By using 454 pyrosequencing we compared ectomycorrhizal cork oak roots with non-symbiotic roots. From the two cDNA libraries sequenced, over 2 million reads were obtained that generated 19,552 cork oak root unique transcripts. A total of 2238 transcripts were found to be differentially expressed when ECM roots were compared with non-symbiotic roots. Identification of up- and down-regulated gens in ectomycorrhizal roots lead to a number of insights into the molecular mechanisms governing this important symbiosis. In cork oak roots, ectomycorrhizal colonization resulted in extensive cell wall remodelling, activation of the secretory pathway, alterations in flavonoid biosynthesis, and expression of genes involved in the recognition of fungal effectors. In addition, we identified genes with putative roles in symbiotic processes such as nutrient exchange with the fungal partner, lateral root formation or root hair decay. These findings provide a global overview of the transcriptome of an ectomycorrhizal host root, and constitute a foundation for future studies on the molecular events controlling this important symbiosis.