Freshwater is an important resource for humans as drinking and power supply (hydroelectric power stations), and as a source of irrigation, production and recreation. Regretfully, accessible freshwater accounts for only 0.01% of the land surface, making this resource limiting to both developed and developing countries. Moreover, use of water for household and production contaminate an already limited resource posing a threat to human and environmental health. Human impact represented by climate change (1), land use (2), use of plastics and microplastics (3) affects a large proportion of freshwater lakes and reservoirs worldwide. Public health risks associated with polluted water include increased carcinogenesis, immunodeficiency, lower cognitive performance and other behavioural deficits. Environmental health risk associated with polluted water includes decrease of ecosystem and recreational services as well as drastic reduction in biodiversity.

This project will, for the first time, investigate water organism resilience to common pollutants mediated by the microbiome. This is important because it is becoming increasingly apparent that the microbiome plays an important role in human and animal health. However, the effects of exposures to mixtures of pollutants on the microbiome, and in turn animal physiology and viability, are poorly understood.

Daphnia is the quintessential ecological model species central to the majority of standing freshwater habitats around the world and driver of ecosystem dynamics. Daphnia has a life cycle that alternates sexual recombination with asexual (clonal) reproduction enabling one to measure the response of the same genotype to multiple environmental stressors and their mixtures. Previous studies have shown that Daphnia is highly responsive to environmental change via both plastic and genetic responses (4, 5). Here, we will study the role of Daphnia gut microbiome in individual resilience to common pollutants and their mixtures. In addition, we will investigate whether microbiome transinfection from resistant to susceptible strains improves adaptive responses of natural populations to environmental mixtures of pollutants. The potential applications of these discoveries are far-reaching.

The interaction between host biology and its microbiome is key to understand adaptation to mixtures of pollutants and resilience of freshwater habitats.


Objective 1: We will screen specimens of the keystone aquatic grazer Daphnia magna from natural environments to identify susceptible and resistant strains to common pollutants and their mixtures.

Objective 2: Using transcriptomics and life history trait assays we will measure the impact of pollutants and their mixtures on animal physiology and fitness. Using metagenomics we will assess the effect of pollutants and their mixtures on the microbiome of the same animals.

Objective 3. Using advanced computational tools and biostatistic approaches we will perform an integrative analysis of transcriptome, fitness and metagenome to uncover the mechanisms of resistance to pollutants and their mixtures.

Objective 4. From Objective 3 we will identify resistant strains in which response to pollutants (e.g. microplastics) is mediated by the microbiome. We will then perform transinfection experiments to assess whether transplanted microbiomes improve resistance to pollutants in susceptible strains.


Training and Skills

CENTA students complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to the student's projects and themes. 

The supervisor team, collectively, has a long track record of graduate and postgraduate supervision. The DR will receive multisciplinary training by this supervisor team spanning from evolutionary biology, multiomics technologies, advanced computational and biostatistics skills, and microbiology. The DR will have access to the Environmental Omics Sequencing facility of which Dr Orsini is director and to one of the largest Daphnia facilities in England managed by a specialized technician who provides hands-on training for undergraduate and graduate students. Finally, the DR will have access to a fully equipped molecular microbiology laboratory in the Institute of Microbiology and Infection under the supervision of Dr Lund.


Year 1: experimental exposures to pollutants and their mixtures and measure of impact on animal fitness via life history trait measurements under chronic exposure. Collection of material for transcriptomics and metagenomics. Preparation of first thesis chapter describing the impact of key pollutants on Daphnia fitness.

Year 2: generation of transcriptomic and metagenomics data with the support of the Environmental Omics Sequencing facility. First data quality screening and transcriptome assembly will be completed by the end of year 2. The student will be taking bioinformatics training during year 2.   

Year 3:integrative data analysis of transcriptome and metagenome leading to the identification of strains with resistant microbiomes to common pollutants. Validation in the laboratory with transinfection of susceptible strains with the microbiome from resistant strains and assessment of effects on phenotype. Prepration of second thesis chapter describing the molecular mechanisms of resistace to mixtures of pollutants and third thesis chapter outlining the applications of microbiome transinfection.

Partners and collaboration (including CASE)

This project is a multidisciplinary partnership among three research groups. The supervisor team has expertise in evolutionary biology and genomics on the model species Daphnia (LO), computation and biostatics (JB) and molecular microbiology (PL). The project builds on a recently awarded NERC highlights grant, for which 7PI and 4 postdoc currently work, to discover the molecular targets of natural selection and their contributions to the process of adaptation. This PhD project will benefit from the resources and expertise of the NERC grant, providing the student with access to some of the most advanced multiomics facilities.

Further Details

For questions about the project contact:

Dr Luisa Orsini (l.orsini@bham.ac.uk)

School of Biosciences

University of Birmingham