Biological sciences

Our river systems face multiple threats. Summer 2022’s drought, followed by rain and discharge of sewage from overflows, and the widespread problem of plastic pollution, highlight the challenges that we face in managing our water resources under climate change. Chalk streams are among the rarest of freshwater habitats globally and are critical for biodiversity as well as having substantial cultural value1, yet their microbial communities are poorly characterized. Of particular concern are microbes with genes encoding antimicrobial resistance that could contribute to treatment-resistant infections. For example, agricultural run-off of nutrients and pesticides, or pharmaceutical compounds escaping from sewage works, or the contamination with plastic waste2 could all be leading to the enrichment of antibiotic-resistant bacterial populations. We hypothesise that antibiotic resistance genes (ARGs) accumulate at specific sites, such as downstream of wastewater treatment works, or specifically within biofilms on plastics or microplastics. The objective of this project is to assess bacterial communities in different locations in chalk rivers and identify factors that lead to the selection of antibiotic-resistant bacteria.

Marine plankton communities are a fundamental component of the Earth system. They support food webs, drive global biogeochemical cycles, and play a central role in the regulation of Earth’s climate1.  These ecosystem functions are carried out by an extremely diverse microbial community, and predicted changes in biodiversity and biogeography are therefore likely to have important impacts within the Earth system. Species distribution models (SDMs) have proved to be a powerful method for estimating contemporary plankton biogeography and biodiversity. However, they make a number of important and somewhat unrealistic assumptions2, especially in relation to marine microbial communities. Most notably, they neglect the known capacity of microbial species to rapidly evolve, and they do not account for dispersal by ocean currents. With SDMs increasingly being applied to predict the future response of marine communities to environmental change it is important that these sources of error and uncertainty are quantified. The aim of this project is to use a simulated ‘virtual ecosystem’3 to assess how evolution, dispersal and a range of other potentially important factors may impact the predictive skill of SDMs. This will improve our ability to understand how marine microbial biodiversity and biogeography will continue to be impacted by ongoing climate change. For full project details visit the Inspire project page.

The diamondback moth (DBM), Plutella xylostella, is an agricultural pest with worldwide impact on brassica crops (>$5 billion in annual damages). Its unique glucosinolate sulfatase (GSS) enzymes allow it to specialize on cruciferous host plants by evading their glucosinolate/myrosinase defence system1. In preliminary studies, we established that herbivory by DBM caterpillars is controlled both by environmental light and their internal daily timekeeping systems. Moreover, the expression of DBM GSS genes exhibits circadian rhythmicity. This project aims to elucidate abiotic and biological determinants of DBM herbivory of its host plants. It will complement ongoing research focused on circadian control of herbivory in the DBM caterpillar by concentrating on environmentally-controlled defence mechanisms in cruciferous plants (Brassica rapa and Arabidopsis thaliana). The following Specific Objectives will be pursued:  SO1: Identify how host plant glucosinolate production and herbivory by DBM are affected by (a) glucosinolate biosynthesis and daily timekeeping in the host plant, (b) daily environmental cycles in light and temperature. The latter will simulate representative light/temperature cycles for the UK and explicitly explore the predicted impact of light pollution and global warming.  SO2: Identify changes in plant and DBM expression profiles that are closely associated with changes in herbivory across different environmental contexts. For full project details visit the Inspire project page.

One of the global challenges is to achieve food security in the face of an expanding world population. This challenge is particularly relevant to PNG, where 85% of the population depend on swidden agriculture, within the third largest area of tropical forest worldwide. A key part of the swidden agricultural cycle is the fallow period. Due to increased demand for agricultural plots because of population growth, fallow periods are reducing. One approach to adapting to this could be to speed up the ecological processes that take place during the fallow period by facilitating soil and forest restoration.  This would likely involve: (1) Quantifying biodiversity and ecosystem functioning, particularly below-ground, across a range of ages of fallow plots; (2) Testing novel ways of managing the fallow period to restore ecosystem functioning faster, e.g. soil inoculations or planting cover crops; (3) Investigating whether and which fallow management methods are likely to be adopted by local farmers using socio-ecological surveys; and (4) Given results for (2) and (3), determining which methods of fallow management are most likely to enable plots to be reused successfully after a shorter fallow period. The student tackling this project will accomplish original science in a tropical ecosystem, alongside delivering feasible adaptations to address a challenge faced by many tropical countries. For full project details visit the Inspire project page.

Noctiluca scintillans (the sea sparkle) and other dinoflagellates are responsible for most bioluminescence in European marine environments and familiar blue-glow blooms. The ecological role of dinoflagellate bioluminescence is currently not clear, and its apparent importance in marine food webs highlights the need to understand its environmental regulation and molecular underpinning. Fundamental gaps in knowledge include how bioluminescence varies within natural populations and how dinoflagellates produce luciferin. We hypothesize that: Bioluminescence intensity and gene expression vary among individual cells and are circadian-regulated. Luciferin is generated by an oxygenase enzyme from a chlorophyll-related molecule. The investigation of these issues will help illuminate the environmental role of bioluminescence and accelerate the industrial use of dinoflagellate luciferin. Three innovative approaches will be used: Studying non-photosynthetic Noctiluca which, unlike other bioluminescent dinoflagellates, lacks endogenous photosynthetic chlorophylls and has non-bioluminescent strains, both advantages when analyzing luciferin tetrapyrroles. Single-cell sequencing to profile expression and circadian regulation of bioluminescence genes in natural populations on a cell-by-cell basis. Identifying new bioluminescence-associated genes by their unique day/night expression profile, specifically oxygenases that could synthesize dinoflagellate luciferin in a single catalytic step, followed by their functional assessment after heterologous expression. For full project details visit the Inspire project page.

Freshwater lakes are a major source of atmospheric methane (CH4), a potent greenhouse gas. However, the importance of freshwater CH4 cycling in our future warm climate remains unknown. One way to better understand methane cycling in lakes is to assess changes in the past, and this project will focus on methane cycling and impacts on ecosystem community. Project aims will be to reconstruct (1) ecosystem communities through microfossil analyses (e.g. chironomids, Cladocera) from varved lake sediments; (2) methane ebullition by analyzing the stable carbon isotopic composition (δ13C) of chironomids and Cladocera; (3) methane production by analysing the abundance of archaeal lipid biomarkers; (4) methane oxidation through δ13C analysis of bacterial lipid biomarkers (e.g., hopanoids), and (5) bacterial communities that are involved in methane oxidation, via sedimentary ancient DNA (sedaDNA) analyses. This will enable the differentiation between Type I or Type II methanotrophs and will provide additional insights into methane flux (i.e., high vs low). These results can then be compared, enabling us to detect if there is a change in community structure over time (protist and/or primary consumers), and thus our interpretation of the methane cycle in the past as well as considering warmer futures. For full project details visit the Inspire project page.

Symmetry is a fundamental property of the animal body plans that emerged over half a billion years ago, during the Ediacaran–Cambrian. While a few animal groups display radial symmetry or are asymmetrical, the vast majority are bilaterally symmetrical. However, determining why different types of symmetry evolved is challenging, in part because most phyla are characterized by only a single form. Echinoderms (starfish, sea urchins and their allies) are an exception; all modern species exhibit pentaradial (five-fold) symmetry, but the phylum also possesses an extensive fossil record that includes bilateral, asymmetrical and radial forms [1,2]. The aim of the proposed research is to investigate the evolution of symmetry in echinoderms as an exemplar for understanding the evolutionary significance of symmetry in animals more broadly. This will be achieved by studying the form, function and phylogeny of early fossil echinoderms using cutting-edge methods, including X-ray tomography, computational fluid dynamics and Bayesian inference. Furthermore, the ecology and environments inhabited by early echinoderms will be characterized and analyzed quantitatively using phylogenetic comparative methods. The results will transform our understanding of the evolution of symmetry in echinoderms, with broad implications for animal body plan assembly.  For full project details visit the Inspire project page.

Climate change provides a major challenge for plants as they cope with increases in abiotic stresses such as high or low temperature and drought. These conditions will negatively affect responses to biotic stresses caused by insect herbivores and pathogens, and contribute to the ongoing problem of providing sufficient food for an increasing World population (1). Temperature stress and drought can result in the production of reactive oxygen species including singlet oxygen, which signals to the rest of the plant that it is in a stressful environment. Seedling development is a particularly sensitive time during the plant life cycle and seedling damage is a major cause of crop loss. We have shown that singlet oxygen production in seedlings has a similar transcriptional signature to heat stress (2) and we hypothesise that singlet oxygen signalling from the chloroplast sends an SOS signal to the seedling that permits acclimation to environmental stresses. In this project we will test this hypothesis by examining the ability of Arabidopsis mutants (e.g. 3) compromised in SOS to withstand different stress regimes including heat and drought. We will then use our Arabidopsis findings to investigate the SOS response in important crop species including wheat and rice. For full project details visit the Inspire project page.

Phytoplankton are often considered as drifters that are at the mercy of oceanic currents. However, many phytoplankton species are motile and can exhibit motile responses to light, temperature and nutrients. The prevalence of motility as a trait (e.g. >50% of Baltic Sea phytoplankton species were classed as motile) suggests that this ability is of major ecological significance, with evidence for important roles both at the microscale (e.g. exploiting heterogeneous nutrient patches) and the mesoscale (e.g. vertical migration or formation of thin layers). However, the many aspects of phytoplankton motility remain poorly understood, making it difficult to understand the wider contribution of this trait to phytoplankton physiology and ecology.   This project will address the following major questions:  How do abundant phytoplankton groups with distinct physiologies (e.g. haptophytes, cryptophytes and dinoflagellates) differ in their motile responses to light, temperature and nutrients?  Can microbially-derived organic nutrients act as chemoattractants for marine phytoplankton?  How are these motile responses influenced by physiological status (e.g. nutrient limitation, availability of light)?  What cellular mechanisms do phytoplankton use to integrate inputs from multiple stimuli to coordinate motile responses (e.g. molecular coordination of phototaxis and chemotaxis)?  For full project details visit the Inspire project page.