Comparison of root-associated communities of native and non-native ectomycorrhizal hosts in an urban landscape

EFECTO DE BORDE EN LA DIVERSIDAD Y COLONIZACIÓN DE ECTOMICORRIZAS DE Quercus humboldtii (FAGACEAE) EN ARCABUCO- BOYACÁ-COLOMBIA

Los robledales en Colombia están dominados por la especie Quercus humboldtii Bonpl. Esta especie se encuentra en categoría de vulnerable debido a la deforestación para generar cultivos, zonas ganaderas y plantaciones de especies exóticas, ocasionando la formación de bordes por el deterioro del ecosistema. Estos bosques establecen asociaciones simbióticas con especies de hongos ectomicorrícicos, permitiendo el intercambio de nutrientes entre las hifas de los hongos y las raíces de las plantas. Este estudio analiza el efecto de borde en un área al interior (BNI-C) y al borde de un bosque de roble no intervenido (BNI-B), además de dos bordes de bosque con intervención antropogénica, una en contacto con plantación de Eucalyptus sp. (BE) y otro con ganadería (BG). Se estableció el borde de bosque mediante variables ambientales (temperatura ambiente, luminosidad temperatura y humedad del suelo). Se colectaron raicillas de siete árboles tanto de interior como de borde para medir la colonización y caracterizar morfológicamente las ectomicorrizas asociadas a las raíces de roble. Se evidenció el efecto de borde en el grado de colonización ectomicorrícica en las raíces de Q. humboldtii con porcentajes de 18 a 30 % en BNI, 15 % en BE y 47 % en BG. Los géneros ectomicorrícicos Cenococcum sp. y Lactarius sp.  presentaron la mayor abundancia en  los tres bosques, variando considerablemente cerca a los bordes en BG y BE. Se evidenciaron cambios de porcentaje de colonización y diversidad de  morfotipos de ectomicorrizas en los bordes de los dos bosques intervenidos.

Mycorrhizal associations of the exotic hickory trees, Carya laciniosa and Carya cordiformis, grown in Kórnik Arboretum in Poland

We studied mycorrhizal associations of North American Carya laciniosa and Carya cordiformis trees, successfully acclimated to local habitat conditions of the historic Kórnik Arboretum in Poland, in order to better understand mycorrhizal host range extensions in new environments. The root systems of Carya seedlings (1-3 years old), regenerated under a canopy of mature hickory trees, were analyzed using microscopic, morphological, and molecular techniques. Our results, for the first time, indicate that C. laciniosa and C. cordiformis have both arbuscular and ectomycorrhizal associations. In the cleared and stained roots of both Carya species, typical structures of arbuscular mycorrhizae (vesicles, arbuscules, hyphal coils, and intercellular nonseptate hyphae) were detected. On the basis of ITS rDNA sequencing, 40 ectomycorrhizal fungal taxa were revealed, with 25 on C. laciniosa and 19 on C. cordiformis. Only four fungal species (Cenococcum geophilum sensu lato, Russula recondita, Xerocomellus cisalpinus, Humaria hemisphaerica) were shared by both Carya species. The high number of infrequent fungal taxa found, as well as the calculated richness estimator, indicates that the real ectomycorrhizal community of C. laciniosa and C. cordiformis is probably richer. The ability of the exotic Carya species to form arbuscular and ectomycorrhizal linkages with native fungi could be a factor in the successful establishment of these tree species under the conditions of Kórnik Arboretum.

Recent Insights on Biological and Ecological Aspects of Ectomycorrhizal Fungi and Their Interactions

The roots of most terrestrial plants are colonized by mycorrhizal fungi. They play a key role in terrestrial environments influencing soil structure and ecosystem functionality. Around them a peculiar region, the mycorrhizosphere, develops. This is a very dynamic environment where plants, soil and microorganisms interact. Interest in this fascinating environment has increased over the years. For a long period the knowledge of the microbial populations in the rhizosphere has been limited, because they have always been studied by traditional culture-based techniques. These methods, which only allow the study of cultured microorganisms, do not allow the characterization of most organisms existing in nature. The introduction in the last few years of methodologies that are independent of culture techniques has bypassed this limitation. This together with the development of high-throughput molecular tools has given new insights into the biology, evolution, and biodiversity of mycorrhizal associations, as well as, the molecular dialog between plants and fungi. The genomes of many mycorrhizal fungal species have been sequenced so far allowing to better understanding the lifestyle of these fungi, their sexual reproduction modalities and metabolic functions. The possibility to detect the mycelium and the mycorrhizae of heterothallic fungi has also allowed to follow the spatial and temporal distributional patterns of strains of different mating types. On the other hand, the availability of the genome sequencing from several mycorrhizal fungi with a different lifestyle, or belonging to different groups, allowed to verify the common feature of the mycorrhizal symbiosis as well as the differences on how different mycorrhizal species interact and dialog with the plant. Here, we will consider the aspects described before, mainly focusing on ectomycorrhizal fungi and their interactions with plants and other soil microorganisms.

Ectomycorrhizal Fungal Communities in Urban Parks Are Similar to Those in Natural Forests but Shaped by Vegetation and Park Age

Ectomycorrhizal (ECM) fungi are important mutualists for the growth and health of most boreal trees. Forest age and its host species composition can impact the composition of ECM fungal communities. Although plentiful empirical data exist for forested environments, the effects of established vegetation and its successional trajectories on ECM fungi in urban greenspaces remain poorly understood. We analyzed ECM fungi in 5 control forests and 41 urban parks of two plant functional groups (conifer and broadleaf trees) and in three age categories (10, ∼50, and >100 years old) in southern Finland. Our results show that although ECM fungal richness was marginally greater in forests than in urban parks, urban parks still hosted rich and diverse ECM fungal communities. ECM fungal community composition differed between the two habitats but was driven by taxon rank order reordering, as key ECM fungal taxa remained largely the same. In parks, the ECM communities differed between conifer and broadleaf trees. The successional trajectories of ECM fungi, as inferred in relation to the time since park construction, differed among the conifers and broadleaf trees: the ECM fungal communities changed over time under the conifers, whereas communities under broadleaf trees provided no evidence for such age-related effects. Our data show that plant-ECM fungus interactions in urban parks, in spite of being constructed environments, are surprisingly similar in richness to those in natural forests. This suggests that the presence of host trees, rather than soil characteristics or even disturbance regime of the system, determine ECM fungal community structure and diversity.IMPORTANCE In urban environments, soil and trees improve environmental quality and provide essential ecosystem services. ECM fungi enhance plant growth and performance, increasing plant nutrient acquisition and protecting plants against toxic compounds. Recent evidence indicates that soil-inhabiting fungal communities, including ECM and saprotrophic fungi, in urban parks are affected by plant functional type and park age. However, ECM fungal diversity and its responses to urban stress, plant functional type, or park age remain unknown. The significance of our study is in identifying, in greater detail, the responses of ECM fungi in the rhizospheres of conifer and broadleaf trees in urban parks. This will greatly enhance our knowledge of ECM fungal communities under urban stresses, and the findings can be utilized by urban planners to improve urban ecosystem services.

Plant species differ in early seedling growth and tissue nutrient responses to arbuscular and ectomycorrhizal fungi

Experiments with plant species that can host both arbuscular mycorrhizal fungi (AMF) and ectomycorrhizal fungi (EMF) are important to separating the roles of fungal type and plant species and understanding the influence of the types of symbioses on plant growth and nutrient acquisition. We examined the effects of mycorrhizal fungal type on the growth and tissue nutrient content of two tree species (Eucalyptus grandis and Quercus costaricensis) grown under four nutrient treatments (combinations of low versus high nitrogen (N) and phosphorus (P) with different N:P ratios) in the greenhouse. Trees were inoculated with unidentified field mixtures of AMF or EMF species cultivated on root fragments of AMF- or EMF-specific bait plants. In E. grandis, inoculation with both AMF and EMF positively affected belowground plant dry weight and negatively affected aboveground dry weight, while only inoculation with AMF increased tissue nutrient content. Conversely, Q. costaricensis dry weight and nutrient content did not differ significantly among inoculation treatments, potentially due to its dependence on cotyledon reserves for growth. Mineral nutrition of both tree species differed with the ratio of N to P applied while growth did not. Our results demonstrate that both tree species' characteristics and the soil nutrient environment can affect how AMF and EMF interact with their host plants. This research highlights the importance of mycorrhizal fungal-tree-soil interactions during early seedling growth and suggests that differences between AMF and EMF associations may be crucial to understanding forest ecosystem functioning.

Mycorrhizal detection of native and non-native truffles in a historic arboretum and the discovery of a new North American species, Tuber arnoldianum sp. nov

During a study comparing the ectomycorrhizal root communities in a native forest with those at the Arnold Arboretum in Massachusetts (USA), the European species Tuber borchii was detected on the roots of a native red oak in the arboretum over two successive years. Since T. borchii is an economically important edible truffle native to Europe, we conducted a search of other roots in the arboretum to determine the extent of colonization. We also wanted to determine whether other non-native Tuber species had been inadvertently introduced into this 140-year-old Arboretum because many trees were imported into the site with intact soil and roots prior to the 1921 USDA ban on these horticultural practices in the USA. While T. borchii was not found on other trees, seven other native and exotic Tuber species were detected. Among the North American Tuber species detected from ectomycorrhizae, we also collected ascomata of a previously unknown species described here as Tuber arnoldianum. This new species was found colonizing both native and non-native tree roots. Other ectomycorrhizal taxa that were detected included basidiomycetes in the genera Amanita, Russula, Tomentella, and ascomycetes belonging to Pachyphlodes, Helvella, Genea, and Trichophaea. We clarify the phylogenetic relationships of each of the Tuber species detected in this study, and we discuss their distribution on both native and non-native host trees.

Don't put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

With the increasing democratization of high-throughput sequencing (HTS) technologies, along with the concomitant increase in sequence yield per dollar, many researchers are exploring HTS for microbial community ecology. Many elements of experimental design can drastically affect the final observed community structure, notably the choice of primers for amplification prior to sequencing. Some targeted microbes can fail to amplify due to primer-targeted sequence divergence and be omitted from obtained sequences, leading to differences among primer pairs in the sequenced organisms even when targeting the same community. This potential source of taxonomic bias in HTS makes it prudent to investigate how primer choice will affect the sequenced community prior to investing in a costly community-wide sequencing effort. Here, we use Fluidigm's microfluidic Access Arrays (IFC) followed by Illumina(®) MiSeq Nano sequencing on a culture-derived local mock community to demonstrate how this approach allows for a low-cost combinatorial investigation of primer pairs and experimental samples (up to 48 primer pairs and 48 samples) to determine the most effective primers that maximize obtained communities whilst minimizing taxonomic biases.

Ectomycorrhizal fungal assemblages of Abies alba Mill. outside its native range in Poland

Abies alba (Mill.) is an important forest tree species, native to the mountainous regions of Europe but has been also widely introduced in the lowlands outside its native range. Like most forest tree species, A. alba forms obligate mutualisms with ectomycorrhizal (ECM) fungi. This investigation sought to examine ECM fungal communities of A. alba when the species grows 400 km north of its native range in the region of Pomerania in Poland. We surveyed for ECM fungi by sampling live roots from four mature forest stands where the A. alba component ranged from 20 to 100%. Ectomycorrhizal fungal symbionts were identified based on morphotyping and sequencing of the internal transcribed spacer (ITS) of nuclear ribosomal DNA (rDNA). Thirty-five ECM fungal taxa were distinguished on root tips of A. alba from all tested stands with 22 to 27 ECM fungal taxa in the individual stand. The diversity and similarity metrics revealed a lack of statistical differences in the structure of the ECM fungal community between stands varying in overstory tree composition. Cenococcum geophilum was the most common fungal species at all investigated A. alba stands, with an abundance of 50 to 70%. The ECM community was characterized by the lack of Abies-specific fungal symbionts and a rich and diverse suite of host-generalist mycobionts that seem to be sufficient for successful growth and development of A. alba outside of its native range.

Commercial Sphagnum peat moss is a vector for exotic ectomycorrhizal mushrooms

Sphagnum peat moss is one of the most commonly used substrates for forest plant and houseplant production. It is extracted from peat bogs in the circumboreal region and exported worldwide. Commercial peat moss is pasteurized, and is therefore believed to be free of viable ectomycorrhizal propagules. We used a bioassay with Pinus montezumae to demonstrate that commercial peat moss carries viable ectomycorrhizal spores, able to form mycorrhizae. Ectomycorrhizal fungi on seedling root-tips were sequenced for phylogenetic analyses using the ITS rDNA barcode region. We found three species: Suillus brevipes, Sphaerosporella brunnea, and Thelephora terrestris. S. brevipes and T. terrestris were found as viable inoculum transported in the peat moss, while S. brunnea was a greenhouse contaminant. S. brevipes and T. terrestris have biological characteristics (such as heat resistant and long living spores) that facilitate their survival to the extraction, transport, and storage processes of peat moss. This allows them to colonize nursery seedlings and to become potential invasive species in plantation areas. S. brevipes and T. terrestris are two of the most introduced fungi by anthropic activities; it has been argued that the vehicle for the introductions are their pine symbionts. This is the first time it has been demonstrated that peat moss is an important vehicle for the introduction of these fungi; a fact potentially related to the pattern of introduction of these ectomycorrhizal species from the northern hemisphere to elsewhere in the world.

Analyses of Sporocarps, Morphotyped Ectomycorrhizae, Environmental ITS and LSU Sequences Identify Common Genera that Occur at a Periglacial Site

Periglacial substrates exposed by retreating glaciers represent extreme and sensitive environments defined by a variety of abiotic stressors that challenge organismal establishment and survival. The simple communities often residing at these sites enable their analyses in depth. We utilized existing data and mined published sporocarp, morphotyped ectomycorrhizae (ECM), as well as environmental sequence data of internal transcribed spacer (ITS) and large subunit (LSU) regions of the ribosomal RNA gene to identify taxa that occur at a glacier forefront in the North Cascades Mountains in Washington State in the USA. The discrete data types consistently identified several common and widely distributed genera, perhaps best exemplified by Inocybe and Laccaria. Although we expected low diversity and richness, our environmental sequence data included 37 ITS and 26 LSU operational taxonomic units (OTUs) that likely form ECM. While environmental surveys of metabarcode markers detected large numbers of targeted ECM taxa, both the fruiting body and the morphotype datasets included genera that were undetected in either of the metabarcode datasets. These included hypogeous (Hymenogaster) and epigeous (Lactarius) taxa, some of which may produce large sporocarps but may possess small and/or spatially patchy genets. We highlight the importance of combining various data types to provide a comprehensive view of a fungal community, even in an environment assumed to host communities of low species richness and diversity.

From genus to phylum: large-subunit and internal transcribed spacer rRNA operon regions show similar classification accuracies influenced by database composition

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5' section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets.