UK Meeting on Soil-Bio Interactions and Engineering

Kenichi Soga, University of CambridgeSteven Banwart, University of SheffieldRichard Whalley, Rothamsted Research

“Biotechnologies for manufacturing insitu systems”6 July 2007

At Rothamsted Research

Geological and Geotechnical Engineering in the New Millennium:

Opportunities for Research and Technological Innovation

Geo-Knowledge and Technology Development Needs (US National Research Council, 2006)

• Better ability to “see into the earth”• Better sensing and monitoring methods• Better understanding and prediction of long term behavior• Better characterization of properties and variability• Better ability to deal with materials between hard soil and soft rock• Better understanding of biogeochemical processes• Better ground improvement materials and methods• Better understanding of the effects of extreme loadings and

environments• Better geotechnical data bases and information systems

Biotechnology• Cumulative effects can shape

the earth and impact properties and behavior

• 109 to 1012 microorganisms per kg in upper few m

• Processes work on small scale and in short times

• Microorganisms are same in size as silt and clay

• Processes and effects– Capture inorganic

compounds from solution– Precipitate inorganics– Release enzymes and

proteins that change pH and chemical conditions

– Change mineral characteristics

Some Possibilities• Stabilize liquefiable soils• Self-healing infrastructure• Grow foundations in-situ• Preconditioning of soil and

rock foundations prior to excavation, tunneling, and mining.

Bio-Soil Interactions & Engineering Workshop

April 1April 1--4, 20074, 2007

MIT Endicott HouseMIT Endicott HouseBoston, MA, USABoston, MA, USA

Kenichi SogaSteven BanwartRichard Whalley

Jason DeJongKlaus NussleinCarlos SantamarinaJames Mitchell

Program Summary

Sunday, April1, 2007Arrival, Check-in, and Welcome ReceptionDinner, Vision & Scope, and Introductions

Evening Lecture: “Current Boundaries and Needs of our Disciplines” – Geotechnical

Monday, April 2, 2007Geotechnical Engineering Lectures, Poster Presentations, and Discussion

Microbiology & Geochemistry Lectures, Poster Presentations, and Discussion

Evening Lecture: “Current Boundaries and Needs of our Disciplines” – Microbiology & Geochemistry

Program Summary, continuedTuesday, April 3, 2007

Soil Science & Geoenvironmental Lectures, Poster Presentations, and Discussion

Process Monitoring & Measurements – the Interdisciplinary Toolbox

Brainstorming Breakout SessionsDiscipline – State Variable and Hard ScienceInterdisciplinary Research Application

Wednesday, April 4, 2007Interdisciplinary Breakout Sessions (continued)Synthesis of Research Opportunities LectureSynthesis of Educational Opportunities

Soil, Our Most Important Resource

• All terrestrial life depends on it– It’s where we look for life

on other planets• We are wasting it

– >18% reduction in organic matter in UK since 1985

– 2.2M Tonnes lost to erosion each year in UK

– Globally, at current loss rates, there is about 60 years of productive topsoil left

POST report, July 2006Env. Agency 2004 report

(Ian Young 2007)

The Future?

(modified withoutpermission from Hayward Baker)

Brina Mortensen

≈1000 μm ≈200 μm ≈100 μm

Ligh

t MIC

P

Cem

ent

Hea

vy M

ICP

C

emen

tU

ntre

ated

Willem van der Zon, GeoDelft

Jason DeJong

Microbiologically Induced Calcium Carbonate Precipitation (MICCP) Process

• Bacillus (Sporosarcina) pasteurii−Gram+ bacillus− Facultative anaerobe−Common in soil− Endospore former −Urease producer− alkalophile

Jason DeJong

Flow

Transformation Feldspar into clay

Fermentation and EPS forming

Capturing of clay particles

Biomass clogging

BioSealing

Hypotheses of mechanism

Waldo Molendijk

Identify and Localize In Situ

Klaus Nusslein

Geotechnical-Biological Compatibility

Microbe – Soil Particle Size Relationship

(modified from Mitchell and Santamarina, 2005)

Å nm μm mm

atoms

small molecules

polymers

clay minerals silt sand

microorganisms cannot pass pore-throatsbut may be entrapped during formation

unhindered microbial motion and easy nutrient transport

(?) nanobacteria

eukaryaviruses

gravel

# microorganisms perparticle-particle contactdecreases, minimizing relevance

bacteria archea

Biomedical Micro/NanosystemsAshwin A. Seshia (aas41@cam.ac.uk)

We are developing technologies for the highly sensitive and minimally disruptive monitoring of biological systems. These include sensitive micromechanical sensor arrays for the label-free study of protein-protein and protein-small molecule interactions, protein crystallisation devices and microphysiometers to study and monitor the behaviour of single-cell organisms in controlled environments. Ongoing projects involve significant collaboration within the IRC for Nanotechnology and the Biochemistry and Biotechnology departments in Cambridge University. Integrated resonant output gyroscope

Microphysiometers

SU-8 sensor arrays

0 2000 4000 6000-50

0

50

100

150

200Biotin

PEG

Biotin

PEG

100 nM 1 nM

Surf

ace

Stre

ss(m

N/m

)

Time(s)

10 nM

Label free biomolecular detection

BBSRC-SuperGraSS ProjectUsing water with greater efficiency

morphogenesis

Rootingdepth

Plant water status

MAXIMISE

MAXIMISEMAXIMISE

MINIMISE

Testing: soil-penetration, effects on soil structure & water-extraction capabilities of fescues : abilities of fescues for reducing run-off

Leaf area

Absorption

Transpiration

Mike Humphreys“Reclaiming and greening land in East London intended for the Olympics in 2012”

Combining desirable ryegrass and fescue traits

Over a few generations ryegrass & fescue chromosomes during cultivar development exchange genes at very high frequencies

The initial hybrid

Mike Humphreys

“Significant change – move from reactive to proactive consideration of microbiology”

“Can we manage any biologically controlled reactions as opposed to microbiologically induced reactions?”

Stephan Jefferis

Biotechnology for Manufacturing In situ Systems

• Characteristics– Reduced uncertainty– Understanding based on 1st principles– Predictive behavior– Proactive instead of reactive control– Reduced embodied energy– Small CO2 footprint– Resource recovery & minimization of waste

Biotechnology for Manufacturing In situ Systems

• Example Applications– Nutrient control in agricultural systems– Construction systems (e.g. foundation stabilization)– Clean water (e.g. decontamination)

In 2020, we want to design with predictiveconfidence sufficient for a Safety Factor → 1

Framework• Discipline Breakout Sessions

– Participants were grouped into common discipline groups to discuss their discipline’s state variables and their ability to characterize those variables (ranked 1(min) to 5(max))

– Disciplines:• Geotechnical Engineering• Environmental Engineering• Geochemistry and Biogeochemistry• Microbiology and Biology• Agriculture and Soil Science

Discipline Synthesis

• Common Variables – Heterogeneity– Soil Structure and Pore Space Distribution– Fluid Movement and Transport– Scale Issues– Biodiversity: community composition and distribution

All of these variables lack sufficient understanding across the disciplines!

• Application Breakout Sessions

– Participants were then grouped into common applications to discuss state variables and their ability to characterize them, the national needs, and the hard science involved

– Application Groups:• Mechanical Control• Hydraulic Control• Remediation and Waste Treatment• Energy and Carbon Sequestration• Soil-Plant Interactions

http://www.sil.ucdavis.edu/workshop.htm

http://www-civ.eng.cam.ac.uk/BioSoil/

What are we going to do today?

Documents

• UK meeting details, list of participants• Boston Workshop summary• Outcomes of Application breakout session• Feedback form• Claim form

In the morning….10.20-12.30 Review documents, define priorities, develop research

ideas and identify discipline gaps

10.20 – 10.40 Energy and carbon sequestration (David Manning and Jon Lloyd)

10.40 – 11.10 Soil Plant interactions (Steve McGrath)11.10 – 11.30 Hydraulic control (Stephan Jefferis)11.30 – 11.50 Mechanical control (John McDougall)11.50 – 12.10 Remediation and waste treatment (Ian Thompson)

12.10 – 12.30 Synthesis (Steven Banwart)

Identify Research Project Titles

Objectives

(1) To review papers that were generated from the Boston Meeting and define priority areas.

(2) To develop a UK programme in this area and find if there are any discipline gaps

(3) To draft outline proposals for responsive mode research

In the afternoon…13.30 – 14.15 Further synthesis with RCs (Whalley)

Cross-councils research programme under “Planning for change”initiative.

Dr Claire Tansely (EPSRC)Dr Paul Burrows (BBSRC)Dr Frances Collingborn (NERC)

EPSRCGeotechnical and GeoenvironmentalResearchSoil mechanics

BBSRCGeneticsMolecular biologySoil Science and Soil Biology

NERCLandscape scale problems

BBSRC/ NERCSoil Science Steering committee

In the afternoon…

14.15 – 15.30 Draft outline proposals – group sessions

a. Research objectives - how will this meet the research need?b. How will this will create a step change in 5 yearsc. What do we achieve working across disciplines that we cannot

achieve working separately?d. Research tools and methods needede. Identify research and knowledge gaps - the scope of the

researchf. Rationale for cross-council funding

Next steps• Large consortiums? Individual projects?

• 20 July – KS, SB&RW visiting EPSRC/NERC/BBSRC(DEFRA?)

• 31 August – EPSRC project end date

• 21 August – KS&JD US-NSF presentations

• 20 September – US-NSF members visiting UK (EPSRC?) Discussion about Memorandum for US-UK collaborations

• 31 September – EPSRC final report

Other Actions

Living with environmental change

• Sustainable natural resources NERC– Action plans– Living with environmental change– Developing countries

• EPSRC– Energy, nanotechnology– Consortium scheme– Focus, can joint councils