The Tree Root Microbiome: A faster pathway to climate resilient forests

Overview

The Tree Root Microbiome Programme is a New Zealand-led research project investigating how tree root microbiomes influence forest performance. APPN contributed advanced phenotyping capabilities to test how manipulating these microbiomes affects seedling growth and stress responses.

Why

Forestry systems face increasing pressure from climate change, while traditional tree management operates on long timeframes that may not keep pace. New approaches are needed to accelerate the development of resilient trees able to thrive under future conditions.

Outcomes

Researchers demonstrated that different root microbiomes can influence seedling growth and drought responses. APPN also developed and applied high-throughput phenotyping protocols to reliably measure these effects over time without destructive sampling.

Impact

This work enables faster pathways to climate resilient trees by identifying microbiome-based approaches that could complement traditional breeding. It also unlocks new research capabilities for studying slow-growing species, supporting future innovation in forestry systems

The Tree Root Microbiome Programme: At the root of climate proofing forests, is a New Zealand-backed research program that positions Pinus radiata (Radiata pine or Monterey pine) as a model species for tree microbiome research. Beginning in 2020, the five-year project has highlighted the important role tree microbiomes can have in the adaptability of forest systems. 

Notably, proof-of-concept work undertaken by the Bioeconomy Science Institute (formerly Scion) utilised APPN’s high-throughput phenotyping capabilities to demonstrate that intentional manipulation of the tree root microbiome can influence tree responses to different environmental stressors. 

This finding helps highlight the unique possibilities tree root microbiomes may have as a key biotechnology for enhancing tree productivity and resilience within the global forestry sector.

The forestry industry is one of New Zealand’s most important export sectors, generating ~NZD $6.28 billion in revenue in 2025. Similarly, forestry is a critical industry in Australia, where large plantations support a strong domestic demand for construction timber. 

Australia currently has over 1.71 million hectares of timber plantations^ which are managed in accordance with ongoing replanting regimes and multi-decadal business plans. However, existing and future trees remain sensitive to the effects of a changing climate.

The Tree Root Microbiome Project, funded by the New Zealand Ministry of Business, Innovation and Employment (MBIE) and the Forest Growers Levy Trust is a research program seeking to build the resilience of New Zealand’s forestry sector through improved understanding of the tree root microbiome. It is expected that the findings from this program will inform forestry research globally. The project has explored the factors shaping tree microbiomes – including environment and host genetics and their implications for tree phenotype and resilience. 

Research at APPN focused on the influence of tree root microbiomes on water stress responses in Radiata pine – a globally significant softwood timber species. It is found in a variety of climates throughout the world, although in New Zealand Radiata pine accounts for over 90% of the nation’s forestry plantation area making it a critical focus for the research program.

^Australian Bureau of Agricultural and Resource Economics and Sciences (ABARES) (2025). Australian forest and wood products statistics: Trade to 2024–25 and production to 2023–24.

Trees can be long-lived however, in plantation settings, Radiata pine is typically harvested at 25 to 35 years of age. Therefore, it can take decades for breeding programs to achieve meaningful improvements in climate resilience, disease tolerance, wood quality, or other productivity enhancements. 

Given that climate change is projected to outpace such breeding programs, this is problematic. Therefore, alternative strategies need to be explored so trees planted today will be able to thrive under future growing conditions. 

Inoculating tree seedlings with beneficial microbiomes is one approach New Zealand scientists are closely considering. Microbiomes are communities of microorganisms (such as bacteria and fungi) that live in close association with a biological host (like humans) or an environmental system (like soil). Interactions between a microbiome and its biological host can alter the host’s health or function, as seen in the human gut microbiome. 

Plant species—including trees— have been shown to harbour their own microbiomes, which have been implicated in plant responses to various stressors. 

However, gaps remain in our understanding of whether microbiomes can be manipulated to improve plant performance. Gaps also exist in the methods for studying tree–microbiome interactions and their associated phenotypes.

The slow growing nature of trees can be a challenge within forestry research, as changes in biomass are not always immediately evident. To address this, APPN, in collaboration with the Bioeconomy Science Institute, developed a new phenotyping protocol to assess the impact of microbiome manipulation on pine seedlings.  

Using the LemnaTec Scanalyzer 3D high-throughput imaging system in APPN’s Smarthouse meant researchers were able to monitor seedling growth non‑destructively at regular intervals.

This approach was critical for detecting small changes in biomass over time – something that would not have been possible without the labour‑intensive destruction of hundreds of plants at each timepoint. 

The experiment showed that inoculating Radiata pine seedlings with different root microbiomes impacted seedling responses to water restrictions. Root soil microbiomes were collected from around trees located in South Australian areas thought to be representative of New Zealand’s future climatic conditions (see map). 

It was also shown that the different microbiomes themselves impacted both seedling establishment and growth response, with the growth rate of the seedlings varying up to 30% across the different microbiomes (in the absence of water restriction). The findings provide compelling evidence of a meaningful, and potentially causal relationship between root microbiomes and phenotypic expression in trees. 

As part of the broader program, these findings will support further investigations into microbiome‑based technologies. 

The prospective impact of the Tree Root Microbiome Project as a whole is broad and powerful when considering the potential applications of microbiome-based technologies and strategies. 

The work undertaken at APPN contributed to the program’s overarching aim of establishing a strong foundation for tree microbiome research. This was a critical step forward in the development of technologies and strategies capable of building climate resilient forests, and showing relationships between root microbiomes and tree phenotypes is an essential part of this process.

Findings from the project showed that root microbiomes can affect drought tolerance and growth in tree seedlings. This indicates microbiomes could potentially be used to enhance the drought tolerance of trees, an approach which operates on shorter timeframes than breeding alone. 

In practical terms, this may translate to improving the survival rate of tree seedlings in different environments or could even lead to development of new management strategies. This has positive implications for both productive forestry and reforestation efforts.

Improving the climate resilience of trees ‘sooner rather than later’ will help support both New Zealand’s large forestry export market, and its approximately 42,000 employees. The underlying approach has broad relevance and could offer significant benefits for forest systems internationally, including in Australia.

The project also demonstrates how high‑throughput phenotyping can unlock insights into slow-growing species that would be difficult or impractical to measure otherwise.

The Tree Root Microbiome Programme is being undertaken by the Bioeconomy Science Institute (formerly known as Scion) and is supported by the 2020 MBIE Endeavour Fund and the Forest Growers Levy Trust. The program has a range of partners, including APPN at Adelaide University. 

Greenhouses at APPN’s Adelaide University Node were used to grow Radiata pine seedlings, following work with the team at the Bioeconomy Science Institute to establish suitable growing conditions, including germination protocols and growth‑media selection. 

APPN’s Smarthouse, which includes an automated conveyor-based imaging and watering system, was used to monitor inoculated seedlings over time under both stressed and well-watered conditions. This has enabled measurement of projected shoot area as a proxy for biomass. 

The Smarthouse infrastructure enabled repeated imaging of the same tree seedlings throughout the experiment, instead of costly and time-consuming destructive harvesting across multiple time points.