Linking the soil microbiome to climate resilience

The tree microbiome project: at the root of climate proofing forests (The Tree Microbiome Programme or ‘TrmP’) is a five-year research project being undertaken by the Bioeconomy Science Institute (formerly known as Scion). The program is led by Dr Steve A. Wakelin and supported by the 2020 MBIE Endeavour Fund and the New Zealand Forest Owners Association.

Its primary aim is to identify elements of P. radiata soil microbiomes that are critical to tree performance under arid growing conditions. Using this knowledge, the ultimate goal is then to utilise root microbiomes to expand the phenotype of trees. This may be for climate resilience, but also disease tolerance, wood quality, and productivity enhancement.

With a growing cycle of over 25 years, trees planted today must be able to survive in future growing conditions. 

Using APPN’s facilities, the research team has definitively shown that deliberate alteration of radiata pine soil microbiome leads to directed, reproducible changes to the trees’ phenotype and dramatically increase their drought tolerance.

This discovery opens the door to microbiome management of trees and supplying bespoke microbiomes with nursery plants to ‘climate proof’ P. radiata plantations. 

The Bioeconomy Science Institute’s team had already worked with TPA® to establish suitable growing conditions, including germination protocols and growth media selection. Then, in 2024-25, Bioceonomy Science and TPA® began work to deliberately engineer root microbiomes for P. radiata and demonstrate their potential to confer measurable phenotypic changes under drought stress.

Ten soil microbiomes from South Australian sites deemed to match future conditions in New Zealand’s forests were used for inoculation. Trees were grown under controlled conditions in a TPA® greenhouse, before being transferred to the conveyor-based imaging and watering system in the Smarthouse. 

While in the greenhouse, these trees were well watered over several months. Then, once they moved to the imaging-phase in the Smarthouse, water restriction was applied to measure the impact of the soil microbiome on seedling growth under water limited conditions

The controlled environment and precision watering available at TPA® reduced environmental variability from the experiment, while the conveyor-based imaging system in the Smarthouse allowed non-destructive measurement of growth over time. 

Each individual tree was photographed regularly using the Smarthouse’s LemnaTec Scanalyzer RGB cameras, to accurately measure differences in their phenotypic development.

In a surprise discovery, the resulting data also demonstrated that soil microbiomes collected from different sites across South Australia impacted seedling growth rates by up to 30 percent in the absence of drought. This shows the profound importance of having a ‘good root microbiome' in overall productivity. It also indicates that microbiome inoculation could be a powerful tool in modulating seedling establishment and growth.

The project is now moving to understand the causal link between climate, tree root microbiomes and tree phenotypes, to explore how these associations vary with environmental conditions and confer benefits to the plant.

The final step will be to deliberately engineer specific elements of the soil microbiome to improve the resilience and performance of P. radiata plantations in New Zealand’s future climate.

Watch more here 
(on the Bioeconomy Science Institute YouTube Channel)

8 December 2025