Bespoke microbiome therapy to manage plant diseases

Abstract

Information gathered with advanced nucleotide sequencing technologies, small molecule detection systems and computational biology is revealing that a community of microbes and their genes, now termed “the microbiome,” located in gut and rhizosphere, is responsible for maintaining the health of human beings and plants, respectively. Within the complete microbiome a “core-microbiome” exists that plays the pivotal role in well being of humans and plants. Recent studies in medicine have shown that an artificial mixture of bacteria representing the core gut microbiome of healthy person when transferred into gut of diseased person results in re-establishment of normal microflora in the latter leading to alleviation from diseased condition. In agriculture, though not exactly in similar manner as in medicine, success in plant disease management has been achieved through transfer of microbiome by mixing disease suppressive soils with disease conducive soils. A study more similar to artificial gut microbiome transfer in medical field has been recently reported in agriculture, in which transfer of microbiome via soil solutions (filtered and unfiltered) has shown ability to alleviate drought stress in Arabidopsis thaliana. However, the exact practice of transferring artificially cultivated core-microbiome as in medicine has not thus far been attempted in plant disease management. Nonetheless, as the gut and rhizosphere microbiome are known to share many common traits, there exists a good scope for accomplishing similar studies in agriculture. Based upon the information drawn from all recent works in microbiome studies of gut and rhizosphere, we propose that tailor-made core-microbiome transfer therapy can be a success in agriculture too and it could become a viable strategy for management of plant diseases in future.

Engineering Microbiomes to Improve Plant and Animal Health

“…Such a final cross-factoring experiment of microbiomes that were artificially selected under different treatments (see Experimental Contrasts, Box 3) can also be a powerful approach to test whether microbiomes evolved with Method 1 have treatment-specific effects on a host. A new research horizon in medicine and agriculture aims to improve animal and plant performance by altering their microbiomes [28,31,32]. Towards this end, a novel and underutilized approach employs artificial selection on a host-microbial association to engineer microbiome function [33,34], a process that we term host-mediated microbiome selection, or more simply microbiome engineering (Boxes 2 and 3).…”

“…Third, the taxonomic makeup of microbiomes can be experimentally manipulated to test hypotheses about microbiome function. For example, gnotobiotic hosts can be maintained with a defined set of microorganisms, and microbiomes can be manipulated with antibiotic treatments or transfer of microbiomes between hosts [25][26][27][28][29]. With any of these approaches, it remains challenging to elucidate specific functional roles of the microbiome in shaping host performance traits (e.g., growth, health, enemy deterrence, mate attraction, fertility, and overall fitness).…”

“…Microbiomes can be manipulated experimentally to test their contributions to host fitness, for example by inoculating gnotobiotic hosts with specific microbial strains, synthetic communities, or natural communities (e.g., experimental substitution of entire microbiome [25][26][27][28]), or by manipulating microbiomes (e.g., alteration of pH or other abiotic parameters, addition of amendments, knockout of specific taxa with antibiotics [29]). Advantages: Experimental manipulation can elucidate causal roles of microbiomes in affecting host performance, overcoming the inferential limits of the above correlational analyses.…”

The science, development, and commercialization of postharvest biocontrol products

“…Massart et al (2015a) suggested the use of microbiota-derived products or the microbiota itself, directly or indirectly, to develop novel tools for the protection of plants against pathogens. An initial approach could be the use of a synthetic or natural consortium (Gopal et al, 2013) that could be applied to a harvested commodity to see if it results in better disease control due to the expression of a variety of modes of action against the pathogen. Maintaining the right balance and diversity inside the consortium before and after its application, however, may prove to be difficult.…”

Microbiome engineering: Current applications and its future

“…Plants Native root-associated microbiota transplant [33,34] Inhibit plant diseases, resist environmental stresses, promote growth…”