Profundae diversitas: the uncharted genetic diversity in a newly studied group of fungal root endophytes

Abstract

Endophytes associated with crops have potential as beneficial inoculants in agriculture, but little is known about their genetic diversity and phylogenetic relationships. We carried out the first ever ecological and phylogenetic survey of the culturable fungal root endophytes of a wild barley species. Fungal root endophytes were isolated from 10 populations of wall barley (Hordeum murinum), and 112 taxa of fungi were identified based on internal transcribed spacer sequence similarity. We found representatives from 8 orders, 12 families and 18 genera. Within this group, only 34 isolates (30% of the total) could be confidently assigned to a species, and 23 of the isolates (21% of the total) had no significant match to anything deposited in GenBank (based on <85% sequence similarity). These results suggest a high proportion of novel fungi, with 28% not assigned to a known fungal order. This includes three endophytes that have been shown to significantly improve agronomic traits in cultivated barley. This study has, therefore, revealed a profound diversity of fungal root endophytes in a single wild relative of barley. Extrapolating from this, the study highlights the largely unknown, hugely diverse and potentially useful resource of crop wild relative endophytes.

Beauveria bassiana and Metarhizium anisopliae endophytically colonize cassava roots following soil drench inoculation

“…This localization is in contrast to other studies that have found B. bassiana can establish as an endophyte throughout the entire plant, particularly after seed inoculation ( Akutse et al, 2013 , Ownley et al, 2008 , Quesada-Moraga et al, 2009 ). However, for M. anisopliae, our results are not surprising given that species of Metarhizium are more often reported as endophytes of roots and not the upper parts of plants ( Akello and Sikora, 2012 , Behie et al, 2015 , Murphy et al, 2015 ). We do not know if systemic endophytic colonization by entomopathogens would be important in cassava for protecting the plant against pests of the leaves, such as the whitefly A. socialis .…”

“…Metarhizium species are less well known as endophytes but have been successfully introduced into tomato ( García et al, 2011 ), fava bean ( Akello and Sikora, 2012 ), oilseed rape ( Batta, 2013 ), and haricot bean ( Behie et al, 2015 , Sasan and Bidochka, 2012 ). Two unidentified Metarhizium species and M. anisopliae have been found naturally as endophytes in roots of wall barley ( Hordeum murinum L.) ( Murphy et al, 2015 ).…”

Host Specificity of Endophytic Fungi from Stem Tissue of Nature Farming Tomato (Solanum lycopersicum Mill.) in Japan

“…This may be an implication of a possible higher colonization intensity of fungal endophytes in nature farming crops than conventional cropping or wild plants. Indeed, previous studies that compared fungal endophytes of tomato, soybean and grapevines grown organically reported higher overall colonization than those grown under conventional practice [12,[70][71][72]. However, further studies to compare endophyte isolation from the same crop grown under different cultivation systems may reveal the potential differences and the cause of differences in colonization intensity.…”

Endophyte ecology, diversity and utilisation

“…1 million endophytic fungal species in the world (Deshmukh et al 2015). This diversity has been amply demonstrated in a study by Murphy et al (2015) which revealed a high alpha diversity of fungal root endophyte species in a single wild relative of barley. The same study found a high proportion of novel fungi in the same dataset, with 28% not assigned to a known fungal order.…”