An acceptable elitism? Getting the best out of nitrogen-fixing bacteria

Nitrogen is essential for life on Earth, mainly because it is a key component of amino acids, the building blocks of proteins. Plants are no exception to this and must obtain usable nitrogen to survive. Some plants famously form symbiotic relationships with soil bacteria that are capable of fixing gaseous nitrogen into a form usable by the plant. Agriculturally-important legumes are a significant proportion of the plants known to enter these symbiotic relationships. The efficiency of this relationship can vary depending on factors including environment conditions and the type of bacteria involved. Maximising this efficiency is of interest both in terms of getting the best yield possible out of leguminous crops, and for returning nitrogen to the soil for use by other crops. In a recent paper published in PNAS, Marcela Mendoza-Suárez and colleagues develop a method for measuring the efficiency of this relationship from the bacterial perspective. An exciting possible use of this method will be selecting the best bacteria to get the most out of this symbiosis in agricultural scenarios.

Nitrogen-fixing bacteria (also known as rhizobia) are hosted by leguminous plants to obtain usable nitrogen in specialised root structures called nodules (see image below). Leguminous crops are a major global food source and one particularly close to the first author’s heart. As Marcela Mendoza-Suárez told Botany One: ‘I’m originally from Mexico, where beans are part of our basic food, and for low-income families that do not have access to animal products, they are the major source of proteins, minerals, fibre, carbohydrates and vitamins. A similar situation happens throughout Latin American, in many African countries and in India, where legumes are the main source of proteins. Unfortunately, in all these areas, low-income farmers cannot access chemical fertilisers due to their high cost.’

In order to measure the efficiency of different rhizobia strains in their interaction with plants, Mendoza-Suárez and colleagues set out to measure two key parameters. First is the amount of nitrogen-fixing enzymes being produced. In other words how ‘effective’ a certain rhizobia strain might be at nitrogen fixation. In order to measure this, the authors built DNA sequences that express a fluorescent protein from a synthetic gene promoter, similar to that upstream of genes encoding nitrogen-fixing enzymes. When inserted into rhizobia, this causes production of the fluorescent protein proportional to the amount of nitrogen-fixing enzymes the bacteria are producing. A readout of this can be obtained by measuring the amount of fluorescence coming from root nodules.

The second parameter to measure is how ‘competitive’ different rhizobia strains are, such as whether they are capable of out-competing all other rhizobia in a nodule, or of colonising all nodules on the root system. To do this, the authors introduced unique ‘barcode’ sequences into each DNA construct they made for each rhizobia strain. Using these sequences, they were able to identify which rhizobial strains were present in each nodule, and whether some strains were more capable of spreading across all nodules compared to others. From this a competitiveness index was calculated for each rhizobia strain. One strain, G083, had a higher competitiveness index than any other and appeared in all of the plants the authors tested. G083 also produced high amounts of fluorescence in nodules compared to other strains. G083 is therefore a possible ‘elite’ rhizobia strain in the conditions used in this study, as it is both competitive and effective. This and other high-performing strains could be an alternative to expensive chemical fertilisers.

As the authors point out, whether G083 and other high-performing strains perform the same in different environmental conditions remains to be seen. However, the methods they develop provide a platform for further study of this. Whilst the authors also do most of their measurements on different strains of one rhizobia species (Rhizobium leguminosarum) in pea plants, they do show that the DNA constructs they use are also capable of being at least partially expressed by some other rhizobia species. This means that the method developed by the authors develop could be applied in the future to a variety of rhizobia species in different leguminous plants. Mendoza-Suárez says: ‘I have been given the opportunity to test this tool in a big Sustainable Crop Production project called ProFaba. Our ultimate goal is to find the best faba bean breeding techniques. Thanks to this project, I’m now searching for elite rhizobial strains in many field sites around Denmark, Germany, France, Ireland, Finland, the UK and Spain’. Watch this space then!