The term ‘endophyte’ is derived from the Greek term ‘endo’ (within) and ‘phyte’ (plant), and may apply to both fungi and bacteria that reside in plant tissues during all or part of their life cycle and cause no apparent harm (Wilson 1995). It is estimated that every plant species has at least one associated bacterial endophyte (Strobel et al. 2004), and they belong to diverse classes of bacteria including alpha, beta, and gamma subdivisions of Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria (Rosenblueth and Martinez-Romero 2006). These bacteria thrive within plants where they successfully colonize roots, translocate to leaves, stems, and even to reproductive organs where they may be vertically transmitted to the next generation, ensuring a stable interaction with its host plant.

The number of microorganisms present in natural ecosystems is tremendous. In fact, estimates of the number of bacterial endophytes in the Brazilian Atlantic forest indicate the possibility of 2-13 million species in the aboveground plant parts alone (Lambais et al. 2006). Of the bacterial species identified, 97% were previously not described. A single plant species may also have a wide range of different bacterial genera associated. In wheat, culture based studies have shown that 88 bacterial species representing 37 genera inhabit the aboveground plant tissue (Legard et al. 1994), which likely underestimate the number of microorganisms as molecular studies yield much larger population numbers (Rasche et al. 2006). Both culture based and molecular based analyses indicate that alpha and beta Proteobacteria are the most numerous colonizers of the phyllosphere (Thompson et al. 1993). In total, 853 bacterial endophytes were isolated from aboveground parts of four agronomic crops and 27 prairie plants including switchgrass. Cellulomonas, Clavibacter, Curtobacterium, and Microbacterium isolates showed high levels of colonization and had the ability to persist in host plants (Zinniel et al. 2002).

Diazotrophs, or atmospheric nitrogen-fixing bacteria have been isolated from bioenergy crops, including Miscanthus spp. and Pennisetum purpureum, where Herbaspirillum frisingense sp. nov. (Kirchhof et al. 2001), Azospirillum doebereinerae (Eckert et al. 2001), and Herbaspirillum frisingense (Rothballer et al. 2008) were found. Similarly, different nitrogen-fixing bacteria belonging to genera Stenotrophomona, Pseudomonas and Burkholderia were isolated from sand dune grasses (Ammophila arenaria and Elymus mollis) in Oregon, which may biologically fix nitrogen and promote the growth of these plants under poor soil conditions (Dalton et al. 2004). Nitrogen-fixing bacteria have also been isolated from different plant species, such as Kallar grass (Leptochoa fusa) (Reinhold-Hurek et al. 1993), lodgepole pine (Pinus contorta), western red cedar (Thuja plicata) (Bal et al. 2012), and hybrid poplar (Populous trichocarpa) (Taghavi et al. 2010). While general surveys of endophytic populations in switchgrass have been undertaken (Zinniel et al. 2002), there are no detailed analysis on native bacterial endophytic interactions in switchgrass.

Fungal endophytic populations may also be substantial, particularly in longer lived plants, as 340 genetically distinct taxa were recovered from two tropical understory plant species (Arnold et al. 2000). Endophytic fungi can also have a significant beneficial impact on switchgrass performance (Kleczewski et al. 2012). While much emphasis has been placed on the study of clavicipitaceous fungal endophytes (Neotyphodium/Epichloe) with cool — and warm-season grasses (Rodriguez et al. 2009), two recent surveys of switchgrass endophytes have failed to identify members of the Clavicipitaceae family (Ghimire et al. 2011; Kleczewski et al. 2012), suggesting that the major endophytic fungi inhabiting switchgrass are of the non-clavicipitaceous type, representing primarily ascomycetous fungi (Kleczewski et al. 2012). These endophytes may be found colonizing tissues above — and/or below-ground (Rodriguez et al. 2009). Recently, 18 taxonomic orders of fungal endophytes were isolated from switchgrass plants in northern Oklahoma belonging to the genera Alternaria, Codinaeopsis, Fusarium, Gibberella, Hypoerea and Periconia, and switchgrass shoot tissues showed a significantly higher diversity of fungal endophytic species compared to the root tissues (Ghimire et al. 2011). Similar fungal endophytic genera were isolated from switchgrass plants growing in a range of habitats across Indiana and Illinois, such as Alternaria, Epicoccum, Phoma, Phaeosphaeria and Stagonospora (Kleczewski et al. 2012). Since switchgrass is one of the most promising bioenergy crops, several laboratories in the US have been working on isolation and characterization of bacterial and fungal endophytes from switchgrass. Identifying and harnessing beneficial endophytic microorganisms that have a broad spectrum of plant growth promotion traits and possess various mechanisms for stress tolerance may aid in the development of a low input and sustainable switchgrass feedstock production system, particularly on marginal land.

Mycorrhizae are symbiotic fungi that interact with the roots of vascular plants. These fungi are typically divided into two groups: ectomycorrhizas which have hyphae that do not penetrate individual cells within the root and endomycorrhizas which, as the name implies, have hyphae that penetrate the cell wall and invaginate the cell membrane. Eighty to 92% of land plant species surveyed are associated with mycorrhizal fungi, among them, arbuscular mycorrhizal (AM) fungi are the predominant type (Wang and Qiu 2006), and are placed in the phylum (division) Glomeromycota. AM fungus is characterized by highly branched fungal structures located within the plant root cortical cells. Generally, AM fungi comprise 130 species of fungi classified as Zygomycotina (Simon et al. 1993). AM fungi from the order Glomales (Glomeromycota) are associated with most plant species including angiosperms, gymnosperms, pteridophytes, lycopods, and mosses (reviewed in Hause and Fester 2005). The fungi involved in the AM interaction are obligate biotrophs and reproduce asexually. As obligate biotrophs, AM fungi are not culturable without their host plant, making the study of these organisms difficult. AM fungal associations are important to help switchgrass tolerate unfavorable soil conditions (Parrish and Fike 2005). It has been reported that AM fungi play essential roles in switchgrass growth in acidic soil, which has high levels of exchangeable aluminum and immobile minerals, such as phosphorus (Koslowsky and Boerner 1989; Brejda et al. 1993; Johnson 1998). AM fungal associations may be more critical in warm-season grasses, such as switchgrass because from an evolutionary perspective, both are of tropical origin (Hetrick et al. 1988).