Bioenergy production will become increasingly important in the future to relieve dependence on fossil fuels and lower greenhouse gas emissions because fossil-based energy is limited and its demand is continually increasing due to economic and population growth around the world. Switchgrass is one of the most promising bioenergy crops due to persistent high yields and its ability to grow on marginal land. Development of a low input and sustainable switchgrass feedstock production system is imperative as the use of chemical fertilizers causes deleterious environmental effects, such as water pollution and N2O release to atmosphere, a potential greenhouse gas. Endophytes and AM fungi have the potential to help address these challenges due to their enhancement of nutrient acquisition, including nitrogen fixation and mobilization of mineral nutrients as well as increased biotic and abiotic stress tolerance, which together will reduce the amount of fertilizer application and/or pesticide and fungicide use. It will also open a door to growing potential bioenergy crops, such as switchgrass on marginal land or achieving the same yield while reducing fertilizer use, resulting in lower cost and contributing to sustainable rural development.

Plants live in complex environmental conditions containing various microorganisms, both beneficial and detrimental. Although endophytes and AM fungi could benefit plant growth, other microorganisms may have negative effects, and different endophytes and AM fungi may not be compatible, therefore the specific functional compatibility of endophytes and AM fungi needs to be further investigated to develop multi-functional bio-inoculants (Podile and Kishore 2007) in switchgrass production. Additionally, while studies with endophytes as well as other plant growth promoting microorganisms in laboratories have been encouraging, there have also been reports of a general decrease in performance from the laboratory to the field (Riggs et al. 2001; Gyaneshwar et al. 2002). As with any ecosystem, the variables of field conditions and native microbial populations will have to be addressed to maximize the beneficial effects of bacteria and fungi. Therefore, screening endophytes having a broad spectrum of growth promotion that continues throughout the life of the plant will be another topic for endophyte application.

Genotype specific responses of host plants to endophytes are also a large barrier in application. For example, in poplar, different cultivars had different responses to different endophytes (Taghavi et al. 2009). One of the most studied plant growth promoting bacterium, B. phytofirmans strain PsJN, has a beneficial effect on many species, such as potato, tomato, and grape. However, PsJN is also genotype specific. In switchgrass, PsJN promoted growth of the lowland cultivar Alamo but not the upland cultivar Cave-in-Rock (Kim et al. 2012). Understanding these differences will also help in developing a more reliable, stable, and broad spectrum of growth promotion in plants.

Complete understanding of the mechanisms of various beneficial symbioses is the foundation for effectively applying these microorganisms in a sustainable switchgrass feedstock production and to achieve their synergistic activities (Podile and Kishore 2007). As more is learned from functional genomics of endophytic microorganisms in growth promotion, it may be possible to share these important genes between similar microorganisms through horizontal gene transfer via transformation, conjugation, or transduction, all common occurrences in the bacterial world. Researchers first reported in planta horizontal gene transfer in the bioenergy crop hybrid poplar when they found Burkholderia cepacia VM1468 transferred its toluene degradation gene to other endophytes (Taghavi et al.

2005) . This suggests that such transfer may be used to modify and improve the growth-promoting effects of other endophytes via gene sharing. The phenomenon of horizontal gene transfer may also occur in nature between different genera as the gene encoding the anti-fungal agent pyrrolnitrin in Burkholderia was likely horizontally transferred from Pseudomonas (de Souza and Raaijmakers 2003). Since AM fungi are coenocytic (many nuclei coexist in a common cytoplasm), genetic exchange was recently reported in different AM fungus Glomus intraradices strains (Colard et al. 2011), which could be beneficial for host plant growth. Generating novel AM fungus genotypes through genetic exchange will be a powerful tool in developing AM fungi that are more beneficial in bioenergy crop production.

Compared with plant genetic engineering, it is much easier for microorganisms to be genetically modified. One could easily transform some useful foreign genes into bacteria or fungi. For instance, the Bacillus thuringiensis cry1Ac7 and Serratia marcescens chiA genes were transformed to sugarcane-associated endophytic bacteria, which helped increase the tolerance of sugarcane plant to the sugarcane borer Eldana saccharina (Downing et al. 2000). These applications indicate that we may be able to genetically engineer endophytes with useful genes, such as the Bacillus thuringiensis toxin gene, to protect host plants against herbivorous insects, herbicide resistance genes to impart host plant resistance to herbicides, and genes related to abiotic stress tolerance to enhance host plant tolerance to abiotic stresses. An efficient endophyte transformation method by Agrobacterium was developed by Abello et al. (2008), which will help in the transfer and expression of agronomically important genes in host plants via endophytes. As functional genomics research is continually advanced, scientists will better understand the mechanisms under which beneficial microorganisms promote host plant growth and enhance stress tolerance to effectively utilize these microbes in bioenergy crop production. For example, endophytes having the ability to fix atmospheric nitrogen could be combined with endophytes having the ability to enhance host plant tolerance to abiotic stresses or endophytes inhibiting pathogen growth or with an AM fungus to improve nutrient uptake or, possibly, all could be combined.

Since 1999, over 15 new patents have been registered for microbial endophytes (Mei and Flinn 2010). The worldwide market for microbial inoculants is experiencing an annual growth rate of approximately 10% (Berg 2009). As world population demand for food is continually increasing, bioenergy crops should be grown on poor or marginal lands or contaminated soil, not competing with food crops for fertile lands. The use of endophytes and AM fungi may help bioenergy crops, such as switchgrass, grow on these lands via their normal mechanisms of action or genetic modification by introducing nitrogen fixation genes, heavy metal accumulation genes, or contaminated compound degradation genes.

Acknowledgements

This work was funded through Special Grants (2003-38891-02112, 2008­38891-19353 and 2009-38891-20092) and HATCH funds (Project No. VA — 135816) from the United States Department of Agriculture, the Office of Science (BER), U. S. Department of Energy for Plant Feedstock Genomics for Bioenergy Program (DE-SC0004951), and operating funds from the Commonwealth of Virginia to the Institute for Advanced Learning and Research.