Understanding metabolic interactions in plant root associated bacterial communities


Plants might not move, but are far from being a static system. They respond to a variety of biotic and abiotic stresses and need to adapt either quickly to temporary conditions or on the long run for evolutionary purposes. Indeed plants have evolved to colonize very diverse environments and to conquer different ecological niches, but they have never been alone in their struggle for survival and adaptation.

Earth formed 4.5 billion years ago, and the first forms of life were little more than RNA pieces. Prokaryotes are known to have appeared at least 3.5 billion years ago when the atmosphere was very different from what we have today. Bacteria started to slowly change the biogeochemistry of Earth, allowing finally life as we know it to appear about half a billion years ago during the so-called “Cambrian explosion”.

Considering that bacteria are some billion years older than land plants, and that no plant is an island (except some in extremely clean labs), it follows that plants have evolved in biotic environments. It is not surprising then to see that they depend on bacteria for certain things, like mineral nutrition. Bacteria on the other hand need to eat as well, and unless they can do photosynthesis (but only a small percentage can, for example cyanobacteria can), they need external sources of carbon, which plants are often happy to provide. Sometimes these exchanges of resources culminate in symbiotic relationships resembling old-fashion love stories. Legumes of the Medicago genus (e.g. Medicago truncatula) create nodules in their roots to host their favorite nitrogen fixing bacteria (e.g. Sinorhizobium meliloti), providing a comfortable space where the bacteria can thrive protected from external competitors and environmental damage. I will not argue here if this is true love or exploitation, but there is a lot of research interest into understanding the principles driving altruistic behavior.

However, not all bacteria are so lucky to get free accommodation with full board, and most of them need to fight in order to gain a seat at the carbon buffet gently offered by the plant. Whether such buffet is the result of careful and dedicated cooking by the plant or rather a disordered lump of leftovers and crumbs, we still don’t know for sure. In my research, my goal is to better understand the characteristics of the places available at the table, also called “ecological niches”, and how their features can shape the composition and stability of the bacterial party. I mean, you do not want to sit next to that friend that always steals the last slice of pizza, do you?1 And if this same friend happens to sit next to someone that really, really wanted that last slice of pizza, how high is the chance that they will fight, and one (or both) gets kicked out of the party? Then of course, if you expect your host to treat you well, you do not show up at the party empty handed. Who will the plant like best, the one coming with cheap beer or the one bringing a nice bottle of Cabernet Sauvignon?2

With my work, I study how different bacteria would fit different metabolic niches. In order to grasp the complexity of plant-microbes-environment ecosystems, the first step is to actually reduce such complexity and choose powerful tools to work with. I use computational methods that translate the information contained in the sequenced genomes of bacteria into metabolic network models, and then represent them with mathematical formalism. With these so-called “Stoichiometric Genome-Scale Metabolic Network Models”, I can identify the metabolic configuration of the organism under a certain environment, and by gradually changing the external conditions, I can put together different “snapshots” of metabolic states, approximating a dynamic response to a varying environment.

The final aim of my research is to exploit the knowledge of community behavior in dynamic ecological niches in order to design “recipes” of bacterial cocktails to improve plant nutrition. My collaborator Richard Jacoby explained in a previous Planter’s Punch how such bacterial cocktails can help improve our farming systems. Towards this challenging goal, it is fundamental to remember that crops are grown in open fields, not under well controlled laboratory conditions. Therefore we should not only combine bacteria that are good to the plant, but bacteria that also get along well with each other and can resist external perturbations. In other words, we have to get the party started and make sure it will keep going!


1 This is another version of “the olive theory” by comedian Paul Rieser and made popular by the show “How I met your mother”.

2 Disclaimer: I do like pizza and good wine, however any similarity to any person or event is to be considered merely coincidental.

Planter’s Punch

Under the heading Planter’s Punch we present each month one special aspect of the CEPLAS research programme. All contributions are prepared by our young researchers.

Further Reading

Review and perspective on mathematical modeling of microbial ecosystems.  SuccurroEbenhöh. Biochemical Society Transactions (2018) [link]

A Diverse Community To Study Communities: Integration of Experiments and Mathematical Models To Study Microbial Consortia. Succurro, Moejes, Ebenhöh. Journal of Bacteriology (2017) [link]

Planter's Punch Richard Jacoby[link]


About the Author

The article was written by Antonella Succurro, who is a member of the CEPLAS Postdoc Programme. She aims to understand what drives the assembly of microbial communities associated with plant roots under different environmental conditions.