Life on Earth depends on soil. The biggest risk factors that could destabilize Earth system and endanger our future are loss of genetic diversity and disturbed biochemical flow of nitrogen. Agriculture is in a key role.
Soil is a rich mixture of organic and inorganic material. The biological, living part of soil includes both macroscopic and microscopic organisms. One gram of soil may include ten thousand bacterial species.
Healthy soil supports plant growth and minimizes nutrient emission and run-off. Also, healthy soil buffers against environmental perturbations, e.g. contamination by chemicals. Since the biogeochemical flows in soil are driven by microbes, the soil microbiome is a key component of healthy soil.
Currently the quality of soil is analysed based on physico-chemical measurements. However, these analyses do not result in precise estimates of biological processes. For example, modelling nitrous oxide emissions based on physico-chemical parameters yields contradictory results. Thus there is a need to search for biological indicators of soil health, and to develop soil health assay that would provide farmers information on how their practices affect soil, with a goal to motivate change towards more sustainable agricultural practices.
Modern metagenomics methods have increased the sensitivity of soil microbiome analysis. We can detect thousands of microbial species in one sample to answer the question “Who’s there?”. The question “What are they capable of doing?” is answered by sequencing millions of genes in a shotgun metagenomics analysis. “What are they doing right now?” is answered by analysing soil mRNA. Metagenomics methods can be accompanied with accurate quantitation of gene and mRNA abundances using digital PCR. These methods have finally made it feasible to assess soil health though microbiological indicators. The soil microbiome is a very sensitive indicator. For example, there are detectable differences in microbiome composition between conventional and organic farming.
Results from scientific studies change the way we see the world. The change is slow. To increase the speed of change, we need to communicate the results to stakeholders and to cooperate with them. Focusing on research questions that are meaningful for the stakeholders increases the chance to promote change. Adaptation of new practices is easier when stakeholders understand the value of change; not only the economic value but also the opportunity to act more sustainably. This cultural change requires a transdisciplinary approach, where results from social and natural sciences are integrated with each other and with the know-how of farmers and consumers for increasing the impact of research.
Our aim is first to define microbiological indicators of soil health, and then apply the indicators to design a gene based assay for soil health estimation. The value of the test for the farmers is discussed with them and demonstrated through on-farm visits and by showing the connection of soil management practices to soil health indicators.