Mycorrhization of Pecan trees (Carya illinoinensis) with commercial truffle species: Tuber aestivum Vittad. and Tuber borchii Vittad

Pecan (Carya illinoinensis) is an economically important nut tree native to the Mississippi basin and cultivated worldwide. In North America, species of truffles are regularly found fruiting in productive pecan orchards and the truffle genus Tuber appears to be abundant in pecan ectomycorrhizal (EM) communities. As an initial step to determine the feasibility of co-cropping European truffle species with pecan, we evaluated whether mycorrhizae of highly esteemed European truffle species (Tuber aestivum Vittad. T. borchii and T. macrosporum) could be formed on pecan seedlings. Seedlings were inoculated with truffle spores and were grown in a greenhouse for 10?months. Levels of EM colonization were estimated visually and quantified by counting EM tips. Ectomycorrhizae were identified both morphologically and molecularly with species-specific amplification and by sequencing of the ITS region of the nuclear ribosomal DNA (nrDNA). Both T. borchii and T. aestivum spores produced well-formed ectomycorrhizae on pecan seedlings with average root colonization levels of about 62% and 42%, respectively, whereas no ectomycorrhizae of T. macrosporum were formed. The anatomy and morphology of these truffle ectomycorrhizae on pecan was characterized. The co-cropping of T. aestivum and T. borchii may hold promise as an additional stream of revenue to pecan growers, although, further studies are needed to assess whether this symbiosis is maintained after planting in the field and whether truffle production can be supported by this host species.     

Tuber aestivum Vittad. mycelium quantified: advantages and limitations of a qPCR approach

A quantitative real-time PCR (qPCR) marker Ta0 with hydrolysis probe (“TaqMan”), targeted to the internal transcribed spacer region of the ribosomal DNA, has been developed for quantification of summer truffle (Tuber aestivum) mycelium. Gene copy concentrations determined by the qPCR were calibrated against pure culture mycelium of T. aestivum, enabling quantification of the mycelium in soil and in host roots from the fields. Significant concentrations of the fungus were observed not only in the finest roots with ectomycorrhizae but also in other root types, indicating that the fungus is an important component of the microbial film at the root surface. The concentration of T. aestivum in soil is relatively high compared to other ectomycorrhizal fungi. To evaluate the reliability of the measurement of the soil mycelium density using qPCR, the steady basal extracellular concentration of the stabilized T. aestivum DNA should be known and taken into account. Therefore, we addressed the stability of the qPCR signal in soil subjected to different treatments. After the field soil was sieved, regardless of whether it was dried/rewetted or not, the T. aestivum DNA was quickly decomposed. It took just about 4 days to reach a steady concentration. This represents a conserved pool of T. aestivum DNA and determines detection limit of the qPCR quantification in our case. When the soil was autoclaved and recolonized by saprotrophic microorganisms, this conserved DNA pool was eliminated and the soil became free of T. aestivum DNA.     

Comparison of Chemical Composition in Tuber aestivum Vittad. of Different Geographical Origin

Truffles are prized and nutrition‐rich edible hypogeous fungi. The aim of this study was a comprehensive investigation of chemical composition of Burgundy truffle (Tuber aestivum Vittad .). We tried to answer the question: what is the impact of the environment on the truffle quality. To know the nutritional value of Burgundy truffle we compared lipids, proteins, saccharides, polyphenolics, flavonoids, total sterols, ergosterol, volatile flavour and aroma compounds content in fruit bodies of the fungus collected in three different geographical regions, i.e., Poland, Slovakia, and Italy. A comparison of the above mentioned compounds is especially interesting due to environmental and climatic differences among the studied geographical regions. Results revealed that fruit bodies of T. aestivum from Poland and Slovakia possessed nearly similar content of proteins, total sterols, and saccharides. The fruiting bodies from Italy contained significantly larger amounts of most of the investigated compounds. In turn, Polish specimens had higher content of lipids and polyphenolics than Slovak and Italian ones. We have found higher similarity of volatile compounds composition between Polish and Italian specimens than those of Polish and Slovak origin.     

Phylogenetic Characterization and In Situ Detection of a Cytophaga-Flexibacter-Bacteroides Phylogroup Bacterium in Tuber borchii Vittad. Ectomycorrhizal Mycelium

Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5′ and 3′ ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of T. borchii Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each T. borchii mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to the Cytophaga-Flexibacter-Bacteroides (CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus T. borchii was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the Cytophaga-Flexibacter phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genus Tuber.     

The cultivation of oak seedlings inoculated with Tuber aestivum Vittad. in the boreal region of Finland

Despite recent findings, truffles are rarely found in Finland. In 2006, we began to explore the cultivation potential of Tuber aestivum/uncinatum in Finland. In 2006–2008, roughly 1,200 Quercus robur seedlings and 200 Q. pubescens seedlings were planted in 20 orchards. We aimed to challenge the Southern European (France) tree provenances of oak seedlings in a boreal climate. Additional winter coverings made up of fabric or plastic and twigs prevented the seedlings’ mortality even when the air temperature was below ?30 °C during the second winter. The results showed that the top soil temperature at 15 cm depth has to be above ?5 °C to guarantee the survival of seedlings. Q. pubescens was more sensitive to low soil temperatures than Q. robur. Morphological and PCR analysis of root samples collected over 2007–2010 confirmed the presence of T. aestivum in all orchards despite unfavorable temperatures during the winter time. The first T. aestivum sporocarps were found under Q. robur in October 2012 in the orchards established in 2006 on old agricultural land, showing truffle cultivation to be successful in the boreal climate.     

Detection of summer truffle (Tuber aestivum Vittad.) in ectomycorrhizae and in soil using specific primers

Tuber aestivum is becoming an important commodity of great economical value in some European countries. At the same time, it is a highly protected organism in other countries, where it needs careful treatment. A reliable method of detection in roots and soil is thus needed for assessment of geographic distribution, ecological studies and inoculation efficiency testing in man-made experiments. A PCR-based method of detection of T. aestivum using specific primers was therefore developed. A pair of PCR primers Tu1sekvF/Tu2sekvR selective for T. aestivum and some genotypes of Tuber mesentericum was designed on the basis of the known internal transcribed spacer T. aestivum sequences. TaiI restriction cleavage was then used to distinguish the two species. The selectivity of the designed primer pair was evaluated using DNA extracted from specimens of a further 13 Tuber spp. Subsequently, the selectivity and robustness to false-positive results with nontarget DNA of the designed primers was compared with two other primer pairs (UncI/UncII and BTAE-F/BTAEMB-R). The occurrence of T. aestivum in soil and ectomycorrhizae collected in its native habitat has been successfully detected using the designed primers and nested PCR. The method is reliable and thus suitable for detection of T. aestivum in the field.     

Deconstructing spatial patterns in species composition of ectoparasite communities: the relative contribution of host composition,environmental variables and geography

Aim We determined whether dissimilarity in species composition between parasite communities depends on geographic distance, environmental dissimilarity or host faunal dissimilarity, for different subsets of parasite species with different levels of host specificity. Location Communities of fleas parasitic on small mammals from 28 different regions of the Palaearctic. Method Dissimilarities in both parasite and host species composition were computed between each pair of regions using the Bray–Curtis index. Geographic distances between regions were also calculated, as were measures of environmental dissimilarity consisting of the pairwise Euclidean distances between regions derived from elevation, vegetation and climatic variables. The 136 flea species included in the dataset were divided into highly host‐specific species (using 1–2 host species per region, on average), moderately host‐specific species (2.2–4 hosts per region) and generalist species (>4 hosts per region). The relative influence of geographic distance, host faunal dissimilarity and environmental dissimilarity on dissimilarity of flea species composition among all regions was analysed for the entire set of flea species as well as for the three above subsets using multiple regressions on distance matrices. Results When including all flea species, dissimilarity in flea species composition was affected by all three independent variables, although the pure effect of dissimilarity in host species composition was the strongest. Results were different when the subsets of fleas differing in host specificity were treated separately. In particular, dissimilarity in species composition of highly host‐specific fleas increased solely with environmental dissimilarity, whereas dissimilarity for both moderately specific and non‐specific fleas increased with both geographic distance and dissimilarity in host species composition. Main conclusions Host specificity seems to dictate which of the three factors considered is most likely to affect the dissimilarity between flea communities. Counter‐intuitively, environmental dissimilarity played a key role in determining dissimilarity in species composition of highly host‐specific fleas, possibly because, although their presence in a region relies on the occurrence of particular host species, their abundance is itself mostly determined by climatic conditions. Our results show that deconstructing communities into subsets of species with different traits can make it easier to uncover the mechanisms shaping geographic patterns of diversity.     

Enolase from the ectomycorrhizal fungus Tuber borchii Vittad.: biochemical characterization, molecular cloning, and localization

Enolase from Tuber borchii mycelium was purified to electrophoretical homogeneity using an anion-exchange and a gel permeation chromatography. Furthermore, the corresponding gene (eno-1) was cloned and characterized. The purified enzyme showed a higher affinity for 2-PGA (0.26 mM) with respect to PEP; the stability and activity of enolase were dependent of the divalent cation Mg2+. T. borchii eno-1 has an ORF of 1323 bp coding for a putative protein of 440 amino acids and Southern blotting analysis revealed that the gene is present as a single copy in T. borchii. The enzymatic activity and the mRNA expression level evaluated in mycelia grown either in different carbon sources, in pyruvate or during starvation were the same in all the conditions tested, while biochemical and Northern blotting analyses performed with mycelia at different days of growth showed T. borchii eno-1 regulation in response to the growth phase. Finally, Western blotting analysis demonstrated that enolase is localized only in the cytosolic fraction confirming its important role in glycolysis.     

Ectomycorrhizal fungal communities in late-successional Swedish boreal forests, and their composition following wildfire

This study was conducted to evaluate the effects of wildfires on ectomycorrhizal (EM) fungal communities in Scots pine ( Pinus sylvestris ) stands. Below- and above-ground communities were analysed in terms of species richness and evenness by examining mycorrhizas and sporocarps in a chronosequence of burned stands in comparison with adjacent unburned late-successional stands. The internal transcribed spacer (ITS)-region (rDNA) of mycobionts from single mycorrhizas was digested with three restriction enzymes and compared with an ITS–restriction fragment length polymorphism (RFLP) reference database of EM sporocarps. Spatial variation seemed to be more prominent than the effects of fire on the EM fungal species composition. Most of the common species tended to be found in all sites, suggesting that EM fungal communities show a high degree of continuity following low-intensity wildfires. Species richness was not affected by fire, whereas the evenness of species distributions of mycorrhizas was lower in the burned stands. The diversity of EM fungi was relatively high considering that there were only three EM tree species present in the stands. In total, 135 EM taxa were identified on the basis of their RFLP patterns; 66 species were recorded as sporocarps, but only 11 of these were also recorded as mycorrhizas. The species composition of the below-ground community of EM fungi did not reflect that of the sporocarps produced. EM fungal species present in our ITS–RFLP reference database accounted for 54–99% of the total sporocarp production in the stands, but only 0–32% of the mycorrhizal abundance.     

Sponge communities of the Antarctic Peninsula: influence of environmental variables on species composition and richness

Sponge communities on the Antarctic continental shelf currently represent one of the most extensive sponge grounds in the world, and all sponge classes are known to occur in the Southern Ocean. Main objectives of this study conducted at the tip of the Antarctic Peninsula were (1) to identify all sampled sponges and (2) to investigate whether the species composition and species richness of Southern Ocean sponge communities in the area of the Antarctic Peninsula are significantly influenced by environmental variables. The studied material originated from 25 AGT catches and was sampled during the expedition ANT-XXIX/3 of RV Polarstern. Samples were collected in three large-scale areas in the vicinity of the Antarctic Peninsula: Bransfield Strait, Drake Passage and Weddell Sea. The following six environmental variables were measured from bottom water samples (except for sea-ice cover): depth (m), light transmission (%), oxygen (µmol/kg), salinity, sea-ice cover (%) and temperature (°C). Two hundred and sixty-three sponge samples were analyzed, and 81 species of 33 genera from all Porifera classes (Calcarea, Demospongiae, Hexactinellida and Homoscleromorpha) were identified. Total numbers of sponge species per sample station ranged from 1 to 29. A detrended correspondence analysis and a backward-stepwise model selection were performed to check whether species composition and richness were significantly influenced by environmental variables. The analyses revealed that none of the measured environmental variables significantly influenced species composition but that species richness was significantly influenced by (1) temperature and (2) the combination of temperature and depth. Results of this study are of crucial importance for development, performance and assessment of future protection strategies in case of ongoing climatic changes at the Antarctic Peninsula.     

Root hemiparasites in productive communities should attack competitive host,and harm them to make regeneration gaps

Demey et al. (2015, this issue) present evidence that root hemiparasitic plants can affect their host community through selectively parasitizing the species within it (with large differences between host species within functional groups), and by promoting seedling establishment through creating gaps. The hemiparasite needs to maintain the host for its water and nutrient supply, but also limit competition for light.     

A global meta-analysis of Tuber ITS rDNA sequences: species diversity, host associations and long-distance dispersal

Truffles (Tuber) are ectomycorrhizal fungi characterized by hypogeous fruitbodies. Their biodiversity, host associations and geographical distributions are not well documented. ITS rDNA sequences of Tuber are commonly recovered from molecular surveys of fungal communities, but most remain insufficiently identified making it difficult to determine whether these sequences represent conspecific or novel taxa. In this meta-analysis, over 2000 insufficiently identified Tuber sequences from 76 independent studies were analysed within a phylogenetic framework. Species ranges, host associates, geographical distributions and intra- and interspecific ITS variability were assessed. Over 99% of the insufficiently identified Tuber sequences grouped within clades composed of species with little culinary value (Maculatum, Puberulum and Rufum). Sixty-four novel phylotypes were distinguished including 36 known only from ectomycorrhizae or soil. Most species of Tuber showed 1-3% intraspecific ITS variability and >4% interspecific ITS sequence variation. We found 123 distinct phylotypes based on 96% ITS sequence similarity and estimated that Tuber contains a minimum of 180 species. Based on this meta-analysis, species in Excavatum, Maculatum and Rufum clades exhibit preference for angiosperm hosts, whereas those in the Gibbosum clade are preferential towards gymnosperms. Sixteen Tuber species (>13% of the known diversity) have putatively been introduced to continents or islands outside their native range.     

Nonhost species reduce parasite infection in a focal host species within experimental fish communities

The dilution effect describes the negative association between host biodiversity and the risk of infectious disease. Tests designed to understand the relative roles of host species richness, host species identity, and rates of exposure within experimental host communities would help resolve ongoing contention regarding the importance and generality of dilution effects. We exposed fathead minnows to infective larvae of the trematode, Ornithodiplostomum ptychocheilus in minnow‐only containers and in mixed containers that held 1–3 other species of fish. Parasite infection was estimated as the number of encysted worms (i.e., brainworms) present in minnows following exposure. The results of exposure trials showed that nonminnow fish species were incompatible with O. ptychocheilus larvae. There was no reduction in mean brainworm counts in minnows in mixed containers with brook sticklebacks or longnose dace. In contrast, brainworm counts in minnows declined by 51% and 27% in mesocosms and aquaria, respectively, when they co‐occurred with emerald shiners. Dilution within minnow + shiner containers may arise from shiner‐induced alterations in minnow or parasite behaviors that reduced encounter rates between minnows and parasite larvae. Alternatively, shiners may act as parasite sinks for parasite larvae. These results highlight the role of host species identity in the dilution effect. Our results also emphasize the complex and idiosyncratic effects of host community composition on rates of parasite infection within contemporary host communities that contain combinations of introduced and native species.     

Tissue age,orchard location and disease management influence the composition of fungal and bacterial communities present on the bark of apple trees

Plants host microbial communities that can be affected by environmental conditions and agronomic practices. Despite the role of bark as a reservoir of plant pathogens and beneficial microorganisms, no information is available on the effects of disease management on the taxonomic composition of the bark-associated communities of apple trees. We assessed the impact of disease management strategies on fungal and bacterial communities on the bark of a scab-resistant apple cultivar in two orchard locations and for two consecutive seasons. The amplicon sequencing revealed that bark age and orchard location strongly affected fungal and bacterial diversity. Microbiota dissimilarity between orchards evolved during the growing season and showed specific temporal series for fungal and bacterial populations in old and young bark. Disease management did not induce global changes in the microbial populations across locations and seasons, but specifically affected the abundance of some taxa according to bark age, orchard location and sampling time. Therefore, the disease management applied to scab-resistant cultivars, which is based on a limited use of fungicides, partially changed the taxonomic composition of bark-associated fungal and bacterial communities, suggesting the need for a more accurate risk assessment regarding possible pathogen outbreaks.     

Phylogenetic characterization and in situ detection of a Cytophaga-Flexibacter-Bacteroides phylogroup bacterium in Tuber borchii vittad. Ectomycorrhizal mycelium

Mycorrhizal ascomycetous fungi are obligate ectosymbionts that colonize the roots of gymnosperms and angiosperms. In this paper we describe a straightforward approach in which a combination of morphological and molecular methods was used to survey the presence of potentially endo- and epiphytic bacteria associated with the ascomycetous ectomycorrhizal fungus Tuber borchii Vittad. Universal eubacterial primers specific for the 5' and 3' ends of the 16S rRNA gene (16S rDNA) were used for PCR amplification, direct sequencing, and phylogenetic analyses. The 16S rDNA was amplified directly from four pure cultures of T. borchii Vittad. mycelium. A nearly full-length sequence of the gene coding for the prokaryotic small-subunit rRNA was obtained from each T. borchii mycelium studied. The 16S rDNA sequences were almost identical (98 to 99% similarity), and phylogenetic analysis placed them in a single unique rRNA branch belonging to the Cytophaga-Flexibacter-Bacteroides (CFB) phylogroup which had not been described previously. In situ detection of the CFB bacterium in the hyphal tissue of the fungus T. borchii was carried out by using 16S rRNA-targeted oligonucleotide probes for the eubacterial domain and the Cytophaga-Flexibacter phylum, as well as a probe specifically designed for the detection of this mycelium-associated bacterium. Fluorescent in situ hybridization showed that all three of the probes used bound to the mycelium tissue. This study provides the first direct visual evidence of a not-yet-cultured CFB bacterium associated with a mycorrhizal fungus of the genus Tuber.     

Ectomycorrhizal mycelial species composition in apatite amended and non-amended mesh bags buried in a phosphorus-poor spruce forest

We studied the effect of apatite amendment on ectomycorrhizal (EM) mycelial biomass production and species composition in a phosphorus-poor spruce forest using sand-filled mesh bags. Control and apatite-amended bags were buried in pairs in the lower part of the organic horizon for one growth season. DNA extraction, PCR of the ITS region, cloning and random sequencing were used to examine the fungal species composition in each bag. Sequences were identified by comparison with the UNITE database and GenBank. Our study confirmed previous results that the major fungal ingrowth in mesh bags was of EM origin. On average 13 species were detected in each bag. Tylospora fibrillosa, Amphinema sp., Tomentellopsis submollis, and Xerocomus badius made up almost 80 % of the EM sequences. High biomass was related to increased dominance of specific species. There were no statistically significant differences in biomass production estimated from PLFA 18:2ω6, 9, or between fungal communities of apatite-amended and control bags estimated from DNA after one growth season. The potential of the mesh bag method in studies of functional diversity of EM mycelia in the field is discussed.     

The influence of fluctuating light intensities on species composition and diversity of natural phytoplankton communities

The influence of fluctuating light intensities on phytoplankton composition and diversity was investigated for 49 days under semi-continuous culture conditions with sufficient nutrient supply, using phytoplankton assemblages from Lake Biwa, Japan. Light conditions were either periodically changed from high intensity (100 µmol photons m^-2 s^-1) to low intensity (20 µmol photons m^-2 s^-1) at intervals of 1, 3, 6 and 12 days, or fixed to constant intensities (permanent high and low light levels). All treatments additionally experienced a day:night cycle of 16:8 h. Phytoplankton abundance increased and reached a saturation level on day 19 of the treatment with permanent high light, but increased continuously until the end of the experiment (day 49) in the treatment with permanent low light intensity. In treatments with periodically changing light intensities, the phytoplankton abundance reached saturation levels between these dates. Under phytoplankton abundance saturation, chlorophytes predominated in the treatment with permanent high light, while either cyanophytes or diatoms were abundant under permanent low light intensity. Treatments with changing light supply had chlorophyte- and cyanobacteria-dominated replicates as well as replicates with balanced proportions of both. Furthermore, species diversity, measured by the Shannon index, was low in cultures under permanent light intensity, while slow fluctuating light at the scale of 3 -12 days resulted in an increased diversity index. These results indicate that species composition and diversity of the phytoplankton were affected by the periodically changing light regime in the order of days, and suggest that temporal changes in weather conditions are a major impediment to competitive exclusion of phytoplankton species in nature.     

Leaf-trait responses to environmental gradients in moorland communities: contribution of intraspecific variation,species replacement and functional group replacement

The values of many important traits of plants in a community change along environmental gradients. Such changes may involve intraspecific variation and replacement by species that have different trait values. We hypothesized that they also involve the variation within and among functional groups (FGs) to the environmental dependence of trait values at the community level. We studied environmental dependence of trait values in 27 moorlands at various scales and analyzed to what extent intraspecific variation, species replacement within FGs and FG replacement contribute to the gradient of community trait values. The community structure in moorlands was influenced mainly by two environmental factors: temperature and water condition. Plants inhabiting sites with low temperature and low-pH generally tended to have lower maximum leaf height, greater leaf mass per area, and smaller leaf size. At the community level, site-mean of maximum leaf height and leaf size generally increased with increasing temperature and water pH. Our analysis demonstrated that the relative contributions of intraspecific variation, species replacement within FGs and FG replacement differed depending on combinations of the traits and environments. The contribution of FG replacement varied considerably among cases (0.6–34.5 %). Species replacement within FGs, which has received little attention in previous studies, was most responsible for the community-level changes (31.6–65.3 %) and intraspecific variation also made a large contribution (22.9–57.9 %). Understanding such various mechanisms involving intraspecific variation and species replacement should help us better predict how the structure and functioning of moorland plant communities will respond to climate change.