Plant micro-ecology: How host genes shape the plant microbial community

Plants harbor unique microbial communities

Studies on the human microbiome have revealed the amazing diversity of commensal bacteria and fungi living on and within us.  We’ve been co-evolving with these tiny, but ubiquitous communities of microbes since the beginning.  They have shaped us into complex reservoirs with fully populated ecosystems and in turn, we have shaped them into friendly tenants that greatly influence the way we develop, metabolize nutrients and fight infection.  These relationships are ancient and complex, so it should come as no surprise that even organisms such as plants harbor unique microbial communities. Yet, how hosts and microbes maintain this deep-rooted commensalism is mysterious.

Matthew Horton, PhD, and colleagues in the laboratory of Joy Bergelson, PhD, professor and chair of the department of ecology and evolution, begin to address this question by searching for genes in the plant model species, Arabidopsis thaliana, that contribute to the make-up of its microbial ecosystem.  They find that genes associated with the “defense response” against pathogens shape this microbial ecosystem, which likely holds true for crop plants as well.  They reported their findings in a recent article published in Nature Communications.

horton

Matthew Horton, PhD

“Our study demonstrates that host-associated microbial communities are heritable,” said Horton, who is currently a post-doctoral fellow at the Gregor Mendel Institute in Vienna. “What’s more, we were able to pinpoint candidate genes, in the host, implicated in the structure of the microbial community.”

Horton and colleagues show that genes responsible for forming and repairing the plant cell wall – a protective and selectively permeable barrier that separates the plant cell from the outside world – are particularly important for shaping the microbial community.  These genes and others that play roles in the “defense response” against pathogens greatly influence the composition of both the bacterial and fungal communities.

“This finding is highly logical,” Horton said. “The first interface for communication between the plant host and its microbial residents is at this barrier between the cells.”

Other important genes are involved in trafficking of cellular components and in signal transduction – these genes encode proteins that allow the cell to recognize and respond to external messages and communicate with each other.

Genes involved in the cell wall – a protective and selectively permeable barrier that separates the plant cell from the outside world – are particularly important for shaping the microbial community.

Genes involved in the cell wall – a protective and selectively permeable barrier that separates the plant cell from the outside world – are particularly important for shaping the microbial community.

Model species, such as A. thaliana, make for useful genetic tools in the lab.  This study, which relies on a panel of 196 previously sequenced genetic variants of A. thaliana, illustrates this point clearly.  With the genomes for these genetic variants in hand, the team could study how genetic differences affected the plants’ microbial communities.

To identify the thousands of different bacterial and fungal inhabitants, the researchers used ribosomal DNA sequencing, which yields the species-specific DNA sequences of the ribosome (the cellular protein factory).  To identify the host genes most crucial for shaping the microbial communities, the authors performed a genome-wide association study (GWAS), a method used to relate genetic variations to a specific trait.

Their findings have the potential to guide agricultural research, where scientists are using similar methods to select for genes that control the microbial communities on crop plants allowing for greater resistance to pathogens. It may also inform future studies looking at how genetic variation among humans impacts the composition of an individuals’ microbiota.

With this study and others like it, it is becoming increasingly clear that the genetic make-up of an individual greatly influences the structure of the microbial community within that individual.  This ought to add some fuel to the fiery nature vs. nurture dialogue.

About Charlie Dulberger (1 Article)
Charlie Dulberger is a PhD candidate in the department of Biochemistry and Molecular Biophysics at the University of Chicago and a contributor to ScienceLife. His research focuses on the molecular details of antigen presentation and recognition by T cells and other immune cells. Other topics of interest include, the human microbiota, pregnancy and fertility, rational drug design and protein crystallography.
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