Patent Publication Number: US-8975489-B2

Title: Grass fungal endophytes and uses thereof

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application claims the priority of U.S. Provisional Application No. 61/419,242, filed Dec. 2, 2010, the entire disclosure of which is incorporated herein by reference. 
    
    
     STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT 
     This invention was made with government support under grant number DE-AC05-00OR22725 awarded by the U.S. Department of Energy. The United States government has certain rights in the invention. 
    
    
     INCORPORATION OF SEQUENCE LISTING 
     The Sequence Listing, which is a part of the present disclosure, includes a computer readable 473 KB file entitled “NBLE076US_ST25.txt” comprising nucleotide and/or amino acid sequences of the present invention submitted via EFS-Web. The subject matter of the Sequence Listing is incorporated herein by reference in its entirety. 
     BACKGROUND OF THE INVENTION 
     1. Field of the Invention 
     The invention relates to fungal endophytes of host plants, such as grass plants. In particular, the invention relates to prairie grass endophytes and combinations of these endophytes with agronomically elite grass plants. 
     2. Description of the Related Art 
     Endophytes are fungal or bacterial organisms that live within plants. Fungal endophytes, such as mycorrhiza, survive within various host plant tissues, often colonizing the intercellular spaces of host leaves, stems, flowers or roots. The symbiotic endophyte-host relationships can provide several fitness benefits to the host plant, such as enhancement of nutrition, increased drought tolerance and/or chemical defense from potential herbivores and often enhanced biomass production. Root-colonizing mycorrhizae survive on photosynthetic carbohydrates from the plant, and in return, aid in the solublization and uptake of water and minerals to the host, which can lead to the promotion of seed germination and plant growth. Additionally, the association of a fungal endophyte with a host plant often provides protection from pathogens or tolerance to a variety of biotic and abiotic stresses, such as insect infestation, grazing, water or nutrient deficiency, heat stress, salt or aluminum toxicity, and freezing temperatures. Host growth and fitness promotion and protection are thought to be achieved through multiple beneficial properties of the endophyte-host association. For instance, the endophytic organisms may produce growth-regulating substances to induce biomass production and alkaloids or other metabolites that have anti-insect and anti-herbivore properties. Additionally, fungal endophytes may directly suppress or compete with disease-causing microbes, protecting the plant from potential pathogens. 
     SUMMARY OF THE INVENTION 
     In a first embodiment, the invention provides an isolated fungal endophyte that has been initially identified from a prairie grass species. For example, the isolated endophyte may be selected from those provided in Table 2 or may be defined as comprising a ribosomal DNA (rDNA) sequence comprising one of the sequences of SEQ ID NOs: 1-555. 
     In a further embodiment, the invention provides a synthetic combination of a grass plant and a fungal endophyte provided herein. In one embodiment, the endophyte comprises a rDNA sequence selected from the group consisting of SEQ ID NOs: 1-555. In certain aspects, the fungal endophyte may primarily colonize a root or stem tissue of the plant. In further aspects, the synthetic combination may comprise two or more different fungal endophytes. For example, a grass plant may comprise at least a first fungal endophyte that colonizes a root tissue and at least a first fungal endophyte that colonizes a stem tissue. In some aspects, a grass plant comprises two, three, four, five, six, or more different endophytes, such as bacterial endophytes or fungal endophytes, including one or more of those provided in Table 2. 
     In certain embodiments, a synthetic combination according to the invention comprises an agronomically elite grass plant and a fungal endophyte. For example, the grass plant may comprise one or more agronomically elite traits, such as drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, cold tolerance, salt tolerance, increased yield, enhanced nutrient use efficiency, increased fermentable carbohydrate content, reduced lignin content, or resistance to biotic or abiotic stress. In certain aspects, the grass plant may comprise a transgene, such as a transgene that confers an agronomic trait. For example, a transgene may confer herbicide tolerance, drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, male sterility, cold tolerance, salt tolerance, increased yield, enhanced nutrient use efficiency, increased fermentable carbohydrate content, or reduced lignin content. Grass plants that may be used in the synthetic endophyte combinations according to the invention include, but are not limited to, switchgrass ( Panicum virgatum ), wheat, durum wheat, tall wheatgrass, western wheatgrass, maize, rice, sorghum, meadow fescue, tall fescue, cereal rye, Russian wild rye, oats, bermudagrass, Kentucky bluegrass, big bluestem, little bluestem,  Miscanthus  sp.,  Miscanthus×giganteus , blue grama, black grama, side-oat grama, johnsongrass, buffalograss, creeping bentgrass, or sugarcane. In certain aspects, the host plant is a forage grass host plant. In one embodiment, the host plant is switchgrass ( Panicum virgatum ). 
     In some further embodiments, combinations of grass plants and fungal endophytes according to the invention display increased biomass, enhanced drought tolerance, increased nitrogen use efficiency, increased phosphorus utilization, disease resistance, and/or increased vigor relative to a host grass plant of the same genotype that lacks the endophyte, when grown under the same conditions. In another aspect, the endophyte protects the host grass plant from biotic stresses such as insect infestation, nematode infestation, and herbivore grazing, and/or abiotic stresses, such as water deficiency, nutrient deficiency, heat stress, fungal infection, salt toxicity, aluminum toxicity, heavy metal toxicity, and freezing temperatures. 
     In certain embodiments, the host grass plant is artificially inoculated with the endophyte. The endophyte-host combination may be achieved, for example, by introduction of the endophyte to the host grass plant by a method selected from the group consisting of: inoculation, infection, grafting, and combinations thereof. 
     In a yet another embodiment, the invention provides a seed comprising a grass plant embryo and a fungal endophyte (e.g., an endophyte comprising a rDNA sequence selected from the group consisting of SEQ ID NOs: 1-555). In certain aspects, a fungal endophyte according to the invention is provided into or onto the exterior of the seed. In still yet another aspect, the invention relates to a method for propagating a host grass plant-fungal endophyte combination comprising: a) obtaining a synthetic combination of a fungal endophyte and a host grass plant, and b) vegetatively reproducing the host grass plant tissue colonized by the endophyte. 
     In still yet another embodiment, the invention provides a method for cultivating a host grass plant comprising: contacting the host grass plant or a seed (or other propagating material) that produces the plant with a fungal endophyte, such that the endophyte colonizes the plant. In one aspect, colonization of the host grass is achieved by a method selected from the group consisting of: inoculation, infection, grafting, and combinations thereof. In another aspect, the host grass plant has enhanced root growth, more tillers, enhanced total biomass, or enhanced seed yield relative to a host grass plant of the same genotype that lacks the endophyte, when grown under the same conditions. In yet other aspects, the host grass plant displays tolerance to stress as relative to a host grass plant of the same genotype that lacks the endophyte, when grown under the same conditions. The stress may be selected from the group consisting of a biotic stress, a pest stress, an insect stress, an abiotic stress, and a water deficit stress. In one embodiment, the stress may be biotic stress caused by at least one organism selected from the group consisting of a mammalian or insect herbivore, or a microbial pathogen (e.g., nematode, fungus, bacteria, or virus). In a further aspect, the stress is abiotic stress selected from the group consisting of: water deficiency, nutrient deficiency, heat stress, salt toxicity, aluminum toxicity, heavy metal toxicity, and freezing temperatures. 
     In still yet another embodiment, the invention provides a method for cultivating a host grass plant comprising: contacting the host grass plant or a seed thereof with a filtrate of a cultured fungal endophyte strain, wherein the plant has enhanced root growth, more tillers, enhanced total biomass, or enhanced seed yield or germination relative to a host grass plant of the same genotype that lacks the filtrate, when grown under the same conditions. In one aspect, the host grass plant displays tolerance to stress relative to a host grass plant of the same genotype that lacks the endophyte, when grown under the same conditions, wherein the stress is selected from the group consisting of a biotic stress, a pest stress, an insect stress, an abiotic stress, and a water deficit stress. 
     In another embodiment, the invention relates to a method for increasing the biomass of a plant or increasing the fermentable biomass of a plant comprising: contacting the host grass plant with an endophyte provided herein, such that the endophyte colonizes the plant, wherein the plant exhibits increased biomass relative to a host grass plant of the same genotype that lacks the endophyte, when grown under the same conditions. 
     In a further embodiment, the invention provides a commodity product obtained from a plant comprising a synthetic combination of the invention, such as comprising an endophyte with a rDNA sequence selected from the group consisting of SEQ ID NOs: 1-555. For example, a commodity product may be an animal feed, a biofuel (e.g., ethanol or biodiesel), a paper or paper pulp, silage, or a fermentable biofuel feedstock. In certain aspects, the invention provides an isolated nucleic acid molecule comprising a sequence selected from the group consisting of SEQ ID NOs: 1-555. 
     In still a further embodiment, there is provided a method for the manufacture of a commercial product comprising obtaining a grass plant or grass plant part comprising a fungal endophyte according to the invention and producing a commercial product therefrom. For example, a plant or plant part described herein can be manufactured into a product such as paper, paper pulp, ethanol, biodiesel, silage, animal feed, or fermentable biofuel feedstock. 
     In yet another embodiment, the invention provides a method of producing ethanol comprising: (a) obtaining a grass plant comprising a fungal endophyte according to the invention; (b) treating tissue from the plant to render carbohydrates in the tissue fermentable; and (c) fermenting the carbohydrates to produce ethanol. 
     In yet another embodiment, the invention provides a method for processing lignocellulosic biomass from a plant or plant part described herein. In one embodiment, the method for processing lignocellulosic biomass from a plant or plant part may comprise acid and/or enzymatic treatment(s). The enzymatic treatment(s) may comprise treatment with one or more cellulolytic enzymes, such as a cellulase. In another embodiment, the method comprises an acid treatment prior to or during a treatment to render carbohydrates in the plant fermentable. In yet another embodiment, no acid treatment is performed. 
     The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.” 
     Other objects, features, and advantages of the present invention will become apparent from the following detailed description. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the invention, are given by way of illustration only, since various changes and modifications within the spirit and scope of the invention will become apparent to those skilled in the art from this detailed description. 
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Endophytic fungi are ubiquitous in nature, infecting virtually all plants in both natural and agronomic ecosystems. Provided herein are endophytic fungi initially identified from switchgrass and having utility for improving the phenotype of a grass plant. Given the constraints involved in producing a bioenergy crop, for example, these beneficial endophytes can be used to maximize the sustainability and minimize the economic cost of growing biofuel crops, such as switchgrass. Novel combinations of fungal endophytes with grasses can be used to enhance agronomic characteristics of grass, such as nutrient use efficiency and stress tolerance, as well as to increase yield. Combining grass species with fungal endophytes thus represents a technique that can be used in parallel with plant breeding and transgenic technologies to improve yield from grass crops and reduce the cost of cellulosic biofuel production. 
     Thus, in one aspect, the invention provides a combination (also termed a “symbiotum”) of a host plant and an endophyte that allows for improved agronomic properties of host plants. The combination may be achieved by artificial inoculation, application, or other infection of a host plant, such as a grass plant, or host plant tissues, with a fungal endophyte strain of the present invention. Thus, a combination achieved by such an inoculation is termed a “synthetic” combination. The fungal endophyte may be present in intercellular spaces within plant tissue, such as the root. Its presence may also occur or may also be maintained within a grass plant or plant population by means of grafting or other inoculation methods. 
     These endophytes may also be introduced or maintained by such procedures, into various grasses, such as switchgrass, wheat ( Triticum aestivum ), durum wheat ( Triticum turgidum  ssp. durum), tall wheatgrass ( Thinopyrum ponticum ), western wheatgrass ( Pascopyrum smithii ), maize ( Zea mays ), rice ( Oyrza sativa ), sorghum ( Sorghum bicolor ), meadow fescue ( Festuca pratensis ), tall fescue ( Festuca arundinacea ), cereal rye ( Secale cereale ), Russian wild rye ( Psathyrostachys juncea ), oats ( Avena sativa ), bermudagrass ( Cynodon dactylon ), Kentucky bluegrass ( Poa pratensis ), big bluestem ( Andropogon gerardii ), little bluestem ( Schizachyrium scoparium ), blue grama ( Bouteloua gracilis ), black grama ( Bouteloua eriopoda ), side-oat grama ( Bouteloua curtipendula ), johnsongrass ( Sorghum halepense ), buffalograss ( Buchloe dactyloides ), and creeping bentgrass ( Agrostis stolonifera ). In one embodiment, the host plant is defined as a monocot. In an additional embodiment, the host plant is a forage grass host plant or a cereal. In a particular embodiment, the host plant is a grass host plant such as switchgrass ( Panicum virgatum ). 
     Endophytes for use according to the invention include any of those provided in Table 2 below. For example, the endophyte may be an endophyte of the Hypocreales order, such as the clavicipitaceous, seed-borne Neotyphodium endophytes,  Fusarium  spp. or  Acremonium  spp. Thus, a combination according to the invention may comprise a grass plant and one of the  Acremonium strictum  endophytes represented Table 2. 
     In certain embodiments, the agronomic qualities for improvement may be selected from the group consisting of: increased biomass, increased tillering, increased root mass, increased flowering, increased seed yield, and enhanced resistance to biotic and/or abiotic stresses, each of these qualities being rated in relation to plants of the same genotype grown under the same conditions, and differing only with respect to the presence or absence of a fungal endophyte. The stresses may include, for instance, drought (water deficit), cold, heat stress, nutrient deficiency, salt toxicity, aluminum toxicity, heavy metal toxicity, grazing by herbivores, insect infestation, nematode infection, and fungal infection, among others. In a particular embodiment, the enhanced resistance is provided by the endophyte and protects the host plant from subsequent infection by other fungal diseases, such as root rot, powdery mildew,  Fusarium  blight,  Pythium  blight, leaf spot, rust, and snow mold, among others. This resistance may allow for improved biomass or seed yield relative, for instance, to grass plants not colonized by an endophyte. In another embodiment, the invention may be defined as a grass plant seed in combination with an endophyte strain or coated with a fungal endophyte strain of the present invention. 
     The invention also relates to methods for protecting grass plants from biotic or abiotic stress, by means of introducing an endophyte strain of the present invention into a grass plant, and propagating the plant-endophyte combination by vegetative means. Vegetative propagation of the plant allows for propagation of the combination, since fungal propagules (e.g., mycelia, conidia, and chlamydospores) are present in or on plant tissue, or may infect the plant tissue. 
     The invention also provides methods for detecting the presence of a fungal endophyte of the present invention within a host plant. This may be accomplished, for instance, by isolation of total DNA from tissues of a potential plant-endophyte combination, followed by PCR, or alternatively, Southern blotting, western blotting, or other methods known in the art, to detect the presence of specific nucleic or amino acid sequences associated with the presence of a fungal endophyte strain of the present invention (Selosse et al. 2007). Alternatively, biochemical methods such as ELISA, HPLC, TLC, or fungal metabolite assays may be utilized to determine the presence of an endophyte strain of the present invention in a given sample of grass plant tissue. Additionally, methods for identification may include microscopic analysis, such as root staining, or culturing methods, such as grow out tests or other methods known in the art (Deshmukh et al. 2006). In particular embodiments, the roots of a potential grass plant-endophyte combination may be stained with fungal specific stains, such as WGA-Alexa 488, and microscopically assayed to determine fungal root associates, as described below. 
     DEFINITIONS 
     Agronomically elite plants: Refers to a genotype or cultivar with a phenotype adapted for commercial cultivation. Traits comprised by an agronomically elite plant may include biomass, carbohydrate, and/or seed yield; biotic or abiotic stress resistance, including drought resistance, insect resistance, fungus resistance, virus resistance, bacteria resistance, cold tolerance, and salt tolerance; improved standability, enhanced nutrient use efficiency, and reduced lignin content. 
     Biofuel crop species: A plant that may be used to provide biomass for production of lignocellulosic-derived ethanol. Examples of such plants include switchgrass ( Panicum virgatum ), giant reed ( Arundo donax ), reed canarygrass ( Phalaris arundinacea ),  Miscanthus×giganteus, Miscanthus  sp., sericea lespedeza ( Lespedeza cuneata ), corn, sugarcane, sorghum, millet, ryegrass ( Lolium multiflorum, Lolium  sp.), timothy,  Kochia  ( Kochia scoparia ), sunn hemp, kenaf, bahiagrass, bermudagrass, dallisgrass, pangolagrass, big bluestem, indiangrass, fescue ( Festuca  sp.),  Dactylis  sp.,  Brachypodium distachyon , smooth bromegrass, orchardgrass, Kentucky bluegrass, and fonio ( Digitaria  sp.), among others. 
     Biomass: The total mass or weight, at a given time, of a plant or population of plants, usually given as weight per unit area. The term may also refer to all the plants or species in the community (community biomass). 
     Culture filtrate: Broth or media obtained from cultures inoculated with a strain of fungi and allowed to grow. The media is typically filtered to remove any suspended cells, leaving the nutrients, hormones, or other chemicals. 
     Endophyte: An organism capable of living within a plant cell. An endophyte may refer to a fungal organism that may confer an increase in yield, biomass, resistance, or fitness in its host plant. Fungal endophytes may occupy the intracellular or extracellular spaces of plant tissue, including the leaves, stems, flowers, or roots. 
     Genotype: The genetic constitution of a cell or organism. 
     Host plant: Any plant which an endophytic fungi colonizes. 
     Increased yield: An increase in biomass or seed weight, seed size, seed number per plant, seed number per unit area, bushels per acre, tons per acre, kilo per hectare, or carbohydrate yield. 
     Phenotype: The detectable characteristics of a cell or organism, which characteristics are the manifestation of gene expression. 
     Regeneration: The process of growing a plant from a plant cell (e.g., plant protoplast, callus, or explant). 
     Synthetic combination: A combination (also termed a “symbiotum”) of a host plant and an endophyte. The combination may be achieved, for example, by artificial inoculation, application, or other infection of a host plant, such as a grass plant, or host plant tissues with an endophyte. 
     Transgene: A segment of DNA which has been incorporated into a host genome or is capable of autonomous replication in a host cell and is capable of causing the expression of one or more coding sequences. Exemplary transgenes will provide the host cell, or plants regenerated therefrom, with a novel phenotype relative to the corresponding non-transformed cell or plant. Transgenes may be directly introduced into a plant by genetic transformation, or may be inherited from a plant of any previous generation which was transformed with the DNA segment. 
     Transgenic plant: A plant or progeny plant of any subsequent generation derived therefrom, wherein the DNA of the plant or progeny thereof contains an introduced exogenous DNA segment not naturally present in a non-transgenic plant of the same strain. The transgenic plant may additionally contain sequences which are native to the plant being transformed, but wherein the “exogenous” gene has been altered in order to alter the level or pattern of expression of the gene, for example, by use of one or more heterologous regulatory or other elements. 
     EXAMPLES 
     The following examples are included to demonstrate preferred embodiments of the invention. It should be appreciated by those of skill in the art that the techniques disclosed in the examples which follow represent techniques discovered by the inventors to function well in the practice of the invention, and thus can be considered to constitute preferred modes for its practice. However, those of skill in the art should, in light of the present disclosure, appreciate that many changes can be made in the specific embodiments which are disclosed and still obtain a like or similar result without departing from the concept, spirit and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the invention as defined by the appended claims. 
     Example 1 
     Isolation of Wild Grass Endophytes 
     Plant samples were collected from Alfalfa, Grant, Kay, and Osage counties of Northern Oklahoma. The sampling points were located between the GPS coordinates of 36°38′38″ to 36°48′48″ N latitude and 96°10′26″ to 08°16′11″ W longitude (Table 1). This region has a sub-humid continental climate, with a mean annual temperature of 15° C. and a growing season of 177 to 220 days. Mean annual precipitation ranges from 76 to 112 cm, of which more than 70% usually falls in April through October (USDA 1985; USDA 2007a; USDA 2007b; USDA 2008). Although all four counties studied are part of the North American tallgrass prairie, sampling sites from Alfalfa, Grant, and Kay counties were from quite diverse habitats (e.g., grassland, pasture, lake shores, salt plains, or marshy land). Conversely, those from Osage county were predominantly composed of natural grassland from the Tallgrass Prairie Preserve (TGPP). Since 1989, the Nature Conservancy has owned and managed the TGPP by recreating a semi-natural grazing and disturbance regime with bison herds and a stochastic fire regime (Hamilton 1996). In addition to habitat differences, Alfalfa, Grant, and the western part of Kay counties receive significantly lower average annual precipitation than Osage county (82 cm versus 112 cm). Sampling sites from Alfalfa, Grant, and Kay counties are henceforth referred to as the west part and those from Osage county are referred to as the east part of the study area. 
     
       
         
           
               
             
               
                 TABLE 1 
               
             
            
               
                   
               
               
                 Sample collection sites. 
               
            
           
           
               
               
               
               
            
               
                   
                 Location 
                 Coordinates 
                   
               
            
           
           
               
               
               
               
            
               
                   
                 ID 
                 Lat. 
                 Lon. 
               
               
                   
                   
               
               
                   
                 E1 
                 36.38.38 
                 96.23.47 
               
               
                   
                 E2 
                 36.38.39 
                 96.23.50 
               
               
                   
                 E3 
                 36.38.39 
                 96.23.47 
               
               
                   
                 E4 
                 36.38.40 
                 96.23.52 
               
               
                   
                 E5 
                 36.41.39 
                 96.20.02 
               
               
                   
                 E6 
                 36.41.40 
                 96.20.01 
               
               
                   
                 E7 
                 36.41.40 
                 96.20.02 
               
               
                   
                 E8 
                 36.41.41 
                 96.20.00 
               
               
                   
                 E9 
                 36.44.11 
                 96.11.13 
               
               
                   
                 E10 
                 36.44.12 
                 96.11.12 
               
               
                   
                 E11 
                 36.44.13 
                 96.11.11 
               
               
                   
                 E12 
                 36.44.16 
                 96.11.12 
               
               
                   
                 E13 
                 36.44.31 
                 96.21.50 
               
               
                   
                 E14 
                 36.44.32 
                 96.21.50 
               
               
                   
                 E15 
                 36.44.32 
                 96.21.49 
               
               
                   
                 E16 
                 36.44.33 
                 96.21.49 
               
               
                   
                 E17 
                 36.45.10 
                 96.21.47 
               
               
                   
                 E18 
                 36.45.10 
                 96.21.46 
               
               
                   
                 E19 
                 36.45.10 
                 96.21.46 
               
               
                   
                 E20 
                 36.45.10 
                 96.21.47 
               
               
                   
                 E21 
                 36.45.23 
                 96.22.56 
               
               
                   
                 E22 
                 36.45.24 
                 96.22.56 
               
               
                   
                 E23 
                 36.45.24 
                 96.22.56 
               
               
                   
                 E24 
                 36.45.25 
                 96.22.56 
               
               
                   
                 E25 
                 36.45.45 
                 96.10.27 
               
               
                   
                 E26 
                 36.45.45 
                 96.10.29 
               
               
                   
                 E27 
                 36.45.45 
                 96.10.26 
               
               
                   
                 E28 
                 36.45.47 
                 96.10.26 
               
               
                   
                 E29 
                 36.45.48 
                 96.10.26 
               
               
                   
                 E30 
                 36.46.08 
                 96.23.24 
               
               
                   
                 E31 
                 36.46.08 
                 96.23.26 
               
               
                   
                 E32 
                 36.46.08 
                 96.23.26 
               
               
                   
                 E33 
                 36.46.09 
                 96.23.24 
               
               
                   
                 E34 
                 36.47.10 
                 96.23.49 
               
               
                   
                 E35 
                 36.47.10 
                 96.23.49 
               
               
                   
                 E36 
                 36.47.10 
                 96.23.48 
               
               
                   
                 E37 
                 36.47.11 
                 96.23.49 
               
               
                   
                 E38 
                 36.47.56 
                 96.24.48 
               
               
                   
                 E39 
                 36.47.56 
                 96.24.48 
               
               
                   
                 E40 
                 36.47.57 
                 96.24.48 
               
               
                   
                 E41 
                 36.47.57 
                 96.24.48 
               
               
                   
                 E42 
                 36.48.39 
                 96.26.03 
               
               
                   
                 E43 
                 36.48.39 
                 96.26.03 
               
               
                   
                 E44 
                 36.48.39 
                 96.26.02 
               
               
                   
                 E45 
                 36.48.40 
                 96.26.02 
               
               
                   
                 E46 
                 36.48.48 
                 96.26.22 
               
               
                   
                 E47 
                 36.48.48 
                 96.26.23 
               
               
                   
                 E48 
                 36.48.48 
                 96.26.23 
               
               
                   
                 W1 
                 36.48.44 
                 97.18.15 
               
               
                   
                 W2 
                 36.48.44 
                 97.18.15 
               
               
                   
                 W3 
                 36.48.44 
                 97.18.13 
               
               
                   
                 W4 
                 36.48.40 
                 97.27.14 
               
               
                   
                 W5 
                 36.48.40 
                 97.27.14 
               
               
                   
                 W6 
                 36.48.37 
                 97.31.34 
               
               
                   
                 W7 
                 36.48.37 
                 97.31.37 
               
               
                   
                 W8 
                 36.48.37 
                 97.31.40 
               
               
                   
                 W9 
                 36.48.42 
                 97.40.41 
               
               
                   
                 W10 
                 36.48.41 
                 98.01.19 
               
               
                   
                 W11 
                 36.48.46 
                 97.40.41 
               
               
                   
                 W12 
                 36.48.41 
                 98.01.19 
               
               
                   
                 W13 
                 36.48.42 
                 98.01.18 
               
               
                   
                 W14 
                 36.48.41 
                 98.01.15 
               
               
                   
                 W15 
                 36.48.38 
                 98.04.59 
               
               
                   
                 W16 
                 36.48.36 
                 98.05.00 
               
               
                   
                 W17 
                 36.48.36 
                 98.05.01 
               
               
                   
                 W18 
                 36.45.01 
                 98.09.42 
               
               
                   
                 W19 
                 36.45.04 
                 98.09.44 
               
               
                   
                 W20 
                 36.45.04 
                 98.07.45 
               
               
                   
                 W21 
                 36.45.06 
                 98.07.43 
               
               
                   
                 W22 
                 36.45.06 
                 98.07.44 
               
               
                   
                 W23 
                 36.41.04 
                 98.12.09 
               
               
                   
                 W24 
                 36.41.04 
                 98.12.10 
               
               
                   
                 W25 
                 36.40.51 
                 98.14.07 
               
               
                   
                 W26 
                 36.40.52 
                 98.14.08 
               
               
                   
                 W27 
                 36.40.52 
                 98.14.08 
               
               
                   
                 W28 
                 36.42.35 
                 98.16.10 
               
               
                   
                 W29 
                 36.42.34 
                 98.16.11 
               
               
                   
                 W30 
                 36.42.34 
                 98.16.11 
               
               
                   
                 W31 
                 36.42.28 
                 98.16.10 
               
               
                   
                 W32 
                 36.42.25 
                 98.16.10 
               
               
                   
                 W33 
                 36.42.22 
                 98.16.08 
               
               
                   
                 W34 
                 36.42.23 
                 98.16.11 
               
               
                   
                 W35 
                 36.42.22 
                 98.16.08 
               
               
                   
                   
               
            
           
         
       
     
     Plant samples were collected during early vegetative, full reproductive, and senescence stages of switchgrass growth in the months of April, July, and October of 2009, respectively. Each sampling consisted of up to 83 whole plant samples (5 to 10 tillers per sample) from different parts of the tallgrass prairie that included at least 35 samples each from the east and west. GPS coordinates were recorded for each sampling site in the April sampling, and the same general coordinates (within the same field) were used for subsequent samplings. More than 210 total plant samples were collected and all samples were processed for shoot and root inhabiting endophytic fungal communities. Twenty-four representative soil samples from these GPS locations, 12 each from the east and west parts of prairie were collected and analyzed for pH, organic matter, phosphorus, potassium, calcium, magnesium, and sodium content. 
     Collected plants with approximately 25-35 cm of both above- and below-ground tissues were transported to the laboratory on ice and processed within 24 h of collection. Each plant sample was divided into two parts. The roots from the first half were harvested immediately for endophyte isolation, while the second half was cut back at 10-12 cm above ground level, transplanted into 3.8 L containers with Metro-mix 350 and maintained in the greenhouse for six weeks prior to endophyte isolation from shoot tissues. This was done to minimize excessive saprophytic fungal contamination. 
     Processing of the root tissues involved thorough rinsing of multiple roots (5-10/plant), with tap water to remove excess soil. The basal portion of shoots was collected from the plants maintained in the greenhouse. Root and shoot samples were cut into 3-4 cm pieces prior to rigorous surface sterilization (95% ethanol for 30 s, 70% ethanol for 5 min followed by 3% sodium hypochlorite for 25-30 min). Surface sterilized tissue were rinsed three times with sterile water, blot dried, cut into small pieces (1-1.5 cm) and plated on PDA plates amended with 100 ppm ampicillin sodium salt, 50 ppm chloramphenicol, and 50 ppm streptomycin sulfate. Plates were incubated in the dark for up to two months at 24° C. and examined regularly for emerging fungal colonies. Emerging fungal colonies were passed through two rounds of subculture prior to preparing agar slants for long-term storage and collecting fungal materials for DNA extraction. 
     Example 2 
     Characterization of Isolated Endophytes 
     Fungal material for DNA extraction was harvested from 1 to 2 week-old cultures grown on potato dextrose agar (PDA) by cutting an agar block of 1.5 cm 3 . Agar blocks were placed in a 1.5 ml micro-tube with a single 4.5 mm stainless steel bead. These micro-tubes were arranged in a rack and covered with an AirPore® filter, stored at −80° C. overnight and lyophilized for 24 h. The DNA was extracted from lyophilized tissue using QIAGEN MagAttract® 96 DNA Plant Core Kit according to the manufacturer&#39;s instructions. 
     The internal transcribed spacer (ITS) regions of fungal ribosomal DNA (rDNA) are highly variable in sequence, and thus of great importance in distinguishing fungal species (White et al. 1990). The fungal-specific primers ITS 1F and ITS4, amplifying the highly variable ITS 1 and ITS2 sequences surrounding the 5.8S-coding sequences, were used in this study. These primer sets have been used widely (Gardes &amp; Bruns 1993; Martin &amp; Rygiewicz 2005) and are thus well represented in the NCBI nucleotide database. PCR primers were used to sequence the purified PCR products as described previously (Puckette et al. 2009). Gene sequences were manually inspected, edited, and appended into contigs using DNA sequence assembly software Sequencher® version 4.9 (Gene Code Corporation, Ann Arbor, Michigan). Test sequences were compared to the NCBI fungal database and the top three hits with ≧99% sequence similarities were used to determine the identity of test isolates to the deepest possible taxonomic resolution. 
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Identification of fungal endophytes by rDNA sequence. 
               
            
           
           
               
               
               
               
               
            
               
                 SEQ 
                   
                   
                 Plant 
                   
               
               
                 ID NO 
                 Isolate ID 
                 Location* 
                 Part 
                 Initial ID/(Accession No.) 
               
               
                   
               
            
           
           
               
               
               
               
               
            
               
                 1 
                 April09_Shoot_13ES1 
                 W13 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 2 
                 April09_Shoot_18ES1 
                 E18 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 3 
                 April09_Shoot_18ES2 
                 E18 
                 Shoot 
                   Cladosporium colombiae  (FJ936159) 
               
               
                 4 
                 April09_Shoot_19ES2 
                 E18 
                 Shoot 
                 Uncultured Ascomycete sp. (EU489902) 
               
               
                 5 
                 April09_Shoot_1WS1 
                 W14 
                 Shoot 
                   Phoma glomerata  (AY183371) 
               
               
                 6 
                 April09_Shoot_20WS3 
                 W20 
                 Shoot 
                   Acremonium  sp. (AM901698) 
               
               
                 7 
                 April09_Shoot_21WS1 
                 W21 
                 Shoot 
                   Stachybotrys elegans  (AF081481) 
               
               
                 8 
                 April09_Shoot_21WS2 
                 W21 
                 Shoot 
                   Myrothecium melanosporum  (FJ235086) 
               
               
                 9 
                 April09_Shoot_22WS1 
                 W22 
                 Shoot 
                   Gibberella  sp. (FJ466715) 
               
               
                 10 
                 April09_Shoot_22WS2 
                 W22 
                 Shoot 
                   Gibberella  sp. (FJ466715) 
               
               
                 11 
                 April09_Shoot_22WS3 
                 W22 
                 Shoot 
                 Ascomycete sp. (AY243057) 
               
               
                 12 
                 April09_Shoot_23WS1 
                 W223 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 13 
                 April09_Shoot_24WS3 
                 W24 
                 Shoot 
                   Bionectria rossmaniae  (AM944351) 
               
               
                 14 
                 April09_Shoot_26WS1 
                 W26 
                 Shoot 
                   F. oxysporum f.  sp.  vasinfectum   
               
               
                   
                   
                   
                   
                 (AF322074) 
               
               
                 15 
                 April09_Shoot_26WS2 
                 W26 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 16 
                 April09_Shoot_26WS5 
                 W27 
                 Shoot 
                   F. oxysporum f.  sp.  vasinfectum   
               
               
                   
                   
                   
                   
                 (AF322074) 
               
               
                 17 
                 April09_Shoot_27WS3 
                 W27 
                 Shoot 
                 Uncultured endophytic fungus 
               
               
                   
                   
                   
                   
                 (EF505542) 
               
               
                 18 
                 April09_Shoot_28ES1 
                 E28 
                 Shoot 
                 Uncultured endophytic fungus 
               
               
                   
                   
                   
                   
                 (EF505542) 
               
               
                 19 
                 April09_Shoot_28WS2 
                 W28 
                 Shoot 
                   Myrothecium melanosporum  (FJ235086) 
               
               
                 20 
                 April09_Shoot_29ES1 
                 E29 
                 Shoot 
                   Hypocrea lixii  (EF392760) 
               
               
                 21 
                 April09_Shoot_29ES2 
                 E29 
                 Shoot 
                   Hypocrea lixii  (EF392760) 
               
               
                 22 
                 April09_Shoot_29ES3 
                 E29 
                 Shoot 
                   Hypocrea lixii  (EF392760) 
               
               
                 23 
                 April09_Shoot_29WS1 
                 W29 
                 Shoot 
                   Buergenerula spartinae  (AF422960) 
               
               
                 24 
                 April09_Shoot_29WS2 
                 W29 
                 Shoot 
                   Gibberella acuminata  (U85533) 
               
               
                 25 
                 April09_Shoot_2WS1 
                 W2 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 26 
                 April09_Shoot_2WS2 
                 W2 
                 Shoot 
                 Ascomycete sp. (AJ279460) 
               
               
                 27 
                 April09_Shoot_30WS2 
                 W30 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 28 
                 April09_Shoot_32ES1 
                 E32 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 29 
                 April09_Shoot_32WS 
                 W32 
                 Shoot 
                   Stachybotrys elegans  (AF081481) 
               
               
                 30 
                 April09_Shoot_34ES2 
                 E34 
                 Shoot 
                   Eutypa scoparia  (AF373064) 
               
               
                 31 
                 April09_Shoot_34ES3 
                 E34 
                 Shoot 
                 Sordariomycete sp. (EU680539) 
               
               
                 32 
                 April09_Shoot_35WS1 
                 W35 
                 Shoot 
                 Uncultured soil fungus (EU479884) 
               
               
                 33 
                 April09_Shoot_35WS4 
                 W35 
                 Shoot 
                   Myrothecium melanosporum  (FJ235086) 
               
               
                 34 
                 April09_Shoot_35WS5 
                 W35 
                 Shoot 
                   Leptosphaeria avenaria f.  sp.  triticea   
               
               
                   
                   
                   
                   
                 (U77357) 
               
               
                 35 
                 April09_Shoot_35WS6 
                 W35 
                 Shoot 
                   Acremonium  sp. (AM901698) 
               
               
                 36 
                 April09_Shoot_3WS1 
                 W3 
                 Shoot 
                   Penicillium citreonigrum  (EU497942) 
               
               
                 37 
                 April09_Shoot_44ES1 
                 E44 
                 Shoot 
                 Fungal endophyte sp. (EU977213) 
               
               
                 38 
                 April09_Shoot_46ES1 
                 E46 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 39 
                 April09_Shoot_46ES2 
                 E46 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 40 
                 April09_Shoot_4ES1 
                 E4 
                 Shoot 
                   Emericellopsis terricola  (FJ430737) 
               
               
                 41 
                 April09_Shoot_5WS2 
                 W5 
                 Shoot 
                   Acremonium strictum  (EU497953) 
               
               
                 42 
                 April09_Shoot_6ES2 
                 E6 
                 Shoot 
                   Emericellopsis minima  (U57675) 
               
               
                 43 
                 April09_Shoot_6WS2 
                 W6 
                 Shoot 
                   Alternaria mali  (AY154683) 
               
               
                 44 
                 April09_Shoot_8ES1 
                 E8 
                 Shoot 
                   Bipolaris heveae  (AB179834) 
               
               
                 45 
                 April09_Shoot_9ES1 
                 E9 
                 Shoot 
                   Stachybotrys bisbyi  (AF081480) 
               
               
                 46 
                 April09_Shoot_9WS1 
                 W9 
                 Shoot 
                 Dothideomycete sp. (EU680559) 
               
               
                 47 
                 July09_Shoot_10WS2 
                 W10 
                 Shoot 
                   Acremonium strictum  (GU219467) 
               
               
                 48 
                 July09_Shoot_12WS1 
                 W12 
                 Shoot 
                   Pleosporaceae  sp. (EU330624) 
               
               
                 49 
                 July09_Shoot_12WS2 
                 W12 
                 Shoot 
                   Alternaria  sp. (FJ210481) 
               
               
                 50 
                 July09_Shoot_12WS3 
                 W12 
                 Shoot 
                   Fusarium moniliformae  (EU364864) 
               
               
                 51 
                 July09_Shoot_12WS4 
                 W12 
                 Shoot 
                   Fusarium moniliformae  (AB369908) 
               
               
                 52 
                 July09_Shoot_12WS5 
                 W12 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 53 
                 July09_Shoot_16WS2 
                 W16 
                 Shoot 
                   Alternaria  sp. (FJ037742, GQ389617) 
               
               
                 54 
                 July09_Shoot_16WS3 
                 W16 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 55 
                 July09_Shoot_17ES2 
                 E17 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 56 
                 July09_Shoot_17ES3 
                 E17 
                 Shoot 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 57 
                 July09_Shoot_17ES4 
                 E17 
                 Shoot 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 58 
                 July09_Shoot_17WS1 
                 W17 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 59 
                 July09_Shoot_19ES1 
                 E19 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 60 
                 July09_Shoot_19ES2 
                 E19 
                 Shoot 
                   Fusarium moniliformae  (AB369908) 
               
               
                 61 
                 July09_Shoot_19ES3 
                 E19 
                 Shoot 
                   Fusarium proliferatum  (EU888923) 
               
               
                 62 
                 July09_Shoot_19ES4 
                 E19 
                 Shoot 
                   Fusarium moniliformae  (EU364864) 
               
               
                 63 
                 July09_Shoot_19WS3 
                 W19 
                 Shoot 
                   Acremonium strictum  (EU497953) 
               
               
                 64 
                 July09_Shoot_1ES1 
                 E1 
                 Shoot 
                   Myrothecium verrucaria  (AY303603) 
               
               
                 65 
                 July09_Shoot_20ES1 
                 E20 
                 Shoot 
                   Fusarium subglutinans  (GQ167234) 
               
               
                 66 
                 July09_Shoot_20ES2 
                 E20 
                 Shoot 
                   Leptosphaeria bicolor  (AF455415) 
               
               
                 67 
                 July09_Shoot_20WS1 
                 W20 
                 Shoot 
                   Acremonium  sp. (AM901698) 
               
               
                 68 
                 July09_Shoot_20WS2 
                 W20 
                 Shoot 
                   Acremonium strictum  (U57671) 
               
               
                 69 
                 July09_Shoot_20WS3 
                 W20 
                 Shoot 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 70 
                 July09_Shoot_22WS1 
                 W22 
                 Shoot 
                 
                   Fusarium pseudograminearum 
                 
               
               
                   
                   
                   
                   
                 (DQ4598710) 
               
               
                 71 
                 July09_Shoot_22WS2 
                 W22 
                 Shoot 
                   Acremonium  sp. (AM924149) 
               
               
                 72 
                 July09_Shoot_23ES2 
                 E23 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 73 
                 July09_Shoot_25ES1 
                 E25 
                 Shoot 
                   Gibberella  sp. (FJ008984) 
               
               
                 74 
                 July09_Shoot_25ES2 
                 E25 
                 Shoot 
                   Colletotrichum graminicola  (GQ221855) 
               
               
                 75 
                 July09_Shoot_25WS3 
                 W25 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 76 
                 July09_Shoot_26ES1 
                 E26 
                 Shoot 
                   Monographella  sp. (FJ228195) 
               
               
                 77 
                 July09_Shoot_26ES2 
                 E26 
                 Shoot 
                   Myrothecium verrucaria  (AY303603) 
               
               
                 78 
                 July09_Shoot_27ES1 
                 E27 
                 Shoot 
                   Alternaria arborescens  (AY154706) 
               
               
                 79 
                 July09_Shoot_27ES3 
                 E27 
                 Shoot 
                   Alternaria alternata  (FJ872066) 
               
               
                 80 
                 July09_Shoot_27ES4 
                 E27 
                 Shoot 
                 
                   Parasarcopodium ceratocaryi 
                 
               
               
                   
                   
                   
                   
                 (AY344479) 
               
               
                 81 
                 July09_Shoot_27WS1 
                 W27 
                 Shoot 
                   Acremonium  sp. (AM924149) 
               
               
                 82 
                 July09_Shoot_29WS1 
                 W29 
                 Shoot 
                   Acremonium strictum  (EU497953) 
               
               
                 83 
                 July09_Shoot_29WS2 
                 W29 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 84 
                 July09_Shoot_2ES1 
                 E2 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 85 
                 July09_Shoot_2WS2 
                 W2 
                 Shoot 
                   Acremonium  sp. (AM924149) 
               
               
                 86 
                 July09_Shoot_30ES1 
                 E30 
                 Shoot 
                   Alternaria mali  (AY154683) 
               
               
                 87 
                 July09_Shoot_30ES2 
                 E30 
                 Shoot 
                   Gibberella  sp. (AM901682) 
               
               
                 88 
                 July09_Shoot_30ES3 
                 E30 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 89 
                 July09_Shoot_30ES4 
                 E30 
                 Shoot 
                   Alternaria mali  (AY154683) 
               
               
                 90 
                 July09_Shoot_31ES1 
                 E31 
                 Shoot 
                   Pseudozyma flocculosa  (DQ411535) 
               
               
                 91 
                 July09_Shoot_32WS1 
                 W32 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 92 
                 July09_Shoot_33WS1 
                 W33 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 93 
                 July09_Shoot_33WS2 
                 W33 
                 Shoot 
                   Nigrospora oryzae  (EU272488) 
               
               
                 94 
                 July09_Shoot_33WS3 
                 W33 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 95 
                 July09_Shoot_33WS4 
                 W33 
                 Shoot 
                   Acremonium strictum  (EU497953) 
               
               
                 96 
                 July09_Shoot_33WS5 
                 W33 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 97 
                 July09_Shoot_33WS6 
                 W33 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 98 
                 July09_Shoot_33WS7 
                 W33 
                 Shoot 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 99 
                 July09_Shoot_34WS1 
                 W34 
                 Shoot 
                 Uncultured endophytic fungus 
               
               
                   
                   
                   
                   
                 (EF505485) 
               
               
                 100 
                 July09_Shoot_34WS3 
                 W34 
                 Shoot 
                   Gibberella  sp. (FJ008984) 
               
               
                 101 
                 July09_Shoot_34WS4 
                 W34 
                 Shoot 
                   Acremonium strictum  (EU497953) 
               
               
                 102 
                 July09_Shoot_35ES1 
                 E35 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 103 
                 July09_Shoot_35ES2 
                 E35 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 104 
                 July09_Shoot_35ES3 
                 E35 
                 Shoot 
                   Acremonium  sp. (AM901698) 
               
               
                 105 
                 July09_Shoot_35WS1 
                 W35 
                 Shoot 
                   Gibberella  sp. (AM901682) 
               
               
                 106 
                 July09_Shoot_35WS2 
                 W35 
                 Shoot 
                   Gibberella  sp. (FJ008984) 
               
               
                 107 
                 July09_Shoot_35WS3 
                 W35 
                 Shoot 
                   Gibberella  sp. (AM901682) 
               
               
                 108 
                 July09_Shoot_35WS4 
                 W35 
                 Shoot 
                   Gibberella  sp. (AM901682) 
               
               
                 109 
                 July09_Shoot_35WS5 
                 W35 
                 Shoot 
                   Fusarium proliferatum  (EU272509) 
               
               
                 110 
                 July09_Shoot_35WS6 
                 W35 
                 Shoot 
                   Alternaria alternata  (AY433814) 
               
               
                 111 
                 July09_Shoot_36ES1 
                 E36 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 112 
                 July09_Shoot_42ES2 
                 E42 
                 Shoot 
                 Sordariomycete sp. (EU680539) 
               
               
                 113 
                 July09_Shoot_45ES1 
                 E45 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 114 
                 July09_Shoot_45ES2 
                 E45 
                 Shoot 
                   Fusarium moniliformae  (AB369908) 
               
               
                 115 
                 July09_Shoot_48ES1 
                 E48 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 116 
                 July09_Shoot_48ES2 
                 E48 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 117 
                 July09_Shoot_48ES3 
                 E48 
                 Shoot 
                   Fusarium nygamai  (U34568) 
               
               
                 118 
                 July09_Shoot_4ES1 
                 E4 
                 Shoot 
                   Exserohilum rostratum  (GQ169762) 
               
               
                 119 
                 July09_Shoot_5ES1 
                 E5 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 120 
                 July09_Shoot_6WS1 
                 W6 
                 Shoot 
                   Fusarium moniliformae  (EU364864) 
               
               
                 121 
                 July09_Shoot_6WS2 
                 W6 
                 Shoot 
                   Fusarium moniliformae  (AB369908) 
               
               
                 122 
                 July09_Shoot_7ES1 
                 E7 
                 Shoot 
                   Bipolaris oryzae  (DQ300203) 
               
               
                 123 
                 July09_Shoot_7ES2 
                 E7 
                 Shoot 
                   Gibberella  sp. (FJ008984) 
               
               
                 124 
                 July09_Shoot_8ES1 
                 E8 
                 Shoot 
                   Colletotrichum graminicola  (EU400146) 
               
               
                 125 
                 July09_Shoot_8ES3 
                 E8 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 126 
                 July09_Shoot_8ES4 
                 E8 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 127 
                 July09_Shoot_9ES2 
                 E9 
                 Shoot 
                   Fusarium moniliformae  (AB369908) 
               
               
                 128 
                 July09_Shoot_9ES3 
                 E9 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 129 
                 July09_Shoot_9ES4 
                 E9 
                 Shoot 
                   Sporisorium everhartii  (AY740159) 
               
               
                 130 
                 Oct09_Shoot_10ES2 
                 E10 
                 Shoot 
                 Sordariomycete sp. (EU680539) 
               
               
                 131 
                 Oct09_Shoot_10ES3 
                 E10 
                 Shoot 
                 Sordariomycete sp. (EU680539) 
               
               
                 132 
                 Oct09_Shoot_28ES1 
                 E28 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 133 
                 Oct09_Shoot_30ES1 
                 E30 
                 Shoot 
                   Fusarium acuminatum  (GQ505462) 
               
               
                 134 
                 Oct09_Shoot_37ES1 
                 E37 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 135 
                 Oct09_Shoot_37ES2 
                 E37 
                 Shoot 
                   Fusarium proliferatum  (AF291061) 
               
               
                 136 
                 Oct09_Shoot_48ES1 
                 E48 
                 Shoot 
                 Leaf litter ascomycetes (AF502815) 
               
               
                 137 
                 Oct09_Shoot_10WS1 
                 W10 
                 Shoot 
                   Acremonium strictum  (U57671) 
               
               
                 138 
                 Oct09_Shoot_14WS1 
                 W14 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 139 
                 Oct09_Shoot_16WS1 
                 W16 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 140 
                 Oct09_Shoot_16WS2 
                 W16 
                 Shoot 
                   Fusarium nygamai  (X94174) 
               
               
                 141 
                 Oct09_Shoot_24WS1 
                 W24 
                 Shoot 
                   Stachybotrys elegans  (AF081481) 
               
               
                 142 
                 Oct09_Shoot_24WS2 
                 W24 
                 Shoot 
                   Stachybotrys elegans  (AF081481) 
               
               
                 143 
                 Oct09_Shoot_24WS3 
                 W24 
                 Shoot 
                   Stachybotrys elegans  (AF081481) 
               
               
                 144 
                 April09_Root_10WR1 
                 W10 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 145 
                 April09_Root_10WR2 
                 W10 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 146 
                 April09_Root_11WR1 
                 W11 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 147 
                 April09_Root_12ER1 
                 E12 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 148 
                 April09_Root_12ER2 
                 E12 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 149 
                 April09_Root_12ER3 
                 E12 
                 Root 
                   Fusarium  sp. (EF453116) 
               
               
                 150 
                 April09_Root_12ER-A 
                 E12 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 151 
                 April09_Root_12WR1 
                 W12 
                 Root 
                   Fusarium annulatum  (AY213654) 
               
               
                 152 
                 April09_Root_13ER1 
                 E13 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 153 
                 April09_Root_14ER2 
                 E14 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 154 
                 April09_Root_15ER1 
                 E15 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 155 
                 April09_Root_16ER1 
                 E16 
                 Root 
                   Coprinus auricomus  (FM163186) 
               
               
                 156 
                 April09_Root_16ER2 
                 E16 
                 Root 
                   Coprinus auricomus  (FM163186) 
               
               
                 157 
                 April09_Root_16ER-A 
                 E16 
                 Root 
                   Amyloathelia crassiuscula  (DQ144610) 
               
               
                 158 
                 April09_Root_16WR1 
                 W16 
                 Root 
                   Alternaria longissima  (EU030349) 
               
               
                 159 
                 April09_Root_18WR2 
                 W18 
                 Root 
                   Kabatiella microsticta  (EU167608) 
               
               
                 160 
                 April09_Root_19ER1 
                 E19 
                 Root 
                   Fusarium annulatum  (AY213654) 
               
               
                 161 
                 April09_Root_19ER2 
                 E19 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 162 
                 April09_Root_19ER3 
                 E19 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 163 
                 April09_Root_19WR1 
                 W19 
                 Root 
                   Alternaria mali  (AY154683) 
               
               
                 164 
                 April09_Root_19WR-A 
                 W19 
                 Root 
                   Fusarium moniliformae  (EU364865) 
               
               
                 165 
                 April09_Root_1ER1 
                 E1 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 166 
                 April09_Root_1ER3 
                 E1 
                 Root 
                 Uncultured soil fungus (EU480242) 
               
               
                 167 
                 April09_Root_20ER1 
                 E20 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 168 
                 April09_Root_20ER2 
                 E20 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 169 
                 April09_Root_20WR2 
                 W20 
                 Root 
                   Eutypella  sp. (FJ172283) 
               
               
                 170 
                 April09_Root_21ER1 
                 E21 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 171 
                 April09_Root_22WR1 
                 W22 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 172 
                 April09_Root_22WR2 
                 W22 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 173 
                 April09_Root_22WR3 
                 W22 
                 Root 
                   Fusarium  sp. (AY143085) 
               
               
                 174 
                 April09_Root_24WR2 
                 W24 
                 Root 
                 Fungal endophyte (FJ449944) 
               
               
                 175 
                 April09_Root_26ER1 
                 E26 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 176 
                 April09_Root_26WR1 
                 W26 
                 Root 
                   Alternaria mali  (AY154683) 
               
               
                 177 
                 April09_Root_26WR2 
                 W26 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 178 
                 April09_Root_27ER1 
                 E27 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 179 
                 April09_Root_27WR1 
                 W27 
                 Root 
                   Microdochium  sp. (FJ536210) 
               
               
                 180 
                 April09_Root_29WR1 
                 W29 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 181 
                 April09_Root_29WR2 
                 W29 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 182 
                 April09_Root_29WR3 
                 W29 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 183 
                 April09_Root_2ER1 
                 E2 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 184 
                 April09_Root_2WR1 
                 W2 
                 Root 
                 Uncultured Ascomycete sp. (EU358786) 
               
               
                 185 
                 April09_Root_2WR2 
                 W2 
                 Root 
                 Uncultured Ascomycete sp. (EU358786) 
               
               
                 186 
                 April09_Root_2WR3 
                 W2 
                 Root 
                 Uncultured Ascomycete sp. (EU003079) 
               
               
                 187 
                 April09_Root_2WR4 
                 W2 
                 Root 
                 Uncultured Ascomycete sp. (EF154350) 
               
               
                 188 
                 April09_Root_30ER1 
                 E30 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 189 
                 April09_Root_31ER2 
                 E31 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 190 
                 April09_Root_31ER3 
                 E31 
                 Root 
                   Fusarium  sp. (GQ505756) 
               
               
                 191 
                 April09_Root_31ER4 
                 E31 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 192 
                 April09_Root_31WR1 
                 W31 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 193 
                 April09_Root_31WR2 
                 W31 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 194 
                 April09_Root_32WR1 
                 W32 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 195 
                 April09_Root_33ER1 
                 E33 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 196 
                 April09_Root_33ER2 
                 E33 
                 Root 
                   Microdochium  sp. (FJ536210) 
               
               
                 197 
                 April09_Root_33ER3 
                 E33 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 198 
                 April09_Root_33ER4 
                 E33 
                 Root 
                   Anthostomella brabeji  (EU552098) 
               
               
                 199 
                 April09_Root_33WR1 
                 W33 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 200 
                 April09_Root_34ER1 
                 E34 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 201 
                 April09_Root_34ER2 
                 E34 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 202 
                 April09_Root_37ER1 
                 E37 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 203 
                 April09_Root_37ER2 
                 E37 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 204 
                 April09_Root_37ER3 
                 E37 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 205 
                 April09_Root_3ER1 
                 E3 
                 Root 
                   Halorosellinia  sp. (EU715636) 
               
               
                 206 
                 April09_Root_3ER2 
                 E3 
                 Root 
                   Fusarium  sp. (EU750677) 
               
               
                 207 
                 April09_Root_3ER3 
                 E3 
                 Root 
                   Halorosellinia  sp. (EU715636) 
               
               
                 208 
                 April09_Root_3ER-A 
                 E3 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144759) 
               
               
                 209 
                 April09_Root_3WR1 
                 W3 
                 Root 
                   Penicillium verruculosum  (AF510496) 
               
               
                 210 
                 April09_Root_3WR2 
                 W3 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 211 
                 April09_Root_3WR3 
                 W3 
                 Root 
                   Gibberella  sp. (GQ389619) 
               
               
                 212 
                 April09_Root_3WR4 
                 W3 
                 Root 
                   Fusarium moniliformae  (EU364865) 
               
               
                 213 
                 April09_Root_41ER1 
                 E41 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 214 
                 April09_Root_41ER2 
                 E41 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 215 
                 April09_Root_41ER2- 
                 E41 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                   
                 Green 
               
               
                 216 
                 April09_Root_41ER3- 
                 E41 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                   
                 Ash 
               
               
                 217 
                 April09_Root_41ER-A 
                 E41 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 218 
                 April09_Root_42ER1 
                 E42 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 219 
                 April09_Root_44ER1 
                 E44 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 220 
                 April09_Root_45ER1 
                 E45 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 221 
                 April09_Root_45ER2 
                 E45 
                 Root 
                   Macrophomina phaseolina  (EF545133) 
               
               
                 222 
                 April09_Root_45ER3 
                 E45 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 223 
                 April09_Root_46ER1 
                 E46 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 224 
                 April09_Root_46ER2 
                 E46 
                 Root 
                   Microdochium  sp. (FJ536210) 
               
               
                 225 
                 April09_Root_47ER1 
                 E47 
                 Root 
                 Uncultured Nectriaceae (EF068175) 
               
               
                 226 
                 April09_Root_47ER2 
                 E47 
                 Root 
                 Ascomycete sp. (AJ279488) 
               
               
                 227 
                 April09_Root_4ER1 
                 E4 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 228 
                 April09_Root_4ER2 
                 E4 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 229 
                 April09_Root_4ER3 
                 E4 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 230 
                 April09_Root_4ER4 
                 E4 
                 Root 
                   Microdochium  sp. (FJ536210) 
               
               
                 231 
                 April09_Root_4ER5 
                 E4 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 232 
                 April09_Root_5ER1 
                 E5 
                 Root 
                 Uncultured Leptosphaeriaceae 
               
               
                   
                   
                   
                   
                 (AY744286) 
               
               
                 233 
                 April09_Root_5ER2 
                 E5 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 234 
                 April09_Root_5ER3 
                 E5 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 235 
                 April09_Root_5WR1 
                 W5 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 236 
                 April09_Root_5WR2 
                 W5 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 237 
                 April09_Root_5WR3 
                 W5 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 238 
                 April09_Root_6ER1 
                 E6 
                 Root 
                 Ascomycete sp. (DQ657853) 
               
               
                 239 
                 April09_Root_6ER2 
                 E6 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 240 
                 April09_Root_7ER1 
                 E7 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 241 
                 April09_Root_7ER2 
                 E7 
                 Root 
                 Uncultured fungus (FJ776560) 
               
               
                 242 
                 April09_Root_7ER-A 
                 E7 
                 Root 
                 Uncultured Helotiales (FJ475783) 
               
               
                 243 
                 April09_Root_7WR1 
                 W7 
                 Root 
                 Fungal endophyte (DQ979674) 
               
               
                 244 
                 April09_Root_7WR2 
                 W7 
                 Root 
                 Fungal endophyte (FN394695) 
               
               
                 245 
                 April09_Root_8ER1 
                 E8 
                 Root 
                 Uncultured  Hypocreales  (FJ708608) 
               
               
                 246 
                 April09_Root_8ER2 
                 E8 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 247 
                 April09_Root_8WR1 
                 W8 
                 Root 
                   Hypocrea lixii  (EF392760) 
               
               
                 248 
                 July09_Root_10ER1 
                 E10 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 249 
                 July09_Root_10ER2 
                 E10 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 250 
                 July09_Root_10ER3 
                 E10 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 251 
                 July09_Root_10ER4 
                 E10 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 252 
                 July09_Root_10ER5 
                 E10 
                 Root 
                 Fungal endophyte (DQ979674) 
               
               
                 253 
                 July09_Root_10WR1 
                 W10 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 254 
                 July09_Root_10WR2 
                 W10 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 255 
                 July09_Root_12WR1 
                 W12 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 256 
                 July09_Root_12WR10 
                 W12 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 257 
                 July09_Root_12WR3 
                 W12 
                 Root 
                 Uncultured  Hypocreales  (FJ708608) 
               
               
                 258 
                 July09_Root_13ER1 
                 E13 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 259 
                 July09_Root_13ER2 
                 E13 
                 Root 
                   Fusarium moniliformae  (EU364856) 
               
               
                 260 
                 July09_Root_13ER4 
                 E13 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 261 
                 July09_Root_13WR1 
                 W13 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 262 
                 July09_Root_15WR1 
                 W15 
                 Root 
                   Fusarium oxysporum  (FJ478116) 
               
               
                 263 
                 July09_Root_17ER1 
                 E17 
                 Root 
                 Mycorrhizal fungal sp. (FJ236025) 
               
               
                 264 
                 July09_Root_17WR2 
                 W17 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 265 
                 July09_Root_17WR3 
                 W17 
                 Root 
                 Uncultured  Hypocreales  (FJ708608) 
               
               
                 266 
                 July09_Root_18ER1 
                 E18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 267 
                 July09_Root_18ER2 
                 E18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 268 
                 July09_Root_18ER3 
                 E18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 269 
                 July09_Root_18ER4 
                 E18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 270 
                 July09_Root_18WR1 
                 W18 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 271 
                 July09_Root_18WR2 
                 W18 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 272 
                 July09_Root_18WR2 
                 W18 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 273 
                 July09_Root_18WR3 
                 W18 
                 Root 
                   Fusarium moniliformae  (EU364856) 
               
               
                 274 
                 July09_Root_18WR4 
                 W18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 275 
                 July09_Root_19ER1 
                 E19 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144806) 
               
               
                 276 
                 July09_Root_19WR2 
                 W19 
                 Root 
                   Fusarium  sp. (EU750682) 
               
               
                 211 
                 July09_Root_19WR3 
                 W19 
                 Root 
                 
                   Fusarium oxysporum f. ciceris 
                 
               
               
                   
                   
                   
                   
                 (EU442590) 
               
               
                 278 
                 July09_Root_1ER1 
                 E1 
                 Root 
                   Microdochium  sp. (FJ536210) 
               
               
                 279 
                 July09_Root_1ER2 
                 E1 
                 Root 
                   Fusarium acuminatum  (GQ505462) 
               
               
                 280 
                 July09_Root_1WR1 
                 W1 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 281 
                 July09_Root_1WR2 
                 W1 
                 Root 
                   Fusarium moniliformae  (EU364865) 
               
               
                 282 
                 July09_Root_1WR3 
                 W1 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144806) 
               
               
                 283 
                 July09_Root_1WR4 
                 W1 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (FJ362205) 
               
               
                 284 
                 July09_Root_1WR5 
                 W1 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 285 
                 July09_Root_20ER1 
                 E20 
                 Root 
                   Fusarium nygamai  (U34568) 
               
               
                 286 
                 July09_Root_20ER10 
                 E20 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 287 
                 July09_Root_20WR2 
                 W20 
                 Root 
                 Uncultured  Hypocreales  (FJ708608) 
               
               
                 288 
                 July09_Root_21ER1 
                 E21 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 289 
                 July09_Root_21ER3 
                 E21 
                 Root 
                 Uncultured soil fungus (DQ420771) 
               
               
                 290 
                 July09_Root_21ER4 
                 E21 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 291 
                 July09_Root_21WR1 
                 W21 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 292 
                 July09_Root_21WR2 
                 W21 
                 Root 
                 Dothideomycete sp. (EU680535) 
               
               
                 293 
                 July09_Root_21WR3 
                 W21 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 294 
                 July09_Root_22WR2 
                 W22 
                 Root 
                   Didymella fabae  (GQ305306) 
               
               
                 295 
                 July09_Root_22WR3 
                 W22 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 296 
                 July09_Root_23WR1 
                 W23 
                 Root 
                   Macrophomina phaseolina  (EF545133) 
               
               
                 297 
                 July09_Root_23WR3 
                 W23 
                 Root 
                   Rhizopycnis  sp. (DQ682600) 
               
               
                 298 
                 July09_Root_23WR4 
                 W23 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (FJ361993) 
               
               
                 299 
                 July09_Root_24WR10 
                 W24 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 300 
                 July09_Root_24WR4 
                 W24 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 301 
                 July09_Root_24WR5 
                 W24 
                 Root 
                   Phoma medicaginis  (EU167575) 
               
               
                 302 
                 July09_Root_25ER1 
                 E25 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 303 
                 July09_Root_25WR4 
                 W25 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 304 
                 July09_Root_26ER1 
                 E26 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 305 
                 July09_Root_26ER2 
                 E26 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 306 
                 July09_Root_26ER3 
                 E26 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 307 
                 July09_Root_26WR1 
                 W26 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 308 
                 July09_Root_26WR2 
                 W26 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 309 
                 July09_Root_26WR3 
                 W26 
                 Root 
                 Uncultured Ascomycete sp. (EU490093) 
               
               
                 310 
                 July09_Root_27WR2 
                 W27 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 311 
                 July09_Root_27WR3 
                 W27 
                 Root 
                 Ascomycete sp. (EF672299) 
               
               
                 312 
                 July09_Root_27WR5 
                 W27 
                 Root 
                 Fungal endophyte (FN392299) 
               
               
                 313 
                 July09_Root_28ER2 
                 E28 
                 Root 
                   Fusarium moniliformae  (EU364865) 
               
               
                 314 
                 July09_Root_28WR1 
                 W28 
                 Root 
                 Uncultured Leptosphaeriaceae 
               
               
                   
                   
                   
                   
                 (AY744286) 
               
               
                 315 
                 July09_Root_29ER1 
                 E29 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 316 
                 July09_Root_29WR2 
                 W29 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 317 
                 July09_Root_29WR3 
                 W29 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 318 
                 July09_Root_2ER2 
                 E2 
                 Root 
                 Uncultured fungus (FN397215) 
               
               
                 319 
                 July09_Root_2ER3 
                 E2 
                 Root 
                   Fusarium nygamai  (U34568) 
               
               
                 320 
                 July09_Root_2ER5 
                 E2 
                 Root 
                   Fusarium oxysporum  (AY928417) 
               
               
                 321 
                 July09_Root_2WR3 
                 W2 
                 Root 
                   Fusarium solani  (FJ478128) 
               
               
                 322 
                 July09_Root_31ER1 
                 E31 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 323 
                 July09_Root_31ER4 
                 E31 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 324 
                 July09_Root_31WR1 
                 W31 
                 Root 
                   Myrothecium cinctum  (DQ135998) 
               
               
                 325 
                 July09_Root_31WR2 
                 W31 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 326 
                 July09_Root_32WR1 
                 W32 
                 Root 
                   Fusarium nygamai  (U34568) 
               
               
                 327 
                 July09_Root_32WR2 
                 W32 
                 Root 
                   Fusarium nygamai  (U34568) 
               
               
                 328 
                 July09_Root_33WR2 
                 W33 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 329 
                 July09_Root_33WR3 
                 W33 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 330 
                 July09_Root_35ER2 
                 E35 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 331 
                 July09_Root_35ER4 
                 E35 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 332 
                 July09_Root_35WR2 
                 W35 
                 Root 
                 Uncultured Ascomycete sp. (EF154351) 
               
               
                 333 
                 July09_Root_35WR3 
                 W35 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 334 
                 July09_Root_35WR4 
                 W35 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 335 
                 July09_Root_36ER1 
                 E36 
                 Root 
                 Uncultured soil fungus (EU480242) 
               
               
                 336 
                 July09_Root_36ER2 
                 E36 
                 Root 
                 Uncultured fungus (FN397215) 
               
               
                 337 
                 July09_Root_36ER3 
                 E36 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 338 
                 July09_Root_36ER4 
                 E36 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 339 
                 July09_Root_36WR1 
                 W36 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 340 
                 July09_Root_36WR2 
                 W36 
                 Root 
                   Eladia saccula  (FJ914702) 
               
               
                 341 
                 July09_Root_36WR2-2 
                 W36 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 342 
                 July09_Root_36WR5 
                 W36 
                 Root 
                   Fusarium moniliformae  (EU364865) 
               
               
                 343 
                 July09_Root_37ER1 
                 E37 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 344 
                 July09_Root_37ER2 
                 E37 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 345 
                 July09_Root_37ER3 
                 E37 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 346 
                 July09_Root_39ER1 
                 E39 
                 Root 
                   Fusarium  sp. (EU750677) 
               
               
                 347 
                 July09_Root_39ER3 
                 E39 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 348 
                 July09_Root_39ER5 
                 E39 
                 Root 
                 Uncultured endophytic fungus 
               
               
                   
                   
                   
                   
                 (FJ524302) 
               
               
                 349 
                 July09_Root_3ER1-2 
                 E3 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 350 
                 July09_Root_3ER2 
                 E3 
                 Root 
                   Fusarium oxysporum  (FJ154076) 
               
               
                 351 
                 July09_Root_3ER3 
                 E3 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 352 
                 July09_Root_3WR1 
                 W3 
                 Root 
                 Uncultured endophytic fungus 
               
               
                   
                   
                   
                   
                 (EF505610) 
               
               
                 353 
                 July09_Root_3WR2 
                 W3 
                 Root 
                 Ascomycete sp. (EF672299) 
               
               
                 354 
                 July09_Root_3WR3 
                 W3 
                 Root 
                 Uncultured Ascomycete sp. (EF154351) 
               
               
                 355 
                 July09_Root_40ER1 
                 E40 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 356 
                 July09_Root_40ER2 
                 E40 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 357 
                 July09_Root_40ER3 
                 E40 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 358 
                 July09_Root_41ER1 
                 E41 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 359 
                 July09_Root_42ER1 
                 E42 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 360 
                 July09_Root_42ER2 
                 E42 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 361 
                 July09_Root_43ER1 
                 E43 
                 Root 
                 Uncultured Ascomycete sp. (EU490093) 
               
               
                 362 
                 July09_Root_43ER2 
                 E43 
                 Root 
                 Uncultured  Hypocreales  (FJ708608) 
               
               
                 363 
                 July09_Root_43ER3 
                 E43 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 364 
                 July09_Root_43ER4 
                 E43 
                 Root 
                 Fungal endophyte (FN392299) 
               
               
                 365 
                 July09_Root_44ER1 
                 E44 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 366 
                 July09_Root_45ER1 
                 E45 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 367 
                 July09_Root_45ER4 
                 E45 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 368 
                 July09_Root_47ER1 
                 E47 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 369 
                 July09_Root_47ER2 
                 E47 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 370 
                 July09_Root_47ER3 
                 E47 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 371 
                 July09_Root_47ER4 
                 E47 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 372 
                 July09_Root_48ER1 
                 E48 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 373 
                 July09_Root_48ER2 
                 E48 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 374 
                 July09_Root_48ER3 
                 E48 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 375 
                 July09_Root_4ER1 
                 E4 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 376 
                 July09_Root_4ER2 
                 E4 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 377 
                 July09_Root_4ER3 
                 E4 
                 Root 
                   Fusarium  sp. (GU257897) 
               
               
                 378 
                 July09_Root_4ER4 
                 E4 
                 Root 
                   Fusarium  sp. (AF158312) 
               
               
                 379 
                 July09_Root_4WR1 
                 W4 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 380 
                 July09_Root_4WR3 
                 W4 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 381 
                 July09_Root_5ER2 
                 E5 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 382 
                 July09_Root_5ER3-1 
                 E5 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 383 
                 July09_Root_5ER3-2 
                 E5 
                 Root 
                   Codinaeopsis  sp. (EF488392), 
               
               
                 384 
                 July09_Root_5ER5 
                 E5 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 385 
                 July09_Root_5WR1 
                 W5 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 386 
                 July09_Root_5WR10 
                 W5 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 387 
                 July09_Root_5WR2 
                 W5 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 388 
                 July09_Root_5WR20 
                 W5 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 389 
                 July09_Root_5WR3 
                 W5 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 390 
                 July09_Root_6ER1 
                 E6 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 391 
                 July09_Root_6ER2 
                 E6 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 392 
                 July09_Root_6WR1 
                 W6 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 393 
                 July09_Root_7ER1 
                 E7 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 394 
                 July09_Root_7ER2 
                 E7 
                 Root 
                   Diaporthe phaseolorum  (AF001016) 
               
               
                 395 
                 July09_Root_7WR1 
                 W7 
                 Root 
                   Fusarium moniliformae  (EU364865) 
               
               
                 396 
                 July09_Root_7WR10 
                 W7 
                 Root 
                 Uncultured fungus (AM260913) 
               
               
                 397 
                 July09_Root_8ER1 
                 E8 
                 Root 
                   Trichoderma koningiopsis  (EU280108) 
               
               
                 398 
                 July09_Root_8ER2 
                 E8 
                 Root 
                 Uncultured Helotiales (FJ475783) 
               
               
                 399 
                 July09_Root_9ER1 
                 E9 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 400 
                 Oct09_Root_10WR1 
                 W10 
                 Root 
                 Ascomycete sp. (EU520609) 
               
               
                 401 
                 Oct09_Root_10WR2 
                 W10 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 402 
                 Oct09_Root_10WR3 
                 W10 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 403 
                 Oct09_Root_11WR1 
                 W11 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 404 
                 Oct09_Root_11WR2 
                 W11 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 405 
                 Oct09_Root_11WR5 
                 W11 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 406 
                 Oct09_Root_12WR1 
                 W12 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 407 
                 Oct09_Root_12WR2 
                 W12 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 408 
                 Oct09_Root_12WR4 
                 W12 
                 Root 
                 Grass root mycorrhizal sp. (AY599235) 
               
               
                 409 
                 Oct09_Root_13ER1 
                 E13 
                 Root 
                   Periconia macrospinosa  (FJ536208) 
               
               
                 410 
                 Oct09_Root_13ER2 
                 E13 
                 Root 
                   Periconia macrospinosa  (FJ536207) 
               
               
                 411 
                 Oct09_Root_13ER3 
                 E13 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 412 
                 Oct09_Root_13WR1 
                 W13 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 413 
                 Oct09_Root_13WR2 
                 W13 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 414 
                 Oct09_Root_13WR3 
                 W13 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 415 
                 Oct09_Root_14WR2 
                 W14 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 416 
                 Oct09_Root_15WR1 
                 W15 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 417 
                 Oct09_Root_15WR2 
                 W15 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 418 
                 Oct09_Root_16WR2 
                 W16 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 419 
                 Oct09_Root_17ER1 
                 E17 
                 Root 
                   Fusarium proliferatum  (AF291061) 
               
               
                 420 
                 Oct09_Root_17WR1 
                 W17 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 421 
                 Oct09_Root_17WR2 
                 W17 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 422 
                 Oct09_Root_17WR5 
                 W17 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 423 
                 Oct09_Root_18ER1 
                 E18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 424 
                 Oct09_Root_18ER2 
                 E18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 425 
                 Oct09_Root_18ER3 
                 E18 
                 Root 
                 Uncultured  Lachnum  (FJ440910) 
               
               
                 426 
                 Oct09_Root_18WR2 
                 W18 
                 Root 
                   Trichoderma aureoviride  (AF194010) 
               
               
                 427 
                 Oct09_Root_18WR3 
                 W18 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 428 
                 Oct09_Root_18WR4 
                 W18 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 429 
                 Oct09_Root_19ER1 
                 E19 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 430 
                 Oct09_Root_19ER2 
                 E19 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 431 
                 Oct09_Root_19ER3 
                 E19 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 432 
                 Oct09_Root_19ER4 
                 E19 
                 Root 
                   Fusarium moniliformae  (EU364856) 
               
               
                 433 
                 Oct09_Root_19WR1 
                 W19 
                 Root 
                   Fusarium nygamai  (U34568) 
               
               
                 434 
                 Oct09_Root_1ER1 
                 E1 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 435 
                 Oct09_Root_1ER3 
                 E1 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 436 
                 Oct09_Root_1ER4 
                 E1 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 437 
                 Oct09_Root_1WR1 
                 W1 
                 Root 
                   Fusarium  sp. 14018 (EU750682) 
               
               
                 438 
                 Oct09_Root_1WR2 
                 W1 
                 Root 
                 Ascomycete sp. (EF672299) 
               
               
                 439 
                 Oct09_Root_1WR3 
                 W1 
                 Root 
                 Ascomycete sp. (EF672299) 
               
               
                 440 
                 Oct09_Root_1WR4 
                 W1 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 441 
                 Oct09_Root_21ER2 
                 E212 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 442 
                 Oct09_Root_22ER3 
                 E22 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 443 
                 Oct09_Root_22ER4 
                 E22 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 444 
                 Oct09_Root_22WR1 
                 W22 
                 Root 
                   Alternaria alternata  (DQ023279) 
               
               
                 445 
                 Oct09_Root_22WR2 
                 W22 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 446 
                 Oct09_Root_22WR3 
                 W22 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 447 
                 Oct09_Root_23ER1 
                 E23 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 448 
                 Oct09_Root_23ER2 
                 E23 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 449 
                 Oct09_Root_23ER4 
                 E23 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 450 
                 Oct09_Root_23WR1 
                 W23 
                 Root 
                   Marasmius nigrobrunneus  (EU935578) 
               
               
                 451 
                 Oct09_Root_23WR2 
                 W23 
                 Root 
                   Hypocrea lixii  (AF194011) 
               
               
                 452 
                 Oct09_Root_23WR3 
                 W23 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 453 
                 Oct09_Root_23WR4 
                 W23 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 454 
                 Oct09_Root_23WR5 
                 W23 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 455 
                 Oct09_Root_24WR1 
                 W24 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 456 
                 Oct09_Root_24WR2 
                 W24 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 457 
                 Oct09_Root_24WR3 
                 W24 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 458 
                 Oct09_Root_24WR4 
                 W24 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 459 
                 Oct09_Root_25ER1 
                 E25 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 460 
                 Oct09_Root_25ER2-1 
                 E25 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 461 
                 Oct09_Root_25ER2-2 
                 E25 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 462 
                 Oct09_Root_25ER3 
                 E25 
                 Root 
                   Waitea circinata  var.  zeae  (GQ221863) 
               
               
                 463 
                 Oct09_Root_25WR1 
                 W25 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 464 
                 Oct09_Root_25WR2 
                 W25 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 465 
                 Oct09_Root_25WR3 
                 W25 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 466 
                 Oct09_Root_25WR4 
                 W25 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 467 
                 Oct09_Root_25WR5 
                 W25 
                 Root 
                   Penicillium  sp. (FJ571475) 
               
               
                 468 
                 Oct09_Root_26ER1 
                 E26 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 469 
                 Oct09_Root_26ER2 
                 E26 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 470 
                 Oct09_Root_26ER3 
                 E26 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 471 
                 Oct09_Root_26ER4 
                 E26 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 472 
                 Oct09_Root_26WR1 
                 W26 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 473 
                 Oct09_Root_26WR2 
                 W26 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 474 
                 Oct09_Root_26WR3 
                 W26 
                 Root 
                 Grass root mycorrhizal sp. (AY599235) 
               
               
                 475 
                 Oct09_Root_27WR1 
                 W27 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 476 
                 Oct09_Root_28ER1 
                 E28 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 477 
                 Oct09_Root_28ER2 
                 E28 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 478 
                 Oct09_Root_28ER4 
                 E28 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 479 
                 Oct09_Root_28ER5 
                 E28 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 480 
                 Oct09_Root_28WR1 
                 W28 
                 Root 
                   Myrothecium melanosporum  (FJ235086) 
               
               
                 481 
                 Oct09_Root_29ER1 
                 E29 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 482 
                 Oct09_Root_2WR1 
                 W2 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 483 
                 Oct09_Root_2WR2 
                 W2 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 484 
                 Oct09_Root_2WR3 
                 W2 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 485 
                 Oct09_Root_2WR4 
                 W2 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 486 
                 Oct09_Root_2WR5 
                 W2 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 487 
                 Oct09_Root_2WR6 
                 W2 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 488 
                 Oct09_Root_2WR7 
                 W2 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 489 
                 Oct09_Root_2WR8 
                 W2 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 490 
                 Oct09_Root_31ER1 
                 E31 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 491 
                 Oct09_Root_32WR2 
                 W32 
                 Root 
                 Uncultured soil fungus (EU490117) 
               
               
                 492 
                 Oct09_Root_32WR3 
                 W32 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 493 
                 Oct09_Root_32WR4 
                 W32 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 494 
                 Oct09_Root_33WR1 
                 W33 
                 Root 
                   Fusarium moniliforme  (EU364856) 
               
               
                 495 
                 Oct09_Root_33WR2 
                 W33 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 496 
                 Oct09_Root_33WR3 
                 W33 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 497 
                 Oct09_Root_34WR2 
                 W34 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 498 
                 Oct09_Root_34WR4 
                 W34 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 499 
                 Oct09_Root_34WR5 
                 W34 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 500 
                 Oct09_Root_35ER1 
                 E35 
                 Root 
                   Gibberella  sp. 1893 (FJ008984) 
               
               
                 501 
                 Oct09_Root_35ER2 
                 E35 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 502 
                 Oct09_Root_35ER3 
                 E35 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 503 
                 Oct09_Root_35ER4 
                 E35 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 504 
                 Oct09_Root_36ER1 
                 E36 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 505 
                 Oct09_Root_36ER2 
                 E36 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 506 
                 Oct09_Root_3ER1 
                 3E 
                 Root 
                   Fusarium  sp. (EU750677) 
               
               
                 507 
                 Oct09_Root_3ER2 
                 3E 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 508 
                 Oct09_Root_3ER3 
                 3E 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 509 
                 Oct09_Root_3ER4 
                 3E 
                 Root 
                   Rhizoctonia praticola  (DQ223780) 
               
               
                 510 
                 Oct09_Root_3WR1 
                 3W 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 511 
                 Oct09_Root_3WR3 
                 3W 
                 Root 
                 Ascomycete sp. (EF672299) 
               
               
                 512 
                 Oct09_Root_40ER4 
                 E40 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 513 
                 Oct09_Root_42ER1 
                 E42 
                 Root 
                   Gaeumannomyces graminis  var.  tritici   
               
               
                   
                   
                   
                   
                 (AJ246153) 
               
               
                 514 
                 Oct09_Root_42ER2 
                 E42 
                 Root 
                   Gaeumannomyces graminis  var.  tritici   
               
               
                   
                   
                   
                   
                 (AJ246153) 
               
               
                 515 
                 Oct09_Root_42ER3 
                 E42 
                 Root 
                   Gaeumannomyces graminis  var.  tritici   
               
               
                   
                   
                   
                   
                 (AJ246153) 
               
               
                 516 
                 Oct09_Root_43ER1 
                 E42 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 517 
                 Oct09_Root_43ER2 
                 E42 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 518 
                 Oct09_Root_43ER3 
                 E43 
                 Root 
                   Fusarium nygamai  (U34568) 
               
               
                 519 
                 Oct09_Root_45ER1 
                 E45 
                 Root 
                 Uncultured root associated fungus 
               
               
                   
                   
                   
                   
                 (EU144855) 
               
               
                 520 
                 Oct09_Root_45ER3 
                 E45 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 521 
                 Oct09_Root_45ER4 
                 E45 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 522 
                 Oct09_Root_47ER1 
                 E47 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 523 
                 Oct09_Root_48ER1 
                 E48 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 524 
                 Oct09_Root_48ER2 
                 E48 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 525 
                 Oct09_Root_4ER1 
                 E4 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 526 
                 Oct09_Root_4ER2 
                 E4 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 527 
                 Oct09_Root_4ER3 
                 E4 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 528 
                 Oct09_Root_4WR1 
                 W4 
                 Root 
                 Ascomycete sp. (EF672299) 
               
               
                 529 
                 Oct09_Root_4WR2 
                 W4 
                 Root 
                   Fusarium  sp. (EU750677, EU750686) 
               
               
                 530 
                 Oct09_Root_5ER1 
                 E5 
                 Root 
                 Sordariomycete sp. (EU680539) 
               
               
                 531 
                 Oct09_Root_5ER2 
                 E5 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 532 
                 Oct09_Root_5ER3 
                 E5 
                 Root 
                   Gaeumannomyces incrustans  (U17214) 
               
               
                 533 
                 Oct09_Root_5WR1 
                 W5 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 534 
                 Oct09_Root_5WR2 
                 W5 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 535 
                 Oct09_Root_6ER1 
                 E6 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 536 
                 Oct09_Root_6ER2 
                 E6 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 537 
                 Oct09_Root_6ER3 
                 E6 
                 Root 
                   Diaporthe phaseolorum  (AF001016) 
               
               
                 538 
                 Oct09_Root_6ER4 
                 E6 
                 Root 
                   Diaporthe phaseolorum  (AF001016) 
               
               
                 539 
                 Oct09_Root_6ER5 
                 E6 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 540 
                 Oct09_Root_6WR1 
                 W6 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 541 
                 Oct09_Root_7ER2 
                 E7 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 542 
                 Oct09_Root_7ER3 
                 E7 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 543 
                 Oct09_Root_7ER4 
                 E7 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 544 
                 Oct09_Root_8ER1 
                 E8 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 545 
                 Oct09_Root_8ER2 
                 E8 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                 546 
                 Oct09_Root_8ER4 
                 E8 
                 Root 
                   Fusarium nygamai  (X94174) 
               
               
                 547 
                 Oct09_Root_8WR1 
                 W8 
                 Root 
                   Fusarium  sp. (EF152423) 
               
               
                 548 
                 Oct09_Root_9ER1 
                 E9 
                 Root 
                   Magnaporthe rhizophila  (DQ528791) 
               
               
                 549 
                 Oct09_Root_9ER2 
                 E9 
                 Root 
                   Microdiplodia  sp. (EF432267) 
               
               
                 550 
                 Oct09_Root_9ER3 
                 E9 
                 Root 
                   Rhizopycnis  sp. (DQ682600) 
               
               
                 551 
                 Oct09_Root_9ER4 
                 E9 
                 Root 
                   Penicillium camemberti  (DQ681326) 
               
               
                 552 
                 Oct09_Root_9ER7 
                 E9 
                 Root 
                   Fusarium moniliformae  (EU364856) 
               
               
                 553 
                 Oct09_Root_9WR1 
                 W9 
                 Root 
                   Rhizopycnis  sp. (DQ682600) 
               
               
                 554 
                 Oct09_Root_9WR2 
                 W9 
                 Root 
                   Codinaeopsis  sp. (EF488392) 
               
               
                 555 
                 Oct09_Root_9WR3 
                 W9 
                 Root 
                 Uncultured root-associated fungus 
               
               
                   
                   
                   
                   
                 (EU144817) 
               
               
                   
               
               
                 *GPS coordinates for each location are provided in Table 1. 
               
            
           
         
       
     
     Example 3 
     Endophyte Population Analysis 
     Two comprehensive endophyte species lists, one for shoot and one for root, were generated for each collection date. Comparisons were made between species from the east and west parts of the tallgrass prairie, as well as between sampling dates. In addition, fungal species from shoot and root tissue were grouped according to their higher taxonomic level (ordinal level) to allow ordinal frequencies to be evaluated. 
     Species diversity in each of these fungal “communities” was estimated using the Shannon diversity index (Bowman et al. 1971) as implemented in the PROC IML program, SAS software version 9.1.3 (SAS 2004). Differences in Shannon diversity indices of any two fungal communities were compared using Student&#39;s t-test at a 95% confidence level. The mean organic matter, macronutrients, sodium, and pH content in soils from the east and west parts of the tallgrass prairie were compared using PROC TTEST in SAS software version 9.1.3 (SAS 2004). 
     A total of 736 culturable fungal taxa were obtained from three collection trips. 
     Out of these isolates, 69% originated from roots, while 31% came from shoot tissues. Quality ITS sequences were obtained for 555 isolates, representing 75.4% of the total isolates obtained in this study. Of those sequenced, 74% were from root tissue and 26% were from shoot tissues. The results presented below are based on the sequence data from these 555 isolates. 
     Endophyte Community Structure in Shoot Tissues 
     The shoot fungal endophyte community was composed of 143 fungal taxa representing at least 51 different species (Table 3). The number of fungal taxa isolated from shoot tissues varied between study months. The numbers of taxa isolated in April, July, and October were 83, 46, and 14, respectively. 
     Endophyte Community Structure in Root Tissues 
     The root fungal endophyte community was composed of 412 taxa representing at least 58 different species (Table 4). The number of fungal taxa isolated from root tissue also varied between study months. The numbers of taxa isolated in April, July, and October were 104, 156, and 152, respectively. 
     Species Diversity in Endophyte Communities in Different Sampling Months 
     The species diversity in endophyte communities varied between sampling months (Table 5). The shoot community had the highest species diversity in April (HS=3.241), and the lowest in October (HS=1.730). The shoot endophyte community was significantly more diverse than the root community in April, whereas the root community was significantly more diverse than the shoot community in the October sampling date (P&lt;0.001; Table 5). 
     Species Diversity in Fungal Communities from East and West Parts of the Tallgrass Prairie 
     Fungal communities from the east and west parts were similar in species diversity (Table 6). However, a combined analysis of species from three collections revealed that the root endophyte community from the west had significantly higher species diversity than that of the east (HS=2.957 vs. 2.787; P&lt;0.001; Table 6). 
     Soils from East and West Parts of the Tallgrass Prairie 
     Soils from the east and west parts of tallgrass prairie were significantly different in organic matter, phosphorus, calcium, and sodium contents (P≦0.049; Table 7). The organic matter and calcium content was high in soils from the east part, whereas phosphorus and sodium content was high in the soils from the west part. 
     Diversity in Endophyte Communities at the Ordinal Level 
     Endophytic fungal isolates from the 2009 collections belonged to at least 18 orders (Table 8). Isolates from shoot tissues were assigned to nine orders and root isolates to 15 orders. Three orders were unique to shoot tissues, whereas nine orders were unique to root tissues. At least seven orders were common between shoot and root tissues. Members of the order Hypocreales were the most commonly isolated fungi, constituting approximately 64% and 39% of the fungal communities in shoot and root tissue, respectively. 
     
       
         
           
               
             
               
                 TABLE 3 
               
             
            
               
                   
               
               
                 Temporal distributions of endophytic fungal species in 
               
               
                 switchgrass shoot tissues from the tallgrass prairie. 
               
            
           
           
               
               
            
               
                   
                 Month &amp; Species Distribution 
               
            
           
           
               
               
               
               
               
               
            
               
                 Species 
                 April 
                 July 
                 October 
                 Total 
                 Percent 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                   Acremonium  sp. 
                 2 
                 5 
                 0 
                 7 
                 4.90 
               
               
                 
                   Acremonium strictum 
                 
                 1 
                 6 
                 1 
                 8 
                 5.59 
               
               
                 
                   Alternaria alternata 
                 
                 0 
                 2 
                 0 
                 2 
                 1.40 
               
               
                 
                   Alternaria arborescens 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Alternaria mali 
                 
                 1 
                 2 
                 0 
                 3 
                 2.10 
               
               
                   Alternaria  sp. 
                 0 
                 2 
                 0 
                 2 
                 1.40 
               
               
                 Ascomycete sp. 
                 2 
                 0 
                 0 
                 2 
                 1.40 
               
               
                 
                   Bionectria rossmaniae 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Bipolaris heveae 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Bipolaris oryzae 
                 
                 1 
                 1 
                 0 
                 2 
                 1.40 
               
               
                 
                   Buergenerula spartinae 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Cladosporium colombiae 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                   Codinaeopsis  sp. 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Colletotrichum graminicola 
                 
                 0 
                 2 
                 0 
                 2 
                 1.40 
               
               
                 Dothideomycete sp. 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Emericellopsis minima 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Emericellopsis terricola 
                 
                 6 
                 0 
                 0 
                 6 
                 4.20 
               
               
                 
                   Eutypa scoparia 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Exserohilum rostratum 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Fusarium acuminatum 
                 
                 0 
                 0 
                 1 
                 1 
                 0.70 
               
               
                 
                   Fusarium moniliformae 
                 
                 0 
                 8 
                 0 
                 8 
                 5.59 
               
               
                 
                   Fusarium nygamai 
                 
                 1 
                 9 
                 5 
                 15 
                 10.49 
               
               
                   F. oxysporum f.  sp.  vasinfectum   
                 2 
                 0 
                 0 
                 2 
                 1.40 
               
               
                 
                   Fusarium proliferatum 
                 
                 2 
                 10 
                 1 
                 13 
                 9.09 
               
               
                 
                   Fusarium pseudograminearum 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Fusarium subglutinans 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Gibberella acuminata 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                   Gibberella  sp. 
                 2 
                 8 
                 0 
                 10 
                 6.99 
               
               
                 
                   Hypocrea lixii 
                 
                 3 
                 0 
                 0 
                 3 
                 2.10 
               
               
                 Leaf litter ascomycetes 
                 0 
                 0 
                 1 
                 1 
                 0.70 
               
               
                   Leptosphaeria avenaria f.  sp. 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   triticea 
                 
               
               
                 
                   Leptosphaeria bicolor 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                   Monographella  sp. 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Myrothecium melanosporum 
                 
                 3 
                 0 
                 0 
                 3 
                 2.10 
               
               
                 
                   Myrothecium verrucaria 
                 
                 0 
                 2 
                 0 
                 2 
                 1.40 
               
               
                 
                   Nigrospora oryzae 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Parasarcopodium ceratocaryi 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Penicillium citreonigrum 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Periconia macrospinosa 
                 
                 0 
                 2 
                 0 
                 2 
                 1.40 
               
               
                   Phaeosphaeria  sp. 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Phoma glomerata 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 Pleosporaceae sp. 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 
                   Pseudozyma flocculosa 
                 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 Sordariomycete sp. 
                 1 
                 1 
                 2 
                 4 
                 2.80 
               
               
                 
                   Sporisorium everhartii 
                 
                 0 
                 10 
                 0 
                 10 
                 6.99 
               
               
                 
                   Stachybotrys bisbyi 
                 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 
                   Stachybotrys elegans 
                 
                 2 
                 0 
                 3 
                 5 
                 3.50 
               
               
                 Uncultured Ascomycete sp. 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                 Uncultured endophytic fungus 
                 2 
                 1 
                 0 
                 3 
                 2.10 
               
               
                 Uncultured root-associated 
                 0 
                 1 
                 0 
                 1 
                 0.70 
               
               
                 fungus 
               
               
                 Uncultured soil fungus 
                 1 
                 0 
                 0 
                 1 
                 0.70 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Temporal distributions of endophytic fungal species in 
               
               
                 switchgrass root tissues from the tallgrass prairie. 
               
            
           
           
               
               
            
               
                   
                 Month &amp; Species Distribution 
               
            
           
           
               
               
               
               
               
               
            
               
                 Species 
                 April 
                 July 
                 October 
                 Total 
                 Percent 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 
                   Alternaria alternata 
                 
                 0 
                 0 
                 1 
                 1 
                 0.24 
               
               
                 
                   Alternaria longissima 
                 
                 1 
                 0 
                 0 
                 1 
                 0.24 
               
               
                 
                   Alternaria mali 
                 
                 2 
                 0 
                 0 
                 2 
                 0.49 
               
               
                 
                   Amyloathelia crassiuscula 
                 
                 1 
                 0 
                 0 
                 1 
                 0.24 
               
               
                 
                   Anthostomella brabeji 
                 
                 1 
                 0 
                 0 
                 1 
                 0.24 
               
               
                 Ascomycete sp. 
                 2 
                 2 
                 5 
                 9 
                 2.18 
               
               
                   Codinaeopsis  sp. 
                 3 
                 1 
                 4 
                 8 
                 1.94 
               
               
                 
                   Coprinus auricomus 
                 
                 2 
                 0 
                 0 
                 2 
                 0.49 
               
               
                 
                   Diaporthe phaseolorum 
                 
                 0 
                 1 
                 2 
                 3 
                 0.73 
               
               
                 
                   Didymella fabae 
                 
                 0 
                 1 
                 0 
                 1 
                 0.24 
               
               
                 Dothideomycete sp. 
                 0 
                 1 
                 0 
                 1 
                 0.24 
               
               
                 
                   Eladia saccula 
                 
                 0 
                 1 
                 0 
                 1 
                 0.24 
               
               
                   Eutypella  sp. 
                 1 
                 0 
                 0 
                 1 
                 0.24 
               
               
                 Fungal endophyte 
                 3 
                 3 
                 0 
                 6 
                 1.46 
               
               
                 
                   Fusarium acuminatum 
                 
                 2 
                 1 
                 0 
                 3 
                 0.73 
               
               
                 
                   Fusarium moniliformae 
                 
                 2 
                 6 
                 3 
                 11 
                 2.67 
               
               
                 
                   Fusarium nygamai 
                 
                 31 
                 23 
                 29 
                 83 
                 20.15 
               
               
                 
                   Fusarium oxysporum 
                 
                 0 
                 3 
                 0 
                 3 
                 0.73 
               
               
                 
                   Fusarium oxysporum f. ciceris 
                 
                 0 
                 1 
                 0 
                 1 
                 0.24 
               
               
                 
                   Fusarium proliferatum 
                 
                 0 
                 21 
                 2 
                 23 
                 5.58 
               
               
                 
                   Fusarium solani 
                 
                 0 
                 1 
                 0 
                 1 
                 0.24 
               
               
                   Fusarium  sp. 
                 4 
                 4 
                 4 
                 12 
                 2.91 
               
               
                   Gaeumannomyces graminis  var. 
                 0 
                 0 
                 3 
                 3 
                 0.73 
               
               
                 
                   tritici 
                 
               
               
                 
                   Gaeumannomyces incrustans 
                 
                 7 
                 16 
                 34 
                 57 
                 13.83 
               
               
                   Gibberella  sp. 
                 1 
                 0 
                 1 
                 2 
                 0.49 
               
               
                 Grass root mycorrhizal sp. 
                 0 
                 0 
                 2 
                 2 
                 0.49 
               
               
                   Halorosellinia  sp. 
                 2 
                 0 
                 0 
                 2 
                 0.49 
               
               
                 
                   Hypocrea lixii 
                 
                 1 
                 0 
                 1 
                 2 
                 0.49 
               
               
                 
                   Kabatiella microsticta 
                 
                 1 
                 0 
                 0 
                 1 
                 0.24 
               
               
                 
                   Macrophomina phaseolina 
                 
                 1 
                 1 
                 0 
                 2 
                 0.49 
               
               
                 
                   Magnaporthe rhizophila 
                 
                 0 
                 14 
                 22 
                 36 
                 8.74 
               
               
                 
                   Marasmius nigrobrunneus 
                 
                 0 
                 0 
                 1 
                   
                 0.24 
               
               
                   Microdiplodia  sp. 
                 0 
                 0 
                 1 
                   
                 0.24 
               
               
                   Microdochium  sp. 
                 4 
                 1 
                 0 
                 5 
                 1.21 
               
               
                 Mycorrhizal fungal sp. 
                 0 
                 1 
                 0 
                   
                 0.24 
               
               
                 
                   Myrothecium cinctum 
                 
                 0 
                 1 
                 0 
                   
                 0.24 
               
               
                 
                   Myrothecium melanosporum 
                 
                 0 
                 0 
                 1 
                   
                 0.24 
               
               
                 
                   Penicillium camemberti 
                 
                 0 
                 0 
                 1 
                   
                 0.24 
               
               
                   Penicillium  sp. 
                 0 
                 0 
                 1 
                   
                 0.24 
               
               
                 
                   Penicillium verruculosum 
                 
                 1 
                 0 
                 0 
                   
                 0.24 
               
               
                 
                   Periconia macrospinosa 
                 
                 20 
                 9 
                 2 
                 31 
                 7.52 
               
               
                 
                   Phoma medicaginis 
                 
                 0 
                 1 
                 0 
                   
                 0.24 
               
               
                 
                   Rhizoctonia praticola 
                 
                 0 
                 0 
                 1 
                   
                 0.24 
               
               
                   Rhizopycnis  sp. 
                 0 
                 1 
                 2 
                 3 
                 0.73 
               
               
                 Sordariomycete sp. 
                 0 
                 2 
                 13 
                 15 
                 3.64 
               
               
                 
                   Trichoderma aureoviride 
                 
                 0 
                 0 
                 1 
                 1 
                 0.24 
               
               
                 
                   Trichoderma koningiopsis 
                 
                 0 
                 1 
                 0 
                 1 
                 0.24 
               
               
                 Uncultured Ascomycete sp. 
                 4 
                 4 
                 0 
                 8 
                 1.94 
               
               
                 Uncultured endophytic fungus 
                 0 
                 2 
                 0 
                 2 
                 0.49 
               
               
                 Uncultured Fungus 
                 1 
                 3 
                 0 
                 4 
                 0.97 
               
               
                 Uncultured Helotiales 
                 1 
                 1 
                 0 
                 2 
                 0.49 
               
               
                 Uncultured  Hypocreales   
                 1 
                 3 
                 0 
                 4 
                 0.97 
               
               
                 Uncultured  Lachnum   
                 0 
                 0 
                 1 
                 1 
                 0.24 
               
               
                 Uncultured Leptosphaeriaceae 
                 1 
                 2 
                 0 
                 3 
                 0.73 
               
               
                 Uncultured Nectriaceae 
                 1 
                 0 
                 0 
                 1 
                 0.24 
               
               
                 Uncultured root-associated 
                 1 
                 17 
                 16 
                 34 
                 8.25 
               
               
                 fungus 
               
               
                 Uncultured soil fungus 
                 1 
                 2 
                 1 
                 4 
                 0.97 
               
               
                   Waitea circinata  var.  zeae   
                 0 
                 0 
                 1 
                 1 
                 0.24 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Fungal taxa, species, and species diversity in switchgrass 
               
               
                 endophytic fungal communities from the tallgrass prairie. 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Number of 
                 Shannon 
                   
                 Degree of 
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Parameter 
                 Comparisons 
                 taxa 
                 species 
                 Index (H S ) 
                 t-value 
                 freedom 
                 P value 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Shoot 
                 April vs. July 
                 46 vs. 83 
                 30 vs. 28 
                 3.241 vs. 2.898 
                 2.775 
                 127 
                 &lt;0.001 
               
               
                 Shoot 
                 April vs. October 
                 46 vs. 14 
                 30 vs. 7  
                 3.241 vs. 1.730 
                 7.158 
                 58 
                 &lt;0.001 
               
               
                 Shoot 
                 July vs. October 
                 83 vs. 14 
                 28 vs. 7  
                 2.898 vs. 1.730 
                 6.167 
                 95 
                 &lt;0.001 
               
               
                 Root 
                 April vs. July 
                 104 vs. 152 
                 30 vs. 34 
                 2.610 vs. 2.865 
                 4.476 
                 254 
                 &lt;0.001 
               
               
                 Root 
                 April vs. October 
                 104 vs. 156 
                 30 vs. 28 
                 2.610 vs. 2.512 
                 1.631 
                 258 
                 &gt;0.100 
               
               
                 Root 
                 July vs. October 
                 152 vs. 156 
                 34 vs. 28 
                 2.865 vs. 2.512 
                 6.920 
                 306 
                 &lt;0.001 
               
               
                 April 
                 Shoot vs. Root 
                  46 vs. 104 
                 30 vs. 30 
                 3.241 vs. 2.610 
                 5.311 
                 148 
                 &lt;0.001 
               
               
                 July 
                 Shoot vs. Root 
                  83 vs. 152 
                 28 vs. 34 
                 2.898 vs. 2.865 
                 0.497 
                 233 
                 &gt;0.500 
               
               
                 October 
                 Shoot vs. Root 
                  14 vs. 156 
                  7 vs. 28 
                 1.730 vs. 2.512 
                 4.237 
                 168 
                 &lt;0.001 
               
               
                 All three months 
                 Shoot vs. Root 
                 143 vs. 412 
                 51 vs. 58 
                 3.456 vs. 3.006 
                 9.857 
                 553 
                 &lt;0.001 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
             
            
               
                   
               
               
                 Fungal taxa, species, and species diversity in switchgrass endophytic fungal 
               
               
                 communities from the east and west parts of the tallgrass prairie. 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Number of 
                 Shannon 
                   
                 Degree of 
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                 Month 
                 Plant Part 
                 Part of Prairie 
                 taxa 
                 species 
                 Index (H S ) 
                 t-value 
                 freedom 
                 P value 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
            
               
                 April 
                 Shoot 
                 East vs. West 
                 18 vs. 28 
                 14 vs. 19 
                 2.553 vs. 2.818 
                 1.060 
                 44 
                 &gt;0.200 
               
               
                   
                 Root 
                 East vs. West 
                 67 vs. 37 
                 20 vs. 17 
                 2.292 vs. 2.358 
                 0.555 
                 102 
                 &gt;0.500 
               
               
                 July 
                 Shoot 
                 East vs. West 
                 44 vs. 39 
                 21 vs. 15 
                 2.752 vs. 2.486 
                 1.965 
                 81 
                 &gt;0.050 
               
               
                   
                 Root 
                 East vs. West 
                 82 vs. 70 
                 23 vs. 25 
                 2.647 vs. 2.770 
                 1.477 
                 150 
                 &gt;0.100 
               
               
                 October 
                 Shoot 
                 East vs. West 
                 7 vs. 7 
                 5 vs. 3 
                 1.550 vs. 1.004 
                 1.491 
                 12 
                 &gt;0.100 
               
               
                   
                 Root 
                 East vs. West 
                 81 vs. 75 
                 19 vs. 19 
                 2.319 vs. 2.420 
                 1.407 
                 154 
                 &gt;0.100 
               
               
                 All three months 
                 Shoot 
                 East vs. West 
                 69 vs. 74 
                 33 vs. 29 
                 3.166 vs. 3.071 
                 0.949 
                 141 
                 &gt;0.300 
               
               
                   
                 Root 
                 East vs. West 
                 230 vs. 182 
                 38 vs. 42 
                 2.787 vs. 2.957 
                 4.464 
                 410 
                 &lt;0.001 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
             
            
               
                   
               
               
                 Organic matter, macronutrients and sodium contents, and pH content 
               
               
                 in the soils from the east and west parts of the tallgrass prairie. 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 Part of 
                   
                 Standard 
                 t-value 
                   
               
               
                 Parameter 
                 Prairie 
                 Mean 
                 error 
                 (at 22 df) 
                 P value 
               
               
                   
               
            
           
           
               
               
               
               
               
               
            
               
                 Organic matter (%) 
                 East 
                 4.90 
                 0.34 
                 4.460 
                 0.0002 
               
               
                   
                 West 
                 2.48 
                 0.42 
               
               
                 Phosphorus (ppm) 
                 East 
                 9 
                 0.99 
                 2.370 
                 0.0267 
               
               
                   
                 West 
                 35 
                 11 
               
               
                 Potassium (ppm) 
                 East 
                 354 
                 63 
                 0.350 
                 0.7310 
               
               
                   
                 West 
                 395 
                 99 
               
               
                 Calcium (ppm) 
                 East 
                 7684 
                 654 
                 3.540 
                 0.0018 
               
               
                   
                 West 
                 4154 
                 751 
               
               
                 Magnesium (ppm) 
                 East 
                 412 
                 41 
                 1.540 
                 0.1380 
               
               
                   
                 West 
                 599 
                 114 
               
               
                 Sodium (ppm) 
                 East 
                 40 
                 8 
                 2.080 
                 0.0491 
               
               
                   
                 West 
                 96 
                 26 
               
               
                 pH (1 to 14) 
                 East 
                 7.5 
                 0.16 
                 0.090 
                 0.9310 
               
               
                   
                 West 
                 7.5 
                 0.24 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 8 
               
             
            
               
                   
               
               
                 Ordinal distributions of switchgrass fungal endophytes 
               
               
                 in shoot and root tissues at different sampling months. 
               
            
           
           
               
               
               
               
            
               
                   
                 Sampling months &amp; number of taxon 
                 Total Number of 
                 Percentage of 
               
            
           
           
               
               
               
               
               
               
            
               
                   
                 April 
                 July 
                 October 
                 Isolates 
                 Population 
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 Order 
                 Shoot 
                 Root 
                 Shoot 
                 Root 
                 Shoot 
                 Root 
                 Shoot 
                 Root 
                 Shoot 
                 Root 
               
               
                   
               
            
           
           
               
               
               
               
               
               
               
               
               
               
               
            
               
                 Agaricales 
                 0 
                 2 
                 0 
                 0 
                 0 
                 1 
                 0 
                 3 
                 0.00 
                 0.73 
               
               
                 Boletales 
                 0 
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 1 
                 0.00 
                 0.24 
               
               
                 Botryosphaeriales 
                 0 
                 7 
                 0 
                 2 
                 0 
                 1 
                 0 
                 10 
                 0.00 
                 2.43 
               
               
                 Cantharellales 
                 0 
                 0 
                 0 
                 0 
                 0 
                 1 
                 0 
                 1 
                 0.00 
                 0.24 
               
               
                 Capnodiales 
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 1 
                 0 
                 0.70 
                 0.00 
               
               
                 Chaetosphaeriales 
                 0 
                 1 
                 1 
                 1 
                 0 
                 4 
                 1 
                 6 
                 0.70 
                 1.46 
               
               
                 Corticiales 
                 0 
                 0 
                 0 
                 0 
                 0 
                 1 
                 0 
                 1 
                 0.00 
                 0.24 
               
               
                 Diaporthales 
                 0 
                 0 
                 0 
                 1 
                 0 
                 2 
                 0 
                 3 
                 0.00 
                 0.73 
               
               
                 Dothideales 
                 0 
                 1 
                 0 
                 0 
                 0 
                 0 
                 0 
                 1 
                 0.00 
                 0.24 
               
               
                 Eurotiales 
                 1 
                 1 
                 0 
                 1 
                 0 
                 2 
                 1 
                 4 
                 0.70 
                 0.97 
               
               
                 Helotiales 
                 0 
                 1 
                 0 
                 1 
                 0 
                 1 
                 0 
                 3 
                 0.00 
                 0.73 
               
               
                 Hypocreales 
                 28 
                 43 
                 52 
                 75 
                 11 
                 44 
                 91 
                 162 
                 63.64 
                 39.32 
               
               
                 Incertae sedis 
                 1 
                 0 
                 1 
                 2 
                 2 
                 13 
                 4 
                 15 
                 2.80 
                 3.64 
               
               
                 Magnaporthales 
                 0 
                 7 
                 0 
                 19 
                 0 
                 39 
                 0 
                 65 
                 0.00 
                 15.78 
               
               
                 Not assigned 
                 2 
                 0 
                 2 
                 16 
                 0 
                 22 
                 4 
                 38 
                 2.80 
                 9.22 
               
               
                 Pleosporales 
                 6 
                 24 
                 12 
                 12 
                 0 
                 3 
                 18 
                 39 
                 12.59 
                 9.47 
               
               
                 Trichosphaeriales 
                 0 
                 0 
                 1 
                 0 
                 0 
                 0 
                 1 
                 0 
                 0.70 
                 0.00 
               
               
                 Unknown 
                 6 
                 12 
                 2 
                 22 
                 1 
                 22 
                 9 
                 56 
                 6.29 
                 13.59 
               
               
                 Ustilaginales 
                 0 
                 0 
                 11 
                 0 
                 0 
                 0 
                 11 
                 0 
                 7.69 
                 0.00 
               
               
                 Xylariales 
                 1 
                 4 
                 1 
                 0 
                 0 
                 0 
                 2 
                 4 
                 1.40 
                 0.97 
               
               
                 Total 
                 46 
                 104 
                 83 
                 152 
                 14 
                 156 
                 143 
                 412 
                 100 
                 100 
               
               
                   
               
            
           
         
       
     
     All of the compositions and methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this invention have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit, and scope of the invention. More specifically, it will be apparent that certain agents which are both chemically and physiologically related may be substituted for the agents described herein, while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope, and concept of the invention as defined by the appended claims. 
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