Abiotic stresses include various environmental factors such as hot and cold extremes, drought, salinity, metal contamination and synthetic chemicals, among others, and all may decrease performance of bioenergy crops like switchgrass in the field. To help the host plant tolerate abiotic stresses, endophytes and AM fungi have evolved a number of mechanisms that improve plant growth and health.

Symbiotic microorganisms help with drought tolerance through the production of protective compounds such as peroxidase, ascorbate, and proline (Fan and Liu 2011; Ruiz-Sanchez et al. 2011). Plant associated microbes may also benefit the host plant by changing stomatal conductance, water potential, and net photosynthesis during drought (Bae et al. 2009).

Endophytes and AM fungi may modify carbohydrate metabolism and photosynthesis, or produce beneficial compounds to enhance cold tolerance in the host plant. When grapevine plants were exposed for five days to chilling conditions, net photosynthesis was higher compared with the levels of the control plants, helping them to withstand long periods of cold exposure (Fernandez et al. 2012a). Recently, it was found that B. phytofirmans PsJN modified trehalose metabolism, which may be a part of the mechanism under which B. phytofirmans PsJN increased chilling tolerance to grapevine (Fernandez et al. 2012b). In tomato plants, the AM fungus Glomus mosseae reduced membrane lipid peroxidation, increased photosynthetic pigments, accumulated osmotic adjustment compounds, and increased antioxidant enzyme activities (superoxide dismutase, catalase, peroxidase and ascorbate peroxidase), which lead to alleviating the damage caused by cold temperatures (Abdel Latef and He 2011). Chemical compounds produced by fungal endophytes may play important roles in host plant tolerance to cold temperatures. For example, a native grass Anchnatherun robustum (sleepygrass) infected with Neotyphodium spp. produced high levels of ergot alkaloids and demonstrated higher overwintering survival compared with non-infected plants, or even plants infected with Neotyphodium spp. with no alkaloid production (Faeth et al. 2010). These results indicate that alkaloids may protect plants against winter conditions.

Beneficial microbes could offer host plant tolerance to high salinity to aid in plant growth. To achieve increased tolerance to high salinity soils, beneficial organisms, both bacterial and fungal, may display a combination of traits such as the production of IAA, phosphate solubilisation, siderophore production, and ACC deaminase activity (Jha et al. 2012). The salt-tolerant Azospirillum brasilenses isolate NH produced IAA under salt — stress conditions, and it is believed that the production of this plant growth regulator may contribute to the increase in salt tolerance of inoculated wheat plants (Nabti et al. 2010). Under similar conditions, the endophytic strains, B. subtilis, B. pumilus, and P. putida isolated from the roots of Prosopis strombulifera (Argentine screwbean) produced significantly higher IAA (Sgroy et al. 2009).