Bacteria: our geo-hazard defence soldiers

Soil is a large terrestrial biodiversity pool that delivers critical ecosystem services. The biological and biochemical processes that occur in soils influences their compositions, mineralogy, fabric, strength, stiffness, and permeability. Conventional geotechnical practice considers that soil is an inert construction material and its engineering properties do not change with time. However, soil is a living ecosystem, and its engineering properties naturally change as a stable ecological system is gradually established following initial construction. Up until very recently, when biogeotechnics emerged as a field of study, biological activity was rarely acknowledged, except when it impacted negatively on geotechnical properties of soils. It is now recognised that some of those microorganisms’ activities could be harnessed to solve problems in geotechnical engineering. Over the last couple of decades, microbial applications have been explored more widely.

The physical effects of climate variability and change will affect infrastructure networks but will also play an important role in building resilience to these impacts. According to the Geological Society, geo-hazards cost billions to the UK economy each year; as well as occasional injury or loss of life and even poses significant threats to cultural and natural heritage sites. Amongst the most common natural geo-hazards experienced in the UK are landslides and floods. Impacts related to changes in heavy precipitation events leading to floods and landslides have increased in the UK and are projected to increase further in the future due to changing climate. Ensuring climate resilience of infrastructures can help minimise direct losses and reduce the indirect cost of damage since many of these changes are inevitable even if we achieve carbon neutrality.

The aim of this project is the understanding of key biological soil processes to develop nature-based solutions for mitigating ‘diffuse’ geotechnical hazards. This will be achieved by engineering the soil through bio-chemical processes involving bacteria with the added value of carbon sequestration and biodiversity enhancement. In order to achieve the objective proposed, the research will focus on understanding key microbiological activities that can be applied to mitigate flood embankments failures.

To better illustrate the innovative aspects of the research proposed, the fundamental mechanisms leading to failure of flood embankments is briefly introduced. Major mechanisms of failure of flood embankments differ depending on the material forming the embankment. For the case of coarse-grained earthfill, water flows through the embankment increasing the degree of saturation (and the pore-water pressure) at the toe eventually triggering failure on the landside. For the case of fine-grained earthfill, waterfront hardly penetrates the embankment. However, if water overflows, inward infiltration occurs at the landside slope, and this triggers the formation of a head-cut and initiate the breaching. Remedial measures should therefore aim at reducing water infiltration by, for instance, making the soil surface hydrophobic.

To make surfaces hydrophobic, binders such as mucilage or Exopolysaccharides (EPS) producing bacteria will be investigated. In addition, the process of decomposing plant by saprophytic bacteria will also be looked at, since it leads to the release of wax-like complex organic acids that form a coating on the particles of soil, repelling in turn the water due to their apolar nature.

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Bacteria the geohazard soldier


We will seek to investigate bio-chemical processes already occurring in the soil and their direct and indirect interaction with the local ecosystem – this is a less invasive approach with more chances of success. We will avoid the use of foreign bacteria, which could compete with native species resulting in unpredictable effects in terms of soil biodiversity.

Firstly, in order to make the research practicable and attainable, efforts will be concentrated on understanding key points associated with biological activity responsible to the formation of hydrophobicity in soil surface.

Since soil type can play a role into the biological process. Thus, as a starting point, soil collected at the BIONICS embankment will be used.

The soil material collected will be assessed microstructurally (Scanning Electron Microscopy – SEM, X-ray Diffraction – XRD among other imaging techniques) and hydraulically (hydraulic conductivity, Soil Water Retention Curve – SWRC). This information will be used as reference.

Of equal importance is the bacteria to be used in the inoculation process. Bacteria present in the soil samples will be identified through molecular and nonmolecular methods; an informed decision will then be made, based on previous studies, to select bacteria for use in the inoculation process. At first soil will be sterilized and inoculated with the selected bacteria. Eventually, the process will be repeated without sterilizing the soil.

The ability of the bacteria to induce soil hydrophobicity will be assessed microstructurally through SEM, XRD and other imaging techniques and quantitatively through water repellence tests, SWRC, hydraulic conductivity, and infiltration mock-up Electrical Resistivity Tomography (ERT) instrumented column tests.

Through the information collected and observed in experimental tests, numerical stability assessments will be carried out to investigate whether the hydrological and hydraulic parameter changes can stabilize flood embankment structures.

Also based on the information gathered throughout the microstructural testing, a conceptual framework will be proposed to account for key biological activities affecting soil geotechnical properties over time hence soil hydro-mechanical behaviour.

Project Timeline

Year 1

Task 1.1. Literature review
Task 1.2. Sample collection at Paull Holme
Task 1.3. Identification of bacteria
Task 1.4. Bacteria selection
Task 1.5. Selection of nutrient growth media for bacteria cultivation
Task 1.6. Microstructural characterisation of block samples collected
Task 1.7. Hydraulic characterisation of block samples collected
MS 1: Characterization of microorganisms present in soil samples, bacteria selection and cultivation
MS 2: Microstructural & hydraulic characterisation of block samples collected

Year 2

Task 2.1. Sample inoculation
Task 2.2. Microstructural investigation
Task 2.3. Hydraulic investigation
Task 2.4. Mock-up test
MS 3: Microstructural & hydraulic assessment of inoculated and sterilised samples
Deliverable 1: Paper submission to Peer-reviewed Int. Journal

Year 3

Task 2.1. Sample inoculation
Task 2.2. Microstructural investigation
Task 2.3. Hydraulic investigation
Task 2.4. Mock-up test
MS 4: Microstructural & hydraulic assessment of inoculated and non-sterilised samples

Year 3.5

Task 4.1. Stability assessment
Task 4.2. Development of conceptual framework
Deliverable 2: Paper submission to Peer-reviewed Int. Journal
Deliverable 3: PhD Thesis

& Skills

The School of Engineering requires each student to collect at least 60 PGRDP credits, corresponding to attendance of in-school delivered workshops, taught modules and other activities. Training is provided through five mechanisms: (i) a programme of taught modules; (ii) internal training ‘workshops’ that focus on key research skills and techniques; (iii) input from supervisors; (iv) School and research group seminars by visiting and internal speakers and presentations by postgraduate students themselves; and (v) external workshops.

In addition to generic training offered by the University, the School provides training through a series of in-house ‘workshops’. Engineering research postgraduates normally take the following Workshops: ‘Scientific Writing’, ‘Research Ethics (Theory)’, ‘Data Management’, ‘Time management’, ‘Document Management’, ‘Introduction to Learning and Teaching’ during their first year.

The student will benefit from the wide range of taught modules associated with MSc courses in ‘Engineering Geology’, ‘Geotechnical Engineering’ and ‘Agriculture and Environmental Science`. Modules particularly relevant for the project are ‘Ground Investigation, Contamination, and Improvement, ‘Geohazards and Deformation of the Earth’ and ‘Ecosystem Management`. Most of these modules are delivered in one intensive week so well suited for PhD students.

Bespoke technical training will also be provided by the research supervisors (DNA sequencing, ERT data processing and interpretation, and other experimental techniques as required) and by attending external workshops.

References & further reading

Kim et al (2019) DOI: 10.12989/gae.2019.17.5.485
McPherson et al (2018) DOI: 10.3791/57932
Beckett et al. (2016) DOI: 10.1051/e3sconf/20160911011
Doerr et al (2006) DOI: 10.1111/j.1365-2389.2006.00818.x

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