Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

Genotypes of Fraxinus excelsior with different susceptibility to the ash dieback pathogen Hymenoscyphus pseudoalbidus and their response to the phytotoxin viridiol - a metabolomic and microscopic study

Eight European ash (Fraxinus excelsior) genotypes with different known susceptibility to Hymenoscyphus pseudoalbidus were tested against the phytotoxin viridiol and their response described at the microscopic and metabolomic level. All ash genotypes were sensitive to the toxin and necrosis was detectable after 24h. Among the three viridiol concentrations used in the experiment, the lowest concentration (14.7μM) yielded markedly lower mean damage scores compared to those resulting from seedlings tested at higher dosages. The highest damage scores were associated with the susceptible ash clones S-101, S-106 and S-125, but also with resistant clone R-104. Three resistant clones (R-131, R-121, and R-118) had lower mean damage scores compared to susceptible clones. Wilting of leaves was more common 48h after treatment and more pronounced on seedlings with high damage scores. The resulting lesions generally lacked browning of tissue and displayed only surface disruption of cells in direct contact with the toxin. A delay in symptom development was evident on all five resistant clones tested with the two higher concentrations of viridiol. LC-HRMS and MS/MS analyses of ash seedling extracts suggest several secoiridoid compounds as well as compounds related to abscisic acid (ABA) to be produced in response to viridiol. ABA-cysteine and xanthoxin were found at significantly higher concentrations in susceptible clones compared to resistant clones after treatment with viridiol, suggesting a primary role of ABA in response to stress. The results observed in this study suggest that genetic resistance to H. pseudoalbidus among ash genotypes may be explained, in part, by the varied response to phytotoxins produced by the fungus.

Distribution and evolution of het gene homologs in the basidiomycota

In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.

Biogeographical patterns and determinants of invasion by forest pathogens in Europe

A large database of invasive forest pathogens (IFPs) was developed to investigate the patterns and determinants of invasion in Europe. Detailed taxonomic and biological information on the invasive species was combined with country-specific data on land use, climate, and the time since invasion to identify the determinants of invasiveness, and to differentiate the class of environments which share territorial and climate features associated with a susceptibility to invasion. IFPs increased exponentially in the last four decades. Until 1919, IFPs already present moved across Europe. Then, new IFPs were introduced mainly from North America, and recently from Asia. Hybrid pathogens also appeared. Countries with a wider range of environments, higher human impact or international trade hosted more IFPs. Rainfall influenced the diffusion rates. Environmental conditions of the new and original ranges and systematic and ecological attributes affected invasiveness. Further spread of established IFPs is expected in countries that have experienced commercial isolation in the recent past. Densely populated countries with high environmental diversity may be the weakest links in attempts to prevent new arrivals. Tight coordination of actions against new arrivals is needed. Eradication seems impossible, and prevention seems the only reliable measure, although this will be difficult in the face of global mobility.

Retracing the routes of introduction of invasive species: the case of the Sirex noctilio woodwasp

Understanding the evolutionary histories of invasive species is critical to adopt appropriate management strategies, but this process can be exceedingly complex to unravel. As illustrated in this study of the worldwide invasion of the woodwasp Sirex noctilio, population genetic analyses using coalescent-based scenario testing together with Bayesian clustering and historical records provide opportunities to address this problem. The pest spread from its native Eurasian range to the Southern Hemisphere in the 1900s and recently to Northern America, where it poses economic and potentially ecological threats to planted and native Pinus spp. To investigate the origins and pathways of invasion, samples from five continents were analysed using microsatellite and sequence data. The results of clustering analysis and scenario testing suggest that the invasion history is much more complex than previously believed, with most of the populations being admixtures resulting from independent introductions from Europe and subsequent spread among the invaded areas. Clustering analyses revealed two major source gene pools, one of which the scenario testing suggests is an as yet unsampled source. Results also shed light on the microevolutionary processes occurring during introductions, and showed that only few specimens gave rise to some of the populations. Analyses of microsatellites using clustering and scenario testing considered against historical data drastically altered our understanding of the invasion history of S. noctilio and will have important implications for the strategies employed to fight its spread. This study illustrates the value of combining clustering and ABC methods in a comprehensive framework to dissect the complex patterns of spread of global invaders.

Gene expression associated with vegetative incompatibility in Amylostereum areolatum

In filamentous fungi, vegetative compatibility among individuals of the same species is determined by the genes encoded at the heterokaryon incompatibility (het) loci. The hyphae of genetically similar individuals that share the same allelic specificities at their het loci are able to fuse and intermingle, while different allelic specificities at the het loci result in cell death of the interacting hyphae. In this study, suppression subtractive hybridization (SSH) followed by pyrosequencing and quantitative reverse transcription PCR were used to identify genes that are selectively expressed when vegetatively incompatible individuals of Amylostereum areolatum interact. The SSH library contained genes associated with various cellular processes, including cell-cell adhesion, stress and defence responses, as well as cell death. Some of the transcripts encoded proteins that were previously implicated in the stress and defence responses associated with vegetative incompatibility. Other transcripts encoded proteins known to be associated with programmed cell death, but have not previously been linked with vegetative incompatibility. Results of this study have considerably increased our knowledge of the processes underlying vegetative incompatibility in Basidiomycetes in general and A. areolatum in particular.

Genetic linkage map for Amylostereum areolatum reveals an association between vegetative growth and sexual and self-recognition

Amylostereum areolatum is a filamentous fungus that grows through tip extension, branching and hyphal fusion. In the homokaryotic phase, the hyphae of different individuals are capable of fusing followed by heterokaryon formation, only if they have dissimilar allelic specificities at their mating-type (mat) loci. In turn, hyphal fusion between heterokaryons persists only when they share the same alleles at all of their heterokaryon incompatibility (het) loci. In this study we present the first genetic linkage map for A. areolatum, onto which the mat and het loci, as well as quantitative trait loci (QTLs) for mycelial growth rate are mapped. The recognition loci (mat-A and het-A) are positioned near QTLs associated with mycelial growth, suggesting that the genetic determinants influencing recognition and growth rate in A. areolatum are closely associated. This was confirmed when isolates associated with specific mat and het loci displayed significantly different mycelial growth rates. Although the link between growth and sexual recognition has previously been observed in other fungi, this is the first time that an association between growth and self-recognition has been shown.

Afforestation of abandoned farmland with conifer seedlings inoculated with three ectomycorrhizal fungi - impact on plant performance and ectomycorrhizal community

The aim of a 3-year study was to investigate whether inoculation of Pinus sylvestris L. and Picea abies (L.) Karst. seedlings with mycorrhizas of Cenococcum geophilum Fr., Piceirhiza bicolorata, and Hebeloma crustuliniforme (Bull.) Quel. has any impact on: 1) survival and growth of outplanted seedlings on abandoned agricultural land, and 2) subsequent mycorrhizal community development. For inoculation, the root system of each plant was wrapped in a filter paper containing mycelium, overlaid with damp peat-sand mixture and wrapped in a paper towel. In total, 8,000 pine and 8,000 spruce seedlings were planted on 4-ha of poor sandy soil in randomized blocks. Already after the first year natural mycorrhizal infections prevailed in the inoculated root systems, and introduced mycorrhizas were seldom found. Yet, the seedlings that had been pre-inoculated with C. geophilum and the P. bicolorata during the whole 3-year period showed significantly higher survival and growth as compared to controls. Moreover, the independent colonization of roots by C. geophilum and the P. bicolorata from natural sources was also observed. A diverse mycorrhizal community was detected over two growing seasons in all treatments, showing low impact of inoculation on subsequent fungal community development. A total of 19 additional ectomycorrhizal morphotypes was observed, which clustered into two well-separated groups, according to host tree species (pine and spruce). In conclusion, the results showed limited ability to increase tree survival and growth, and to manipulate the mycorrhizal community even by extensive pre-inoculations, indicating that fungal community formation in root systems is governed mainly by environmental factors.

Parental tracking in the postfire wood decay ascomycete Daldinia loculata using highly variable nuclear gene loci

The origin of the male and female gametes involved in fertilization events within a local population of the postfire wood decay ascomycete Daldinia loculata was investigated by genotyping the mycelia growing in the wood and the sexual ascospores, using three highly variable nuclear gene loci. The study was conducted in a geographically isolated burned forest site in southern Sweden. An intensive sampling was performed by collecting stromata containing ascospores and wood samples containing mycelia. In total, from 32 mapped burned birches, cultures of 22 haploid genets from decayed wood and six ascospores from each of 19 stromata were isolated and analysed. In 80% of the investigated burned branches, only one genet was found. From the analysis of the ascospore genotypes, we detected 30 fertilization events and 60% of them were the result of mating between conidia (clonal propagules) acting as male gametes and the genets in the branches representing the female gametes. The male parents producing the conidia were detected within the same local population as the female parents in 27% of the fertilization events and originated either from the same branch or from different trees located at 0.5-36 m away from the female parents. In 33% of the fertilization events, conidia originated from three male parents that were not found within the local population sampled. These parents could be anywhere inside or outside the sampled area. For the remaining fertilization events, we could not rule out the ascospores or the conidia as fertilizing propagules. No strong evidence for fertilization by recombinant propagules (ascospores) was detected in this study. The pyrophilous insect species associated with conidia of D. loculata are suggested to be essential vectors for the realization of the sexual cycle of this fungal species. By feeding on the conidia and flying between nearby trees inhabiting wood decay mycelia, these insects allow the transfer of conidia and therefore the opposite mating types to meet within a localized burned forest site.

Genetic differentiation in Eurasian populations of the postfire ascomycete Daldinia loculata

The genetic population structure of the postfire ascomycete Daldinia loculata was studied to test for differentiation on a continental scale. Ninety-six samples of spore families, each comprising mycelia from six to 10 spores originating from single perithecia, were sampled from one Russian and six Fennoscandian forest sites. Allelic distribution was assayed for six nuclear gene loci by restriction enzyme analyses of polymerase chain reaction (PCR)-amplified gene fragments. In addition, the full sequence of the gene fragment was analysed for a subset of haploid single-ascospore isolates in a multiallelic approach. A third data set was generated by using arbitrary-primed PCR with the core sequence of the phage M13 as primer. Although there was a reduction in heterozygosity in the total population from what would have been expected at random mating, the levels of genetic differentiation among the Eurasian subpopulations of D. loculata were low. All subpopulations were found to be in Hardy-Weinberg equilibrium and gametic equilibrium was observed between all investigated nuclear gene loci. The results obtained by the different markers were consistent; we confirmed low levels of genetic differentiation among the Eurasian subpopulations of D. loculata. The differentiation did not increase with distance; the Russian subpopulation, sampled more than 7000 km from the Fennoscandian subpopulations, was only moderately differentiated from the others (FST = 0.00-0.14). In contrast, one of the Swedish populations was the most highly differentiated from the others, with FST and GST values of 0.10-0.16. The results suggest that D. loculata consists of a long-lived background Eurasian population of latent mycelia in nonburned forests, established by sexual ascospores dispersed from scattered burned forest sites. Local differentiation is probably due to founder effects of populations in areas with low fire frequency. A tentative life cycle of D. loculata is presented.

Mitochondrial control of fungal hybrid virulence

Hybrid species of fungal pathogens that infect wild and cultivated plants are emerging with new virulence and host ranges, posing a threat to agriculture and forestry. Here we show that the virulence of hybrid species of the basidiomycete fungus Heterobasidion annosum (Fr) Bref, a causal agent of root and butt rot in conifers and one of the most economically important forest pathogens, is controlled by their mitochondrial genome. Our results indicate that cooperation between organelles that contain genetic information may influence the phenotype of hybrid phytopathogens.

Pyrone and pyridone compounds in the liquid culture of Physisporinus sanguinolentus

Chromatographic separation of the liquid culture filtrate of the basidiomycete fungus Physisporinus sanguinolentus has yielded three new compounds viz., 2-methyl-4-pyrone, 2-methyl-5,6-dihydro-4-pyrone and the pyridone form of 4-hydroxy-2-methylpyridine, together with the known triacetic acid lactone, the sesquiterpene dialdehyde merulidial and a derivative of merulidial. Their structures were elucidated by spectroscopic analysis and by comparison to literature data and a synthetic sample. One of the compounds, merulidial, was shown to inhibit the germination of spores and the hyphal growth of the wood-rotting basidiomycete Heterobasidion annosum and the saprophytic mould Cladosporium cucumerinum.

Diversity and abundance of resupinate thelephoroid fungi as ectomycorrhizal symbionts in Swedish boreal forests

Resupinate thelephoroid fungi (hereafter called tomentelloid fungi) have a world-wide distribution and comprise approximately 70 basidiomycete species with inconspicuous, resupinate sporocarps. It is only recently that their ability to form ectomycorrhizas (EM) has been realized, so their distribution, abundance and significance as mycobionts in forest ecosystems is still largely unexplored. In order to provide baseline data for future ecological studies of tomentelloid fungi, we explored their presence and abundance in nine Swedish boreal forests in which the EM communities had been analysed. Phylogenetic analyses were used to compare the internal transcribed spacer of nuclear ribosomal DNA (ITS rDNA) sequence data obtained from mycobionts on single ectomycorrhizal tips with that obtained from sporocarps of identified tomentelloid fungi. Five species of Tomentella and one species of Pseudotomentella were identified as ectomycorrhizal fungi. The symbiotic nature of Tomentella bryophila, T. stuposa, T. badia and T. atramentaria is demonstrated for the first time. T. stuposa and Pseudotomentella tristis were the most commonly encountered tomentelloid fungi, with the other species, including T. sublilacina, only being recorded from single stands. Overall, tomentelloid fungi were found in five of the studies, colonizing between 1 and 8% of the mycorrhizal root tips. Two of the five sites supported several tomentelloid species. Tomentelloid fungi appear to be relatively common ectomycorrhizal symbionts with a wide distribution in Swedish coniferous forests. The results are in accordance with accumulating data that fungal species which lack conspicuous sporocarps may be of considerable importance in EM communities.

Spatiotemporal Patterns of Laccase Activity in Interacting Mycelia of Wood-Decaying Basidiomycete Fungi

A BSTRACTInterspecific fungal interactions are important ecological processes, whereas their physiological mechanisms are little understood. The aim of this work was to study how activity of fungal extracellular laccase was changed across mycelia during interactions between white- and brown-rot basidiomycetes from different wood decay stages. Qualitative assay of eight species interacting with each other in all combinations showed four spatial patterns of laccase activity: (I) laccase activity present both in contact zone and mycelium, (II) laccase activity only in contact zone, (III) laccase activity in mycelium but not in contact zone, (IV) no laccase activity. Presence of laccase activity only in the contact zone was more frequent than expected from random samples associated with mycelia that replaced other ones. On the other hand, the presence of laccase activity in the mycelium but not in the contact zone was only attributed to fungal species that were replaced by their antagonists. After one month, laccase activity was distributed over mycelia more homogeneously than after 6 days of interactions. In interacting mycelia, laccase activity was higher than in control and increasing with time. Saprotrophic fungi from late successional stages of wood decay generally had higher laccase activity than early succession saprotrophic and pathogenic fungi. The qualitative assays were confirmed by quantitative assay of total laccase activity. Significance of the results in antagonistic fungal interactions as well as in the processes of hyphal tip growth and mycelium senescence is discussed.

Biochemical interactions of conifer seedling roots with Fusarium spp

The importance of root and spore surface molecules in the interactions of Fusarium spp. with conifer roots, and cellular localization of proteins presumed to be involved in host defence, were investigated. For adhesion studies, using a combination of fluorescein isothiocyanate (FITC) labelled lectins and high perfomance liquid chromatography (HPLC), several sugars (pinitol, xylitol, galactose, mannose, and glucose) were detected in root surface mucilage. Both artificial substrata and detached living roots were used to evaluate the significance of selective removal of root or spore surface components on the adhesion process. The spores or roots were pretreated with either periodic acid, pronase E, potassium hydroxide or diethyl ether. Pretreatment of the spores with diethyl ether reduced significantly the level of spore adhesion, which suggests that the adhesive component is either a lipid, or is bound to lipid. Since oxidation of carbohydrate reactive sites with periodic acid on the root surface almost completely abolished the development of germ tubes by adherent spores, it was presumed that some of these periodate-sensitive substances serve as a nutrient source for the fungus. On inoculated roots, F. avenaceum and F. culmorum were significantly pathogenic to both Norway spruce and Scots pine seedlings. Cytochemical labelling of sites of accumulation of host defence molecules within infected root tissues using anti-peroxidase demonstrated increased peroxidase activity in host cell walls. With anti-chitinase and anti-glucanase, gold labelling was found mainly on pathogen hyphal walls.Key words: conifer seedlings, adhesion, Fusarium spp., PR proteins, immunolocalization, lectins.

Population structure of the wood decay fungus Fomitopsis pinicola

Three populations of the wood decay fungus Fomitopsis pinicola, one from each of three countries (Sweden, Russia and Lithuania), were studied by means of arbitrary primed PCR. The genetic structure of the populations was assessed by inferring the genotype of the genets by studying the haplotypes of several single-spore isolates from one sporocarp for each individual. Heterozygotes could therefore be detected with a dominant genetic marker. The amplified band and the null allele of all loci segregated in a way that was in agreement with a 50:50 ratio. Genetic analysis showed that the total population as well as the subpopulations had heterozygote frequencies in agreement with Hardy-Weinberg expectations. No population differentiation was detected in spite of large geographical distances among the populations studied. We also compared the methods of somatic incompatibility and AP-PCR in terms of their value in detecting fungal genets. This was tested for a sample of dikaryotic mycelia from Switzerland. For the tested material the two methods gave congruent results.

Genetic differentiation in Fomitopsis pinicola (Schwarts: Fr.) Karst studied by means of arbitrary primed-PCR

Genetic variation within and among one Finnish and three Swedish populations of Fomitopsis pinicola (Schwarts: Fr.) Karst. were studied by amplifying DNA from haploid isolates originating from single spore cultures using two arbitrary primers. Analysis offspring from single fruit bodies revealed only three pairs of codominant alleles among 42 variable genetic markers, the remaining 38 segregated independently. Genetic similarity was measured in terms of Euclidean distance. Individuals in the Finnish population tended to form a distinct cluster in the principal component analysis. Variation within and among populations/regions was partitioned by Analysis of Molecular Variance-AMOVA. Within population variation accounted for 91.6% of the total genetic variation. The remaining 7.68% was accounted for by variation between the Finnish population and each of the three Swedish ones. Variation among the Swedish populations accounted for only 0.72% of the total variation. Wright's Fst was 0.17 for all four populations and 0.13 for the three Swedish populations. These relatively low values indicate that there is gene flow among all populations or that they are derived from a common ancestral population. The observed pattern of genetic variation is probably the result of effective spore dispersal and the continuous distribution of this common early successional species.

Population structure and decay pattern of Phellinus tremulae in Populus tremula as determined by somatic incompatibility

Isolates of the wood-decaying basidiomycete Phellinus tremulae were obtained from four different stands of aspen Populus tremula in the south of Sweden. Studies were made of somatic incompatibility among all isolated within each site. No genet could be found in more than one tree. From one stand, two trees were felled and samples were taken from stem discs every half metre up to 13 m. Eight genets were isolated from the two trees, four in each tree. Fungal DNA was amplified from five isolates representing three different genets in one tree. The core sequence of M13 was used as primer. The results agreed with those of the somatic incompatibility test. Forty-five samples were taken from small twigs from healthy-looking branches and trees, and isolates of Phellinus tremulae were obtained from three of them. The likely route of infection of Phellinus tremulae in aspen is discussed. Key words: somatic incompatibility, Phellinus tremulae, Populus tremula.

Tansley Review No. 19 Environmental and endogenous controls of developmental pathways: variation and its significance in the forest pathogen, Heterobasidion annosum

Cultural studies of the forest root pathogen Heterobasidion annosum (Fr.) Bref. have shown that the mycelium of the fungus possesses a high degree of developmental versatility, being able to grow in a variety of distinctive functional modes. Consequently the fungus can alternate between conidiogenous and meiotic reproductive pathways, rapid, sparsely branched and slow, densely branched mycelial extension, nutritive and non-nutritive modes, and'juvenile'and 'senescent'phases. This ability is probably of considerable importance in natural infection cycles and provides an interesting model for examining interrelationships between developmental regulation and host-pathogen interactions generally. It also raises important questions about the interface between environmental and endogenous controls of developmental pathways. CONTENTS Summary 245 I. Introduction 245 II. Spore germination and mycelial extension 246 III. Production of non-nutritive mycelium 249 IV. Sporophore production, senescence, somatic incompatibility and extracellular enzyme production 251 V. Discussion 254 Acknowledgements 255 References 255.