Biology Education

The loss of plant diversity is a growing global concern, driven by changes in land-use and climate. Maintaining plant diversity is important for ecosystem functions, such as carbon storage which is regulated by soil microbial communities. Plant diversity is particularly important during more frequent and intense drought events under climate change. While it is well known that ecosystems with high plant diversity are better to maintain functional stability under drought, less is understood about how plant diversity influences soil microbial responses during drought cycles. Soil moisture is a key factor controlling soil microbial communities, and as such drought will affect their ability to regulate soil functions. Therefore, understanding how plant diversity impact soil microbial functions during drought is crucial.

Objectives
This project aims to determine how plant diversity affect soil microbial tolerance and recovery to drought. We will set up two different plant diversity and drought treatments using a greenhouse pot experiment. The experiment will represent Swedish grasslands using common grass species, including a high diversity and a low diversity grassland community. We will evaluate the microbial ability to deliver soil functions and sensitivity to drought by resolving responses of growth and respiration both during and after drought, as well as associated soil and plant characteristics. The project will focus on soil microbial communities and is open to a tailored design that matches your interest within the topic. By combining the effect of plants and microbial communities we will determine how climate change impact soil microbial communities and their processes such as CO2 in different plant treatments, along with carbon and nitrogen-use efficiencies.

Methodology

• Determine bacterial and fungal growth rates by radioactive isotope tracing
• Estimate plant and soil respiration using both gas chromatography and continuous fluxes
• Estimate GPP, NPP and NEP using light and dark chamber systems
• Learn how to assess micrometeorological assessments of soil moisture and temperature
• Assess key plant traits, including height, biomass, root production, and nutrient contents
• Determine soil characteristic including soil moisture, C, N, pH, organic matter etc.
• Asses microbial community composition using 16S/ITS amplicon assessments of extracted
• DNA, and the size and abundance of microbial groups using PLFA
• Determine gross and net nitrogen mineralization and nitrification using 15N pool dilution

Skills and techniques acquired

• Design and manage a greenhouse experiment with focus on grass mesocosms
• Learn about plant traits and link them to microbial community responses
• Assess the soil carbon budget during drought cycles
• Developed problem-solving strategies and explore various approaches related to running a
• greenhouse experiment
• Statistical analysis and curve fitting to interpret patterns of microbial drought responses and
• correlate them with other measured variables

Application process

Flexible starting date, but preferably autumn 2024
If you are interested, please contact: Sara Winterfeldt, sara.winterfeldt@biol.lu.se and/or Johannes Rousk, johannes.rousk@biol.lu.se

Soil microbial decomposers, including bacteria and fungi, are the gatekeepers of the soil carbon cycle, determining the fraction of decomposed carbon that becomes part of their biomass or is released into the atmosphere through respiration. In the context of climate change, understanding how rising temperatures will affect these microbial communities is crucial for predicting global carbon fluxes. Elevated temperatures could either increase or decrease the amount of carbon released into the atmosphere by soil microbes.
Numerous studies have shown that soil bacteria and fungi exposed to rising temperatures in situ exhibit shifts in their growth rate temperature dependencies, with both their minimum and optimal growth temperatures moving upward in response to the warming conditions. However, these adaptations are often measured at the community level, which limits our understanding of the ecological mechanisms involved. It remains unclear whether these changes are due to shifts in community composition toward warm-adapted taxa or physiological acclimation and evolution within existing taxa—possibly through mechanisms like horizontal gene transfer.

Objectives
This project aims to elucidate the mechanisms by which soil microbial communities adapt to increasing temperatures at the species level. By comparing the thermal traits of bacterial and fungal strains isolated from artificially warmed soils, we seek to determine whether thermal adaptation results from species sorting or physiological changes within species. Bacterial and fungal populations will be isolated from both control (ambient temperature) and warmed soils. These strains will be identified using DNA barcoding, and their thermal traits will be analyzed in relation to their phylogeny. The findings will be compared with previously acquired community-level thermal trait data to assess whether community-level thermal adaptation is primarily associated with microbial species sorting or physiological adaptation, and to determine if these processes differ between bacteria and fungi.

Methodolog

• Isolate bacteria and fungi from artificially warmed soils.
• Identify bacterial and fungal strains using DNA barcoding techniques.
• Measure growth rates of bacterial and fungal isolates at different temperatures.
• Model growth rates as a function of temperature to determine thermal traits.

Skills and techniques acquired

• Microbiology techniques for isolating and identifying microbes the molecular level.
• Methods for axenic bacterial and fungal cultivation and phenotyping.
• Analyzing thermal adaptation traits in relation to microbial phylogeny.
• Advanced data analysis and visualization skills.

 Application process

• Flexible starting date,
• 45-60 cr
• Interested candidates should contact Dr. François Maillard at francois.maillard@biol.lu.se.

Bacteria and fungi associated with plants play critical roles in plant growth, fitness, and stress tolerance. These microbial communities inhabit the rhizosphere—the soil zone influenced by root secretions—and internal plant tissues both belowground and aboveground, collectively known as the plant microbiome. While considerable progress has been made in understanding how disturbances like pathogen outbreaks, invasive species, and pollution affect plant microbiomes, there is limited research on the impacts of climate change-associated disturbances.
In boreal and subarctic areas, ericaceous shrubs (members of the family Ericaceae) often dominate the vegetation and form specialized symbiotic relationships with ericoid mycorrhizal fungi, essential for nutrient uptake in nutrient-poor soils. Climate models predict that heatwaves will increase in frequency and intensity in these regions due to climate change. Understanding how these heat stress events affect shrub-associated microbial communities, both belowground and aboveground, is crucial, as alterations in the microbiome can influence shrub health, survival, and ecosystem dynamics.

Objectives
This project aims to understand how acute heatwaves affect microbial communities associated with three different ericaceous shrub species. We will investigate whether such climatic disturbances influence plant-associated microbial diversity and composition in both belowground and aboveground habitats, as well as plant physiology, using an artificial warming experiment at the Abisko Field Station. By combining microbial community sequencing and plant tissue biochemical characterization, we seek to determine how future climatic disturbances might affect shrub microbiomes and identify potential microbial bioindicators of these changes.

Methodology

• Evaluate shrub root fungal colonization.
• Determine bacterial and fungal community diversity and composition from soil and plant
  habitats, including roots and leaves.
• Assess plant biochemical composition.

Skills and techniques acquired

• Root staining and microscopy to assess mycorrhizal and endophytic fungal colonization.
• Bacterial and fungal metabarcoding, including DNA extraction and amplification, to profile
  plant-associated microbial communities.
• Bioinformatics analysis of high-throughput sequencing data to identify microbial taxa and
  assess community diversity.
• Statistical analysis to interpret patterns in microbial communities and correlate them with
  environmental variables.

Application process

• Flexible starting date,
• 45-60 cr
• Interested candidates should contact Dr. François Maillard at francois.maillard@biol.lu.se.

Soils are the largest organic carbon reservoir in terrestrial ecosystems, storing carbon as organic matter derived from decomposed plant, microbial, and animal residues that resist microbial decomposition. Recent research has revealed that organic molecules adsorbed onto soil mineral nanoparticles, such as iron and aluminum oxides, form the most stable and persistent pool of organic carbon in soils. However, the environmental factors driving the formation and destabilization of mineral-associated organic matter (MAOM) remain poorly understoodIn boreal and subarctic regions, climate change is causing trees and shrubs to encroach upon tundra ecosystems, leading to significant decreases in soil organic carbon stocks. While most studies have focused on the organic layers of soils—primarily composed of particulate plant residues—there is limited knowledge about how changes in vegetation types affect organic carbon stored in the mineral soil layers as MAOM.

Objectives
This project aims to understand how the progression of trees and shrubs affects MAOM processes in subarctic soils. To achieve this, we will utilize a natural ecotone from dwarf birch forest to tundra in the Swedish subarctic as our study site. By employing a new probe system, we will quantify MAOM formation and destabilization rates across this gradient. We will then compare these rates with various plant parameters (such as species composition, and tree density), soil parameters (including organic matter stocks, pH, moisture, and temperature), and microbial parameters (bacterial and fungal community diversity and composition). This project aims to identify the abiotic and biotic drivers influencing MAOM processes in subarctic mineral soils.

Methodology

• Analyze MAOM probes to determine stabilization and destabilization rates.
• Assess plant parameters to evaluate their influence on MAOM processes.
• Measure soil parameters to determine their effect on MAOM processes.
• Examine soil microbial parameters to understand their role in MAOM processes.

Skills and techniques acquired

• Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy.
• Stable isotope tracing using ¹³C and ¹⁵N isotopes.
• Soil organic matter fractionation techniques.
• Bacterial and fungal metabarcoding to determine soil microbial community composition.
• Advanced statistical analysis and data visualization.

Application process

• Flexible starting date,
• 45-60 cr
• Interested candidates should contact Dr. François Maillard at francois.maillard@biol.lu.se.

Ectomycorrhizal fungi form symbiotic relationships with trees, playing a pivotal role in forest ecosystems by enhancing plant nutrient uptake in exchange for carbon from photosynthesis. Unlike most mycorrhizal fungi that transfer inorganic nutrients to their host plants, ectomycorrhizal fungi have the unique ability to acquire nutrients—particularly nitrogen—directly from soil organic matter. This process allows them to bypass the typical nutrient mineralization pathways in soils.
In boreal forests, where nutrients predominantly exist in organic forms, the capacity of ectomycorrhizal fungi to access organic nitrogen is especially critical. However, despite their ecological importance, there is limited understanding of the efficiency and mechanisms of organic nitrogen acquisition among the diverse species of ectomycorrhizal fungi. This knowledge gap stems from their high diversity; ectomycorrhizal symbiosis has evolved independently over 80 times, resulting in up to 20,000 different species.

Objectives
The project aims to phenotype a diverse collection of ectomycorrhizal fungi in vitro, encompassing over 50 different genera. By assessing their growth performance on various organic nitrogen sources, quantifying enzyme production that facilitates nutrient acquisition, and analyzing modifications of organic matter induced by fungal activity, this project seeks to evaluate the efficiencies and mechanisms used by ectomycorrhizal fungi for organic nitrogen acquisition. Ultimately, this work will connect the functional diversity of ectomycorrhizal fungi with soil biogeochemical cycles.

Methodology

• Cultivation of fungi: Grow cultures on media containing different organic nitrogen sources.
• Biomass measurement: Quantify fungal growth and nitrogen uptake.
• Enzyme assays: Use fluorometric and colorimetric methods to measure enzyme activity.
• Spectroscopy analysis: Employ Fourier-transform infrared spectroscopy (FTIR) to characterize
  changes in organic matter.
• Data interpretation: Analyze results to determine nutrient acquisition strategies among
  various fungal taxa.

Skills and techniques acquired

• Fungal microbiology: Sterile techniques, media preparation, and high-throughput in vitro
  phenotyping.
• Enzymology: Performing and interpreting enzyme assays.
• Spectroscopy: Utilizing FTIR spectroscopy for organic matter characterization.
• Data Analysis: Statistical analysis and scientific interpretation of experimental data.

 Application process

• Flexible starting date,
• 45-60 cr
• Interested candidates should contact Dr. François Maillard at francois.maillard@biol.lu.se.

Songbirds rely on an endogenous program to follow species-specific routes and schedule their migrations to the annual cycle. Due to competition, birds are often under time stress to complete their migrations, especially in spring when they are heading to the breeding areas. How birds are affected by parasites on migration and in particular, if fueling and expression of migratory activity potentially leading to slower migration speeds decrease in sick birds compared to healthy birds is not well known. We have collected fueling and activity data from a number of migratory songbird species in controlled experiments, from which we have blood samples that will be analyzed with respect to prevalence of avian malaria parasites. We hypothesize that migratory songbirds are affected by chronic avian malaria infections and will show decreased levels of fueling and migratory activity recorded by films.

We aim to test the hypothesis that songbirds can adjust their schedule of migratory fueling, migration activity and orientation to parasite load by exploring already collected data potentially in combination with new data collected during the study period. We are looking for a dedicated master’s student to conduct the avian malaria genotyping and analyses of behavioural and ecophysiological data collected in controlled experiments. There is a possibility to collect additional experimental data during spring or autumn.

Labwork and potential fieldwork starts: Autumn 2024/Spring 2025.

If understanding how songbirds are affected by parasites on migration excites you, then this may be your master’s project.

Please, contact Susanne Åkesson (migration phenotype, behavioural data) or Helena Westerdahl (genetics) for more information.

Professor Susanne Åkesson, Department of Biology
susanne.akesson@biol.lu.se

Professor Helena Westerdahl, Department of Biology
helena.westerdahl@biol.lu.se

The evolutionary ecology of cognition and memory in Caenorhabditis worms

We have two MSc projects (45-60 credits each) to investigate the evolution and ecology of cognition and transgenerational epigenetic memory in Caenorhabditis worms. With as few as c.a. 300 neurons, worms demonstrate a wide range of learning capabilities; they can associate olfactory cues with stress, learn to avoid pathogens, and can transmit their learned memory to their offspring (how convenient!). However, the regulation of their cognitive capacity remains unclear, and the ecology that facilitates the evolution of epigenetic memory inheritance is unknown.

Project 1: Being good at learning may seem universally beneficial. But is it? First, you can make mistakes. Second, there may be physiological costs associated with learning, forming memories, and keeping your nervous system in peak condition. Our recent results indicate that learning is regulated by the RNA interference (RNAi) pathway, but the capacity for RNAi-regulated learning may come with a potential fitness cost. This MSc project aims to investigate the costs of the active process of learning and memory inheritance using several RNAi mutants of Caenorhabditis elegans. 

Project 2: C. elegans worms learn to avoid pathogenic food (Pseudomonas bacteria) and can transmit the learned avoidance through epigenetic mechanisms (in this case, non-coding RNAs) to naïve progeny that have never encountered the pathogen. Such epigenetic memory inheritance has important implications in evolution, but its ecological relevance remains unclear – can other Caenorhabditis species that occupy different ecological niches inherit pathogenic memories? And how does worms’ microbial environment affect their response to pathogenic learning? This MSc project is part of a larger study, where we aim to investigate learning and epigenetic memory inheritance across Caenorhabditis species, as well as explore the interactions between the worms’ microbial environment and epigenetic memory inheritance.

Starting date: flexible

Required qualifications: Strong interests in evolutionary biology. No specific experience required.

Who are we?

We are three groups of researchers based in Lund University (Hwei-yen Chen), Uppsala University (Martyna Zwoinska), and Halmstad University (Martin Lind). Our shared interests include plasticity, cognition, life-history, and aging. Drop us a line if you’re interested in our projects, or if you would like to develop your own project with us!

Hwei-yen Chen, hwei-yen.chen@biol.lu.se

Martin Lind, martin.lind@hh.se

Martyna Zwoinska, martyna.zwoinska@ebc.uu.se