Article: Nature Ecology and Evolution

  1. The ash dieback invasion of Europe was founded by two genetically divergent individuals M McMullan, M Rafiqi, G Kaithakottil, BJ Clavijo, L Bilham, E Orton, …Nature Ecology & Evolution, 1

    Abstract

    Accelerating international trade and climate change make pathogen spread an increasing concern. Hymenoscyphus fraxineus, the causal agent of ash dieback, is a fungal pathogen that has been moving across continents and hosts from Asian to European ash. Most European common ash trees (Fraxinus excelsior) are highly susceptible to H.fraxineus, although a minority (~5%) have partial resistance to dieback. Here, we assemble and annotate a H.fraxineus draft genome, which approaches chromosome scale. Pathogen genetic diversity across Europe and in Japan, reveals a strong bottleneck in Europe, though a signal of adaptive diversity remains in key host interaction genes. We find that the European population was founded by two divergent haploid individuals. Divergence between these haplotypes represents the ancestral polymorphism within a large source population. Subsequent introduction from this source would greatly increase adaptive potential of the pathogen. Thus, further introgression of H.fraxineus into Europe represents a potential threat and Europe-wide biological security measures are needed to manage this disease.

Article: Mycorrhiza

N-Acetylglucosaminidase activity, a functional trait of chitin degradation, is regulated differentially within two orders of ectomycorrhizal fungi: Boletales and Agaricales F Maillard, M Didion, L Fauchery, C Bach, M Buée. Mycorrhiza, 1-7

Abstract

Chitin is one of the most abundant nitrogen-containing polymers in forest soil. Ability of ectomycorrhizal (EM) fungi to utilize chitin may play a key role in the EM symbiosis nutrition and soil carbon cycle. In forest, EM fungi exhibit high diversity, which could be based on function partitioning and trait complementarity. Although it has long been recognized that closely related species share functional characteristics, the phylogenetic conservatism of functional traits within microorganisms remains unclear. Because extracellular N-acetylglucosaminidase activity has been proposed as functional trait of chitin degradation, we screened this activity on 35 EM fungi species with or without chitin in the growth medium to (i) describe the functional diversity of EM fungi and (ii) identify potential links between this functional trait and EM fungal phylogeny. We observed large variations of the extracellular N-acetylglucosaminidase activities among the fungal strains. Furthermore, our results revealed two regulation patterns of extracellular N-acetylglucosaminidase activities. Indeed, these chitinolytic activities were stimulated or repressed in the presence of chitin, in comparison to the control treatment. These profiles of extracellular N-acetylglucosaminidase stimulation/repression might be conserved at a high phylogenetic level in the Basidiomycota phylum, as illustrated by the opposite patterns of regulation between Boletales and Agaricales. Finally, the downregulation of this activity by chitin, for some EM fungal groups, might suggest another chitin degradation pathway.

Article: The New Phytologist

The ectomycorrhizal basidiomycete Laccaria bicolor releases a secreted β-1, 4 endoglucanase that plays a key role in symbiosis development. F Zhang, GE Anasontzis, A Labourel, C Champion, M Haon, … The New phytologist

Abstract

In ectomycorrhiza, root ingress and colonization of the apoplast by colonizing hyphae is thought to rely mainly on the mechanical force that results from hyphal tip growth, but this could be enhanced by secretion of cell-wall-degrading enzymes, which have not yet been identified. The sole cellulose-binding module (CBM1) encoded in the genome of the ectomycorrhizal Laccaria bicolor is linked to a glycoside hydrolase family 5 (GH5) endoglucanase, LbGH5-CBM1. Here, we characterize LbGH5-CBM1 gene expression and the biochemical properties of its protein product. We also immunolocalized LbGH5-CBM1 by immunofluorescence confocal microscopy in poplar ectomycorrhiza. We show that LbGH5-CBM1 expression is substantially induced in ectomycorrhiza, and RNAi mutants with a decreased LbGH5-CBM1 expression have a lower ability to form ectomycorrhiza, suggesting a key role in symbiosis. Recombinant LbGH5-CBM1 displays its highest activity towards cellulose and galactomannans, but no activity toward L. bicolor cell walls. In situ localization of LbGH5-CBM1 in ectomycorrhiza reveals that the endoglucanase accumulates at the periphery of hyphae forming the Hartig net and the mantle. Our data suggest that the symbiosis-induced endoglucanase LbGH5-CBM1 is an enzymatic effector involved in cell wall remodeling during formation of the Hartig net and is an important determinant for successful symbiotic colonization.

Article: BMC Genomics

Intraspecific comparative genomics of isolates of the Norway spruce pathogen (Heterobasidion parviporum) and identification of its potential virulence factors Z Zeng, H Sun, EJ Vainio, T Raffaello, A Kovalchuk, E Morin, S Duplessis, … BMC genomics 19 (1), 220

Abstract

Background

Heterobasidion parviporum is an economically most important fungal forest pathogen in northern Europe, causing root and butt rot disease of Norway spruce (Picea abies (L.) Karst.). The mechanisms underlying the pathogenesis and virulence of this species remain elusive. No reference genome to facilitate functional analysis is available for this species.

Results

To better understand the virulence factor at both phenotypic and genomic level, we characterized 15 H. parviporum isolates originating from different locations across Finland for virulence, vegetative growth, sporulation and saprotrophic wood decay. Wood decay capability and latitude of fungal origins exerted interactive effects on their virulence and appeared important for H. parviporum virulence. We sequenced the most virulent isolate, the first full genome sequences of H. parviporum as a reference genome, and re-sequenced the remaining 14 H. parviporum isolates. Genome-wide alignments and intrinsic polymorphism analysis showed that these isolates exhibited overall high genomic similarity with an average of at least 96% nucleotide identity when compared to the reference, yet had remarkable intra-specific level of polymorphism with a bias for CpG to TpG mutations. Reads mapping coverage analysis enabled the classification of all predicted genes into five groups and uncovered two genomic regions exclusively present in the reference with putative contribution to its higher virulence. Genes enriched for copy number variations (deletions and duplications) and nucleotide polymorphism were involved in oxidation-reduction processes and encoding domains relevant to transcription factors. Some secreted protein coding genes based on the genome-wide selection pressure, or the presence of variants were proposed as potential virulence candidates.

Conclusion

Our study reported on the first reference genome sequence for this Norway spruce pathogen (H. parviporum). Comparative genomics analysis gave insight into the overall genomic variation among this fungal species and also facilitated the identification of several secreted protein coding genes as putative virulence factors for the further functional analysis. We also analyzed and identified phenotypic traits potentially linked to its virulence

Article: Mycorrhiza

Impact of soil pedogenesis on the diversity and composition of fungal communities across the California soil chronosequence of Mendocino PE Courty, M Buée, JJT Tech, D Brulé, Y Colin, JHJ Leveau, S Uroz Mycorrhiza, 1-1

Abstract

Understanding how soil pedogenesis affects microbial communities and their in situ activities according to ecosystem functioning is a central issue in soil microbial ecology, as soils represent essential nutrient reservoirs and habitats for the biosphere. To address this question, soil chronosequences developed from a single, shared mineralogical parent material and having the same climate conditions are particularly useful, as they isolate the factor of time from other factors controlling the character of soils. In our study, we considered a natural succession of uplifted marine terraces in Mendocino, CA, ranging from highly fertile in the younger terrace (about 100,000 years old) to infertile in the older terraces (about 300,000 years old). Using ITS amplicon pyrosequencing, we analysed and compared the diversity and composition of the soil fungal communities across the first terraces (T1 to T3), with a specific focus in the forested terraces (T2 and T3) on soil samples collected below trees of the same species (Pinus muricata) and of the same age. While diversity and richness indices were highest in the grassland (youngest) terrace (T1), they were higher in the older forested terrace (T3) compared to the younger forested terrace (T2). Interestingly, the most abundant ectomycorrhizal (ECM) taxa that we found within these fungal communities showed high homology with ITS Sanger sequences obtained previously directly from ECM root tips from trees in the same study site, revealing a relative conservation of ECM diversity over time. Altogether, our results provide new information about the diversity and composition of the fungal communities as well as on the dominant ECM species in the soil chronosequence of Mendocino in relation to soil age and ecosystem development.

Article: New Phytologist

The origin and evolution of mycorrhizal symbioses: from palaeomycology to phylogenomics. C Strullu-Derrien, MA Selosse, P Kenrick, FM Martin The New phytologist

Abstract

 The ability of fungi to form mycorrhizas with plants is one of the most remarkable and enduring adaptations to life on land. The occurrence of mycorrhizas is now well established in c. 85% of extant plants, yet the geological record of these associations is sparse. Fossils preserved under exceptional conditions provide tantalizing glimpses into the evolutionary history of mycorrhizas, showing the extent of their occurrence and aspects of their evolution in extinct plants. The fossil record has important roles to play in establishing a chronology of when key fungal associations evolved and in understanding their importance in ecosystems through time. Together with calibrated phylogenetic trees, these approaches extend our understanding of when and how groups evolved in the context of major environmental change on a global scale. Phylogenomics furthers this understanding into the evolution of different types of mycorrhizal associations, and genomic studies of both plants and fungi are shedding light on how the complex set of symbiotic traits evolved. Here we present a review of the main phases of the evolution of mycorrhizal interactions from palaeontological, phylogenetic and genomic perspectives, with the aim of highlighting the potential of fossil material and a geological perspective in a cross-disciplinary approach.

Article: Forest pathology

Do higher summer temperatures restrict the dissemination of Hymenoscyphus fraxineus in France? M Grosdidier, R Ioos, B Marçais. Forest Pathology

Summary

Hymenoscyphus fraxineus is an invasive pathogen that severely affects European ashes, jeopardizing the use of this species in forestry. However, even aggressive invasive pathogens require environmental conditions conducive to disease development. Hence, H. fraxineus survival at temperatures above 35°C is limited, which could reduce its impact in southern Europe. This study examined the effect of environmental conditions, mainly summer temperatures, on ash dieback development in southeast France between 2015 and 2016. Fourteen sites were selected according to altitudinal and longitudinal gradients covering a wide range of mean summer temperatures. Disease severity, density of infected and healthy rachises in the litter and quantity of apothecia produced on infected rachises were measured. Results point to limited disease severity in this area because of the occurrence of high summer temperatures that are unfavourable to the pathogen. In a context of global warming, increases in temperatures could have a positive impact on ashes by limiting ash dieback development.

Article: Applied and Environmental Microbiology

Assessing airborne fungal communities by high-throughput sequencing using passive traps J Aguayo, C Fourrier-Jeandel, C Husson, R Ioos Applied and Environmental Microbiology, AEM. 02637-17

ABSTRACT

Techniques based on the high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols including different passive spore traps, spore recovery procedures, DNA extraction kits and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two sub loci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of trap are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.

Importance The advent of high throughput sequencing (HTS) methods such as those offered by next-generation sequencing (NGS) techniques has opened a new era in the study of fungal diversity in different environmental substrates. In this study we show that the assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, comparison of sample processing protocols showed that several methodological biases may impact results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.

Article: Annals of Forest Science

Comparison of teak wood properties according to forest management: short versus long rotation DE Rizanti, W Darmawan, B George, A Merlin, S Dumarcay, H Chapuis, … Annals of Forest Science 75 (2), 39

Context

In Indonesia, teak wood has been supplied from the state forests (Perhutani) for long rotation teak and from community teak plantations for short rotation teak. Short rotation teak has been harvested at 7–10 years and long rotation teak at 40–60 years.

Aims

This paper discusses the characterization of technical properties of short and long rotation teak wood based on the chemical, anatomical, physical, and mechanical properties.

Methods

The properties of short rotation and long rotation teak woods were characterized by measuring their density, extractive contents, chemical composition, swelling, wettability, water sorption isotherm, decay resistance, anatomical properties, bending strength (modulus of rupture (MOR), modulus of elasticity (MOE)), and hardness.

Results

The results indicate that short rotation teak was not particularly different in swelling, MOE and MOR, and Brinell hardness compared to long rotation teak, although it was less dense and less durable due to lower heartwood and extractive contents. Therefore, careful attention should be given to the use of short rotation teak in some wood-processing technologies.

Conclusion

Lower wood density and durability of the short rotation compared to the long rotation teak will restrict its utilization to some extent for both indoor and outdoor applications. Fast-growing teak from community cannot be used as usual heartwood teak from Perhutani because of the very low proportion of useful heartwood in the stem.