IAP-25-139

A beneficial plant-microbial interaction: the ecology of flax retting.

This project investigates the microbial ecology of flax retting as a natural decomposition process with implications for microbial community dynamics, water quality, and sustainable fibre production. Natural plant fibres, including flax, were historically valued for their utility and sustainability to produce textiles with a wide range of applications, but now make up only a small fraction of global fibre production. Instead, there has been a shift towards textiles made from synthetic fibres, which has led to unwelcome environmental consequences including oil consumption, greenhouse gas emissions, and microplastics pollution. One major barrier to the wider industrial adoption of flax fibres is the retting process, which separates useful bast fibres from plant stalks. Retting is typically done in two ways: Dew/Field Retting that relies on natural microbial decomposition in the field and Water/Pool Retting that submerges plant material in water. Water retting produces higher-quality fibres but generates environmentally problematic effluent. Therefore, dew retting is more common despite being climate dependent and yielding inconsistent fibre quality. Despite its limitations, dew-retting can still produce fibres suitable for novel and high-value non-textile applications such as biocomposites and feedstocks for biochemical synthesis.
Microorganisms involved in retting use a complex mix of enzymes to selectively break down different plant cell wall components. This study will contribute to understanding how microbial ecosystems form and respond to controlled environmental inputs with the aim of improving retting efficiency for consistent fibre quality and safe sustainable practise. Historically, microbial studies relied on culture-based techniques, which only capture a small fraction of microbial diversity. Recent developments in high-throughput sequencing (HTS) and environmental DNA have revolutionized the study of microbial communities.
The field of retting microbiomes is in its infancy with a recent systematic review we conducted (July 2025) finding just 13 studies that applied sequencing approaches targeting bacterial or fungal retting communities, only five of which had accessible sequencing data. These studies applied metabarcoding that uses conserved genetic markers (e.g. 16S rRNA for bacteria, ITS for fungi) to identify and quantify microbial taxa, providing insights into both the taxonomic composition and functional potential of retting microbiomes. Despite, the limitations and biases inherent in metabarcoding experiments including: sampling inconsistencies, DNA extraction variability, PCR amplification errors, sequencing platform differences, bioinformatic pipeline discrepancies, they were shown to be a powerful tool for understanding microbial communities.
We propose to draw upon these lessons and generate new high-confidence insights by applying best-practise approaches to characterise and compare the microbial communities associated with dew and water retting of flax in a single study. Our approaches will for the first time in this field: include mock communities in experimental designs to assess data quality; use sufficient replication to account for variability and outliers, use relatively unbiased metagenomics sequencing, and compile comprehensive reporting standards to enhance reproducibility and transparency. Armed with this knowledge, we will attempt to adjust retting conditions to direct microbial community assembly to improve fibre quality and consistency and effluent biosafety. The work supports NERC’s goals by addressing biodiversity, pollution mitigation, and the development of nature-based solutions for sustainable materials.

To achieve the aim of objectively characterising and comparing microbial communities involved in dew and water retting of flax, experiments will be designed that include both retting treatments, with suitable replication across different time points capturing early, mid, and late retting stages. Appropriate mock communities will be included at all steps to assess sequencing and analysis accuracy. Later experiments will be added to control for other variables such as cultivar, harvest time, and environmental conditions. Based on initial findings, microbial inoculants or environmental adjustments (e.g., moisture, pH) will be tested for their ability to steer microbial community assembly and improve. retting outcomes. Comprehensive documentation of methods and metadata following MIEM guidelines will be kept, and raw data and analysis scripts will be deposited in public repositories (e.g., NCBI SRA, GitHub).

Year 1

Pilot experiments will be done to guide final experimental design, build the bioinformatics pipeline and data management plan, and to develop proficiency with the methods. Training will be gained in molecular biology techniques, high-throughput sequencing, and bioinformatics tools.

Year 2

Full-scale retting experiments to understand the environmental factors that influence microbial communities and their function will be performed by collecting plant, soil, and water samples across multiple time points, preparing sequencing libraries (metabarcoding, followed by more targeted metagenomics), and conducting sequencing processing for taxonomic and functional profiling . This will generate results for publication and/or conference presentation.

Year 3

Taxonomic and functional data will be further integrated to identify key microbial indicators. Targeted interventions (e.g., microbial inoculants or environmental adjustments) will be tested to evaluate effects on fibre quality (colour, length, fineness, tensile strength, etc.) and effluent biosafety (final microbial load, total organic carbon).

Year 3.5

Data analysis will be finalised to complete thesis. Manuscripts will be submitted to peer-reviewed journals. Findings will be presented at national/international conferences in the field.

This project will provide experience in microbial ecology and plant–microbe interactions, with a focus on fibre crop systems and in sustainable biotechnology, particularly in optimizing microbial processes for industrial applications like fibre retting. Both Durham and UKCEH have fully equipped molecular labs and in-house facilities for HTS. Both institutes will provide specialist training in experimental design and reproducibility standards in environmental microbiology, high-throughput environmental DNA sequencing (HTS), and bioinformatics analysis.