From metabarcoding to omics: uncovering how soil organisms aid forest adaptation to environmental stress

Jose Alonso — Thu, 06 Feb 2025 09:43:19 +0000

By N. Tourvas, V. Kotina and FA (Phil) Aravanopoulos*
Forest Genetics Lab
Faculty of Agriculture, Forestry and Natural Environment

Aristotle University of Thessaloniki (AUTh)

Thessaloniki, Greece

*email address: aravanop@for.auth.gr

Traditionally, scientists have thought of natural selection, the fundamental, according to Charles Darwin, mechanism of evolution, as a process that helps certain groups of organisms (individuals and populations within a species) succeed and reproduce because of their distinct traits which are better adapted to their environment. However, the story of evolution involves more than just distinct species; it includes how different species interact and evolve together. For example, plants and their insect pollinators have evolved in interconnected ways. This broader view of evolution, known as “community evolution,” suggests that natural selection works across various levels – from genes to ecosystems.

Photo: Example of sampled soil core (Aristotle University of Thessaloniki)

In the case of soil environments, probably the most famous species interaction is mycorrhiza, a symbiotic relationship between fungi and the roots of plants. In this partnership, the fungus helps the plant absorb water and nutrients from the soil more efficiently, while the plant provides the fungus with sugars produced through photosynthesis. This relationship not only is beneficial for both parties, but also plays a crucial role in the health and growth of many plants, enhancing their resilience to environmental stresses and improving soil quality.

An example of this strong relationship is presented in a study by Bazzicalupo et al. (2020) and focuses on the genetic adaptations of Suillus luteus, a mycorrhizal fungus, to environments contaminated with heavy metals. This fungus forms a symbiotic relationship with Scots pine (Pinus sylvestris) forest stands. The researchers compared the genomes of S. luteus populations inhabiting both polluted and proximal non-polluted sites. This comparison aimed to uncover the genetic mechanisms enabling the fungus to survive in heavy metal-contaminated soils.

Photo: Field work in the University forest of Taxiarchis, Greece (Aristotle University of Thessaloniki)

One of the key findings was the minimal genetic divergence between fungal populations from polluted and non-polluted sites. However, the study identified specific areas of the genome that were significantly differentiated between populations from the two environment types, indicating genes which conferred adaptation to heavy metal pollution. A recent preprint followed (Smith et al., 2023) in which the latter results were corroborated by applying another -omic tool, questing this time the gene expression levels (i.e. how active genes were) in S. luteus isolates from the original study. The authors exposed the isolates to varying levels of zinc, a heavy metal, in a controlled environment inside the laboratory. They found that S. luteus zinc tolerance was highly associated with soil contamination level, in particular isolates from polluted sites being more tolerant than isolates collected from non-polluted sites. Furthermore, genes with known function towards heavy metal stress were differentially expressed between tolerant and non-tolerant isolates.

Overall, the findings of both works underscore the importance of genetic adaptation in ecological resilience and survival that influence community evolution. Understanding the underlying mechanisms that shape genetic adaptation, could be crucial for mitigating the adverse effects of human activities (industrial pollution, climate change) on natural ecosystems.

The School of Forestry and Natural Environment of Aristotle University of Thessaloniki (AUTh) along with other departments of the AUTh, participates in the Biodiversity Genomics Europe (BGE) project. Our team collected soil samples across ecological gradients of land abandonment and/or post-disturbance vegetation stages. The soil samples will be analysed with a genomic tool which allow us to concurrently detect the DNA of numerous organisms within a single sample (DNA meta-barcoding). The results of such experiments have the potential to guide research on the evolution (local adaptation) of forest ecosystems, by indicating communities and species associated with each environment. This in turn can lead to more exciting research shading light on the mechanisms that these communities/species employ to thrive in their environments.

Links to original research:

Bazzicalupo et al. 2020 https://onlinelibrary.wiley.com/doi/10.1111/mec.15618
Smith et al. 2023 https://www.biorxiv.org/content/biorxiv/early/2023/12/10/2023.12.08.570832.full.pdf

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From metabarcoding to omics: uncovering how soil organisms aid forest adaptation to environmental stress