Biogeochemical processes and geotechnical applications: Progress, opportunities and challenges

Abstract

Consideration of soil as a living ecosystem offers the potential for innovative and sustainable solutions to geotechnical problems. This is a new paradigm for many in geotechnical engineering. Realising the potential of this paradigm requires a multidisciplinary approach that embraces biology and geochemistry to develop techniques for beneficial ground modification. This paper assesses the progress, opportunities, and challenges in this emerging field. Biomediated geochemical processes, which consist of a geochemical reaction regulated by subsurface microbiology, currently being explored include mineral precipitation, gas generation, biofilm formation and biopolymer generation. For each of these processes, subsurface microbial processes are employed to create an environment conducive to the desired geochemical reactions among the minerals, organic matter, pore fluids, and gases that constitute soil. Geotechnical applications currently being explored include cementation of sands to enhance bearing capacity and liquefaction resistance, sequestration of carbon, soil erosion control, groundwater flow control, and remediation of soil and groundwater impacted by metals and radionuclides. Challenges in biomediated ground modification include upscaling processes from the laboratory to the field, in situ monitoring of reactions, reaction products and properties, developing integrated biogeochemical and geotechnical models, management of treatment by-products, establishing the durability and longevity/reversibility of the process, and education of engineers and researchers.

Full text

DeJong, J. T. et al. (2013). Ge
´otechnique 63, No. 4, 287–301 [http://dx.doi.org/10.1680/geot.SIP13.P.017]
287
Biogeochemical processes and geotechnical applications: progress,
opportunities and challenges
J. T. DEJ ONG1, K. SOGA2, E . K AVA Z A N J I A N 3, S. BURNS4,L.A.VANPAASSEN
5, A. AL QABANY2,
A. AYDILEK6,S.S.BANG
7, M. BURBANK8, L. F. CASLAKE9,C.Y.CHEN
10, X. CHENG11,J. CHU
12,
S. CIURLI13,A.ESNAULT-FILET
14,S. FAURIEL
15,N. HAMDAN
16,T.HATA
17, Y. INAG AKI18,
S. JEFFERIS19,M. KUO
2, L. LALOUI14, J. LARRAHONDO20, D. A. C. MANNING21, B. MARTINEZ22,
B. M. MONTOYA23, D. C. NELSON24,A. PALOMINO
25,P. RENFORTH
26,J.C.SANTAMARINA
4,
E. A. SEAGREN27, B. TANYU28,M. TSESARSKY
29 and T. WEAVER30
Consideration of soil as a living ecosystem offers the potential for innovative and sustainable solutions
to geotechnical problems. This is a new paradigm for many in geotechnical engineering. Realising the
potential of this paradigm requires a multidisciplinary approach that embraces biology and geochem-
istry to develop techniques for beneficial ground modification. This paper assesses the progress,
opportunities, and challenges in this emerging field. Biomediated geochemical processes, which
consist of a geochemical reaction regulated by subsurface microbiology, currently being explored
include mineral precipitation, gas generation, biofilm formation and biopolymer generation. For each
of these processes, subsurface microbial processes are employed to create an environment conducive
to the desired geochemical reactions among the minerals, organic matter, pore fluids, and gases that
constitute soil. Geotechnical applications currently being explored include cementation of sands to
enhance bearing capacity and liquefaction resistance, sequestration of carbon, soil erosion control,
groundwater flow control, and remediation of soil and groundwater impacted by metals and radio-
nuclides. Challenges in biomediated ground modification include upscaling processes from the
laboratory to the field, in situ monitoring of reactions, reaction products and properties, developing
integrated biogeochemical and geotechnical models, management of treatment by-products, establish-
ing the durability and longevity/reversibility of the process, and education of engineers and
researchers.
KEYWORDS: chemical properties; environmental engineering; ground improvement; remediation; soil
stabilisation
Manuscript received 2 March 2012; revised manuscript accepted 23
October 2012.
Discussion on this paper closes on 1 August 2013, for further details
see p. ii.
1Department of Civil and Environmental Engineering, University of
California, Davis, CA, USA.
2Department of Engineering, University of Cambridge, Cambridge,
UK.
3School of Sustainable Engineering and the Built Environment,
Arizona State University, Phoenix, AZ, USA.
4School of Civil and Environmental Engineering, Georgia Institute of
Technology, Atlanta, GA, USA.
5Department of Geoscience and Engineering, Delft University of
Technology, The Netherlands.
6Department ofCivil and Environmental Engineering, University of
Maryland, College Park, MD, USA.
7Department of Chemical and Biological Engineering, South Dakota
School of Mines and Technology, Rapid City, SD, USA.
8Environmental Biotechnology Institute, University of Idaho,
Moscow, ID, USA.
9Department of Biology, Lafayette College, Easton, PA, USA.
10 Department of Earth and Environmental Sciences, National Chung
Cheng University, Taiwan.
11 Department of Civil Engineering, Tsinghua University, Beijing,
China.
12 Department of Civil, Construction and Environmental Engineering,
Iowa State University, Ames, IA, USA.
13 Department of Agro-Environmental Science and Technology,
University of Bologna, Bologna, Italy.
14 Research & Development Department, Soletanche Bachy, Rueil
Malmaison, France.
15 Laboratory for Soil Mechanics, Ecole Polytechnique Fe´de´rale de
Lausanne (EPFL), Lausanne, Switzerland.
16 Department of Civil, Environmental and Sustainable Engineering,
Arizona State University, Tempe, AZ, USA.
17 Department of Civil Engineering, Nagano National College of
Technology, Nagano, Japan.
18 Geology and Geotechnical Engineering Research Group, Public
Works Institute, Japan.
19 Environmental Geotechnics Ltd and Department of Engineering
Science, University of Oxford, Banbury, UK.
20 INGETEC S. A., Bogota, Columbia.
21 School of Civil Engineering & Geosciences, Newcastle University,
Newcastle upon Tyne, UK.
22 Geosyntec Consultants, Oakland, CA, USA.
23 Department of Civil, Construction, and Environmental Engineer-
ing, North Carolina State University, Raleigh, NC, USA.
24 Department of Microbiology, University of California, Davis, CA,
USA.
25 Department of Civil and Environmental Engineering, University of
Tennessee, Knoxville, TN, USA.
26 Department of Earth Sciences, University of Oxford, Oxford, UK.
27 Department of Civil and Environmental Engineering, Michigan
Technological University, Houghton, MI, USA.
28 Department of Civil, Environmental, and Infrastructure Engineer-
ing, George Mason University, Fairfax, VA, USA.
29 Department of Structural Engineering and Department of Geolo-
gical and Environmental Sciences, Ben Gurion University of the
Negev, Beer-Sheva, Israel.
30 Office of Research, Nuclear Regulatory Commission, USA.

INTRODUCTION
Biology in the evolution of geotechnical engineering
The field of geotechnical engineering has advanced steadily
throughout history; the durability of several ancient geotech-
nical systems (e.g. Egyptian dams and canals, Greek strip
and raft foundations, and Roman bridges along the Appian
Way) testifies to a working knowledge of geotechnics by
their creators. However, formal initiation of the discipline
may be attributed to Coulomb’s definitive work on earth
pressures in the 1770s. Numerous advances in mechanics
and water flow followed Coulomb’s work, including Darcy’s
law (Darcy, 1857), Boussinesq stress distribution (1871),
Rankine earth pressure theory (1875), Mohr’s circle of strain
(1885), Reynolds volumetric behaviour (1885), and more.
Karl Terzaghi’s work, from the 1920s onwards (e.g. Terzaghi,
1924), revolutionised the discipline by developing the princi-
ple of effective stress and analyses for the bearing capacity
of foundations and consolidation of soils. Later work by
Gibson on analytical techniques (see the first issue of
Ge
´otechnique), by Taylor (1948) on dilation and interlock-
ing, by Roscoe et al. (1958) and Schofield & Wroth (1968)
on plasticity and critical state, and by many others since
then and through to the present day, have continued the
development of mechanics concepts and analysis methods
for geotechnical systems.
The natural origins of soils, and hence their variability
and changes in properties over time, result in engineering
mechanics alone being insufficient to address many practical
problems. The geologic origin of a soil, its depositional
mode and environment, thixotropic processes, and other
post-depositional phenomena must often be considered.
Early on (e.g. Terzaghi, 1955), the importance of considering
these formational and time-dependent processes was recog-
nised and addressed through the field of geology. Work by
Mitchell (e.g. Mitchell, 1975) and others in the second half
of the 20th century recognised the critically important role
of chemistry in the behaviour of fine-grained soils, and how
macro-scale performance depends directly on micro- (or
nano-) scale conditions. For example, some ground improve-
ment methods specifically target chemical changes in the
clay fabric to stabilise soils for construction (e.g. pozzolanic
changes).
Harnessing of biological processes in soils promises to be
the next transformative practice in geotechnical engineering.
For many years, the influence of plant roots on slope
stability has been recognised and exploited (e.g. Gray &
Sotir, 1996). There is now the opportunity to exploit many
chemical processes that are mediated by biology. Although
ignored for centuries with respect to geotechnical behaviour,
microbes are ubiquitous in soils at surprisingly high concen-
trations, almost regardless of saturation, mineralogy, pH, and
other environmental factors. Near the ground surface, more
than 1012 microbes exist per kilogram of soil (Mitchell &
Santamarina, 2005). At depths typical in geotechnical sys-
tems (e.g. 2 to 30 m), the microbial population decreases to
about 1011 to 106microorganisms per kilogram respectively
(Whitman et al., 1998) (for context, about 1014 bacteria exist
in the typical human body; Berg, 1996). Living organisms at
other length scales are also present. For example, worms at
larger length (cm) scales recompact soil, create preferential
drainage conditions, and otherwise impact on soil character-
istics, and spores at smaller length scales (,1ìm) can be
transported into smaller pore spaces.
A permanent biological presence (microbes have been
active geotechnical engineers for 3+ billion years, much
longer than the 0.0002 billion years for humans; Kohnhau-
ser, 2007) in soil provides opportunities for geotechnical
engineering to consider soil as a living ecosystem rather
than as an inert construction material. Biological activity in
soil can potentially explain observations in some case
histories that have troubled experts (Mitchell & Santamar-
ina, 2005) and provides the opportunity to manipulate soil
using natural or stimulated processes (as expanded upon
herein).
Emergence of bio-soils as a subdiscipline
One of the first explicit discussions of the application of
biological processes in geotechnical engineering was pre-
sented by Mitchell & Santamarina (2005), and in parallel it
was identified as an important research topic by the US
National Research Council (NRC, 2006) for the 21st century.
The first international workshop on biogeotechnical engineer-
ing in 2007 facilitated interdisciplinary discussions and
prioritisation of research topics in this emerging field
(DeJong et al., 2007). Research advanced quickly, with a
bio-geo-civil-engineering conference in 2008, and several
dedicated sessions at national and international conferences,
additional papers assessing the potential of the field (Ivanov
& Chu, 2008; Kavazanjian & Karatas, 2008; Ivanov, 2010;
Seagren & Aydilek, 2010; DeJong et al., 2011; Hata et al.,
2011), and more than 100 technical conference and journal
papers dedicated to this topic since. Research programmes
on biogeotechnical engineering are currently active in more
than 15 countries around the world.
The Second International Workshop on Bio-Soils Engin-
eering and Interactions, funded by the US National Science
Foundation, was held in September 2011 at the University of
Cambridge. This workshop assembled 35 of the leading
researchers in the field, and provided an opportunity to
assess progress to date, identify the primary challenges and
opportunities that lie ahead, and develop strategies for
advancing this rapidly developing field. This paper presents
the outcomes of the workshop, along with a perspective on
the possible role of biological processes in geotechnical
engineering, including examples of their application and a
discussion of salient issues.
POTENTIAL OF BIOLOGY TO MODIFY ENGINEERING
PROPERTIES OF SOILS
Length scales of biological processes
The processes by which biology can modify the engineer-
ing properties of soil depend on the length scale of organ-
isms, both in absolute dimension and relative to the particle
size. Multicellular organisms, ranging from plant roots down
to insects and invertebrates (e.g. ants, worms), alter soils
through both mechanical and biological processes. For ex-
ample, ants are effective at soil grading, densification, and
creating preferential flow paths (macropores); they also adapt
and optimise their efforts considering capillarity forces at
particle contacts (Espinoza & Santamarina, 2010). Similarly,
mucous excretion from worms can strengthen soil along
tunnelling paths, and help bind (geotechnically strong) faecal
pellets to such an extent that the cone penetration test (CPT)
measures the strength increase (Kuo, 2011).
Unicellular microbial organisms in soil consist primarily
of bacteria and archaea (see Woese et al., 1990, for defini-
tions of terms), which typically range in diameter from 0.5
to 3 ìm, and have morphologies that are typically spherical
(coccus) or cylindrical; the latter may be straight (rods),
curved (vibrio), or corkscrew shaped (spirilla). These are
present in soil either through entrapment during deposition
(the typical mode in fine-grained sediments offshore; Reba-
ta-Landa & Santamarina, 2006) or through migration
through pore space via hydraulic flow transport or self-
motility. Geometric compatibility between bacteria and ar-
chaea and the pore space (pore throats to be specific)
288 DEJONG ET AL.

dictates mobility (Mitchell & Santamarina, 2005; DeJong et
al., 2010; Phadnis & Santamarina, 2012) and survivability
(Rebata-Landa & Santamarina, 2006).
Unicellular activity, in general, does not affect soil proper-
ties directly. Rather, it is how biological activity locally
exploits geochemical processes, which in turn affect soil
properties. Microbe activity creates ‘microniche’ conditions
surrounding individual cells that critically alter when, where,
and at what rate geochemical processes occur. A given
geochemical process can often occur in the absence of
biological activity, and indeed, for it to occur as a microbial
process, it must be viable in the absence of biological
activity, although the rate may be exceedingly slow (i.e.
bioprocesses are often regarded as biocatalysis). However,
doing so may result in widely distributed reactions, resulting,
for example, in precipitation in the pore fluid that is subse-
quently transported outside the targeted treatment zone.
The ability of microbes to regulate processes (depending
on the specific process utilised) often stems from the uni-
cells containing the enzyme(s) critical to the geochemical
reaction. The location of the enzyme, usually within the cell
membrane or within the membrane-bound cytoplasm, regu-
lates (through diffusion or active transport) the rate at which
the reaction can occur. Increased enzymatic activity within a
given cell or an increased number of cells both increase the
bulk reaction rate. Although not widely explored to date, it
may also be possible to use free enzymes (a non-biological
approach) to improve soil properties in applications where
the treatment time is relatively brief (e.g. dust suppression;
Bang et al., 2011).
Methods of application: processes and products
Development of a biomediated soil improvement tech-
nique requires an application strategy. The two primary
strategies – bioaugmentation (where the required microbes
are injected into the soil) and biostimulation (where natural
microbes are stimulated) – build on bioremediation tech-
niques developed over the last 30+ years. While the former
has been the primary strategy used to date in exploring
geotechnical applications, the geoenvironmental field is in-
creasingly using biostimulation. Bioaugmentation is gener-
ally considered less favourable than biostimulation, owing to
the introduction of exogenous (non-native) microbes, in
some cases the permissions required, the increased costs, the
practical difficulty of uniform application in the subsurface
due to filtration of microbes (akin to filter design intended
to protect clay cores of dams), and the potential for die-off
or dormancy if the environment is not favourable for their
proliferation. Biostimulation is generally preferable, owing
to the stimulation and growth of native microbes, which are
adapted to the subsurface environment, and to the reduction
in permission difficulties. However, many challenges exist in
applying biostimulation, including obtaining uniform treat-
ment across a site, and accommodating the increased time
associated with stimulation and growth. A compromise be-
tween these two approaches may be bioaugmentation at a
low concentration followed by stimulation in situ, or ‘micro-
dosing’ (Martinez, 2012).
Geochemical processes regulated through biostimulation
or bioaugmentation often result in multiple products. The
primary product is typically the one that is designed to be
the desired outcome (e.g. calcite precipitation to bind soil
particles together). In addition, there are often additional
‘by-products’ generated by the geochemical process (e.g.
ammonium ions). The generation, transport and fate of these
by-products must be addressed, often as a waste, although in
some cases they may be repurposed for other applications
(e.g. ammonium for fertilisation of plants).
Potential improvements to engineering properties with
biogeochemical processes
Biomediated geochemical processes have the potential to
modify physical properties (density, gradation, porosity,
saturation), conduction properties (hydraulic, electrical,
thermal), mechanical properties (stiffness, dilation, compres-
sibility, swell/shrink, cohesion, cementation, friction angle,
erodibility, and soil-water characteristic curve), and chemical
composition (buffering, reactivity, cation exchange capacity)
of soils. This may be conceptualised by considering how
different biogeochemical processes may influence an assem-
blage of sand grains and/or an aggregation of clay platelets.
Biomineralisation processes that precipitate inorganic
solids (including microbially induced calcite precipitation, or
MICP) can clearly have a mechanical effect: for example,
reduction in pore space, brittle cementation at particle con-
tacts, increased fines in the pore space, and increased
stiffness. These effects will predictably result in reduced
hydraulic conductivity, increased small-strain stiffness, in-
creased large-strain strength, and increased dilative behav-
iour.
Biofilm formation, and the production of other extracellu-
lar polymeric substances (EPS), are additional biogeochem-
ical processes that can impact on soil behaviour. These
processes generate organic solids that occupy a portion of
the pore space with a soft, ductile, elastomeric-like material
that reduces pore size, reduces rearrangement of particles
during soil deformation, and increases ductility. These
changes can reduce hydraulic conductivity, and perhaps
reduce rapid strain-softening during undrained shearing.
However, property changes due to biofilm and EPS produc-
tion may be lost, and thus be applicable only for short-term
ground modification, as these living systems must be con-
tinuously nourished or their engineering performance may
become unreliable.
Biogas generation from denitrification or other biogeo-
chemical processes may enable long-term reduction in the
degree of saturation of a soil. Reduction in the degree of
saturation increases pore space compressibility, and may
thereby reduce excess pore pressure build-up during cyclic
loading, mitigating earthquake-induced liquefaction potential
in some soils.
Other processes that have been identified, but are currently
less developed, include algal and fungal growth for near-
surface soil stabilisation, bacteria and worms for methane
oxidation, biopolymers for drilling applications, organic slur-
ries for hydraulic control, and silicate precipitation.
RESEARCH ACTIVITY AND APPLICATIONS
Research activity in biogeotechnical engineering to date
has investigated many of the above potential processes, with
a significant portion of activity focused on biomediated
cementation via calcite precipitation. The following exam-
ples highlight the extent to which soil properties can be
modified or improved by biogeochemical processes. These
examples are not comprehensive, with additional references
provided.
Microbially induced calcite precipitation
Microbially induced calcite precipitation, or MICP, has
been the primary focus of research in biogeotechnical en-
gineering to date. In MICP, the creation of calcium carbo-
nate (calcite) occurs as a consequence of microbial
metabolic activity (Stocks-Fischer et al., 1999; Ramakrish-
nan et al., 2001). Calcite precipitation may be achieved by
many different processes (DeJong et al., 2010), including
urea hydrolysis (Benini et al., 1999; Ciurli et al., 1999);
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 289

denitrification (Karatas et al., 2008; Van Paassen et al.,
2010a; Hamdan et al., 2011b); sulphate reduction, inducing
dolomite precipitation (Warthmann et al., 2000); and iron
reduction, inducing ankerite and other mixed mineral pre-
cipitation (Roden et al., 2002; Weaver et al., 2011). Enzy-
matic hydrolysis of urea by microbes is the most energy
efficient of these processes (DeJong et al., 2010), and urease
activity is found in a wide range of microorganisms and
plants (Bachmeier et al., 2002). Bacillus pasteurii (American
Type Culture Collection 6453), which was recently reclassi-
fied as Sporosarcina pasteurii (ATCC 11859), an alkalophilic
bacterium with a highly active urease enzyme (Ferris et al.,
1996), has been used in laboratory studies where bioaug-
mentation has been performed to produce calcite precipita-
tion (Mortensen et al., 2011). More recently, biostimulation
of native microbes has reportedly been successful (Burbank
et al., 2011, 2012a), and the influence of competing microbe
species/processes has been explored (Gat et al., 2011).
Limited studies have also explored precipitation of other
minerals (e.g. Chu et al., 2011; Weaver et al., 2011).
Research has provided insights into MICP from micro-
metre- to metre-length scales (Fig. 1). Microscopy tech-
niques show that the calcite structure varies with treatment
formulation (Al Qabany et al., 2012), cementation occurs
preferentially at particle contacts (Chou et al., 2008; Marti-
nez & DeJong, 2009), calcite precipitation occurs directly on
or around individual microbes and their aggregates, and
cementation breakage during shearing occurs within the
calcite crystals (DeJong et al., 2011). Laboratory-scale ele-
ment tests have shown substantial (.1033) increases in
strength (DeJong et al., 2006; Whiffin et al., 2007; Van
Paassen et al., 2009; Chu et al., 2011, 2013; Al Qabany &
Soga, 2013), decreases in hydraulic conductivity greater than
two orders of magnitude (Al Qabany, 2011; Rusu et al.,
2011; Martinez et al., 2013), increases in small-strain stiff-
ness by three orders of magnitude (DeJong et al., 2006; Van
Paassen et al., 2010b; Van Paassen, 2011; Esnault-Filet et
al., 2012), and an increase in dilative tendencies (Chou et
al., 2011; Mortensen & DeJong, 2011; Tagliaferri et al.,
2011). Even after cementation degrades owing to shearing,
the reduction in pore space (or increase in solids density)
due to the precipitated calcite alters the behaviour of the
material. Re-establishment of properties following MICP
degradation from shearing can be rapid and efficient (Mon-
toya, 2012). Geophysical methods (shear wave velocity in
particular) are effective for real-time monitoring of the
cementation process, as the precipitated calcite stiffens parti-
cle–particle contacts (Al Qabany et al., 2011; Montoya et
al., 2012; Weil et al., 2012).
One-dimensional column, two-dimensional flow and three-
dimensional model tests have enabled enquiry into treatment
uniformity, formulation optimisation, and self-equilibrating
ability, as well as demonstration of conceptual ideas about
property improvement due to MICP (DeJong et al., 2009;
Martinez & DeJong, 2009; Van Paassen, 2009; Van Paassen
et al., 2009; Inagaki et al., 2011a; Tobler et al., 2012;
Martinez et al., 2013) (Fig. 1). One-dimensional column
experiments have shown pulsed flow injection and flow
reversal to increase uniformity, lowering the molar ratio of
urea to calcium to reduce by-product formation, and geophy-
sical seismic measurement to spatially monitor improvement
(Martinez, 2012). Two-dimensional models of field treatment
patterns have explored the efficacy of bioaugmentation com-
pared with biostimulation, and linkages between microbial
distribution, ureolysis activity, shear wave velocity and total
precipitated calcite (Al Qabany, 2011; Martinez, 2012). Scale
model tests have demonstrated the effectiveness of MICP in
reducing wind- and water-induced erosion (Bang et al.,
2011), improving resistance to liquefaction (Inagaki et al.,
2011b; Montoya et al., 2013), creating impermeable crusts
(f) (g)(e)(b) (c) (d)
350
300
250
200
150
100
50
0
0 3 6 9 12 15
Axial strain, : %εz
Deviatoric stress,: kPaq
(h)
Experimental untreated
Experimental treated
Numerical untreated
Numerical treated
(i) (j) (k) (l) (m)
km
μmmm
Length scale cm
dm m
(a)
cm
Fig. 1. Overview of upscaling of MICP: (a) urease enzyme structure housed within microbes (Benini et al., 1999); (b) Sporosarcina
pasteuri microbe (image supplied by DeJong); (c) bacterial impression within precipitated calcite (Martinez & DeJong, 2009);
(d) structure of precipitated calcite (Day et al., 2003); (e) MICP-cemented sand grains (Chou et al., 2008); (f) CT scan of MICP-cemented
sand (image supplied by DeJong); (g) MICP-cemented triaxial specimen (Mortensen et al., 2011); (h) modelling of MICP triaxial
compression test (Fauriel, 2012); (i) 1D column tests (Martinez, 2012); (j) radial flow treatments (Al Qabany, 2011); (k) MICP
impermeable skin for retention basin (Stabnikov et al., 2011); (l) MICP treatment of 100 m3sand (Van Paassen et al., 2010b; Esnault-Filet
et al., 2012); (m) field trial
290 DEJONG ET AL.

for catchment facilities (Stabnikov et al., 2011; Chu et al.,
2012), healing/stabilising cracks in concrete and masonry
(Ramachandran et al., 2001; Bang et al., 2010; Yang et al.,
2011), treating waste (Chu et al., 2009), immobilising heavy
metals (Fujita et al., 2004, 2008, 2010; Hamdan et al.,
2011a; Li et al., 2011), and performing shallow carbon
sequestration (Manning, 2008; Renforth et al., 2009, 2011;
Washbourne et al., 2012). MICP has also been shown to
increase cone tip resistance (Burbank et al., 2012b).
Modelling of MICP requires coupling of biological, chem-
ical, hydrological, and mechanical processes. Modelling ef-
forts have generally focused either on prediction of biogeo-
chemical processes (Barkouki et al., 2011; Fauriel & Laloui,
2011b, 2012; Laloui & Fauriel, 2011; Martinez et al., 2011;
Van Wijngaarden et al., 2011, 2012; Martinez, 2012) and
calcite distribution, or on prediction of the mechanical be-
haviour of biocemented soils (Fauriel & Laloui, 2011a;
Fauriel, 2012). Models to date have captured and predicted
biogeochemical processes, provided first-order predictions of
precipitated calcite distributions, and captured the mechanic-
al behaviour of MICP-treated sand (Fig. 1(h)).
As discussed later in the section on field applications, two
field trials using MICP have been performed to date.
Biofilm formation
Biofilms form when microorganisms adhere to a surface
and excrete EPS as part of their metabolism. This ‘slimy’
EPS enhances further attachment of more microorganisms
and other particles, thereby forming a biofilm that can affect
the physical properties of soils (Fig. 2(a); Banagan et al.,
2010). Close to the surface in riverine and marine environ-
ments, biofilms play an important role in trapping and
stabilising sediments, and increasing the resistance to erosion
(Stal, 2010). In the subsurface, it has been shown already that
the growth of biofilms can reduce hydraulic conductivity
(Slichter, 1905), a process referred to as bioclogging. Much
of the research on bioclogging is focused on preventing and/
or removing the clogging material (Howsam, 1990), for
example by flushing with formaldehyde, in order to restore or
maintain the functionality of wells or drains (Baveye et al.,
1998). However, some researchers have found that biofilm
formation in soil could also be advantageous (e.g. Mitchell et
al., 2009). For example, Talsma & van der Lelij (1976)
observed that water losses from rice fields were limited,
owing to bacterial clogging. Attempts have been made to use
bioclogging to decrease hydraulic conductivity in situ beneath
and within dams and levees, to reduce infiltration from ponds,
to reduce leakage at landfills, to plug high hydraulic conduc-
tivity layers surrounding oil bearing layers, and to control
groundwater migration with subsurface barriers (Fig. 2(b);
Seki et al., 1998; James et al., 2000; Lambert et al., 2010).
Biogas generation
Biological activity in the subsurface is frequently accom-
panied by the development of discrete gas bubbles in other-
wise saturated environments. A variety of gases can be
produced by microbial processes (e.g. carbon dioxide, hydro-
gen, methane and nitrogen), with both the organism and the
oxidative/reductive environment of the pore fluid influencing
the ultimate products of the reaction. For example, aerobic
microbes (obligate or facultative) use oxygen as the terminal
electron acceptor during the process of microbial respiration.
Typically, an organic molecule is used as the carbon and
energy source, and the products resulting from the reaction
include water and carbon dioxide. By contrast, anaerobic
respiration by methanogenic archaea occurs in the absence
of oxygen, and results in the production of methane and
often carbon dioxide (i.e. part of the carbon is oxidised to
carbon dioxide and part is reduced to methane). The process
uses part of the carbon, as opposed to oxygen, as the
terminal electron acceptor. Respiratory denitrification occurs
through the reduction of nitrate, producing nitrogen and
carbon dioxide gas as the end products of the reaction in
environments that have high ratios of nitrate to carbon.
Numerous laboratory studies have demonstrated the feasibil-
ity of producing microbially generated discrete gas bubbles
at the bench scale, with a review of the processes given in
Rebata-Landa & Santamarina (2012), and shaking-table tests
provided by He et al. (2013). In practical terms, the pre-
sence of gas bubbles within an otherwise saturated soil
results in a decrease in the measured P-wave velocity; this
decrease is transient in coarse-grained soils, but not in fine-
grained soils that can trap the generated gas bubbles (Fig.
3(a); Rebata-Landa & Santamarina, 2012). Even small re-
ductions in the level of saturation of a soil are known to
significantly reduce a soil’s susceptibility to liquefaction
(Fig. 3(b); e.g. Sherif et al., 1977; Chaney, 1978; Yoshimi et
al., 1989; Ishihara et al., 2001; Pietruszczk et al., 2003).
Biopolymers and EPS
Both in situ and ex situ applications of biopolymers for
soil improvement have been explored. Biopolymers mixed
with soils have been shown to reduce hydraulic conductivity
(a)
0
50
100
150
200
250
300
350
400
450
0 102030
Discharge flow: l/h
Time: days
(b)
Drain 2
Drain 1
Fig. 2. Example results of biofilm treatment for permeability
reduction; (a) laser confocal fluorescence microscopy image of
biofilm-coated sand grains; (b) field data showing reduction in
seepage flow in a dam following biofilm hydraulic conductivity
reduction treatment (Blauw et al., 2009; used by permission)
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 291

and increase shear strength (Kavazanjian et al., 2009;
Nugent et al., 2010). Martinez et al. (2011) showed that
mixing silt with 0.3% (by weight) xanthan gum, a commer-
cially available biopolymer, can reduce saturated hydraulic
conductivity by two orders of magnitude (down to
,106cm/s) and increase the drained shear strength by up
to 30%. The observed reduction in hydraulic conductivity is
a function of soil grading and the applied hydraulic gradient
(Jefferis, personal communication, 2012). Biopolymers are
used in biodegradable drilling muds owing to their propen-
sity for bioplugging (Hamed & Belhadri, 2009). They have
also been used as temporary excavation support fluids to
create permeable reactive barriers for groundwater remedia-
tion, with biopolymer degradation accelerated by the intro-
duction of a high-pH ‘enzyme breaker’ after placement of
the permeable reactive material in an open trench (Sivavec
et al., 2003). Khachatoorian et al. (2003) observed per-
meability decreases in less than 2 weeks in sand treated with
a biopolymer slurry. Some investigators have explored in-
creasing soil shear strength in situ by biopolymer generation
(e.g. Cabalar & Canakci, 2005). However, most investiga-
tions of applications of in situ biopolymer growth and EPS
generation have focused on reduction in hydraulic conductiv-
ity to form hydraulic barriers (e.g. Wu et al., 1997; Bonala
& Reddi, 1998; Seki et al., 1998). Furthermore, there are
many case histories of clogging of filters in dams, landfills
and water treatment plants caused by the growth of biofilms
(Cullimore, 1990; Ivanov & Chu, 2008). For example, in
October 1985 an investigation of subsurface drain clogging
at the Ergo Tailings Dam (ETD) in South Africa, after only
6 months’ service, revealed that the geotextile drain filter
was clogged by the growth of arsenic-resistant microorgan-
isms (Legge et al., 1985).
Mechanical processing by marine worms
Many deep ocean clays are subject to thousands of cycles
of biological activity that transform virgin material into
processed material. Burrowing invertebrates (worms), through
the process of bioturbation, digest sediment that has fallen
through the water column to the seabed. They are one
example of a biological agent that has been active for
millennia. During feeding, the ingested sediment, containing
clay, organic matter, foraminifera, diatoms, shell fragments
and other detritus, is processed in the gut, removing material
of nutritional value. The remaining material is expelled by
the worm’s hind gut (Barnes et al., 1988) in the form of
faecal pellets that are compacted and bound by mucus (see
Fig. 4(a)). These resulting pellets are significantly stronger
than the material initially ingested, and have undrained shear
strengths of between 1 kPa and 12 kPa (Kuo & Bolton, 2012).
If sufficiently numerous, these pellets can produce measurable
increases in bulk sediment strength within the top few metres
of deep ocean clay sediments. The sedimentation rate in
many of these locations may only be of the order of 0.1mm
per year (Kuo, 2011). Worms, however, may digest material
at a rate of 0.75 mm each year if hypothetically located at a
plan spacing of 1 m (Gingras et al., 2008). It is therefore
plausible that, over the sediment’s lifetime, worms are biolo-
gically engineering all material settling on the seabed into
robust pellets. These pellets’ collective presence (in some
cases 20–60% of total sediment by dry mass; Kuo, 2011) can
be measured as a crust-like feature during in situ strength
testing with conventional tools, including ball and T-bar full-
flow penetrometers (see Fig. 4(b), following Kuo & Bolton,
2011). Because of their proximity to the seabed, faecal pellets
are of significant engineering interest in the design of off-
shore pipelines and shallow foundations.
Shallow carbon fixation through plant roots
It may be possible to design a carbon sequestration func-
tion in soils through exploiting and extending natural pro-
cesses of pedogenic carbonate function. Widely observed in
natural soils, pedogenic carbonate minerals form as a con-
sequence of reaction between plant root exudates and cal-
cium derived from silicate mineral weathering. It has
recently been shown that this process also occurs in urban
soils, as a consequence of reaction between root exudates
and calcium derived from the dissolution or weathering
of cement-based construction materials (Manning, 2008;
Renforth et al., 2009, 2011; Washbourne et al., 2012). Plants
exude 10– 30% of carbon captured from the atmosphere by
photosynthesis through their roots and associated mycorrhi-
zal fungal associations (Kuzyakov & Domanski, 2000; Tay-
lor et al., 2009). Root tissue compounds are released into
the soil as exudates (Jones et al., 2009), which are complex
materials composed of polysaccharides, proteins, phospho-
lipids, cells that detach from roots, and other compounds.
Respired carbon dioxide and organic acid anions that natu-
rally decompose and can react with calcium-rich silicates
1000100·1
200015001000500
0
200
400
600
800
1000
1200
1400
1600
1800
2000
0·001
P-wave velocity: m/s
Specific surface: m /g
(a)
2
Final values
Initial values
1·0
1·2
1·4
1·6
1·8
2·0
2·2
2·4
0
Normalised cyclic stress ratio
P-wave velocity: m/s
(b)
Ishihara . (1998)et al
Tsukamoto . (2002)et al
Fig. 3. Reduction in saturation monitored by P-wave velocity in
initially saturated sand due to nitrogen gas generation via
biogeochemical treatment process of denitrification: (a) P-wave
velocities pre- and post-treatment, with consistent performance
across a broad range of specific surfaces (grain sizes); (b) published
relationship between P-wave velocity (corollary to saturation) and
cyclic strength, indicating that reduction in saturation (via
denitrification) could increase liquefaction resistance (Rebata-
Landa & Santamarina, 2012; used by permission)
292 DEJONG ET AL.

within soils are of particular interest. Manning (2008),
Renforth et al. (2009, 2011) and others (Sanderson, 2008)
have recorded that this process occurs naturally in soils at
brownfield sites and can be very rapid (Washbourne et al.,
2012). As summarised in Fig. 5, the resequestration of
carbon emitted during cement/lime production into the sub-
surface may be possible through the admixing of recycled
concrete and furnace slag into soils used for non-food crops
and urban revegetation (Manning, 2008).
FIELD APPLICATIONS
Completed/ongoing field trials
To date, only a few field trials have been performed in
which microbes have actively been used to either increase
the strength and stiffness of soils by microbially induced
carbonate precipitation or reduce the hydraulic conductivity
through biofilm formation, although such processes will have
been occurring naturally for millennia.
Two field trials using MICP are reported in the literature,
the first using a bioaugmentation strategy and the second
stimulating the indigenous species to induce precipitation.
Contractor Visser & Smit Hanab applied a MICP treatment
for gravel stabilisation to enable horizontal directional dril-
ling (HDD) for a gas pipeline in the Netherlands in 2010
(Fig. 6; from Van Paassen, 2011). The treatment was applied
to a 1000 m3volume at depths varying between 3 and 20 m
below the surface. The treatment involved injection of a
200 m3bacterial suspension that was cultivated in the
laboratory, two injections of 300–600 m3of reagent solution
containing urea and calcium chloride, and extraction of
groundwater until electrical conductivity and ammonium
concentrations returned to background values. MICP was
monitored using electrical resistivity, groundwater sampling
and physical sampling for calcite content measurements,
with varying degrees of success. Overall, the MICP treat-
ment was a success, as HDD was possible without instability
in the loose gravel deposit.
A second set of MICP field trials using biostimulation to
evaluate the capability of co-precipitation of heavy metals
(strontium-90) with calcium carbonate (to immobilise the
heavy metals) was initiated at the Vadose Zone Research
Park (VZRP) at the Idaho National Laboratory (INL), and is
ongoing at the US Department of Energy site in Rifle,
Colorado, USA (Fujita et al., 2010). These trials have
employed injection of dissolved molasses and urea in the
target treatment zone (calcium available in groundwater),
with contemporaneous withdrawal of groundwater from a
well several metres away from the injection point. At the
Rifle site the well-to-well cycle is closed by reinjection of
withdrawn water. To date, native microbes have been suc-
cessfully stimulated at both sites, and calcite precipitation
appears to be in progress. The rate of precipitation is slower
than in the bioaugmentation application in the Netherlands
(a)
16
12
8
4
(b)
0
0·5
1·0
1·5
2·0
2·5
3·0
3·5
4·0
0
Depth: m
Undrained shear strength: kPa
Deep Pacific (Meadows & Meadows, 1994)
Ehlers . (2005)et al
In situ T-bar (BP Exploration)
Nova Scotia (Baltzer ., 1994)et al
Peru Margin (Grupe ., 2001)et al
Normally consolidated
Fig. 4. Natural example of bioturbation by multicellular organisms such as worms, etc.: (a) image and SEM of faecal pellets from near-
surface offshore fine-grained sediments (note micro- and macropores evident in SEM) (Kuo et al., 2010; used by permission); (b) clearly
detectable crystal layer, formation is attributed largely to bioturbation (Baltzer et al., 1994; Meadows & Meadows, 1994; Grupe et al.,
2001; Ehlers et al., 2005)
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 293

described above, but is nonetheless advancing at a sufficient
rate for the project requirements.
Successful field trials of bioclogging have also been
reported in the Netherlands and Austria, with the objective
of reducing leakage through water-retaining constructions
(Van Meurs et al., 2006; Blauw et al., 2009). In Austria,
nutrient solutions were injected through a screen of injection
wells in the crest of a ‘leaking’ dike along the Danube river
in Greifenstein (Blauw et al., 2009; Lambert et al., 2010).
Injection was performed in two stages. During and following
the first injection phase (November– December), no signifi-
cant flow reduction was observed in downstream drains.
However, during the second treatment phase (July–August),
a significant reduction in discharge rate was observed (Fig.
2(b)). The measurement of a significant reduction in redox
potential indicated biochemical activity in the treated area.
The actual mechanism behind the reduction in permeability
is not yet fully understood (Blauw et al., 2009). Whether it
is the biofilm itself that clogs the pores, or some trapped
particles in the biofilm, or perhaps the biogeochemical
conversions that stimulate attachment, detachment or preci-
pitation of particles that can reduce the hydraulic conductiv-
ity still needs to be resolved.
In southern Ontario, Canada, researchers (Lambert et al.,
2010) have also been successful in reducing hydraulic
conductivity in a fractured dolostone formation in order to
block the flow of contaminated groundwater. Nutrient solu-
tions (molasses) were injected several times into the ground
to stimulate bioclogging. Geochemical measurements indi-
cated that microbial growth and a significant increase in
microbial diversity were observed. The longevity of the
biofilm appeared to be limited, as the hydraulic conductivity
returned to its initial condition 230 days after the nutrient
injections had stopped.
Challenges for field implementation
The process of upscaling to the field, following experi-
mental and modelling research at the element and bench
scales, raises the following challenges that must be consid-
ered and addressed.
Characterisation of subsurface heterogeneity. The treatment
of 100+ m3of naturally deposited soil requires characterisa-
tion of both soil and microbial spatial distributions at different
scales. Similar to chemical injection methods, preferential
flow – and therefore initial treatment – will occur within
zones of larger pore space (hydraulic conductivity). Recent
work indicates that MICP may be ‘self-equilibrating’ to some
extent, as the precipitated calcite does reduce conductivity;
when the level of reduction is sufficient in fine-grained soils,
treatment may redirect towards untreated (and relatively
higher conductivity) zones (Martinez, 2012). The spatial
microbial distribution does not necessarily map with soil
particle variations, and hence targeted delivery of microbes to
the improvement area may be required. From a practical
standpoint, the primary interest is the bulk reactivity level in
the soil (i.e. the rate at which a chemical reaction can occur in
a soil volume) required for a given biogeochemical process;
the exact microbial species, their absolute population, and
other environmental factors are not critically important.
Instead it is the bulk activity level that the biota (all
microbes) provide for a specific process that is the key factor.
For ureolysis-based MICP, the critical bulk activity is the rate
at which urea is hydrolysed. The bulk ureolysis rate can be
tested by injecting and monitoring the spatial degradation of
aqueous urea temporally (Martinez et al., 2013).
Treatment schemes for uniform improvement. The first task in
developing a treatment scheme is to identify the level of
improvement required. Laboratory test results enable identi-
fication of an ideal improvement threshold (akin to grouting
methods), but the actual application level of treatment is often
higher in the field because of allowances for spatial variability.
To minimise the additional application level that must be
achieved in the field, the treatment scheme must be optimised
for treatment uniformity. The treatment scheme selected
depends largely on whether the nutrients and/or microbes
can be delivered relatively uniformly across the treatment
zone through injection; this uniformity is directly a function of
solution viscosity and density as well as microbe size relative
to soil pore throat size and of course, critically, the soil
uniformity. In situ treatment is typically possible in gravels,
sands and silty sands. Uniform treatment using biogeochem-
ical processes can utilise technologies from the ground
improvement, geoenvironmental remediation and oil produc-
tion industries. For example, grouting methods, including
injection/extraction well patterns, point injection sources and
treatment solution mixing equipment, were successfully used
in the MICP field trial in the Netherlands (Van Paassen, 2011).
Bedrock
CO uptake
2
Subsoil
CO and organic acids
2
are released from plant
roots, mycelium and
bacteria
The organic acids are
If sufficient
calcium is present
the solution will
precipitate CaCO
oxidised to CO
(HCO and CO in
solution).
2
33
2⫺⫺
3
CO uptake
2
c
c
c
c
o
o
oca
Plants
Plant root
Topsoil
Fig. 5. Overview of biomediated (plants) near-surface carbon
sequestration observed and documented by Manning & Renforth
(described in Manning, 2008)
294 DEJONG ET AL.

A more localised approach using a five-spot injection/
extraction well pattern with pulsed injections following
geoenvironmental and oil production techniques has also been
successful at both field and model scales (Fujita et al., 2010;
Martinez, 2012). If treatment of fine-grained soils such as clay
is desired, mechanical mixing, either in situ or ex situ, may be
necessary. These methods have been marginally successful in
the laboratory, and implementation using conventional ground
improvement equipment such as deep soil mixing tools may
be problematic, as rapid pressure drops and high shearing
stresses may cause lysing (bursting) of cells. Other variables
that must also be considered but are not yet fully understood
include single versus multiple phase injections schemes,
continuous versus pulsed injection, surficial flooding versus
deep injection, and short, high-concentration treatments versus
slow, low-concentration treatments.
Construction, operation and maintenance. Nearly all research
performed to date has focused on implementation of the
biogeochemical processes for improvement/modification of
the soil properties. However, realising the treatment in situ is
only the first stage of development of an application. As
discussed above, biogeochemical processes may have by-
products (such as ammonia) that must be managed. By-
product management requires consideration of the fate and
transport of the by-products, as well as verification that the
treatment does not degrade with time owing to geotechnical
mechanical loading (e.g. an earthquake), or chemical (e.g.
dissolution by carbon-dioxide-rich waters) or biochemical
processes that may change the rate of chemical processes.
Use of the observational method may be appropriate for this
technology. If degradation over time is of concern, then
retreatment, or ‘healing’, of the biogeochemical treatment
might be a possible solution, although inducing additional
costs and implementation constraints (Montoya, 2012).
Service life. Selection of an appropriate biogeochemical
treatment for a specific application requires compatibility of
its permanence and durability with service life requirements.
MICP-treated sand is expected to be stable for more than 50
years, provided alkaline conditions persist (DeJong et al.,
2009), as its longevity is expected to be consistent with that
of natural calcite-rich geomaterials. A 50+ year time frame is
compatible with the expected service life of many structures,
and occasional retreatment can be applied to extend this
service life. On the other hand, biofilms require a continuous
nutrient source, and therefore may be more suitable for short-
term hydraulic control applications (Cunningham et al.,
1997). In either case, a risk assessment with respect to
treatment longevity, including assessment of the ground-
water– precipitate interaction and a performance-monitoring
programme, may be appropriate.
(a) (b) (c)
⫺6
⫺4
⫺2
⫺15 ⫺10 ⫺50 5 1015
X: m
Z: m
Before treatment
160
120
80
60
40
20
15
10
7·5
5
30
⫺6
⫺4
⫺2
⫺15 ⫺10 ⫺50 51015
X: m
Z: m
During treatment
(d)
Fig. 6. Overview of MICP field trial for stabilisation of loose gravel for horizontal directional drilling (project described by Van Paassen
(2011)): (a) repeating well pattern; (b) sample of MICP-stabilised gravel; (c) pipeline installation after horizontal directional drilling
(provided by Visser & Smit Hanab); (d) resistivity mapping before and during treatment (provided by Deltares)
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 295

Performance monitoring. Central to any improvement method
– biogeochemical or conventional – is monitoring during
treatment to verify that the required distribution and
magnitude of improvement are realised, and, after treatment,
to verify that the improvement level remains adequate
throughout the service life. This typically requires a rigorous
quality assurance/quality control (QA/QC) process during
construction by the contractor to verify the ‘certainty of
execution’ (an issue for conventional ground improvement
techniques). The QA/QC programme would be likely to
include a verification testing programme that specifies the
number of samples obtained, tests to be performed on
samples, field tracer tests, monitoring of reactants and
products during treatment, and/or geophysical measurements.
In addition, a reduced, but continuous, level of monitoring by
the owner/operator throughout the service life (perhaps bi-
monthly to yearly) is likely to be required. Post-improvement
monitoring may also become a regulatory compliance issue
similar to that for geoenvironmental remediation projects.
Modelling of biogeochemical treatment processes. The inter-
disciplinary nature of biomediated geochemical processes
requires integration of the biological and chemical compo-
nents within the hydraulic and mechanical modelling
techniques already established in geotechnical finite-element
and finite-difference modelling codes, as well as the
development of new constitutive models for the behaviour
of bio-treated soil. Current models can predict final spatial
MICP calcite distribution, and model the mechanical element
behaviour of MICP-treated sand. Issues that remain include
the integration of relevant biogeochemical reaction networks,
small-scale biochemical processes (i.e. microbial growth,
enzymatic rates, gas generation, etc.), local changes in
porosity (and hydraulic conductivity) and saturation, model-
ling of degradative processes in treated soils, and more.
Modelling of spatial variability (microbes versus soil
particles) and identifying the appropriate transition from
discrete to continuum scales (i.e. microbes and soil particle
versus bulk reaction rate and porosity) will be particularly
challenging, as the biogeochemical processes occur at the
micrometre length scale.
Sustainability: life cycle analysis and embodied energy. One
of the attractive attributes of biogeotechnology is the
utilisation of natural, biogeochemical processes to improve
soil. These processes have the potential for significant
reduction in embodied energy and carbon emissions, relative
to conventional ground improvement methods such as soil
stabilisation using Portland cement. Sustainability analyses to
date are limited, and challenges regarding the definition of
system boundaries and the service life period must still be
resolved. However, with respect to MICP, soil improvement
with calcite production requires less carbon than cement
stabilisation, but additional analysis is required to study the
energy required for manufacturing of the urea and calcium
chloride, for injection of the improvement media into the
ground, and for treatment of by-products.
Cost. The cost of biogeochemical treatment schemes will be
dependent on the process used, and on details of the specific
field project. With very limited field applications, the actual
costs of the various improvement processes are largely
unknown. Studies and cost estimates to date vary widely,
owing to suboptimised treatment schemes being implemented
to date. Ivanov & Chu (2008) estimated material costs for
MICP (e.g. urea, calcium) of about US$5/m3(range from 0.5
to 9), and total costs of MICP treatment (materials,
equipment, and installation) in saturated soils range from
US$25–75/m3(DeJong, personal communication, 2011) to
about US$500/m3(Esnault-Filet, personal communication,
2011). Recent work by Cheng & Cord-Ruwisch (2012) found
that materials and costs may be reduced through more
efficient cementation. While their estimate encompasses a
wide range, the lower half of this range is competitive with
many conventional ground improvement techniques, such as
deep soil mixing, jet grouting and chemical grouting. It also
shows that, in common with many other ground treatment
processes, the major cost is in delivery. If processes can be
developed that enable biotreatment to be delivered more
economically, then strong potential exists.
Feasibility for different applications
Realistically, biogeochemical-based soil improvement tech-
nologies will never replace all conventional ground improve-
ment techniques. However, the following general attributes
make these technologies potentially favourable in many
instances: they are based on natural processes; they often
require less energy; they are deployable beneath and around
existing structures, and are non-disruptive to those struc-
tures; and they may enable improvement over larger dis-
tances, owing to their low viscosity and injection pressure
requirements. Thanks to these attributes, biogeochemical soil
improvement technologies may provide opportunities to ad-
dress broad societal priorities, such as climate change,
energy, food, shelter, infrastructure, urbanisation, sustainabil-
ity, waste management, safety, water availability and eco-
nomic stability.
Considering the general attributes of biogeochemical pro-
cesses, the challenges for implementation in the field, and
society’s needs, the applications with the highest likelihood
of success will, in general, require simple implementation,
provide a unique answer to a problem, have competitive
costs, and have a potential for rapid take-up by industry and
society. Within this context, 24 different biogeochemical
applications were identified and evaluated in a qualitative
manner against the criteria of cost, implementation, prob-
ability of success, and social acceptance as part of the 2012
Workshop activities. The applications and their approximate
‘ranking’ against these criteria are presented in Table 1.
The applications that seem most feasible in the near term
include erosion control, environmental remediation, dust
control, improvement of rural roads, surface carbon dioxide
sequestration, repair of sandstone structures, and solidifica-
tion of fly ash. All of these applications still require further
development, but they all represent problems for which
current solutions are insufficient. Longer-term ‘blue sky’
applications include the creation of underground space (for
storage or transport), deep carbon dioxide sequestration,
stabilisation of sink holes, and control of underground
hydraulic flow. In all these cases, the current capital-cost-
driven construction industry essentially forces consideration
of a new biogeochemical technique, because current best
practices are insufficient. However, if capital costs are
merely competitive with current industry methods, the tried-
and-true established methods in industry that have decades
of experience will often be preferred.
CLOSURE: RESEARCH AND DEVELOPMENT NEEDS
The rapid development of biomediated soil improvement
methods over the last decade has generated exciting ad-
vances in geotechnology, from the micro scale up through
successful field-scale application. Experimental, analytical
and numerical techniques from the fields of geotechnical
296 DEJONG ET AL.

engineering, geoenvironmental engineering, microbiology
and geochemistry have been integrated, making this a truly
interdisciplinary field. MICP has evidently been the primary
focus of efforts to employ biogeotechnical ground improve-
ment technology to date. The focus on MICP is simultan-
eously encouraging, as this focus has resulted in a successful
field-scale trial within a decade of its initial development in
the laboratory, and unsatisfying, as there are probably so
many other biogeochemical processes that have yet to be
identified and/or be subject to intensive research. Advances
within MICP include the development of biostimulation and
bioaugmentation techniques, quantified improvements in
stiffness, strength, conductivity, etc., developed geophysical
methods for real-time monitoring, optimised treatment in
one-dimensional and two-dimensional models, demonstrated
improvement to liquefaction resistance through centrifuge
modelling, the development and verification of bio-geo-
chemical-mechanical numerical models, field-scale imple-
mentation, and much more. This has clearly validated and
demonstrated the potential influence of biological processes
on engineering soil properties, and on opportunities for
geotechnical field applications.
Many alternative biogeochemical processes have received
little attention compared with MICP, and there are undoubt-
edly many such processes that have yet to be discovered.
Promising results of biogas via denitrification, biofilm for-
mation, biocementation through alternative geochemical
pathways, and the generation of biopolymers and biofilms
for strength enhancement and permeability reduction all
show potential, but require further development.
Monitoring techniques to verify treatment success, and to
monitor durability and performance over the project’s service
life, have been identified as an important consideration.
However, implementation and interpretation of various mon-
itoring techniques in field trials are required to develop
reliable monitoring methods. While appropriate monitoring
techniques will vary, depending on the biogeochemical pro-
cess selected, geophysical methods have a high potential for
indirectly mapping the effect that a treatment process may
have on engineering soil properties. The permanence, or
longevity, of a treatment method must match or exceed the
required service life; this is a challenging criterion to satisfy,
as physical experiments to date extend at most 2 years
(although modelling results indicate a potential service live
of 50 years or more).
While not addressed explicitly herein, a new workforce is
required to embrace and help realise the development of
biogeochemical treatment methods in the geotechnical com-
munity. To develop this workforce, education and training
must include the fundamentals of biology and chemistry,
producing engineers who can intelligibly converse and
engage with experts in these areas on interdisciplinary
teams. Indeed, many emerging fields lie at the intersection
of disciplines, and participation in these discoveries and
advances requires engineers equipped to engage in cross-
disciplinary discovery.
The adoption of biogeotechnical methods in industry will
take time. Often, the primary conventional ground improve-
ment methods that compete with biogeochemical techniques
are likely to be cement-based techniques, which the general
public view largely as harmless/clean, in spite of the energy-
intensive, carbon-producing, manufacturing process for
cementitious materials, which involves the quarrying of large
volumes of raw materials and associated land impairment,
coupled with their high pH. Furthermore, there has often
been public resistance to biotechnologies using exogenous
organisms. Activities designed to raise awareness may be
needed, as well as industry training, as field-scale applica-
tions of biogeotechnology become increasingly common.
ACKNOWLEDGEMENTS
The Second International Workshop on Bio-Soil Engineer-
ing and Interactions was funded in part by the United States
Table 1. Evaluation of application alternatives and their potential, considering implementation feasibility, probability of success, cost/
viability, and social acceptance
Application Implementation
Easy: 5
Difficult: 1
Probability of
success
High: 5
Low: 1
Cost/viability
Economic: 5
Expensive: 1
Societal
acceptance
High: 5
Low: 1
Total score out
of 20
Structural repair 5 5 3 5 18
Erosion control 4 5 4 5 18
Co-precipitation/immobilisation of contaminants 5 4 4 5 18
Dust mitigation 4 5 4 5 18
Ground improvement for rural roads 5 5 3 4 17
Shallow carbon sequestration 5 3 4 5 17
Leak management 4 3 4 5 16
Rehabilitation of ancient monuments 3 3 5 5 16
Ground improvement for urban road subgrading 5 3 3 4 15
Soil liquefaction mitigation (MICP) 3 5 3 3 14
Ground improvement for ash ponds 1 4 4 5 14
Recycling/reuse of dredging materials 3 2 3 5 13
Soil liquefaction mitigation (biogas) 3 3 3 3 12
Enhanced water/oil/gas recovery 1 3 3 5 12
De-desertification 1 5 1 5 12
Sediment weakening by fluidisation 3 2 3 3 11
Underground creation (pipeline) 3 4 1 3 11
Stabilisation of sinkholes 1 3 2 5 11
Landfills as new energy resource 3 4 1 2 10
Construction products (bricks) using soil-biocementation 2 4 1 3 10
Water storage 3 2 2 2 9
De-swelling of clays 1 1 1 4 7
Deep carbon sequestration 1 1 1 3 6
Underground creation (tunnel) 1 1 2 1 5
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 297

National Science Foundation under Grant No. CMMI-
1110409. Any opinions, findings and conclusions or recom-
mendations expressed in this material are those of the
author(s), and do not necessarily reflect the views of the
National Science Foundation.
REFERENCES
Al Qabany, A. (2011). Microbial carbonate precipitation in soils.
Doctoral dissertation, University of Cambridge, UK.
Al Qabany, A. & Soga, K. (2013). Effect of chemical treatment
used in MICP on engineering properties of cemented soils.
Ge
´otechnique 63, No. 4, 331–339, http://dx.doi.org/10.1680/
geot.SIP13.P.022.
Al Qabany, A., Mortensen, B., Martinez, B., Soga, K. & DeJong, J.
(2011). Microbial carbonate precipitation: correlation of S-wave
velocity with calcite precipitation. Proc. Geofrontiers 2011:
Advances in Geotechnical Engineering, Dallas, TX, ASCE Geo-
technical Special Publication 211, 3993–4001.
Al Qabany, A., Soga, K. & Santamarina, J. C. (2012). Factors
affecting efficiency of microbially induced calcite precipitation.
ASCE J. Geotech. Geoenviron. Engng 138, No. 8, 992 –1001.
Bachmeier, K. L., Williams, A.E., Warmington, J. R. & Bang, S. S.
(2002). Urease activity in microbiologically-induced calcite pre-
cipitation. J. Biotechnol.93, No. 2, 171–181.
Baltzer, A., Cochonat, P. & Piper, D. J. W. (1994). In situ
geotechnical characterisation of sediments on the Nova Scotian
Slope, eastern Canadian continental margin. Marine Geol.120,
No. 7, 291– 308.
Banagan, B. L., Wertheim, B. M., Roth, M. J. S. & Caslake, L. F.
(2010). Microbial strengthening of loose sand. Lett. Appl. Micro-
biol.51, No. 2, 138–142.
Bang, S. S., Lippert, J. J., Yerra, U., Mulukutla, S. & Ramakrishnan,
V. (2010). Microbial calcite, a bio-based smart nanomaterial in
concrete remediation. Int. J. Smart Nano Mater.1, No. 1,
28– 39.
Bang, S., Min, S. H. & Bang, S. S. (2011). Application of
microbiologically induced soil stabilization technique for dust
suppression. Int. J. Geo-Engng 3, No. 2, 27–37.
Barkouki, T., Martinez, B. C., Mortensen, B. M., Weathers, T. S.,
DeJong, J. T., Ginn, T. R., Spycher, N. F., Smith, R. W. &
Fujita, Y. (2011). Forward and inverse bio-geochemical model-
ing of microbially induced calcite precipitation in half-meter
column experiments. Transp. Porous Media 90, No. 1, 23–39.
Barnes, R. S. K., Calow, P. & Olive, P. J. W. (1988). The
invertebrates: A new synthesis, 1st edn. Oxford, UK: Blackwell
Scientific.
Baveye, P., Vandevivere, P., Hoyle, B. L., DeLeo, P. C. & Sanchez
de Lozada, D. (1998). Environmental impact and mechanisms of
the biological clogging of saturated soils and aquifer materials.
Crit. Rev. Environ. Sci. Technol.28, No. 2, 123–191.
Benini, S., Rypniewski, W. R., Wilson, K. S., Miletti, S., Ciurli, S.
& Mangani, S. (1999). A new proposal for urease mechanism
based on the crystal structures of the native and inhibited
enzyme from Bacillus pasteurii: why urea hydrolysis costs two
nickels. Structure 7, No. 2, 205– 216.
Berg, R. D. (1996). The indigenous gastrointestinal microflora.
Trends Microbiol.4, No. 11, 430 –435.
Blauw, M., Lambert, J. W. M. & Latil, M. N. (2009). Biosealing: a
method for in situ sealing of leakages. Proceedings of the
International Symposium on Ground Improvement Technologies
and Case Histories, ISGI’09, Singapore, 125– 130.
Bonala, M. V. S. & Reddi, L. N. (1998). Physicochemical and
biological mechanisms of soil clogging: an overview. In Filtra-
tion and drainage in geotechnical/geoenvironmental engineering
(eds L. N. Reddi and M. V. S. Bonalo), ASCE Geotechnical
Special Publication 78, pp. 43– 68. Reston, VA, USA: ASCE.
Burbank, M., Weaver, T., Green, T., Williams, B. & Crawford, R.
(2011). Precipitation of calcite by indigenous microorganisms to
strengthen liquefiable soil. Geomicrobiol. J.28, No. 4, 301–312.
Burbank, M., Weaver, T., Williams, B. & Crawford, R. (2012a).
Urease activity of ureolytic bacteria isolated from six soils in
which calcite was precipitated by indigenous bacteria. Geomi-
crobiol. J.29, No. 4, 389 –395.
Burbank, M., Weaver, T., Lewis, R., Crawford, R. & Williams, B.
(2012b). Geotechnical tests of sands following bio-induced
calcite precipitation catalyzed by indigenous bacteria. ASCE J.
Geotech. Geoenviron. Engng, http://dx.doi.org/10.1061/(ASCE)
GT.1943-5606.0000781.
Cabalar, A. F. & Canakci, H. (2005). Ground improvement by
bacteria. Proc. 3rd Biot Conference on Poromechanics, Norman,
OK, 707– 712.
Chaney, R. (1978). Saturation effects on the cyclic strength of sand.
Proceedings of the ASCE Specialty Conference on Earthquake
Engineering and Soil Dynamics, Pasadena, CA, pp. 342–359.
Cheng, L. & Cord-Ruwisch, R. (2012). In situ soil cementation
with ureolytic bacteria by surface percolation. Ecol. Engng 42,
64– 72.
Chou, C.-W., Seagren, E. A., Aydilek, A. H. & Maugel, T. K.
(2008). Bacterially-induced calcite precipitation via ureolysis.
Washington, DC, USA: ASM Microbe Library, Visual
Media Briefs, http://www.microbelibrary.org/library/laboratory-
test/3174-bacterially-induced-calcite-precipitation-via-ureolysis.
Chou, C.-W., Seagren, E. A., Aydilek, A. H. & Lai, M. (2011).
Biocalcification of sand through ureolysis. ASCE J. Geotech.
Geoenviron. Engng 137, No. 12, 1179– 1189.
Chu, J., Ivanov, V., Lee, M. F., Oh, X. M. & He, J. (2009). Soil and
waste treatment using biocement, Proceedings of the Interna-
tional Symposium on Ground Improvement Technologies and
Case Histories, ISGI’09, Singapore, 165– 170.
Chu, J., Ivanov, V., Naeimi, M., Li, B. & Stabnikov, V. (2011).
Development of microbial geotechnology in Singapore. Proc.
Geofrontiers 2011: Advances in Geotechnical Engineering, Dal-
las, TX, ASCE Geotechnical Special Publication 211, 4070–
4078.
Chu, J., Stabnikov, V. & Ivanov, V. (2012). Microbially induced
calcium carbonate precipitation on surface or in the bulk of soil.
Geomicrobiol. J.29, No. 6, 544 –549.
Chu, J., Ivanov, V., Stabnikov, V. & Li, B. (2013). Microbial method
for construction of aquaculture pond in sand. Ge
´otechnique,
http://dx.doi.org/10.1680/geot.SIP13.P.007.
Ciurli, S., Benini, S., Rypniewski, W. R., Wilson, K. S., Miletti, S.
& Mangani, S. (1999). Structural properties of the nickel ions in
urease: novel insights into the catalytic and inhibition mechan-
isms. Coordination Chem. Rev.190–192, 331 –355.
Cullimore, D. R. (1990). Microbes in civil engineering environ-
ments: biofilms and biofouling. In Microbiology in civil engi-
neering (ed. P. Howsam), pp. 15– 23. London, UK: E & FN
Spon.
Cunningham, A., Warwood, B., Sturman, P. et al. (1997). Biofilm
processes in porous media. In The microbiology of the terrestrial
deep subsurface (eds P. Amy and D. Haldeman), pp. 325–346.
New York, NY, USA: Lewis Publishers.
Darcy, H. (1857). Recherches expe
´rimentales relatives au mouve-
ment de l’eau dans les tuyaux. Paris, France: Imprimerie Impe´r-
iale (in French).
Day, J. L., Ramakrishnan, V. & Bang, S. S. (2003). Microbiologi-
cally induced sealant for concrete crack remediation. Proc. 16th
Engng Mech. Conf., Seattle, WA.
DeJong, J. T., Fritzges, M. B. & Nu
¨sslein, K. (2006). Microbial
induced cementation to control sand response to undrained shear.
ASCE J. Geotech. Geoenviron. Engng 132, No. 11, 1381 –1392.
DeJong, J. T., Mortensen, B. & Martinez, B. (2007). Bio-soils
interdisciplinary science and engineering initiative, Final Report
on Workshop, 84 pp. Arlingon, VA, USA: National Science
Foundation.
DeJong, J. T., Martinez, B. C., Mortensen, B. M., Nelson, D. C.,
Waller, J. T., Weil, M. H., Ginn, T. R., Weathers, T., Barkouki,
T., Fujita, Y., Redden, G., Hunt, C., Major, D. & Tanyu, B.
(2009). Upscaling of bio-mediated soil improvement. Proc. 17th
Int. Conf. Soil Mech. Geotech. Engng, Alexandria, 2300 –2303.
DeJong, J. T., Mortensen, M. B., Martinez, B. C. & Nelson, D. C.
(2010). Biomediated soil improvement. Ecol. Engng 36, No. 2,
197– 210.
DeJong, J. T., Soga, K., Banwart, S. A., Whalley, W. R., Ginn, T.,
Nelson, D. C., Mortensen, B. M., Martinez, B. C. & Barkouki,
T. (2011). Soil engineering in vivo: harnessing natural biogeo-
chemical systems for sustainable, multi-functional engineering
solutions. J. R. Soc. Interface 8, No. 54, 1–15.
Ehlers, C. J., Chen, J., Roberts, H. H. & Lee, Y. C. (2005). The
origin of near-seafloor crust zones in deepwater. Proc. Int. Symp.
298 DEJONG ET AL.

on Frontiers in Offshore Geotechnics: ISFOG 2005, Perth,
927–934.
Esnault-Filet, A., Gadret, J. P., Loygue, M. & Borel, S. (2012).
Biocalcis and its application for the consolidation of sands. In
Grouting and deep mixing 2012 (eds L. F. Johnsen, D. A. Bruce
and M. J. Byle), Geotechnical Special Publication 288, vol. 2,
pp. 1767–1780. Reston, VA, USA: ASCE.
Espinoza, D. & Santamarina, J. C. (2010). Ant tunneling: a granular
media perspective. Granular Matter 12, No. 6, 607– 616.
Fauriel, S. (2012). Bio-chemo-hydro-mechanical modeling of soils in
the framework of microbial induced calcite precipitation. PhD
thesis, Ecole Polytechnique Fe´de´rale de Lausanne, Switzerland.
Fauriel, S. & Laloui, L. (2011a). A bio-hydro-mechanical model for
propagation of biogrout in soils. Proc. Geo-Frontiers 2011:
Advances in Geotechnical Engineering, Dallas, TX, ASCE Geo-
technical Special Publication 211, 4041– 4048.
Fauriel, S. & Laloui, L. (2011b). Modelling of biogrout propagation
in soils. Proc. 2nd Int. Symp. Computat. Geomech., Rhodes,
578– 586.
Fauriel, S. & Laloui, L. (2012). A bio-chemo-hydro-mechanical
model for microbially induced calcite precipitation in soils.
Comput. Geotech.46, 104– 120.
Ferris, F. G., Stehmeier, L. G., Kantzas, A. & Mourits, F. M.
(1996). Bacteriogenic mineral plugging. J. Can. Petrol. Technol.
35, No. 8, 56– 61.
Fujita, Y., Redden, G. D., Ingram, J. S., Cortez, M. M. & Smith,
R. W. (2004). Strontium incorporation into calcite generated by
bacterial ureolysis. Geochim. Cosmochim. Acta 68, No. 15,
3261– 3270.
Fujita, Y., Taylor, J. L., Gresham, T. L. T., Delwiche, M. E.,
Colwell, F. S., McLing, T. L., Petzke, L. M. & Smith, R. W.
(2008). Stimulation of microbial urea hydrolysis in groundwater
to enhance calcite precipitation. Environ. Sci. Technol.42, No.
8, 3025– 3032.
Fujita, Y., Taylor, J. L., Wendt, L. M., Reed, D. W. & Smith, R. W.
(2010). Evaluating the potential of native ureolytic microbes to
remediate a 90Sr contaminated environment. Environ. Sci. Tech-
nol.44, No. 19, 7652– 7658.
Gat, D., Tsesarsky, M. & Shamir, D. (2011). Ureolytic CaCO3
precipitation in the presence of non-ureolytic competing bacter-
ia. Proc. Geo-Frontiers 2011: Advances in Geotechnical Engi-
neering, Dallas, TX, ASCE Geotechnical Special Publication
211, 3966– 3974.
Gingras, M. K., Pemberton, S. G., Dashtgard, S. & Dafoe, L.
(2008). How fast do marine invertebrates burrow? Palaeogeog.
Palaeoclimatol. Palaeoecol.270, No. 3–4, 280 –286.
Gray, D. H. & Sotir, R. B. (1996). Biotechnical and soil bioengi-
neering stabilization. New York, NY, USA: John Wiley & Sons.
Grupe, B., Becker, H. J. & Oebius, H. U. (2001). Geotechnical and
sedimentological investigations of deep-sea sediments from a
manganese nodule field of the Peru Basin. Deep-Sea Res. Part
II 48, No. 17– 18, 3593–3608.
Hamdan, N., Kavazanjian, E. Jr & Rittmann, B. E. (2011a).
Sequestration of radionuclides and metal contaminants through
microbially-induced carbonate precipitation. Proc. 14th Pan
American Conf. Soil Mech. Geotech. Engng, Toronto, 5 pp.
Hamdan, N., Kavazanjian, E. Jr, Rittmann, B. E. & Karatas, I.
(2011b). Carbonate mineral precipitation for soil improvement
through microbial denitrification. Proc. GeoFrontiers 2011: Ad-
vances in Geotechnical Engineering, Dallas, TX, ASCE Geo-
technical Special Publication 211, 3925– 3934.
Hamed, B. S. & Belhadri, M. (2009). Rheological properties of
biopolymer drilling fluids. J. Petrol. Sci. Engng 67, No. 3– 4,
84– 90.
Hata, T., Tsukamoto, M., Mori, H., Kuwano, R. & Gourc, J. P.
(2011). Evaluation of multiple soil improvement techniques
based on microbial functions. Proc. GeoFrontiers 2011: Ad-
vances in Geotechnical Engineering, Dallas, TX, ASCE Geo-
technical Special Publication 211, 3945– 3955.
He, J., Chu, J. & Ivanov, V. (2013). Mitigation of liquefaction of
saturated sand using biogas. Ge
´otechnique,63, No. 4, 267–275,
http://dx.doi.org/10.1680/geot.SIP13.P.004.
Howsam, P. (ed.) (1990). Water wells, monitoring, maintenance and
rehabilitation. London, UK: E & FN Spon.
Inagaki, Y., Tsukamoto, M., Mori, H., Sasaki, T., Soga, K., Al
Qabany, A. & Hata, T. (2011a). The influence of injection
conditions and soil types on soil improvement by microbial
functions. Proc. GeoFrontiers 2011: Advances in Geotechnical
Engineering, Dallas, TX, ASCE Geotechnical Special Publica-
tion 211, 4021– 4030.
Inagaki, Y., Tsukamoto, M., Mori, H., Nakajiman, S., Sasaki, T. &
Kawasaki, S. (2011b). A centrifugal model test of microbial
carbonate precipitation as liquefaction countermeasure. Jiban
Kogaku Janaru 6, No. 2, 157–167.
Ishihara, K., Tsuchiya, H., Huang, Y. & Kamada, K. (2001). Recent
studies on liquefaction resistance of sand: effect of saturation.
Proc. 4th Int. Conf. Recent Adv. Geotech. Earthquake Engng
Soil Dynamics, San Diego, CA.
Ivanov, V. (2010). Microbial geotechniques. In Environmental micro-
biology for engineers, pp. 279 –286. Boca Raton, FL, USA:
CRC Press.
Ivanov, V. & Chu, J. (2008). Applications of microorganisms to
geotechnical engineering for bioclogging and biocementation of
soil in situ. Rev. Environ. Sci. Biotechnol.7, No. 2, 139–153.
James, G. A., Warwood, B. K., Hiebert, R. & Cunningham, A. B.
(2000). Microbial barriers to the spread of pollution. In
Bioremediation (ed. J. J. Valdes), pp. 1 –14. Amsterdam, the
Netherlands: Kluwer Academic.
Jones, D. L., Nguyen, C. & Finlay, R. D. (2009). Carbon flow in
the rhizosphere: carbon trading at the soil–root interface. Plant
and Soil 321, No. 1, 5–33.
Karatas, I., Kavazanjian, E. Jr & Rittmann, B. E. (2008). Micro-
bially induced precipitation of calcite using Pseudomonas
denitrificans. Proc. 1st Int. Conf. Biogeotech. Engng, Delft (CD-
ROM).
Kavazanjian, E. Jr & Karatas, I. (2008). Microbiological improve-
ment of the physical properties of soil. Proc. 6th Int. Conf. on
Case Histories in Geotech. Engng, Rolla, MO (CD-ROM).
Kavazanjian, E. Jr, Iglesias, E. & Karatas, I. (2009). Biopolymer
soil stabilization for wind erosion control. Proc. 17th Int. Conf.
Soil Mech. Geotech. Engng, Alexandria 2, 881 –884.
Khachatoorian, R., Petrisor, I. G., Kwan, C.-C. & Yen, T. F. (2003).
Biopolymer plugging effect: laboratory-pressurized pumping
flow studies. J. Petrol. Sci. Engng 38, No. 1– 2, 13– 21.
Kohnhauser, K. (2007). Introduction to geomicrobiology. Malden,
MA, USA: Blackwell Publishing.
Kuo, M. Y. H. (2011). Deep ocean clay crusts: Behaviour and
biological origin. Doctoral dissertation, University of Cam-
bridge, UK.
Kuo, M. Y. H. & Bolton, M. D. (2011). Faecal pellets in deep
marine soft clay crusts: implications for hot-oil pipeline design.
Proc. 30th Int. Conf. on Ocean, Offshore and Artic Engineering,
Rotterdam, 883– 892.
Kuo, M. Y. H. & Bolton, M. D. (2012). The nature and origin of
deep ocean clay crust from the Gulf of Guinea. Ge
´otechnique,
http://dx.doi.org/10.1680/geot.10.P.012.
Kuo, M.Y.-H., Hill, A., Rattley, M. & Bolton, M. D. (2010). New
evidence for the origin and behaviour of deep ocean crusts.
Proc. 2nd Int. Symp. on Frontiers in Offshore Geotechnics,
Perth, 365–370.
Kuzyakov, Y. & Domanski, G. (2000). Carbon input by plants into
the soil: review. J. Plant Nutrition Soil Sci.163, No. 4, 421–
431.
Laloui, L. & Fauriel, S. (2011). Biogrout propagation in soils.
Proceedings of the international workshop on multiscale and
multiphysics processes in geomechanics, Stanford, CT, pp. 77– 80.
Lambert, J. W. M., Novakowski, K., Blauw, M., Latil, M. N.,
Knight, L. & Bayona, L. (2010). Pamper bacteria, they will help
us: application of biochemical mechanisms in geo-environmental
engineering. In GeoFlorida 2010: Advances in Analysis,
Modeling & Design (eds D. O. Fratta, A. J. Puppala and
B. Muhunthan), ASCE Geotechnical Special Publication 199,
pp. 618– 627. Reston, VA, USA: ASCE.
Legge, K. R., Scheurenburg, R., Clever, C., James, G. & Claus, R.
(1985). Investigation into apparent clogging of a geotextile
recovered from Ergo Tailings Dam wall drain, Preliminary
Report. Pretoria, Republic of South Africa: Department of Water
Affairs and Forestry.
Li, M., Yang, Z., Guo, H. & Cheng, X. (2011). Heavy metals
removal by biomineralization of urea hydrolyzed bacteria iso-
lated from soil. Proc. 1st Int. Conf. on Geomicrobial Ecotoxicol-
ogy, Wuhan, 312–315.
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 299

Manning, D. A. C. (2008). Biological enhancement of soil carbon-
ate precipitation: passive removal of atmospheric CO2:Mineral.
Mag.72, No. 2, 639– 649.
Martinez, B. C. (2012). Experimental and numerical upscaling of
MICP for soil improvement. Doctoral dissertation, University of
California, Davis, CA, USA.
Martinez, B. C. & DeJong, J. T. (2009). Bio-mediated soil improve-
ment: load transfer mechanisms at micro- and macro-scales.
Proc. 2009 ASCE US-China Workshop on Ground Improvement
Technologies, Orlando, FL, 242– 251.
Martinez, B. C., Barkouki, T. H., DeJong, J. T. & Ginn, T. R.
(2011). Upscaling of microbial induced calcite precipitation in
0.5m columns: experimental and modeling results. Proc. Geo-
Frontiers 2011: Advances in Geotechnical Engineering, Dallas,
TX, ASCE Geotechnical Special Publication 211, 4049–4059.
Martinez, B. C., DeJong, J. T., Ginn, T. R., Mortensen, B. M.,
Barkouki, T. H., Hunt, C., Tanyu, B. & Major, D. (2013).
Experimental optimization of microbial induced carbonate pre-
cipitation for soil improvement. ASCE J. Geotech. Geoenviron.
Engng (in press).
Meadows, A. & Meadows, P. S. (1994). Bioturbation in deep-sea
pacific sediments. J. Geol. Soc.151, No. 2, 361–375.
Mitchell, A. C., Phillips, A. J., Hiebert, R., Gerlach, R., Spangler,
L. H. & Cunningham, A. B. (2009). Biofilm enhanced geologic-
al sequestration of supercritical CO2:Int. J. Greenhouse Gas
Control 3, No. 1, pp. 90– 99.
Mitchell, J. K. (1975). Fundamentals of soil behavior. New York,
NY, USA: Wiley.
Mitchell, J. K. & Santamarina, J. C. (2005). Biological considera-
tions in geotechnical engineering. ASCE J. Geotech. Geoenviron.
Engng 131, No. 10, 1222– 1233.
Montoya, B. M. (2012). Bio-mediated soil improvement and the
effect of cementation on the behavior, improvement, and per-
formance of sand. Doctoral dissertation, University of California,
Davis, CA, USA.
Montoya, B. M., Gerhard, R., DeJong, J., Weil, M., Martinez, B.,
Pederson, L. & Wilson, D. (2012). Fabrication, operation, and
health monitoring of bender elements for aggressive environ-
ments. Geotech. Test. J.35, No. 5, 15 pp.
Montoya, B. M., DeJong, J. T. & Boulanger, R. W. (2013).
Dynamic response of liquefiable sand improved by microbial
induced calcite precipitation. Ge
´otechnique,63, No. 4, 302–312,
http://dx.doi.org/10.1680/geot.SIP13.P.019.
Mortensen, B. M. & DeJong, J. T. (2011). Strength and stiffness of
MICP treated sand subjected to various stress paths. Proc.
GeoFrontiers 2011: Advances in Geotechnical Engineering,
Dallas, TX, ASCE Geotechnical Special Publication 211, 4012–
4020.
Mortensen, B. M., Haber, M., DeJong, J. T., Caslake, L. F. &
Nelson, D. C. (2011). Effects of environmental factors on
microbial induced calcite precipitation. J. Appl. Microbiol.111,
No. 2, 338– 349.
NRC (2006). Geological and geotechnical engineering in the new
millennium: Opportunities for research and technological inno-
vation. Washington, DC, USA: National Research Council.
Nugent, R. A., Zhang, G. & Gambrell, R. P. (2010). The effect of
exopolymers on the erosional resistance of cohesive sediments.
Proc. 5th Int. Conf. on Scour and Erosion, San Francisco, CA,
162–171.
Phadnis, H. & Santamarina, J. C. (2012). Bacteria in sediments:
pore size effects. Ge
´otechnique Lett.1, 91– 93.
Pietruszczk, S., Pande, G. N. & Oulapour, M. (2003). A hypothesis
for mitigation of risk of liquefaction. Ge
´otechnique 53, No. 9,
833– 838, http://dx.doi.org/10.1680/geot.2003.53.9.833.
Ramachandran, S. K., Ramakrishnan, V. & Bang, S. S. (2001).
Remediation of concrete using micro-organisms. ACI Mater. J.
98, No. 1, 3– 9.
Ramakrishnan, V., Ramesh, K. P. & Bang, S. S. (2001). Bacterial
concrete. Proc. SPIE 4234, 168– 176.
Rebata-Landa, V. & Santamarina, J. C. (2006). Mechanical limits to
microbial activity in deep sediments. Geochem. Geophys. Geo-
syst.7, No. 11, 1–12.
Rebata-Landa, V. & Santamarina, J. C. (2012). Mechanical effects
of biogenic nitrogen gas bubbles in soils. ASCE J. Geotech.
Geoenviron. Engng 138, No. 2, 128–137.
Renforth, P., Manning, D. A. C. & Lopez-Capel, E. (2009).
Carbonate precipitation in artificial soils as a sink for atmo-
spheric carbon dioxide. Appl. Geochem.24, No. 9, 1757–1764.
Renforth, P., Edmondson, J., Leake, J. R., Gaston, K. J. & Manning, D.
A. C. (2011). Designing a carbon capture function into urban soils.
Proc. ICE – Urban Design and Planning 164, No. 2, 121–128.
Roden, E. E., Leonardo, M. R. & Ferris, F. G. (2002). Immobiliza-
tion of strontium during iron biomineralization coupled to
dissimilatory hydrous ferric oxide reduction. Geochim. Cosmo-
chim. Acta 66, No. 16, 2823–2839.
Roscoe, K. H., Schofield, A. N. & Wroth, C. P. (1958). On the
yielding of soils. Ge
´otechnique 8, No. 1, 22–53, http://dx.doi.
org/10.1680/geot.1958.8.1.22.
Rusu, C., Cheng, X. & Li, M. (2011). Biological clogging in
Tangshan sand columns under salt water intrusion by Sporosar-
cina pasteurii. Adv. Mater. Res.250– 253, 2040– 2046.
Sanderson, K. (2008). Waste concrete could help to lock up carbon.
Nature, http://dx.doi.org/10.1038/news.2008.732.
Schofield, A. N. & Wroth, C. P. (1968). Critical state soil mech-
anics. London, UK: McGraw-Hill.
Seagren, E. A. & Aydilek, A. H. (2010). Biomediated geomechani-
cal processes. In Environmental microbiology, 2nd edn (eds R.
Mitchell and J.-D. Gu), pp. 319 –348. Hoboken, NJ, USA: John
Wiley & Sons.
Seki, K., Miyazaki, T. & Nakano, M. (1998). Effects of micro-
organisms on hydraulic conductivity decrease in infiltration. Eur.
J. Soil Sci.49, No. 2, 231–236.
Sherif, M. A., Ishibashi, I. & Tsuchiya, C. (1977). Saturation effect
on initial soil liquefaction. ASCE J. Geotech. Engng 103, No. 8,
914– 917.
Sivavec, T., Krug, T., Berry-Spark, K. & Focht, R. (2003). Perform-
ance monitoring of a permeable reactive barrier at the Somers-
worth, New Hampshire Landfill Superfund site. In Chlorinated
solvent and DNAPL remediation (eds S. M. Henry and S. D.
Warner), American Chemical Society, Symposium Series, Vol.
837, pp. 259– 277. Washington, DC, USA: ACS Publications.
Slichter, C. S. (1905). Field measurements of the rate of movement
of underground waters, USGS Water Supply and Irrigation
Paper 140. Washington, DC, USA: Government Printing Office.
Stabnikov, V., Naeimi, M., Ivanov, V. & Chu, J. (2011). Formation
of water-impermeable crust on sand surface using biocement.
Cement Concrete Res.41, No. 11, 1143– 1149.
Stal, L. J. (2010). Microphytobenthos as a biogeomorphological
force in intertidal sediment stabilization. Ecol. Engng 36, No. 2,
236– 245.
Stocks-Fischer, S., Galinat, J. K. & Bang, S. S. (1999). Microbio-
logical precipitation of CaCO3:Soil Biol. Biochem.31, No. 11,
1563– 1571.
Tagliaferri, F., Waller, J., Ando, E., Hall, S. A., Viggiani, G.,
Besuelle, P. & DeJong, J. T. (2011). Observing strain localisation
processes in bio-cemented sand using X-ray imaging. Granular
Matter 13, No. 3, 247–250.
Talsma, T. & van der Lelij, A. (1976). Infiltration and water move-
ment in an in situ swelling soil during prolonged ponding. Aust.
J. Soil Res.14, No. 3, 337–349.
Taylor, D. (1948). Fundamentals of soil mechanics. New York, NY,
USA: Wiley.
Taylor, L. L., Leake, J. R., Quirk, J., Hardy, K., Banwart, S. A. &
Beerling, D. J. (2009). Biological weathering and the long-term
carbon cycle: integrating mycorrhizal evolution and function
into the current paradigm. Geobiology 7, No. 2, 171–191.
Terzaghi, K. (1924). Erdbaumechanik. Vienna, Austria: Franz Deu-
ticke (in German).
Terzaghi, K. (1955). Influence of geological factors on the engineer-
ing properties of sediments. Econ. Geol.50, 557–618.
Tobler, D. J., Maclachlan, E. & Phoenix, V. R. (2012). Microbially
mediated plugging of porous media and the impact of different
injection strategies. Ecol. Engng 42, 270– 278.
Van Meurs, G., Van Der Zon, W., Lambert, J., Van Ree, D.,
Whiffin, V. & Molendijk, W. (2006). The challenge to adapt soil
properties. Proc. 5th ICEG: Environ. Geotechnics: Opportu-
nities, Challenges and Responsibilities for Environ. Geotechnics,
2, 1192– 1199.
Van Paassen, L. A. (2009). Biogrout, ground improvement by
microbially induced carbonate precipitation. Doctoral disserta-
tion, Department of Biotechnology, Delft University of Technol-
ogy, the Netherlands.
300 DEJONG ET AL.

Van Paassen, L. A. (2011). Bio-mediated ground improvement:
from laboratory experiment to pilot applications. Proc.
GeoFrontiers 2011: Advances in Geotechnical Engineering,
Dallas, TX, ASCE Geotechnical Special Publication 211, 4099 –
4108.
Van Paassen, L. A., Harkes, M. P., Van Zwieten, G. A., Van der
Zon, W. H., Van der Star, W. R. L. & Van Loosdrecht, M. C.
M. (2009). Scale up of BioGrout: a biological ground reinforce-
ment method. Proc. 17th Int. Conf. Soil Mech. Geotechn. Engng,
Alexandria, 2328–2333.
Van Paassen, L. A., Daza, C. M., Staal, M., Sorokin, D. Y., van der
Zon, W. & van Loosdrecht, M. C. M. (2010a). Potential soil
reinforcement by biological denitrification. Ecol. Engng 36, No.
2, 168– 175.
Van Paassen, L. A., Ghose, R., van der Linden, T. J. M., van der
Star, W. R. L. & van Loosdrecht, M. C. M. (2010b). Quantify-
ing biomediated ground improvement by ureolysis: large-scale
biogrout experiment. ASCE J. Geotech. Geoenviron. Engng 136,
No. 12, 1721– 1728.
Van Wijngaarden, W. K., Vermolen, F. J., van Meurs, G. A. M. &
Vuik, C. (2011). Modelling biogrout: a new ground improvement
method based on microbial-induced carbonate precipitation.
Transp. Porous Media 87, No. 2, 397– 420.
Van Wijngaarden, W. K., Vermolen, F. J., van Meurs, G. A. M. &
Vuik, C. A. (2012). Mathematical model and analytical solution
for the fixation of bacteria in biogrout. Transp. Porous Media
92, No. 3, 847– 866.
Warthmann, R., van Lith, Y., Vasconcelos, C., McKenzie, J. A. &
Karpoff, A. M. (2000). Bacterially induced dolomite precipita-
tion in anoxic culture experiments. Geology 28, No. 12, 1091–
1094.
Washbourne, C.-L., Renforth, P. & Manning, D. A. C. (2012).
Investigating carbonate formation in urban soils as a method for
capture and storage of atmospheric carbon. Sci. Total Env. 431,
166– 175.
Weaver, T., Burbank, M., Lewis, R., Lewis, A., Crawford, R. &
Williams, B. (2011). Bio-induced calcite, iron, and manganese
precipitation for geotechnical engineering applications. Proc.
GeoFrontiers 2011: Advances in Geotechnical Engineering,
Dallas, TX, ASCE Geotechnical Special Publication 211, 3975 –
3983.
Weil, M. H., DeJong, J. T., Martinez, B. C. & Mortensen, B. M.
(2012). Seismic and resistivity measurements for real-time mon-
itoring of microbially induced calcite precipitation in sand.
ASTM Geotech. Test. J.35, No. 2, GTJ103365.
Whiffin, V. S., Van Paassen, L. A. & Harkes, M. P. (2007).
Microbial carbonate precipitation as a soil improvement techni-
que. Geomicrobiol. J.24, No. 5, 417 –423.
Whitman, W. B., Coleman, D. C. & Wiebe, W. J. (1998). Prokar-
yotes: the unseen majority. Proc. Nat. Acad. Sci.95, No. 12,
6578– 6583.
Woese, C. R., Kandler, O. & Wheelis, M. L. (1990). Towards a
natural system of organisms: proposal for the domains of
Archaea, Bacteria, and Eucarya. Proc. Nat. Acad. Sci.87, No.
12, 4576– 4579.
Wu, J. G., Stahl, P. & Zhang, R. (1997). Experimental study on the
reduction of soil hydraulic conductivity by enhanced biomass
growth. Soil Sci.162, No. 10, 741– 748.
Yang, Z., Cheng, X. & Li, M. (2011). Engineering properties of
MICP-bonded sandstones used for historical masonry building
restoration. Proc. GeoFrontiers 2011: Advances in Geotechnical
Engineering, Dallas, TX, ASCE Geotechnical Special Publica-
tion 211, 4031– 4040.
Yoshimi, Y., Tanaka, K. & Tokimatsu, K. (1989). Liquefaction
resistance of a partially saturated sand. Soils Found.29, No. 3,
157– 162.
BIOGEOCHEMICAL PROCESSES AND GEOTECHNICAL APPLICATIONS 301