We study plant-soil-microbial interactions from ecological perspective with an applied twist. Carbon and its stability, as well as key soil nutrients are of particular interest.

Plants and their roots have a major influence on soil biochemical processes. From the point of view of material fluxes, large quantities of carbon assimilated in photosynthesis are allocated below-ground through roots. Carbon compounds in root exudates consist mainly of sugars and are therefore an easily available energy source for a diversity of soil microbes. The microbial activity is particularly high near roots and mycorrhizal fungal hyphae (mycorrhizosphere). Microbes are responsible for most of the important biochemical reactions in soil by producing many process-specific enzymes.

In boreal forest, almost all tree short roots (so called root tips) are colonized by symbiotic ectomycorrhizal (ECM) fungi. ECM fungi form large mycelial networks in forest soil and greatly extend the nutrient-reaching surface area of the root system. In addition to increased nutrient uptake, ECM fungi help trees in many other ways like protecting roots against pathogenic microbes, affecting root and plant drought tolerance.

In agricultural soils, plant roots are colonized by symbiotic arbuscular mycorrhizal (AM) fungi that are shown to be important for plant nutrient uptake especially in nutrient poor conditions. They have also been shown to be involved in soil C stabilization or aggregate formation, and plant health. However, in boreal agriculture, the role of AM fungi is less well investigated. In both forest and agricultural ecosystems, the plants and their symbionts shape the microbial communities with potentially differing functions.

Current projects or experiments
Multi-benefit solutions to climate-smart agriculture (MULTA)

Central idea: Sequestering atmospheric carbon to soil is a great opportunity for the food system to address the climate crisis. In addition, climate-smart agricultural solutions offer many other benefits related to sustainability and health aspects of the food system. These solutions improve productivity and soil health, increase biodiversity and resiliency of ecosystems, improve food quality and the retention of nutrients and water, and decrease nutrient runoff to waterbodies. Implementation of climate-smart agriculture requires a paradigm shift and a holistic approach integrating science and farmer training, policy adjustment, incentives and interaction work.

Our work focuses on Work package 1: WP1 studies processes of carbon sequestration and climate impacts focusing on critical knowledge gaps.

Digital solutions to foster climate-smart agricultural transition (Digi4CSA)

Agriculture is a notable greenhouse gas (GHG) emitter. The European Union has set ambitious emissions reduction goals for this sector. Attempts to improve agriculture’s resilience to climate change and reduce its climate impact are often referred to as climate-smart agriculture (CSA). Despite an impressive start, CSA initiatives remain far from being the industry standard. Digi4CSA will create a digital platform that integrates relevant data streams on CSA farms to facilitate agricultural stakeholders’ decision-making and enable novel business models and market exchanges to foster scaling up CSA initiatives. Digi4CSA will build novel ways of accounting that will holistically capture the climate and other impacts of CSA as it grows in scale. Digi4CSA has an extensive partner network, including Carbon Action, ACCC Flagship, worldwide PEcAn project and Ecological Forecast Initiative, science collaborators, and major companies and foundations working in the food and retail sector.

Our work is under project Work Package 1. ‘Agriculture’: Experimental data on CSA farming practices are still limited. WP1 analyses data from a 5-year carbon farming experiment to be completed on our 100 Carbon Action farms across Finland in 2023. WP1 also synthesizes the data and the knowledge and contributes to developing CSA farming guidelines and education materials. 


Biodiversity may increase carbon sequestration to agricultural soils in many ways. Diverse vegetation assimilates atmospheric CO2 efficiently and roots and root exudates transporting carbon to different depths within the soil. Plant diversity supports diverse microbial communities that induce stable soil carbon formation.

Modern agriculture where monocultures and chemical plant protection (e.g. herbicides, pesticides) are commonly used, has caused a decline in biodiversity in agricultural ecosystems. Currently, it is not well known how the increased plant diversity affects plant production and carbon sequestration.

The aim of the project is to quantify the potential additional agricultural soil carbon sequestration caused by increased plant diversity. In particular, we are interested in understanding which diversity-related processes are essential for soil carbon accumulation.

In addition to scientific research, the emphasis is on the impact on assessing the impact to facilitate informed decision-making and the development of sustainable agricultural practices. 

Our work focuses on plant-soil-microbial interactions and soil C stocks, sequestration and stability.


The great novelty of this research is the focus of our project on deeper soil layers and the combination of factors that play a critical role in SOM stabilization: soil physical properties (mineral-associated and particulate fractions), presence of plant roots as a resource for C inputs, microbiology and biomarkers, and characterization of SOM based on its resistance to thermal decomposition and nutrient stoichiometry. The data produced improves future model predictions and contributes to validation of C sequestration as a climate change mitigation tool.


Soil organic carbon (SOC) is a keystone for most soil functions and associated soil ecosystem services (e.g., biomass production, flood and erosion mitigation, etc.). SOC is also the main part of the large soil organic matter reservoir feeding soil life with energy and nutrients. Moreover, increasing SOC stocks can help mitigate climate change. Over the past millenia, the SOC reservoir has been strongly depleted by human land-use. Restoring SOC stocks using more sustainable management practices has been suggested as a way to improve soil health while ensuring food security and mitigating global warming.

Soils contain organic carbon with highly contrasted residence times, ranging from a few hours to millennia. This is due to the complex combination of mechanisms driving its persistence. The different organic matter forms of SOC support different functions in soils. SOC with short residence times is easily metabolized, and sustains soil biological activity, but is rapidly respired as CO2 and lost to the atmosphere. Conversely, persistent SOC with long residence times can lock up C and thus mitigate climate change but does not fuel biological activity. Our insufficient knowledge of SOC kinetic pools partitioning hampers efforts to estimate soil health and limits the accuracy of model projections of the fate of the SOC reservoir at all spatial scales.

Our work focuses on soil total organic carbon (SOC), mineral-associated and particulate organic matter (MAOM and POM) and aminosugar analysis (see also Soils and Climate Change research group, PI Kristiina Karhu) of Finnish agricultural soil samples.

Continuous cover forestry

Figure: Otto Saikkonen

In 2023, we started to establish new forest experimental sites to study how continuous cover forests (uneven-aged) differs from rotation forest (even-aged) and non-harvested control forest. The first 8 sites were established at Qvidja farm in Parainen, south-western Finland and at Hyytiälä Forest Station of University of Helsinki in Juupajoki, south-central Finland. New sites will be established in the coming years, and several studies are planned on these sites.

The effects of drought on pine (Pinus sylvestris L.) and pine- bilberry (Vaccinium myrtillus) interactions

We work on the effects of short-term drought on ectomycorrhizal Pinus sylvestris seedlings in greenhouse conditions by studying how plant transpiration, root morphology and plant biomass formation are affected when plants are exposed to different ectomycorrhizal fungal and soil inoculum.

We also work on the effects of snow removal on pine and bilberry root growth and microbial biomass and communities in field conditions. In addition, we investigate the external mycelial interactions of pine and bilberry in greenhouse conditions using 13C and 15N-labels.

Past projects

The interactions between trees and ground vegetation for organic nitrogen uptake via ericoid and ectomycorrhizal fungi (NITROFUNGI)

The aim of the project (2012-2017) is to investigate how changes in climatic conditions affect carbon (C) storage ability of the boreal forest soils. It has been shown that nitrogen (N) has a key role in the decomposition of soil organic matter (SOM) because the need for N partly controls SOM decomposition. Fungi are important decomposers of SOM and some fungi form symbiosis with forest trees and shrubs. The interaction between SOM decomposition, soil organic N uptake, symbiotic fungi and forest plants will be studied using modern methods from stable isotopes and radiocarbon dating to molecular biology. The results improve our knowledge on the effect of climate change on soil C and N storage pools, and provide data to improve ecosystem-scale models used to predict forest growth in the changing climate.

The interactions between soil fungal communities and soil organic nitrogen (SON) transformation in boreal forests- the effects of season, geographical location and natural disturbances (PYROFUNGI) 

The main aim of the project (2013-2015) is to identify for the first time the fungal community structure and some of their functions in three main ecosystem stations in Finland. We will connect NGS sequence data (454 pyrosequencing) to organic nitrogen decomposition from several aspects: spatio-temporal dynamics and disturbances in forest ecosystem (fire and reindeer husbandry). 

Revealing sources of biological methane production in boreal upland forests (METAFOR)

The aim of the project (2014-2016) is to quantify the biological sources of CH4 in an upland boreal forest ecosystem, and to identify the microbes, CH4 producing methanogens, involved in the CH4 exchange in each of the compartments: soil, ground vegetation and trees. In order to quantify the contribution of each compartment to the net ecosystem CH4 exchange, the CH4 emission rates from the forest-floor, tree-trunks or the canopy (branches), will be integrated to represent the fluxes over a large forest area. The information of the microbial community structure and the presence of methanogens will be used to further understand the biological mechanisms and the players in the CH4 production. Project leader Doc. Mari Pihlatie.

Decomposition of different fractions of soil organic matter in boreal forest soil; effect of fast cycling carbon and nitrogen on the decomposition of old soil organic matter (FASTCARBON)

In this project (2010-2014) the aim is to study organic matter degradation using stable isotope techniques and to determine what is the age of carbon respired after priming by simple sugars. The adding is done either directly as glucose or by Scots pine plant as a natural mixture of recent photosynthates. Experiments to better understand the priming effect are in progress. Project leader Doc. Jukka Pumpanen.

The cryopreservation of ectomycorrhizal fungi

The MSc project of Ulla Mikkola started in September 2010. The aim of the project is to study how ectomycorrhizal fungi tolerate cryopreservation (-196°C) and whether the survived strains have the same functional properties before and after cryopreservation. Mycorrhiza formation, enzyme production and growth patterns are used as indirect methods to test the functionality. Cryopreservation would greatly facilitate the storage of strains in large culture collections (like FBCC in University of Helsinki) and would allow infinite storage periods.

BVOC production by soil fungi

The project is done in collaboration with e.g. dos. Jaana Bäck and MSc. Hermanni Aaltonen (University of Helsinki). Biogenic volatile organic compounds (BVOCs) are shown to be important for atmosphere chemistry and cloud formation. Boreal forest are shown to produce significant amounts of BVOCs that consist of numerous organic compuons. The aim of the project is to experimentally test whether soil fungi produce BVOCs, what compounds are produced and  how mycorrhizal symbiosis affect tree roots BVOC production. The first paper of the project was published in 2010 (Bäck et al. 2010).

Tree root and mycorrhizal associated archaeal communities

The project is done in collaboration with Dr. Malin Bomberg (VTT, Finland). Archaea are a group of micro-organisms that are not well know but do have a contribution to e.g. global methane cycling. However, the significance of this contribution is largely not quantified. In the project, the archaeal community structure in different tree species and different temperatures was determined. The manuscript is submitted November 2010. 

Evaluating the role of shiro formation of Tricholoma matsutake in natural stand of Pinus sylvestris

The project is led by Dr. Lu-Min Vaario and other collaborators are Drs. Taina Pennanen, Tytti Sarjala and MSc. Eira-Maija Savonen, all from Finnish Forest Research Institute (METLA). My major contribution to the project is the enzyme analysis that are performed from field soil, ectomycorrhiza and bark samples.

Bioactive compounds for drug discovery

This project was started in late 2005 as part of Jussi Heinonsalo's post-doctoral project in collaboration with Viikki Drug Discovery Center and with professors Pia Vuorela, Annele Hatakka and MSc. Päivi Järvinen. The fungal extract were analysed in the drug discovery center to find interesting novel bioactive compounds.

The effects of ectomycorrhizal fungi on carbon balance of Scots pine (Pinus sylvestris) seedlings

The project was started in collaboration with professor Hannu Ilvesniemi (Finnish Forest Research Institute, METLA) and his project ‘Role of older humus and rhizobial exudates in the C-balance of boreal forest soils: Impact of clear-cutting, forest regeneration and tree species' funded by the Academy of Finland. There are experimentation going on related to this topic.

Quorum sensing inhibition by root associated fungi

This collaborative project was done together with Dr. Stephane Uroz from INRA in Nancy, France. The aim of the project was to see whether root-associated fungi can produce bioactive compounds that may affect bacterial quorum sensing. Quorum sensing is an important function in bacterial communities that partly regulates bacterial community responses. See the publication Uroz and Heinonsalo, 2008.

The interactions of ectomycorrhizal and litter-decomposing fungi

The project was done in collaboration with PhD Kari Steffen ( at the University of Helsinki (postdoctoral project of  the Academy of Finland called ‘Comparative evaluation of degradative activities in litter-decomposing and facultative mycorrhiza-forming fungi’), prof. Martin Hofrichter (International Graduate School Zittau, Germany) and doc. Maarit Niemi (Finnish Environment Institute, Helsinki, Finland). A manuscript on a novel enzyme analysis method is in preparation from this project.

Biodiversity of ectomycorrhizal fungi

Jussi Heinonsalo did his PhD thesis under supervision of doc. Robin Sen with a title ‘The effects of Forestry Practices on Ectomycorrhizal Fungal Communities and Seedling Establishment’. The project was part of Academy of Finland’s FIBRE project. Thesis can be found as pdf in Helda - open repository of University of Helsinki.

Bioremediation or hydrocarbon contaminated soil by ectomycorrhizal fungi

I did my MSc. thesis in the bioremediation project. The results were published under title ‘Effects of ectomycorrhizal fungi and associated bacteria on hydrocarbon oxidation in forest and petroleum-contaminated soils’. See Heinonsalo et al. (2000).