Overview

Microbial communities constitute the next research frontier, with several challenging research questions that require an interdisciplinary approach1. Among these challenges, a particularly fascinating one is the structure and function of microbial mats (and other structures)2,3. These are centimetre sized structures, containing possibly 100s of different microbes and interfacing with the external environment – they are akin to mammalian tissues and organs. Currently, we have only limited understanding of the overall and internal physiology of these structures, their individual composing microbes, and the possible metabolic and signalling systems that reside within them3. This ambitious project will start deciphering the structure and function of a particular type of these structures, through application of electrochemical, physical, metabolic, genomic, and microbiological methods.

In a recent pilot project, we discovered that samples, isolated from a freshwater reservoir, form intricate large scale structures when kept in solution and under day-night light cycles (Figure 1A). These structures are highly stable and self-sufficient, with some of them now kept for over a year without any substrate addition. We have discovered that the entire structure is motile and can respond yet to be determined signals, possibly involving light. Preliminary attempts to isolate the key species from the system suggests that the outside of the structure is dominated by a filamentous cyanobacteria, which we preliminarily assigned to Oscillatoria genus based on morphology (Figure 1B). Members of the Oscillatoria genus are commonly found in freshwater environments, yet their function and physiology is significantly under-studied. The few studies conducted on them established that certain species form this genus display electrical properties on their filaments4,5, are able to form intricate patterns in response to light6, and display biotechnologically relevant metabolic capabilities7,8

In this project, we would like to further understand the stabilising factors that lead to the formation and self-sustaining nature of these microbial structures. We would study both the entire structure through physiological and genomic means and individually isolated species for their functional roles. Once the key species are isolated, we would also attempt to re-constitute the system with the smallest number of species, to engineer a synthetic community amenable to further experiment and control9-11.

Figure 1. A: Cyanobacterial microbal mat, kept under laboratory conditions. The whole structure is motile by means of filamentous outgrowths (see on left of the structure). B: A sample from a filament grown on an agar plate and imaged with a fluorescent microscope (image shows overlay of GFP, RED, and Phase channels).

Methodology

In this project, we will use existing and sampled Oscillatoria containing microbial mats from an identified freshwater reservoir. These systems will be setup in the laboratory as self-sustaining microcosms. The system structure will be monitored over time using self-built recording system, and their development recorded. Once ‘mature’ structures are established, their overall physiology will be studied using microelectrodes to measure external and internal metabolite and oxygen gradients. Possible electrical signals and field within and across the structure will be measured using electrochemical electrodes. More invasive methods will also be applied, dissecting the structure and determining metabolite concentrations at diferente locations using metabolite extraction and subsequent determination using Mass Spec and Ion Chromatography. In parallel to these physiological/physical measurements, we will sample genomic DNA and map community composition at diferente parts of the structure. Finally, we will isolate individual key members of the community, such as Oscillatoria, and aim to study their physiology and structure in isolation (using similar techniques as listed above).  

Training and Skills

This multidisciplinary PhD project will offer a unique opportunity for the student to learn state-of-the-art techniques in microbial ecology and physiology and in particular metabolic measurements using Mass Spec and Ion Chromatography, and electrical measurements using electrodes. The student would also learn techniques in metagenomics, and species isolation and culturing. The laboratories of supervisors Prof. Soyer and Dr. Christie-Oleza (School of Life Sciences) are part of the Warwick Integrative Synthetic Biology Centre and are excellently equipped to carry out this cutting-edge project, with full access to WISB technical facilities as well as Mass Spec Technology Platform at the University of Warwick. They also have strong links with Physics and Chemistry departments, where the groups of Marco Polin and Pat Unwin respectively offer additional expertise in motility and electrical measurements.  

Timeline

Year 1: Setting up of new samples and establishing protocols for microcosms in the laboratory. Analysis of existing structures for collective motility (possible publication 1), metabolic gradients and genomic structure (possible publication 2). Initiation of specific species isolation.

Year 2:  Further analysis of metabolic gradients and establishment of electrical measurements. Developing electrical patterns and their link to redox metabolism (possible publication 3). Establishment of isolated species in the lab and study of their physiology and motility.

Year 3: Continued analysis of mat structures, with emphasis on self-sustaining nature of the system. Continued analysis of isolated species with focus on motility and metabolism (possible publication 4). Thesis write up and exploration of future directions with grant and fellowship development.

Partners and collaboration (including CASE)

Besides the collaboration between the Soyer and Oleza groups, this project offers interaction points with the groups of Marco Polin and Pat Unwin (both at UoW). From an industrial perspective, the project might lead to links with Seven Trent Water, where the samples will be collected from and where the PI has already ongoing interactions through a different project.

Further Details

Potential applicants are invited to contact Orkun Soyer (O.Soyer@warwick.ac.uk) for more details and to express an interest in the project.