Celebrating World Soil Day 2019: DNA Metabarcoding Uncovers Tropical Forest Soil Microbiomes

Post provided by KATIE M. MCGEE

Tropical forest in Costa Rica ©Katie M. McGee

How much do you think about the world beneath your feet? Soil is essential for life on earth and provides many ecosystem services, including carbon storage and providing habitats for billions of organisms. But one third of our global soils are already degraded and are at risk of further degradation from human activities, such as unsustainable farming practices, industrial activities, mining and other non-environmentally friendly practices. In 2002, the International Union of Soil Sciences (IUSS) marked the 5th December as World Soil Day, to celebrate the importance of soil as a critical component of the natural system and as a vital contributor to human well-being.

To mark this World Soil Day, I’m going to be highlighting my recent study, which used DNA metabarcoding as a method to investigate soil microbiomes for evaluating the success of forest restoration in Costa Rica.

Importance of Tropical Forests and Deforestation Pressures

Tropical forests are ecosystems which are essential to planetary health. The degradation of tropical forests is often as a result of agriculture, logging, mining and/or other stressors. Effective restoration is needed for these ecosystems to successfully regain pre-disturbed levels of biodiversity. Tropical forests only comprise 7–10% of the Earth’s land surface but contain 20% of the planet’s carbon within the first 3m of their soil, and exchange more carbon dioxide (CO2) with the atmosphere than any other terrestrial ecosystem.

These suites of characteristics make tropical areas critical for hosting a variety of species and for global nutrient cycling. Yet, these unique and important ecosystems are continually under threat from deforestation.

Logging road through tropical forest in Costa Rica ©Katie M. McGee

Deforestation activities across the tropics contribute to the increase of atmospheric CO2 levels almost as much as fossil fuels. If tropical deforestation were a country, it would be ranked third in the world in terms of CO2 emissions (behind China and then United States). One of the main contributing factors for this is that there is a large release of decades (or even centuries) worth of CO2 from the soil when the forests are clear-cut. In addition, the soil in many of these areas has been so degraded that the capacity to recover is significantly reduced.

Secondary Tropical Forests and Soil Microbes

To remediate the consequences of deforestation, restoration attempts have been implemented throughout the tropics. Secondary forests are those that regrow after degradation and make up over half of the world’s tropical forests. Secondary forests tend to be nitrogen limited though. The richness (i.e. number of species) of trees in secondary tropical forests recovers after around 50 years, but there has been little focus on investigating the extent of soil recovery in secondary tropical forests.

Soil microbes are key components in the restoration of tropical forests due to the nutrient cycling processes they carry out. It is thought that certain tree species and their associated soil microbes (i.e. soil microbiome) may be important in restoring degraded soils. Many tropical trees can fix atmospheric nitrogen (N2) through specialised root microbial symbionts by converting nitrogen gas into ammonium. This conversion is critical to the growth and development of plants and soil microbes, yet it is still unclear the influence that N-fixing trees can have on the soil in the immediate vicinity of the tree.

Identifying Soil Microbes

Soil microbes ©Pixabay

Studying the soil microbes using DNA-based identification has been occurring since the 1980s. Popular methods used in the past involved the time-consuming and costly process of PCR amplification and cloning of genes of interest, using older Sanger sequencing equipment.

The development of DNA metabarcoding (i.e. the method of simultaneous multiple species identification) has enabled a more rapid and comprehensive characterisation of soil microbiome. DNA metabarcoding combines traditional marker gene surveys with high throughput sequencing (HTS).

By comparing obtained sequences to a growing standard reference library of known organisms, taxa present in an environmental sample such as soil can be identified with high confidence. This helps us better address ecological questions linked to environmental impact and biomonitoring, and to understand the complexity of soil biotic communities in various ecosystems.

Individual Plant-Soil Microbiomes

Tropical forest plot in Costa Rica ©Katie M. McGee

In our recent study, we looked at investigating individual plant effects of the soil collected around a nitrogen-fixing (Gavilán) and a non-nitrogen-fixing (Almendro) tree, to look at the differences in the soil microbiome.

We found that each plant species contained their own unique soil microbiome, and that the nitrogen-fixing tree supported soil microbes at numbers similar to those measured in primary forests (non-disturbed). This suggests the importance of nitrogen-fixing trees for the recovery of soils to a pre-disturbed state. In particular, the nitrogen-fixing tree, Gavilán, consists of a soil microbial decomposer community that is more efficient in storing soil carbon.

These results highlight the importance of this tree in building back up carbon storage as biomass in the soil. As such, Gavilán and its associated soil microbiome could be an important ecosystem restoration tool used in facilitating early regeneration of secondary forests.

Summary

The method of using soil microbes, through DNA metabarcoding, is a novel approach that can be applied globally to guide restoration ecology and the policy surrounding it. Using DNA metabarcoding to investigate the diversity of soil microbiomes for evaluating the success of forest restoration, is a technique that can be easily applied to identify additional key tree species. Understanding what species of tree are important for the process of forest restoration is vital for the global recovery of tropical forests.

To find out more, read the full Applied Soil Ecology article ‘Soil microbiomes associated with two dominant Costa Rican tree species, and implications for remediation: A case study from a Costa Rican conservation area

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