Marie Thomas - AIMS@JCU

Marie Thomas

School of Chemistry and Molecular Biosciences

Marie Thomas

School of Chemistry and Molecular Biosciences
Quantifying the Impacts of Environmental Stress on Marine Microbial Communities

Marie is originally from Germany, where she spent her time exploring the dark Taunus Forest, far away from any access to the sea. Growing up in a science-oriented family, it was only a matter of time before she followed in the footsteps of her ancestors by pursuing a bachelors in Meteorology and Atmospheric Physics: the only science discipline that hadn’t yet been tackled by another family member. Marie was one of only a handful to survive the course and immediately after graduating, escaped across the world to the beautiful Shire of New Zealand before landing on Australian shores. Here she fell in love with the “chilled” vibe of the Australians and the endless miles of empty beaches.
After arriving back in Germany, she quickly decided to move back to Australia. Inspired by “the jellyfish guy from 72 most dangerous animals of Australia”, Marie was destined to change direction and became a marine biologist at James Cook University. After completing her masters project with Dr Andrew Negri’s team at the Australian Institute of Marine Science, Marie then took on the role as an experimental technician, where she investigated the effects of herbicides and oil on the growth and photosynthetic efficiency on microalgae, corals and sponges. Today, Marie continues her research journey at AIMS by pursuing a PhD on quantifying microbial stress responses to environmental change.
In her free time, Marie enjoys being creative, exploring the great outdoors, camping, collecting dead things and mountain biking, especially if some risky-business is involved.
Fun Fact: By the time she was 17 years old, Marie was very certain that she would either become a fighter pilot (her mum’s dream; she has probably watched TopGun one too many times) or an action stunt double.

Quantifying the Impacts of Environmental Stress on Marine Microbial Communities

2020 to 2023

Project Description

This project resolves the critical methodological and knowledge gaps that are currently preventing derivation of risk thresholds for marine microbial community structure and function. For the first time, Marie will develop (i) species and (ii) functional sensitivity distributions, with a view to include reef microorganisms in marine risk assessments to facilitate early management interventions aimed at preserving coral reef ecosystems. A novel molecular-ecotoxicological framework will be developed to test for the loss of taxa, genes, genomes, and functional pathways of microbial communities in response to pollution and climate stress. Taxa and functional risk thresholds can then be modelled in species and functional sensitivity distributions to derive specific protection values for entire microbial populations.

Project Importance

The capacity of reef ecosystems to resist and adapt to environmental change is strongly influenced by the responses of coral reef associated microbial communities. Marine microorganisms are key drivers of the biogeochemical cycling of essential nutrients and have the capacity to exacerbate or mitigate ecosystem changes. Often these organisms are the first responders when environmental conditions such as water quality and ocean temperature changes, triggering a destabilization of natural microbiomes. Changes to microbial community dynamics, abundance, and metabolic function is likely to result in cascading bottom-up impacts on biogeochemical cycling at higher trophic levels, leading to detrimental large-scale implications for coral reef function, including how corals respond to environmental stress. Identifying stress thresholds for microbial communities and their key functions therefore represents a crucial step towards the development of sensitive, early, and ecologically relevant indicators for assessing tropical ecosystem health to trigger management and mitigation responses long before coral reef health declines.

Project Methods

Taxonomic variations in reef microbial communities will be assessed using 16S rRNA gene amplicon sequence data collected from controlled pollution and climate stress experiments conducted in the National Sea Simulator at AIMS. In parallel, shotgun metagenomic sequencing will be applied to allow the identification of functional pathways within the community. From here, quantitative stress-response relationships will be interpolated for taxonomic and functional groups that remain stable in the control treatment over the duration of exposure, enabling the estimation of stress thresholds (ECx values) that affect 10% and 50% of each taxonomic or functional group. To quantitatively establish links between taxonomic, compositional, and functional changes within the community, the derived stress threshold values of multiple taxa and functional groups will be combined in a species or functional sensitivity distribution (SSD/FSD) model that describes the proportion of taxonomic or functional groups affected as the stress level increases. Protective concentration (PCx) values can then be estimated that are conservative of a given percentage of microbial taxonomic or functional groups in any given population.

Project Results

Fundamental research has shown that understanding the response of microbial communities to environmental disturbances could be of paramount importance to predict alterations of ecosystem functioning. By shifting our focus towards the microbial scale, advances in molecular technologies will allow us to base predictions of the response of coral reef microbial communities to environmental change upon a holistic view of their community composition, interactions, and functional potential. Enhancing Australia’s capacity to establish a novel regulatory framework would facilitate early management intervention to human activities in coral reef ecosystems.


Climate change,
Coastal development,
Coral reefs,
Field based,
Human use,
Management tools,
Manipulative experiments,
Molecular techniques,
Natural disturbance,
Ocean acidification,
Ocean warming,
Qualitative techniques,
Quantitative marine science,

Supervised By:

Heidi Luter (AIMS)

David Bourne (JCU)

Andrew Negri (AIMS)

Inka Vanwonterghem (University of Queensland)

Nicole Webster (JCU)