Research

Linking fine-scale microbial diversity to ecosystem functions

Resolving genome and community dynamics from environmental change by applying newly-developed tools to complex microbiomes.

Summary

Project Summary.

Project Lead: Chris Quince

Funding:

This research is supported by the UKRI Biotechnology and Biological Sciences Research Council (BBSRC).

Earlham Institute Strategic Programme Grant Decoding Biodiversity BBX011089/1 and its constituent work package BBS/E/ER/230002C.

Microbial communities, also known as microbiomes, play a crucial role in various aspects of health and the environment.

At the Earlham Institute we’re applying a diverse set of methods and applications to the study of microbiomes that scale in complexity across human health, biotechnology, and agriculture.

Our goal is to understand the underlying principles of microbial community assembly and function, identifying common aspects across different systems. Our work focuses on three key areas:

High-resolution longitudinal microbiome dynamics
Revealing eukaryotic diversity of soil
Linking microbial genomic diversity to community function

On short ecological timescales, the microbial lineage is the fundamental unit of diversity in a microbiome. Over longer evolutionary timescales and increasing recombination rates, individual genes and gene cassettes may become effectively independent evolving units.

As part of the Decoding Biodiversity strategic programme, we have developed tools that we will apply to the study of complex microbiomes in order to unravel the dynamics of microbial communities over time, and connected to environmental factors.

We are using pangenomics to connect genes to genomes and determine how these two units interact during community assembly and coevolution.

Detail

Details.

High-resolution longitudinal microbiome dynamics

We are using our expertise and technology platforms to apply long, accurate reads at depth in order to characterise - to the lineage genome level - individual microbial communities, and using these resulting genomes to enable profiling from less accurate reads.

This will enable us to quantify the importance of in situ evolution versus immigration as a means of generating new diversity across systems, and track AMR genes moving through communities - determining the significance of the commensal gut microbiota as a resistance reservoir.

The reliability of large-scale short read MAG collections is of relevance to researchers in diverse microbiome fields.

Revealing eukaryotic diversity of soil

Soil is probably the most diverse microbiome on the planet. It has been estimated that a single gram of soil may harbour up to 50,000 different prokaryotic and eukaryotic species and many of these will be in multiple strains. Resolving genomes from metagenomes at this scale, has hitherto proved impossible.

We are addressing this challenge, one that is vital given the critical role these microbes play in making minerals, such as nitrogen and phosphorous, available to plants.

Working with our partners at UK CEH, Rothamsted Research, and the Quadram Institute, we will provide the first comprehensive metagenome-assembled genome collection, revealing the eukaryotic genomic diversity of soil for the first time and informing researchers as to the best methods for profiling soil microbial communities.

Link microbial genomic diversity to community function

Microbial ecosystems support the growth of their members through essential internal and external functions - for example, providing vital nutrients to their host or Nitrogen to plants.

Stable and resilient ecosystems often have several layers of functional redundancy (the presence of multiple species or groups that perform similar roles), which ensures that diversity loss does not lead to loss of vital ecosystem functionality.

We are exploring the functional importance of fine-scale microbial diversity,to improve our understanding of the functional relevance of microbiome diversity.

Tools and data

Collaborators

Impact statement.

We will develop tools and technologies tailored to in-field and in-situ analysis of microbial communities for diverse applications in agriculture, environmental monitoring, and process engineering.

Analysis of soil communities will feed into the development of soil health indicators for better agronomy and land management, thus improving farm profitability. We will engage with stakeholders and policy makers to explore ways our tools could be incorporated into practical methods to measure soil health.