The Department of Biological and Environmental Sciences is seeking applicants for 1–4 fully funded doctoral researcher positions. The positions will begin on August 1, 2026, or as agreed, for a maximum period of 3.5 years.

The Doctoral Programme in Biological and Environmental Sciences offers doctoral education in Aquatic Science, Ecology and Evolution Biology, Cell and Molecular Biology and Environmental Science. The selected doctoral researchers will be assigned to the appropriate research group at the Department.

Open PhD projects

1. Keystone players in soil carbon dynamics: Direct and indirect effects of mesofauna on different forms of carbon pools, supervisors Sten Anslan, Carlos A. Aguilar-Trigueros, Nerea Abrego

Soils teem with life, harboring most terrestrial biodiversity. These megadiverse communities are key to understanding soil carbon cycling dynamics because they underpin the processes of formation, stability, and transition of soil carbon, the largest carbon pool on the globe. However, most of what is understood about these processes is based on studies of the microbial soil component alone, ignoring their interaction effect with the faunal component, that are especially abundant in boreal regions. This PhD project aims to identify the keystone soil faunal species in soil carbon dynamics and investigate their direct and indirect effects on the two main pools of carbon used in carbon dynamic models: particulate organic carbon (POC) and mineral-associated organic carbon (MAOC).

• For more information, please contact the project leader Sten Anslan.

2. Interactions between thermal performance and parasite resistance in genetically distinct salmon populations, supervisor Anssi Karvonen

Climate change is rapidly increasing not only the global temperatures, but also the amplitude of extreme temperature fluctuations. This poses a challenge for biodiversity and particularly to many northern species, such as cold-adapted salmonid fishes. As temperature increases or fluctuates rapidly, these species face conditions close to their upper temperature tolerance limit, which causes stress and changes in important physiological functions. Thermal tolerance and the associated physiological functions may also show genetic variation within a population, which can largely determine the ability of the population to adapt to changing temperature conditions. At the same time, temperature and its fluctuations can change conditions for pathogens and parasites, whose life history characteristics, such as reproduction, transmission and virulence, are strongly controlled by temperature. Such changes may have significant consequences not only for parasite fitness, but also for the magnitude of damage caused by the infections in their hosts. This may be further influenced by corresponding changes in host resistance and tolerance to infections.

This project investigates interactions between thermal physiology, parasitism and host genetics in a unique setup of genetically distinct populations of Atlantic salmon and their hybrids. Using rigorous experimental approaches, this project will investigate how increasing and changing temperature influences short-term and long-term physiological performance and life history traits of both hosts and parasites and evaluates the degree of genetic variation associated with these traits. We are looking for a highly motivated PhD researcher, with a background in evolutionary ecology, physiology, parasitology, or related field, to join our research team. Experience in (experimental) work with animal models and/or laboratory analyses, as well as a valid driving licence to conduct field work, will be considered beneficial. We offer a unique opportunity to combine timely aspects of thermal performance of endangered salmonids and parasitism in a single study system and to acquire PhD training in a multidisciplinary research group including some of the leading experts in the field.

• For more information, please contact the project leader Anssi Karvonen

3. Anthropogenic changes to forest use and effects on wildlife health, supervisors Esa Koskela and Eva Kallio

Forest ecosystems are profoundly influenced by human activities, such as forest management and urbanisation. These activities may alter the health of species communities, populations and individuals. Consequently, changes in forest ecosystems may affect the spread of pathogens within populations, potentially translating also into the health of humans. This project is linked to an ongoing Kone Foundation funded ‘For the Woods’ -project, which studies how human activities shape the diversity of forest soil microbial communities, the well-being of other species living in forests, and the resulting disease threat to humans. In the PhD project, the student will focus on the effects of human-caused environmental changes on the health of a keystone forest species, the bank vole (Clethrionomys glareolus). The work will include intensive fieldwork in dissimilar forest ecosystems and various laboratory methods for measuring the health parameters of individuals. For instance, the infections caused by diverse pathogens, including the zoonotic Puumala hantavirus and Borrelia burgdorferi sensu lato, will be examined using immunofluorescence assays and qPCR-based assays. Host populations and communities will be monitored using camera traps and live trapping. The study will facilitate extensive research into the association between forest management, multispecies communities and wildlife pathogens to improve our understanding of wildlife health.

• For more information, please contact the project leader Esa Koskela and visit the research group's website.

4. Rules of engagement: molecular and evolutionary dynamics between megaphages and bacterial hosts in cold freshwater environments, supervisor Elina Laanto

Phages, the most abundant viruses on Earth, remain strikingly underexplored in their diversity. Recent metagenomic studies have identified so‑called megaphages with genomes exceeding 500 kbp, ten times larger than those of “typical” phages. These giant viruses carry hundreds of genes and have the potential to profoundly reshape the metabolism of their bacterial hosts through novel molecular mechanisms. This PhD project focuses on a set of unique megaphage isolates and investigates how they interact with host cells. Project results will experimentally characterize a group of viruses previously known only from metagenomic data. By combining genomics, transcriptomics, and physiological assays, the project will reveal how megaphages coordinate host takeover and thrive under natural conditions. Beyond advancing our understanding of viral ecology and evolution, the discovery of novel phage-encoded genes could drive innovative applications in biotechnology, including new strategies to combat antibiotic-resistant bacteria. The project will be carried out in close collaboration with the ERC-funded Life of Giant Phages project, which explores the biology of large phages. 

• For more information, please contact the project leader Elina Laanto and visit the research group’s website  

5. The role of phase separation and chromatin compaction in HSV-1 reactivation dynamics, supervisor Salla Mattola

Herpes simplex virus 1 (HSV-1) genomes are maintained extrachromosomally in the host cell nucleus during latent infection. HSV-1 reactivation leads to the transcription of viral immediate early proteins, the formation of viral replication centers, and the reorganization of the nuclear structures, including chromatin. Modulation of both host and viral chromosomes and their transcriptional status is an integral part of the lytic and latent viral life cycle, yet the mechanisms are not fully understood. Understanding the intranuclear mechanisms of herpesvirus reactivation and its effects on host chromatin structure and dynamics is crucial for basic research and for the development of oncolytic virus therapies and novel antivirals.

This Ph.D. project is linked to an ongoing Academy of Finland Research Fellow project in which we aim to unravel the positioning of the HSV-1 genomes within host chromatin during lytic and latent infection. The PhD project aims to elucidate the functions of virus-induced phase-separated compartments and their effects on chromatin transcriptional status and compaction during the reactivation of latently infected neurons. Reactivation dynamics under altered conditions that affect phase separation properties in the nucleus will be examined using super-resolution imaging techniques combined with advanced image analysis.

The specific objectives of the project are: 1) To investigate the role of phase separation in HSV-1 reactivation dynamics, and 2) To characterize changes in chromatin compaction and transcriptional status during reactivation

• For more information, please contact the project leader Salla Mattola and visit the research group website.

6. Eco-evolutionary feedbacks through host-microbiomes, supervisor Katja Räsänen

Human induced changes threaten the persistence of natural populations by causing physiological stress on individual organisms and by altering biotic interactions as well as ecosystem function. At the same time, our activities are a significant evolutionary force, influencing the expression of genetic and phenotypic variation, causing strong natural selection and modifying feedbacks between ecological and evolutionary processes (i.e. eco-evolutionary dynamics). Importantly, the microbiome (the micro-organisms living in a eukaryotic host) is a key component influencing fitness and function in many taxa and has the potential to influence eco-evolutionary dynamics. However, how the responses of host organisms to environmental stressors (such as chemical pollution or resource limitation) and, subsequently, their ecological function and evolutionary responses are mediated by host-associated microbiomes is poorly understood.

This project aims to understand co-adaptation of hosts and their microbiomes to anthropogenic change, and the potential for host-microbiome co-adaptation to influence ecosystem function. The study uses the freshwater isopod Asellus aquaticus - a keystone detritivore with broad environmental tolerance, key role on nutrient cycling, and a diverse gut microbial community - as an empirical model. The research methods include high throughput phenotyping and -omics tools (to assess microbial communities, as well as host phenotypic and genetic variation), as well laboratory and mesocosm experiments (to assess individual fitness and ecosystem function).

The project is led by Prof. Katja Räsänen and is done in collaboration with Assoc. Prof. Suvi Ruuskanen (Univ. of Jyväskylä) and Dr. Blake Matthews (Swiss Federal institute of Aquatic Science and Technology, Switzerland).

• For more information, please contact the project leader Katja Räsänen.

7. From Phytoplankton to People: Climate Change Impacts on Nutritional Pathways in Large Tropical Lakes, supervisor Sami Taipale

Large tropical lakes are more than biodiversity hotspots—they are biochemical engines that convert sunlight and nutrients into essential nutrients for millions. As climate change disrupts these systems, the risk of losing access to high-quality protein and LC-PUFAs grows. Interdisciplinary research that links ecosystem dynamics with nutritional outcomes is crucial for protecting these freshwater resources and the communities that depend on them.

This PhD project aims to produce important information about the ability of phytoplankton communities to produce LC-PUFA in some tropical lakes that are important for fisheries. Moreover, this project unravels the food web structure and the ability of zooplankton and fish species (Tilapia) to produce LC-PUFA endogenously. Fatty acid production, conversion, and storage will be quantified using stable-isotope labeling (¹³C), state-of-the-art lipidomics (LC-MS/MS, GC–FID/MS), and compound-specific isotope analysis (CSIA). Moreover, we will use the fads2 gene expression measurement to estimate the fish's ability to biosynthesize LC-PUFA themselves. When combining all these different methods, we can trace carbon flow through FA pathways up to the food web and also quantify FA turnover rates and biosynthetic capacities under stress.

I am seeking a highly motivated candidate with a master’s degree and a background in environmental analytical chemistry, aquatic ecology, or related fields. Prior experience in a laboratory setting is acknowledged and should be mentioned in the motivation letter.

• For more information, please contact the project leader Sami Taipale

8. Systematic cumulative impact assessment in EIA practice, supervisors Elisa Vallius and Saara Vauramo

Environmental impact assessment (EIA) is a process, in which the significant impacts of a project or activity on the environment is assessed. The process is based on EU directive (2011/92/EU) but implication is directed by national legislation, which leads to varying practices. In Finland, the quality and effectiveness of the project has improved remarkably since 1990’s. There are, however, some parts of the process with more needs for further development. To be able to reliably assess the impacts on valuable environmental components (VECs), cumulative changes affecting them should be considered instead of reflecting the possible changes caused by the planned development only. However, there are often significant practical challenges in its implementation: cumulative impacts are often given very little attention in projects and are carried out hurriedly with inadequate methods towards the end of the project.

The PhD project aims to examine the current Finnish EIA process and develop the cumulative impact assessment (CIA) into a more analytical and transparent practice. The study focuses the starting points of CIA, such as location-based vs. project-based assessment, identification of cumulative and mitigating effects. To create systematic approach for CIA, different data processing and assessment methods are studied to depict complex cumulative impact mechanisms including those created by progress in climate and environmental changes. This project focuses on the CIA  in projects causing land use changes and utilizes, among other methods, spatial data-based analyses. 

• For more information, please contact the project leader Elisa Vallius

Who we are looking for

Suitable candidates should have

• A Master’s degree in a relevant discipline.
• Strong interest to the research project you are applying to.
• Curiosity and interest in fundamental scientific questions.
• Ability and motivation to work as part of a team, combined with independence and problem-solving skills.
• We are seeking a highly motivated, innovative, productive persons, who will contribute intellectually to project development.

The tasks of a Doctoral Researcher focus on research aiming at the completion of a doctoral thesis, doctoral studies, assisting teaching tasks, and other related tasks to these. The duties, qualification requirements, and the language skills of Doctoral Researchers are stipulated by the University of Jyväskylä Regulations and language skills guidelines (Doctoral Students). A good command of English is required. A trial period of six months will be used in the beginning of the employment.

The eligible candidate has, or is about to obtain, a suitable Master's degree. In addition, the Doctoral Researcher must have a permission for post-graduate studies at the University of Jyväskylä. After selection, the selected person must apply for postgraduate study rights through a separate application process at the Faculty of Mathematics and Science if they do not already have them.