A Vavilovian approach to discovering crop-associated microbes with potential to enhance plant immunity

Abstract

Through active associations with a diverse community of largely non-pathogenic microbes, a plant may be thought of as possessing an “extended genotype,” an interactive cross-organismal genome with potential, exploitable implications for plant immunity. The successful enrichment of plant microbiomes with beneficial species has led to numerous commercial applications, and the hunt for new biocontrol organisms continues. Increasingly flexible and affordable sequencing technologies, supported by increasingly comprehensive taxonomic databases, make the characterization of non-model crop-associated microbiomes a widely accessible research method toward this end; and such studies are becoming more frequent. A summary of this emerging literature reveals, however, the need for a more systematic research lens in the face of what is already a metagenomics data deluge. Considering the processes and consequences of crop evolution and domestication, we assert that the judicious integration of in situ crop wild relatives into phytobiome research efforts presents a singularly powerful tool for separating signal from noise, thereby facilitating a more efficient means of identifying candidate plant-associated microbes with the potential for enhancing the immunity and fitness of crop species.

Plant domestication through an ecological lens

“…A plethora of plantmicrobe interactions are potentially influenced by domestication [54]. These include interactions with root mutualists such as rhizobia or arbuscular mycorrhiza.…”

An evolutionary ecology perspective to address forest pathology challenges of today and tomorrow

“…Some mycoviruses have followed the route of invasion of their invasive fungal hosts and have been first detected in the introduced range of their hosts (Bryner et al 2012;Feau et al 2014;Voth et al 2006;Schoebel et al 2014;Martinez-Alvarez et al 2014). However, according to the enemy release hypothesis (Mitchell and Power 2003), hyperparasites are expected be more frequent in the native range of their hosts than elsewhere, and thus, systematic searches should be concentrated in these areas (Roderick and Navajas 2003;Hale et al 2014;Ridout and Newcombe 2015). Such a search for hyperparasites requires a known centre of origin of the parasite, which is far from the rule, as seen before.…”

“…• Adaptation of pathogens after introduction (Gladieux et al 2015 • More systematic search of antagonists and hyperparasites in the native ranges of forest pathogens (Hale et al 2014;Ridout and Newcombe 2015) • Development of platforms for the coupling of metagenomic and phenotypic characterization of microbial communities (Lebeis 2014) • Mycoparasitism by fungi, bacteria, virus -significance in natural ecosystems ) -role of hybridization, admixture and multiple infections on the efficiency and evolution of the biocontrol agents (Feau et al 2014) • Tree endophytic fungi: continuum or shift from opportunistic, weak pathogenicity, and their interaction with true pathogens (Pautasso et al 2014). …”

Beneficial microorganisms for soybean (Glycine max (L.) Merr), with a focus on low root-zone temperatures

“…However, intentional modification of the rhizosphere microbial community through long-term management has been proposed (Ryan et al 2009;Chaparro et al 2012;Hale et al 2014;Lakshmanan et al 2014). Plants actively favor desired species of rhizosphere microorganisms by exuding inorganic and organic compounds and modifying pH and redox conditions (Hartmann et al 2009).…”

“…These products come in various formulations soils (Mazzola and Gu 2002), and response to biocontrol pseudomonads (Meyer et al 2010). As modern plant breeding has taken place under conditions of high nutrient availability and relatively stable environments, modern genotypes are less able to use these mechanisms than older genotypes (Provorov and Tikhonovich 2003;Wissuwa et al 2009); Hale et al (2014) thus suggest introgressing rhizosphere-related traits of wild relatives into modern cultivars.…”