#FEMSmicroBlog: Can microbial communities predict the future?


Usually, farmers perform soil tests to decide on the fertilisation procedure for the oncoming season. However, they base their decisions on the nutrient content of the soil, which is not very precise and often leads to over-fertilization and soil contamination. A new study published in FEMS Microbiology Ecology investigates how farmers could use microbes to guide management decisions. Étienne Yergeau explains for the #FEMSmicroBlog how microbial characteristics of soils can help farmers predict the yields and the grain baking quality of bread wheat. #FascinatingMicrobes


Microbes in soil as biofertilisers

The inefficient use of chemical fertilisers for many decades resulted in the agricultural sector facing serious sustainability issues. This is mainly related to soil microorganisms that are involved in the nitrogen cycle. Indeed, soil microbial communities determine the availability of nitrogen for plants since they are involved in decomposition and fixing nitrogen.

Hence, soil microorganisms are responsible for soil processes and they could be seen as master fertilisers for crop growth. Based on that hypothesis, the research article “Predictive microbial-based modelling of wheat yields and grain baking quality across a 500km transect in Québec” published in FEMS Microbiology Ecology investigated various microbial characteristics of wheat field soil.

Microbes in soil are responsible for decomposition processes and they could be seen as master fertilisers for crop growth.

The study analysed soil samples from 80 bread wheat fields across the province of Québec, Canada, early in the growing season. The samples’ microbial and soil parameters were recorded and compared with yield data from farmers and grain baking quality from the partnered milling company “Les Moulins de Soulanges” at the end of the growing season. With these data, statistical learning techniques modelled yield and grain baking quality.


Microbial communities improve bread quality

The study looked at microbial parameters like the diversity of various taxa, concentrations of specific substrates or the presence of genes involved in nitrification. Interestingly, microbial parameters outperformed soil parameters for all models. Many of the microbial variables selected by the models had potential causal links with the response variables.

Taxa of microbial communities from different soil samples.
Microbial community compositions of soil samples. From Asad et al. (2021).

For example, a good quality grain contains high percentages of gluten and protein. And synthesising these compounds requires nitrogen, so bread wheat needs to have ample nitrogen provisions, ideally in the form of ammonia.

The model found that the presence of ammonia-oxidizers was negatively linked to the quality of wheat grains. This key bacterial group is involved in the transformation of ammonia into nitrate, which is more prone to leach and can be transformed into gaseous compounds. Hence, the presence of ammonia-oxidizers results in more nitrate than ammonia in the soil.

However, for the plant, it is more energetically favourable to uptake and use ammonia than nitrate. Thus, ammonia-oxidizing bacteria in the soil ultimately lead to less efficient nitrogen nutrition by the wheat plant and lower grain quality.

The next step will be to find ways to act on these microbial parameters to prove causality. This is extremely challenging, as approaches to modify efficiently complex microbial communities are not yet available!


Microbes in soil can help us predict future crop yields

It is worth noting that microbial parameters were measured several months before analysing the yield and grain quality. Yet, these parameters were able to predict the outcomes with high accuracy.

Simple models based on microbial characteristics of soil could predict the future.

This could mean that these simple models based on microbes in the soil could indeed predict the future! The vision of the study is that a farmer would measure a few soil microbial parameters before the growing season. They would then base their management strategy on this information: type and rate of fertilizer, wheat variety to seed, etc. This type of microbial approach could help make agriculture more sustainable.


About the author of this blog

Étienne Yergeau is studying microbes that cover the outside and inside of trees, crops, animals, ice, soil and water. Although he grew up in the city, he spent his summers as a kid at the family cottage in the Canadian back-country, where he became fascinated with all life forms and their interconnections. He is now leading a team of enthusiastic scientists toward (hopefully!) exciting discoveries. When he is not busy with science, Étienne enjoys spending time with his three kids and his wife, training for obstacle course races, snorkelling, BBQing, playing ice hockey or building stuff.

About this blog section

The section #FascinatingMicrobes for the #FEMSmicroBlog explains the science behind a paper and highlights the significance and broader context of a recent finding. One of the main goals is to share the fascinating spectrum of microbes across all fields of microbiology.

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