The hologenome hypothesis explains a great deal of how the evolution of plants
may have proceeded as the Earth itself evolved. One could ask the same question of
any organisms, including lichens, for which the hologenome hypothesis was originally described (Frank 1877). The cooperation of multiple microbiomes to make a
complex organism had its roots in earlier times and it also led to major changes in
Planet Earth, i.e., not only in the variety of organisms present, but also in the changes
in soil, atmosphere, and other climatic factors for making an environment more
hospitable to these organisms.
21.4 Engineering Microbiomes
In the last decade, climate related disasters have had a direct impact on factors that
influence agroecosystems and compromise the global food security (Cavicchioli
et al. 2019). Many studies have supported the use of microbes and their metabolites
in improving overall plant growth and also in mitigating plant stress responses
(Rodriguez and Durán 2020; de Vries et al. 2020). However, to fully realize the
potential of microbial technology in enhancing crop production and improving plant
resilience, current research effort is focused on breeding “microbe-optimized
plants.” Accordingly, microbiome engineering has emerged as an alternative to
modify and promote positive interactions between microbes and plants to improve
plant fitness. The goal is to pursue modifications of microbial community compositions that result in improved plant phenotypes and benefit ecosystems. Microbial
strains with desired functions can be selected and combined to form synthetic
microbiomes. For examples, Lebeis et al. (2015) demonstrated that microbiomes
can be optimized for disease resistance in plants by applying phytohormones that
activate plant immune signaling responses.
Advancements in high-throughput “multi-omics” technologies and computational developments have also led to a greater understanding and manipulation of
plant holobionts. Indirect approaches to this research include the use of soil amendments, while direct approaches involve the use of specific microbes, modified
microbial consortia, microbiome breeding, and transplantation. Recently, a method
used typically in human metagenomic studies, MWAS (metagenome-wide association study) has been proposed by Beilsmith et al. (2019) to find associations between
host plant genes and microbial species. MWAS could prove helpful in unravelling
functional associations interplaying in plant-microbe interactions. Finally,
microbiome engineering is an interesting option to improve and enhance the biological capabilities of the plant using a combination of desired selected strains that
prove to be effective, compatible with each other and the soil conditions, and
non-pathogenic. As indicated by Martínez-Hidalgo and Hirsch (2017) in their review
on plant microbiomes for sustainable agriculture, it is essential to test the long-term
persistence and effectiveness of the transfer of microbial technology from lab to
field, especially in fluctuating environmental conditions.
21 The Hologenome Hypothesis and Its Application to Plant-Microbe Interactions on. . .
435
may have proceeded as the Earth itself evolved. One could ask the same question of
any organisms, including lichens, for which the hologenome hypothesis was originally described (Frank 1877). The cooperation of multiple microbiomes to make a
complex organism had its roots in earlier times and it also led to major changes in
Planet Earth, i.e., not only in the variety of organisms present, but also in the changes
in soil, atmosphere, and other climatic factors for making an environment more
hospitable to these organisms.
21.4 Engineering Microbiomes
In the last decade, climate related disasters have had a direct impact on factors that
influence agroecosystems and compromise the global food security (Cavicchioli
et al. 2019). Many studies have supported the use of microbes and their metabolites
in improving overall plant growth and also in mitigating plant stress responses
(Rodriguez and Durán 2020; de Vries et al. 2020). However, to fully realize the
potential of microbial technology in enhancing crop production and improving plant
resilience, current research effort is focused on breeding “microbe-optimized
plants.” Accordingly, microbiome engineering has emerged as an alternative to
modify and promote positive interactions between microbes and plants to improve
plant fitness. The goal is to pursue modifications of microbial community compositions that result in improved plant phenotypes and benefit ecosystems. Microbial
strains with desired functions can be selected and combined to form synthetic
microbiomes. For examples, Lebeis et al. (2015) demonstrated that microbiomes
can be optimized for disease resistance in plants by applying phytohormones that
activate plant immune signaling responses.
Advancements in high-throughput “multi-omics” technologies and computational developments have also led to a greater understanding and manipulation of
plant holobionts. Indirect approaches to this research include the use of soil amendments, while direct approaches involve the use of specific microbes, modified
microbial consortia, microbiome breeding, and transplantation. Recently, a method
used typically in human metagenomic studies, MWAS (metagenome-wide association study) has been proposed by Beilsmith et al. (2019) to find associations between
host plant genes and microbial species. MWAS could prove helpful in unravelling
functional associations interplaying in plant-microbe interactions. Finally,
microbiome engineering is an interesting option to improve and enhance the biological capabilities of the plant using a combination of desired selected strains that
prove to be effective, compatible with each other and the soil conditions, and
non-pathogenic. As indicated by Martínez-Hidalgo and Hirsch (2017) in their review
on plant microbiomes for sustainable agriculture, it is essential to test the long-term
persistence and effectiveness of the transfer of microbial technology from lab to
field, especially in fluctuating environmental conditions.
21 The Hologenome Hypothesis and Its Application to Plant-Microbe Interactions on. . .
435