Nature-based solutions: harnessing Daphnia for pathogen and chemical pollutant removal from surface and wastewater

Secondary Supervisor(s): Dr Jan Ulric-Kreft

University of Registration: University of Birmingham

BBSRC Research Themes: Renewable Resources and Clean Growth (Industrial Biotechnology)

Project Outline

As the world faces increasing pressures from urbanization, population growth, and climate change, the need for sustainable water management solutions is greater than ever. Pathogen contamination and persistent chemical pollutants in waste and surface water pose significant health and environmental risks. Current wastewater treatment methods are costly, energy-intensive, and often fail to remove harmful pathogens and pollutants from treated wastewater.

Building on the successes of Daphne Water Solutions Ltd. and the University of Birmingham, which pioneered the use of Daphnia (water fleas) for removing persistent chemical pollutants from wastewater, this project seeks to expand the applications of Daphnia-based technology to also tackle pathogen removal. This research aims to develop a nature-based, low-energy, and scalable solution for comprehensive wastewater treatment, integrating chemical and pathogen removal to meet the growing demands for safe and sustainable water reuse. The biological agent Daphnia has been shown to efficiently remove up to 90% of persistent chemicals like pharmaceuticals (e.g., diclofenac) and persistent industrial chemicals (PFOS). The innovative use of Daphnia as a biofilter taps into its natural ability to absorb and bioaccumulate/degrade harmful substances in aquatic ecosystems. Chemical pollutants often have complex interactions with biological agents, making their removal particularly challenging. This PhD project builds on that success by extending the scope of the Daphnia-based technology to address biological contaminants, making it a comprehensive and sustainable solution for wastewater treatment. Preliminary work by the primary supervisor’s group has shown potential for antimicrobial resistant bacteria removal by Daphnia. Building on this proof of concept and expanding previous application of the technology to pathogen removal, the project proposes a dual-action system that can address both biological and chemical threats in wastewater, offering an environmentally sustainable alternative to traditional methods.

Objectives

The project has three main objectives co-developed with the non-academic partner for relevance in real-world applications:

1. Quantifying the efficacy of Daphnia for pathogen removal. This objective will involve laboratory experiments to determine how effective Daphnia is at removing or inactivating pathogens, including antibiotic-resistant bacteria and viruses, from wastewater.

2. Investigating mechanisms of combined pollutant and pathogen removal. While Daphnia has shown great success in chemical removal, this project will also explore how the organism's biological pathways respond to both chemical pollutants and pathogens simultaneously.

3. Developing a scalable pilot system for real-world application in collaboration with the non-academic partner. To validate this approach in real-world conditions, a pilot system will be designed and installed at a site managed by the Wildfowl & Wetlands Trust (WWT). This system will build on the prototype developed by Daphne Water Solutions, incorporating modifications to allow for simultaneous pathogen and pollutant removal. Special emphasis will be placed on adapting the Daphnia-based technology to decentralised communities in the UK.

Portable DNA sequencing for real-time biodiversity monitoring has the potential to transform conservation efforts

Secondary Supervisor(s): Dr Jiarui Zhou

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

Ditches play a crucial role in maintaining biodiversity, acting as vital habitats for various species, and contributing to the connectivity of ecosystems. They are linear water features that crisscross landscapes, connecting wetlands, rivers, and terrestrial ecosystems. Ditches act as refuges for a diverse range of species, from plants to amphibians and invertebrates, while also serving as corridors for wildlife movement. However, they are highly vulnerable to anthropogenic pressures, such as agricultural runoff, habitat fragmentation, and pollution. Despite their importance, ditches often receive limited attention in biodiversity conservation efforts. Effective conservation efforts for ditches require robust, real-time biodiversity monitoring to assess and mitigate these threats.

Traditional biodiversity monitoring methods are time-consuming, invasive, and limited in scope, often failing to capture the full spectrum of species diversity, particularly cryptic or elusive species. DNA-based methods, specifically metabarcoding, have revolutionized biodiversity research by allowing for non-invasive, high-throughput screening of species from environmental samples. However, current sequencing platforms require outsourcing to high-throughput sequencing facilities, delaying data analysis and decision-making.

This PhD project proposes the use of Oxford Nanopore Technologies (ONT) to metabarcoding in real-time, directly in the field. Nanopore sequencing technology offers portability, allowing biodiversity data to be collected and analyzed on-site, enabling rapid decision-making and effective conservation measures. The application of this innovative technology will provide real-time, high-resolution data on species presence and relative abundance, filling a critical gap in conservation efforts for small, yet ecologically significant habitats like ditches.

Objectives

The objectives of this projects are:

1. Developing a field-based toolkit for real-time biodiversity monitoring:

The student will design and optimize a portable biodiversity monitoring system using the Oxford Nanopore technology (ONT), enabling real-time identification of species in ditch ecosystems.

2. Testing and validating the toolkit in ditch ecosystems:

Field studies will be conducted in ditches across different landscapes, such as agricultural areas and protected nature reserves, to assess the toolkit's effectiveness.

3. Data analysis and bioinformatics:

The student will apply bioinformatics pipelines to analyze metabarcoding data and identify biodiversity patterns in ditches.

4. Wider application and knowledge transfer:

The student will capitalise on the interactions with the Wildfowl & Wetlands Trust, co-designing this proposal, to learn about stakeholder needs in biodiversity conservation and to enjoy a two-way knowledge transfer during a 6 month internship.