Beneficial bacteria in Oz

This post is by MSU grad student Colleen Friel

Pea fields (with yellow-flowered canola growing in the background) near Esperance, WA.

Increasing agricultural sustainability is an important research focus in the face of climate change, rapid population increase, and growing food insecurity. Synthetic nitrogen fertilizers have fueled a huge boom in agricultural productivity in recent decades, but they come with serious environmental consequences. Fertilizer manufacturing requires large fossil fuel inputs, and fertilizer runoff poses environmental and public health threats such as eutrophication of waterways and marine ecosystems, destruction of coral reefs, and algal blooms. For example, runoff from farms along the Mississippi River has led to a dead zone in the Gulf of Mexico that is 8,776 square miles, or roughly the size of the state of New Jersey.

One alternative source of nitrogen comes from the interactions between a subset of plants called legumes and specialized soil bacteria known as rhizobia. This interaction begins when plants growing in low nitrogen environments release a chemical signal from their roots. If this signal is detected by a compatible rhizobium, the rhizobium releases its own signaling molecules that initiate morphological changes in the plant root. Root hairs curl to encompass the rhizobium, and the plant houses the rhizobium in special organs called nodules. Inside the nodules, rhizobia convert atmospheric nitrogen (N2) to ammonia (NH3), which plants are able to use. In exchange, the plant supplies its rhizobia with sugars from carbon fixed during photosynthesis.

There is a wide range of outcomes in this interaction. Due to incompatibilities in signaling and other molecular events required for successful colonization, not all rhizobia can form nodules on all legumes. In addition, some rhizobia-legume combinations can form nodules but fail to fix nitrogen after nodulation. Evolutionary theory predicts that there is strong pressure on the rhizobia to cheat in a “tragedy of the commons” situation: since a single plant usually is colonized by a number of different rhizobial strains in the wild, each strain faces pressure to dedicate resources to its own reproduction rather than to nitrogen fixation for the plant. This trend is predicted to lead to a total breakdown of the mutualism, where all rhizobia fix little to no nitrogen for their plant hosts. However, this is not the case, suggesting that plants are able to control their rhizobial partners in some way and prevent this “cheating.” This might arise in the form of plants being able reward more effective rhizobia, punish less effective rhizobia, or select for more effective rhizobia during colonization.

The ability to select for more effective rhizobial strains is very important for the application of biological nitrogen fixation in agriculture. When rhizobia are used in agriculture, seeds are usually inoculated with a single rhizobial strain that has been shown to fix large amounts of nitrogen in combination with a given crop plant. However, this inoculant strain is frequently outcompeted by native rhizobia that are able to form nodules on the crop plant but fix little to no nitrogen for their host. Some legumes have demonstrated the ability to pick out the strains of rhizobia that effectively fix nitrogen for them, while excluding ineffective strains. However, not all legumes are very good at this, and we do not know what mechanism plants use for this purpose.

Making friends with the locals.

I spent the summer of 2016 at the Centre for Rhizobium Studies (CRS) at Murdoch University in Perth, Western Australia (WA) to study how plants select for effective rhizobia. Clovers are commonly used as forage crops in WA agriculture, since they are able to tolerate the challenges facing growers in WA, including low rainfall and acidic and sandy soils. The Mediterranean clover Trifolium purpureum and the South African clover Trifolium polymorphum are two such species. Both species have an effective native rhizobial partner that nodulates and effectively fixes nitrogen. If you inoculate one plant with the other’s effective rhizobia, the rhizobia will form nodules but will not fix nitrogen. If the plants are inoculated with a mixture of the two strains, the plant will pick out its effective strain and only form nodules with that strain, even if it is outnumbered 100:1.

To explore how the plants are doing this, we made bacterial mutants in which the gene for one of the proteins necessary for nitrogen fixation was deleted. We then inoculated these mutants onto the plants to see whether they were able to detect the ability to fix nitrogen, or if they used another marker to determine if a strain was an effective partner. We are also testing how the rhizobia strains react to the signals sent out by the plant and how well they are able to grow on the root systems of the different plant species. This will tell us if the the nodulation patterns we see are being determined by competition between the rhizobia rather than selection by the plant.. Understanding how plants select effective rhizobia can help make commercial rhizobial inoculants more efficient.

Planting Lebeckia in a field of nonwetting soil.

While I was in Australia, I traveled throughout much of WA, going 500+ km north of Perth to West Binnu, WA and going 700+ km southeast to Esperance, WA. During these expeditions, I assisted with field work for ongoing projects at the CRS. These projects ranged from assessing the negative effects of various pesticide treatments on rhizobial colonization in pea crops to planting field trials of the newly domesticated crop Lebeckia, which can grow in very sandy and unique nonwetting soils that plague parts of WA. It was an amazing experience to be able to interact with growers across such a large part of the country and learn how different agriculture is in Australia compared to the US. The landscape, flora, and fauna were shockingly different, and it was shocking to be able to drive for hours without seeing much evidence of humans. It was fascinating to learn how agriculture has adapted to the heat, low rainfall, and challenging soils present in WA. I look forward to using the knowledge, techniques, and relationships I developed in Australia to inform my work and increase our understanding of legume-rhizobia interactions.



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