IAP-24-064

Microbial ecological archaeology of Antarctic microbes through single cell genomics

Bacteria are fundamental to Earths ecosystems and play key roles in important mechanisms such as nutrient cycling, the generation of novel bioactive compounds and the decomposition of organic matter. Within Marine ecosystems bacteria are foundational to global carbon and nitrogen cycles, driving climate processes and underpin the oceans’ food webs.
The impact of climate change on these essential networks is largely unknown but is certain to be profound. This project will use single cell sorting and whole genome sequencing to bacteria isolated from well characterised Antarctic marine sediment cores to determine the current and historical microbial diversity. The application of advanced phylogenomic and computational techniques will probe the function and wider context of isolated strains.

Key focuses of the project are:

Theme 1: Single cell sorting and whole genome sequencing of bacteria from Antarctic marine sediments.

Theme 2: Big data, Phylogenomics, and ecological context.

The project is a synergy between genomic and computational method development and will provide insights into understanding microbial life and ecological resilience, the role of bacteria in biogeochemical cycles, and the historical and potential future effects of climate change on Antarctic marine microbial ecosystems.

With the successful completion of the project, the student will be skilled in advanced microbial genomics, including single-cell sorting, high-resolution genome sequencing, and bioinformatics. They will also gain expertise in Antarctic field sampling, environmental data analysis, and interdisciplinary collaboration, preparing them for careers in environmental microbiology, climate science, and biotechnological research and data science.

Cytometry/Cytomics/Single cell: We will use combinations of generic (pan) microbial species fluorescent probes to firstly identify the presence of viable and non-viable bacteria in the samples. This will be done using full spectrum flow cytometry as it also provides a unique label-free capability to assess bacterial heterogeneity by virtue of multiple autofluorescence signature measurements. We will then utilise a suit of novel, targeted fluorescent probes and attempt to uncover/appreciate the heterogeneity of bacterial subtypes within the samples. We will then transfer these stains to an advanced full spectrum fluorescent cell sorting platform that also has the capabilities to image bacteria and sort on morphological and spatially resolved signal features. The sorted samples will then be subject to single or bulk genomic analysis to confirm, correlate and explore subtypes. The use of such technologies in this context is, to our knowledge, highly innovative.

Comparative genomics will be a central approach to uncovering how Antarctic marine bacteria have evolved in response to their unique environmental pressures. By analysing genomes of individual cells from sediment layers representing different historical periods, the student will compare genetic adaptations that have allowed bacterial populations to thrive or decline in this extreme environment.

The current best practices for bacterial population genomics – metagenomic methods, analyse aggregate DNA from environmental samples, which can obscure the genomes of individual species or strains, particularly in low-abundance or highly similar taxa. This pooling can mask subtle genetic distinctions and adaptation patterns, especially where rare or functionally distinct bacteria play critical ecological roles. Additionally, metagenomics faces significant challenges in detecting horizontal gene transfer (HGT), a major mechanism through which bacteria evolve and acquire adaptive genes, as HGT signals are often diluted or misattributed by the metagenomic computational approach.

Single-cell sequencing provides the unique advantage of isolating and sequencing individual bacterial cells, enabling clear resolution of HGT events. By examining the genomes of single cells rather than pooled community DNA, we can identify instances where genes have been acquired from unrelated taxa, pinpointing the exact bacterial lineage and cellular context of HGT. This is especially relevant in the Antarctic environment, where HGT may drive critical adaptations such as antifreeze proteins, osmoprotectants, or antibiotic resistance, which are key to survival in cold, nutrient-limited, and high-stress conditions. The precision of single-cell sequencing reveals not only the occurrence of HGT but also its role in rapid adaptation, as specific genes are acquired and integrated into bacterial genomes to enhance survival and ecological fitness in response to environmental pressures.
Correlating high-resolution single-cell genomic data with environmental factors (such as historical temperature, salinity, and nutrient levels) will reveal how Antarctic bacteria have adapted to historical climate shifts. By linking specific adaptations, including HGT-acquired genes, to environmental events documented by BAS, the project will reconstruct how microbial communities evolved alongside changing conditions in the Southern Ocean. This cell-specific data matched with environmental change offers insights into microbial resilience, critical for predicting responses to future climate shifts.

By overcoming traditional metagenomics’ limitations through single-cell sequencing, this project provides detailed insights into rare taxa, niche adaptation, genome reduction or expansion, and HGT in Antarctic bacteria. This approach enables a nuanced understanding of bacterial resilience and specialization, uncovering previously hidden ecological dynamics essential for adaptation in extreme environments.

Year 1

Foundational

Literature Review – comprehensive review of Antarctic microbial populations, single cell genomics and bacterial sequence analysis. Familiarisation with Antarctic marine sedimentology, ecology and environmental context.
Training – Initial focus on FACS sorting and sample handling, genome sequencing and analysis, and collaboration with BAS for sediment core processing and sampling techniques.
Preliminary Sample Analysis – Initial sorting of environmental bacteria from Antarctic marine sediments.

Year 2

Theme 1

Antarctic sediment cell sorting – cytometry of Antarctic samples based on best-practices developed in Y1.

Genome Sequencing – Genome sequencing (Illumina short read and Nanopore long-read sequencing) of sorted and amplified single cell genomes.

Initial Computational Analysis – Application of variant calling pipelines for phylogenomic reconstruction and comparative genomic analyses including investigation of pangenome and core virulence and metabolic genes.

Output: Literature review – Cytomics of environmental bacterial communities

Year 3

Theme 2

Data Expansion – manual curation of publicly available genome sequence data set to determine the global context of identified taxa.

Phylogenomic and in-depth Computational Analysis – Phylogenomic analyses and sequence clustering for high resolution community structure analysis. Analysis of gene degradation through Hidden Markov Model comparison of coding sequences

Orthogonal Analysis – for example – functional profiling of computationally identified genes of interest, metabolomic profiling of isolated strains etc.

Output: Manuscript – population structure of Antarctic bacterial communities

Year 3.5

Consolidation

Thesis Writing – preparation and submission project thesis

Output: Manuscript – Ecology and Evolution focus

The student should have a degree in Biological Sciences or Similar and an interest in bacterial evolution, method development and data science. Maths A level would be beneficial.

Core handling, sample preparation and processing, relevant sedimentological and chronological analyses.

Cell Sorting: (above)

Genome Sequencing: DNA extraction and QC, DMA amplification and library preparation for whole genome sequencing as well as sequencing using Oxford Nanopore sequencing

Data Analysis: Some experience of computational analyses would be desirable but not essential as the student will be guided through appropriate resources to undertake the project

This project can be completed using existing marine sediment cores. Although not an essential part of the project, if practicable, every effort will be made for the student to participate in a future Antarctic research cruise, providing valuable experience in polar fieldwork and ship-based research skills.