Unlocking the power of the microbiome

Hun­dreds of dif­fer­ent bac­terial spe­cies live in and on leaves and roots of plants. A re­search team led by Ju­lia Vorholt from the In­sti­tute of Mi­cro­bi­o­logy at ETH Zurich, to­gether with col­leagues in Ger­many, first in­vent­or­ied and cat­egor­ised these bac­teria six years ago. Back then, they isol­ated 224 strains from the vari­ous bac­terial groups that live on the leaves of thale cress (Ar­a­bidop­sis thali­ana). These can be as­sembled into sim­pli­fied, or “syn­thetic” plant mi­cro­bi­o­mes. The re­search­ers thus laid the found­a­tions for their two new stud­ies, which were just pub­lished in the journ­als Nature Plants and Nature Mi­cro­bi­o­logy.

Volume con­trol of the plant re­sponse

In the first study, the re­search­ers in­vest­ig­ated how plants re­spond to their col­on­isa­tion by mi­croor­gan­isms. Vorholt’s team dripped bac­terial cul­tures onto the leaves of plants that had, up to that point, been cul­tiv­ated un­der sterile con­di­tions. As ex­pec­ted, dif­fer­ent types of bac­teria triggered a vari­ety of re­sponses in the plants. For ex­ample, ex­pos­ure to cer­tain gen­era of Gammapro­teo­bac­teria caused the thale cress plants to ac­tiv­ate a total of more than 3,000 dif­fer­ent genes, while those of Al­phapro­teo­bac­teria triggered a re­sponse in only 88 genes on av­er­age.

“Des­pite this broad range of re­sponses to the dif­fer­ent bac­teria of the mi­cro­bi­ome, we were as­ton­ished to pin­point a cent­ral re­sponse: the plants prac­tic­ally al­ways ac­tiv­ate a core set of 24 genes,” Vorholt says. But that’s not all the team found: act­ing as a kind of volume con­trol for the plant re­sponse, the ac­tiv­a­tion in­tens­ity of these 24 genes provides in­form­a­tion as to how ex­tens­ively the bac­teria have col­on­ised the plant. This volume con­trol also pre­dicts how many ad­di­tional genes the plant will ac­tiv­ate as it ad­apts to the new ar­rivals.

Plants with de­fects in some of these 24 genes are more sus­cept­ible to harm­ful bac­teria, Vorholt’s team has shown. And since other stud­ies had no­ticed that some genes in the core set are also in­volved in plant re­sponses to os­motic shock or fungal in­fest­a­tion, the ETH re­search­ers in­fer that the 24 genes con­sti­tute a gen­eral de­fens­ive re­sponse. “It looks like an im­mune train­ing, even though the bac­teria we used aren’t patho­gens, but rather part­ners in a nat­ural com­munity,” Vorholt says.

Bac­terial com­munity out of con­trol

In the second study, Vorholt and her team ex­plored how bac­terial com­munit­ies change when muta­tions cause a plant to be de­fi­cient in one or sev­eral genes. The team ex­pec­ted to see that ge­netic de­fects in re­cept­ors, which plants use to de­tect the pres­ence of mi­crobes, play a ma­jor role in the story.

What they didn’t ex­pect was that an­other ge­netic de­fect would have the biggest ef­fect: if the plants were de­fi­cient in a cer­tain en­zyme, an NADPH ox­i­dase, the bac­terial com­munity was thrown off-​kilter. Plants use this en­zyme to pro­duce highly re­act­ive oxy­gen rad­ic­als, which have an an­ti­mi­cro­bial ef­fect. In the ab­sence of this NADPH ox­i­dase, mi­crobes that un­der nor­mal cir­cum­stances lived peace­fully on the leaves de­veloped into what are known as op­por­tun­istic patho­gens.

Is the NADPH ox­i­dase found among the core set of 24 genes re­spons­ible for gen­eral de­fens­ive re­sponse? “No, that would have been too good to be true,” says Se­bastian Pfeil­meier, a mem­ber of Vorholt’s re­search group and lead au­thor of the study. This is be­cause the gene re­spons­ible for the NADPH ox­i­dase is turned on prior to con­tact with mi­crobes and be­cause the en­zyme is ac­tiv­ated by chem­ical re­ac­tions gov­erned by phos­phoryla­tion.

For Vorholt, the two stud­ies show that syn­thetic mi­cro­bi­o­mes are a prom­ising ap­proach to in­vest­ig­at­ing the com­plex in­ter­ac­tions within dif­fer­ent com­munit­ies. “Since we can con­trol and pre­cisely en­gin­eer the com­munit­ies, we can do much more than just ob­serve what hap­pens. In ad­di­tion to simply de­term­in­ing cause and ef­fect, we can un­der­stand them on a mo­lecu­lar level,” Vorholt says. An ideal mi­cro­bi­ome pro­tects plants from dis­eases while also mak­ing them more re­si­li­ent to drought and salty con­di­tions. This is why the ag­ri­cul­tural in­dustry is among those in­ter­ested in the team’s res­ults. They should help farm­ers har­ness the power of the mi­cro­bi­ome in the fu­ture.

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