Rev Environ Sci Biotechnol (2008) 7:139153

DOI 10.1007/s11157-007-9126-3

REVIEW PAPER

Applications of microorganisms to geotechnical engineering

for bioclogging and biocementation of soil in situ
Volodymyr Ivanov Jian Chu

Published online: 23 January 2008

Springer Science+Business Media B.V. 2008

Abstract Microbial Geotechnology is a new branch

of geotechnical engineering that deals with the
applications of microbiological methods to geological
materials used in engineering. The aim of these
applications is to improve the mechanical properties
of soil so that it will be more suitable for construction
or environmental purposes. Two notable applications,
bioclogging and biocementation, have been explored.
Bioclogging is the production of pore-filling materials through microbial means so that the porosity and
hydraulic conductivity of soil can be reduced.
Biocementation is the generation of particle-binding
materials through microbial processes in situ so that
the shear strength of soil can be increased. The most
suitable microorganisms for soil bioclogging or
biocementation are facultative anaerobic and microaerophilic bacteria, although anaerobic fermenting
bacteria, anaerobic respiring bacteria, and obligate
aerobic bacteria may also be suitable to be used in
geotechnical engineering. The majority of the studies
on Microbial Geotechnology at present are at the
laboratory stage. Due to the complexity, the applications of Microbial Geotechnology would require an
integration of microbiology, ecology, geochemistry,
and geotechnical engineering knowledge.

V. Ivanov (&)
J. Chu

Block N1, School of Civil and Environmental
Engineering, Nanyang Technological University,
50 Nanyang Avenue, Singapore 639798, Singapore
e-mail: cvivanov@ntu.edu.sg

Keywords Bacteria
Biocementation

Bioclogging
Geotechnical engineering

1 Introduction
Biogeotechnology is a branch of Geotechnical Engineering that deals with the applications of biological
methods to geotechnical engineering problems. At the
present, biogeotechnologies are related mainly to the
applications of plants or vegetative soil cover for soil
erosion control and slope protection, prevention of
slope failure, and reduction of water infiltration into
slopes. Biogeotechnology have advantages of low
investment and maintenance costs. It also offers
benefits to environment and aesthetics (Karol 2003).
Microbial geotechnology is an emerging branch of
Geotechnical Engineering. Although there are various
potential applications of microorganisms to geotechnical engineering, at the present, promising applications are only concentrated in the bioclogging and
biocementation. Therefore, this review is covering
mainly the recent developments in these two areas.
Bioclogging is to reduce the hydraulic conductivity of soil and porous rocks due to microbial activity
or products. It could be used to reduce drain channel
erosion, form grout curtains to reduce the migration
of heavy metals and organic pollutants, and prevent
piping of earth dams and dikes.
Biocementation is to enhance the strength and
stiffness properties of soil and rocks though microbial

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activity or products. It could be used to prevent soil

avalanching, reduce the swelling potential of clayey
soil, mitigate the liquefaction potential of sand, and
compact soil on reclaimed land sites.
As the scale of geotechnical construction such as
land reclamation is usually large, a microbial treatment could be one of the most cost effective methods.
The major factors that affect the applications of
microorganisms to geotechnical engineering include
the screening and identification of suitable microorganisms for different applications and different
environments, the optimization of microbial activity
in situ, biosafety of the application, cost effectiveness,
and stability of soil properties after biomodification.
Among all the factors, cost effectiveness is the most
important factor for large-scale application.
As an emerging discipline, microbial geotechnology has been developing rapidly in recent years. Some
of the developments have already been summarized
by Baveye et al. (1998), Castainer et al. (1999) and
Mitchell and Santamarina (2005). This review paper
intends to offer an update of the most recent
developments related to bioclogging and biocementation. The aims are to summarize the existing or
potential applications in these two areas, to compare
advantages and disadvantages of different methods,
and to identify some of the physiological groups of
prokaryotes that could be potentially used effectively
for biocogging and biocementations. This paper is
organized in such a way that the applications related
to bioclogging and biocementation are summarized
first before a method for the screening of the suitable
physiological groups of prokaryotes is suggested.

2 Bioclogging: microbial grouting in situ

for water flow control
Chemical grouting is a process to fill the soil voids
with fluid grouts. It is often used to control water flow
(Karol 2003). Common grouts are solution or
suspension of sodium silicate, acrylates, acrylamides,
and polyurethanes. Industrially produced water-insoluble gel-forming biopolymers of microbial origin
such as xantan, chitosan, polyglutamic acid, sodium
alginate, and polyhydroxybutyrate can also be used as
grouts for soil erosion control, enclosing of bioremediation zone, and mitigating soil liquefaction
(Momemi et al. 1999; Yang et al. 1993; Yen et al.

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1996; Etemadi et al. 2003; Gioia and Ciriello 2006).

Suitable microorganisms could be applied to soil to
serve the same purpose through microbial growth and
biosynthesis of extracellular biopolymers.

2.1 Microbial products and processes

It has been observed by Vandevivere and Baveye
(1992) and Bonala and Reddi (1998) that accumulation
of bacterial biomass, insoluble bacterial slime, and
poorly soluble biogenic gas bubbles in soil will make
the soil more impermeable for water. Therefore,
bioclogging can be used to seal a leaking construction
pit, landfill, or dike. One of the bioclogging processes
is the microbial production of water-insoluble polysaccharides in situ. This can be performed by addition
of carbon source and enriched or pure culture of
microorganisms to soil if necessary. Role of microbial
polysaccharides in soil particles aggregation and
clogging of soil pores is well known. Although a lot
of gel-forming water-insoluble microbial polysaccharides are produced in industry (Sutherland 1990), these
materials cannot be used for soil grouting because of
the high cost involved. Only growth of microorganisms, which were added to soil, and accumulation of
water-insoluble microbial slime from cheap raw
materials in situ can be considered as economically
reasonable option for bioclogging. An addition of
microorganisms must be accompanied with medium
that initiates bioclogging. However, this process could
be complicated by transport of microbial cells into soil,
which depends on cell size, cell surface properties, and
cell physiological state (Murphy and Ginn 2000).
Production of bacterial exopolymers in situ can be
used to modify soil properties. This has been adopted
for enhancing oil recovery or soil bioremediation
(Stewart and Fogler 2001). The groups of microorganisms that produce insoluble extracellular
polysaccharides to bind the soil particles and fill in
the soil pores are oligotrophic bacteria from genus
Caulobacter (Ravenscroft et al. 1991; Tsang et al.
2006), aerobic Gram-negative bacteria from genera
Acinetobacter, Agrobacterium, Alcaligenes, Arcobacter, Cytophaga, Flavobacterium, Pseudomonas,
and Rhizobium (Harada 1983; Portilho et al. 2006;
Ross et al. 2001). Other groups of microorganisms
are cellulose-degrading bacteria from species Cellulomonas flavigena (Kenyon et al. 2005) and many

Rev Environ Sci Biotechnol (2008) 7:139153

species of Gram-positive facultative anaerobic and

aerobic bacteria, such as Leuconostoc mesenteroides
that is used for the production of a water-insoluble
exopolymer dextran (Stewart and Fogler 2001). The
strains of Cellulomonas flavigena may be suitable for
large scale soil clogging or soil grouting because
these bacteria are Gram-positive (i.e. resistant to the
changes of osmotic pressure) and can utilize cellulose
for the production of a curdlan-type (beta-1,3-glucan)
exopolysaccharide. In this case, such sources of
carbon as cellulose-containing agricultural and horticultural wastes, and saw dust can be hypothetically
used for the propagation of bacteria in soil and
formation of the pore-clogging polysaccharide.
It is well known that almost all bacteria produce
exopolysaccharides under excess of carbohydrates or
other water soluble sources of carbon over source of
nitrogen (Wingender et al. 1999). Therefore, such
food-processing wastes or sub-products as corn
glucose syrup, cassava glucose syrup and molasses
with C: N ratio [ 20 are used for industrial production
of bacterial water-insoluble polysaccharides (Portilho
et al. 2006).
Probably, nitrifying bacteria that produce extracellular polysaccharides from CO2 of air during
oxidation of ammonium (Stehr et al. 1995) can also
be used for the soil clogging. Almost every natural
nitrifying biofilm contains nitrifying bacteria, which
are embedded into a layer of microbial slime (Ivanov
et al. 2006a). Accumulation of aggregating bacterial
cells in soil pores could also contribute to soil
clogging. Such bacterial strains with fast and strong
cell aggregation are used in wastewater treatment in
fixed biofilm reactors and for the fast formation of
microbial granules (Ivanov et al. 2005; Ivanov 2006;
Ivanov and Tay 2006b).
Exopolysaccharide-producing bacteria may be
used to modify the soil matrix in situ. After growth
of these bacteria in soil, its permeability for water
will be greatly reduced. This approach could be used
for different geotechnical applications such as selective zonal bioremediation, harbor and dam control,
erosion potential minimization, earthquake liquefaction mitigation, construction of reactive barrier, and
long-term stabilization of contaminated soils (Yang
et al. 1993). Organic wastes can be used as a source
of organic matter for fermenting and exopolysaccharideproducing microorganisms in large-scale
applications to diminish the cost of soil clogging.

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For example, municipal solid wastes, sewage

sludge, uncomposted or composted poultry manure
has been added to soil to diminish soil erosion. In
these experiments, a positive correlation between the
stability of soil aggregates and the produced microbial
biomass in soil has been found (Mataix-Solera et al.
2005). It was shown in other experiments that the
introduction of polysaccharideproducing algae and
bacteria in irrigation channel could provide a low cost
technique for seepage control in irrigation channel.
The reduction of hydraulic conductivity by 22% of its
original value within a month of inoculating soil
columns with algae correlated with the amount of
produced polysaccharides (Ragusa et al. 1994).
Laboratory tests have been carried out to identify
the microbial groups that could be used for bioclogging. The study has demonstrated that enrichment
cultures of nitrifying and oligotrophic bacteria can be
used for bioclogging. Enrichment culture of nitrifying
bacteria, grown in sand with dissolved ammonium,
produced microbial polysaccharides from solution of
ammonium and CO2 of air. The application of
ammonium solution decreased the hydraulic conductivity of sand from 10-4 m/s to 10-6 m/s. Enrichment
culture of oligotrophic bacteria, grown in sand with
low concentration of glucose, produced polysaccharides from solution of glucose and reduced the
hydraulic conductivity of the sand from 10-4 m/s to
10-6 m/s (Ivanov and Chu, unpublished data).

2.2 Field tests and applications

Attempts to use bioclogging to diminish the hydraulic
conductivity of the dams and dykes, to reduce infiltration from the ponds and leakage in construction sites or
landfills, to prevent soil erosion, and to make a barrier
on soil pollution site have been made (James et al.
2000; Seki et al. 1998, 2005). Microbial plugging
in situ is also used to increase the extent and rate of
heavy oil production by the selective reduction of the
permeability of zones in an oil-bearing underground
formation after injection of exopolymer-producing
microorganisms and carbon source into the oil-bearing
formation (Thompson and Thomas 1984, 1985).
Experimental studies on the reduction of soil
hydraulic conductivity by enhanced biomass growth in
soil with dextrose-nutrient solution have demonstrated
a positive correlation between attached microbial

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biomass and the soil hydraulic conductivity (Wu et al.

1997). Field bioclogging tests to reduce soil permeability for water and diminish soil erosion have been also
reported (McConkey et al. 1990). If soil has poor
drainage, addition of waste organic matter such as straw
and manure in soil will lead to their microbial aerobic
decomposition and creation of anaerobic conditions in
soil. This soil gleization is accompanied with microbial
reduction of Fe(III) and reduction in soil permeability. It
is considered that the clogging of the soil pores during
gleization is due to the production of exopolysaccharides from the decomposed organic material. However,
soil gleization does not provide satisfactory long-term
seepage control for flooded channels (McConkey et al.
1990). This supports further the above mentioned
conclusion that stable bioclogging is feasible only
under soil conditions favorable for exopolysaccharideproducing microorganisms, but not favorable for exopolysaccharide-degrading microorganisms.
Bouwer (2002) reported that during artificial
recharge of groundwater using surface water, clogging layer of silt on basin bottom was formed. This
type of clogging may also be possible due to the
production of exopolysaccharides by oligotrophic
bacteria in organicpoor soil. Artificial recharge of
groundwater by surface water or effluent of wastewater treatment plant through permeable soil or sand
could promote growth of oligotrophic bacteria and
formation of clogging layer of their slime.
However, biopolymers clogging could be unstable
because of their biodegradability, thermal sensitivity,
and low mechanical resistance to pressure drop across
the plug. In some cases, biological clogging of porous
media and wells is a significant geotechnical problem
due to negative effect of bioclogging on soil bioremediation, sand filtration, and aquifer recharge (Bonala
and Reddi 1998; Dupin and McCarty 2000; Hajra et al.
2000; Ralph and Stevenson 1995).
Stable bioclogging could be due to precipitation of
inorganic substances in the soil pores, for example,
precipitation of calcium carbonate at increased
pH (Bachmeier et al. 2002; Castanier et al. 1999;
Hammes and Verstraete 2002; Stocks-Fischer and
Galinat 1999). This approach is used in the microbesmediated process for reducing the porosity and
permeability of a subsurface geological formation.
Bioclogging due to the precipitation of minerals from
an aqueous system has also been proposed to enhance
the recovery of oil from oil reservoirs or to control the

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flow of a spilled contaminant in a reservoir (Ferris and

Stehmeier 1992; Ferris et al. 1996; Fujita et al. 2000).
One promising application is the formation of the
soil plugs by Bacillus pasteurii in the medium
containing urea and calcium chloride. Bacteria produce enzyme urease that hydrolyzes urea by the
following reaction:


(NH2 )2 CO 3H2 O ! 2NH
4 HCO3 OH

1
Due to this enzymatic reaction, pH is increased and
hydrocarbonate is produced. It is initiating precipitation of calcium carbonate, which clogging the pores
and binding soil particles (cited from Kucharski et al.
2005). The bioclogging could be used in the industry to
decrease permeability of porous media, reduce fluid
flow, enhance the recovery of oil from reservoirs (cited
from Kucharski et al. 2005), and repair cracks in
concrete (Ramachandran et al. 2001). For the formation of new bioclogging materials the following
microbial techniques are used: (a) the bioproduction
of bacterial slime due to supply of saccharides into soil
for the soil obstruction in the dike or dune; (b) bacteriamediated transformation of sand to sandstone using
soil bacteria, urea, and calcium ions. Bacteria hydrolyse urea to ammonium increasing pH, producing
carbonate, and precipitating calcium as calcium carbonate under high pH (http://www.geodelft.com/files/
bacteriabuildbiodikes.pdf and http://www.smartsoils.
nl). A pilot scale test of bioclogging using bioproducton of slime in soil was successfully carried out in 2004.
After 6 weeks, the hydraulic resistance of soil in
experiment was enhanced by a factor five. Afterwards,
the resistance factor increased further to a value of
about thirty. Even more then 3 months after the last
injection of nutrients, the hydraulic resistance
remained stable. In control container, without injection
of the nutrients, the hydraulic resistance around the
inflow was not decreased (Veenbergen et al. 2005).
Another potential application of bioclogging is sealing
of the unforeseen leaks in the sheet piling screens
around the construction wells, which occur at some
10% of all construction pits dug in the Netherlands. It is
estimated that the cost of solving such problems totals
several tens of millions of euros each year. The injection of nutrients into the groundwater ensures that it
flows towards the problem area. If needed group of soil
microorganisms is absent in the porous medium, these

Rev Environ Sci Biotechnol (2008) 7:139153

microorganisms must be injected or infiltrated into

groundwater.

2.3 Limitations and potential problems

A major lmitation or problem in the use of microbial
polysaccharides in situ is the stability of soil properties
after treatment. Many known microorganisms in soil
can degrade water-insoluble microbial exopolysaccharides. Therefore, a successful and stable bioclogging
process is possible only under soil conditions that are
favorable for exopolysaccharide-producing microorganisms, but not favorable for exopolysaccharidedegrading microorganisms. One example is the addition
of ammonium to organic-poor soil or sand, stimulating
growth of nitrifying bacteria, which synthesize polysaccharides from CO2. Another example is the
production of water-insoluble exopolysaccharides in
organic-poor soil or sand by oligotrophic bacteria at
permanent supply into soil a solution with low concentration of energy and carbon source for bacterial growth
and synthesis of polysaccharides (Ivanov and Chu,
unpublished data).
The cases of clogging of sand-filled and gravel-filled
agricultural drains are well known (Baveye et al. 1998).
This is probably due to the production of exopolysaccharides by nitrifying bacteria, oxidizing ammonium in
agricultural drainage. A problem in the application of
nitrifying and oligotrophic bacteria is that they are slow
growing organisms with low rate of exopolysaccharide
production and their applications will require long-term
treatment of soil for its clogging. For example, duration
of exponential accumulation of biomass in soil by
1,000 times from the initial content is from 69 to
690 days when the growth rate of nitrifying or oligotrophic bacteria in situ is ranging from 0.1 d-1 to
0.01 d-1. Any temporarily shortage of ammonia or
oxygen will significantly decrease the growth rate and
content of ammonia-oxidizing bacteria in treated soil
because the decay rate of ammonia-oxidizing bacteria
under ammonia or oxygen depletion is from 0.08 to
0.55 d-1 (Geets et al. 2006), which is comparable with
the growth rate of these bacteria in situ. Therefore,
bioclogging of soil with water-insoluble exopolysaccharides could be used in cases where the long duration
of bioclogging does not limit the application.
Another potential problem of microbial clogging
in situ is that the penetration of microbial cells in

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soil depth is limited by the minimum soil pore size

from 0.5 to 2 lm. Therefore, the method can be
used for limited soil types with suitable hydraulic
conductivity.
One more problem is that the growth of clogging
biofilm in soil pores affects the concentrations and
mass transfer rates of nutrients and microbial metabolites between biofilm and flow through the pores
(Baveye et al. 1998; Rodgers et al. 2004; Ross et al.
2001; Sharp et al. 1999). Concentration of dissolved
oxygen is the most sensitive parameter in soil
clogging. Although, concentrations of carbon, nitrogen, and phosphorous sources, and metabolites such
as hydrocarbonate and organic acids will also affect
significantly the rate of microbial growth and activity
of clogging microorganisms in soil.
Secondary microbial products can be produced
during bioclogging, for example, organic acids due to
fermentation or nitrate due to nitrification. All
residual products of bioclogging must be removed
from soil or converted to neutral products like water,
carbon dioxide, and nitrogen gas.

2.4 Summary on bioclogging

Different possible microbial processes that can lead
potentially to bioclogging are summarized in Table 1.
These include formation of impermeable layer of
algal and cyanobacterial biomass; production of slime
in soil by aerobic and facultative anaerobic heterotrophic bacteria, oligotrophic microaerophilic bacteria
and nitrifying bacteria; production of undissolved
sulphides of metals by sulphate-reducing bacteria;
formation of undissolved carbonates of metals by
ammonifying bacteria; and production of ferrous
solution and precipitation of undissolved ferrous and
ferric salts and hydroxides in soil by iron-reducing
bacteria. Not all of these processes have been tested in
the laboratory and in the field.

3 Biocementation: structural microbial grouting

in situ
Chemical cementation (or chemical grouting) is to fill
the sand voids with fluid chemical grouts to produce
sandstone like masses to carry loads. This method is
widely used in geotechnical engineering (Indraratna

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Table 1 Microbial processes that can lead potentially to bioclogging

Physiological group of
microorganisms

Mechanism of bioclogging

Essential conditions for

bioclogging

Potential geotechnical
applications

Algae and cyanobacteria

Formation of impermeable layer of

biomass

Light penetration and

presence of nutrients

Reduce of water infiltration

into slopes and control
seepage

Aerobic and facultative

Production of slime in soil
anaerobic heterotrophic
slime-producing
bacteria

Presence of oxygen and

medium with ratio of
C:N [ 20

Avoide cover for soil erosion

control and slope protection.

Oligotrophic
Production of slime in soil
microaerophilic bacteria

Low concentration oxygen

and medium with low
concentration of carbon
source

Reduce drain channel erosion

and control seepage

Nitrifying bacteria

Presence of ammonium and

oxygen in soil

Reduce drain channel erosion

Production of slime in soil

Sulphate-reducing bacteria Production of undissolved sulphides of Anaerobic conditions;

metals
presence of sulphate and
carbon source in soil

Form grout curtains to reduce

the migration of heavy
metals and organic
pollutants

Ammonifying bacteria

Formation of undissolved carbonates of Presence of urea and

dissolved metal salt
metals in soil due to increase of pH
and release of CO2

Prevent piping of earth dams

and dikes

Iron-reducing bacteria

Production of ferrous solution and

Anaerobic conditions
precipitation of undissolved ferrous
changed for aerobic
and ferric salts and hydroxides in soil
conditions; presence of
ferric minerals

Prevent piping of earth dams

and dikes

and Chu 2005). The chemicals that are used to bind

soil particles include sodium silicate, calcium chloride, calcium hydroxide (lime), cement, acrylates,
acrylamides, polyurethanes (Karol 2003).
Microbial cementation (or structural microbial
grouting) is to form soil particle-binding material
after introduction of microbes and specific additives
into soil. It is different from biobinding, which is
formation of the particle-binding cellular chains.
Biobinding can be performed by mycelial fungi,
actynomycetes, and filamentous phototrophic and
heterotrophic bacteria. In some experiments, the
added biomass of some fungal strains binds the sand
grains and increases the shear strength of soil
(Meadows et al. 1994). However, biobinding does
not seem to be suitable for large scale operations such
as enhancing the liquefaction resistance of land
reclamation sites because all biological bindings are
unstable and can be degraded by other microorganisms. Only processes that are mediated by microbial
activity, such as oxidation, reduction, dissolution, and
precipitation of inorganic substances in soil pores can
form stable and strong binding of soil particles.

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3.1 Microbial products and processes

Chemical cementation of soil in nature is due to the
precipitation of material in spaces between soil
particles and binding of these particles together into
a hard rock. Microorganisms are often associated
with the cemented sediments containing calcium,
magnesium, iron, manganese, and aluminium, which
are crystallized as carbonates, silicates, phosphates,
sulphides, and hydroxides, especially iron hydroxides
(DeJong et al. 2006). Chemical transformations of
metals and ions in soil are mediated by soil microorganisms. Example of sand cementation in nature is
the formation of ferrihydrite in pores (Ross et al.
1989). Iron hydroxides, depending on its crystallization, can be also an important cementing agent in
soils (Dniker et al. 2003). Drying of soil samples
containing iron hydroxide can produce irreversible
soil hardening and cementation. In areas of soil with
high pH or redox potential the iron hydroxide is
precipitated forming cemented concretions or nodules. Biological cementation with iron hydroxides
can be detected at the roots of all wetland plants

Rev Environ Sci Biotechnol (2008) 7:139153

where Fe(II), produced by iron-reducing bacteria,

reacts with oxygen released by the roots (JohnsonGreen and Crowder 1991; Weiss et al. 2005). To
form ferric hydrates by oxidation and hydrolysis of
Fe(II), iron (III) must be preliminary reduced by ironreducing bacteria. Oxidation of ferrous ions and
chelates in soil is performed chemically or catalyzed by neutrophlic or acidophilic iron-oxidizing
bacteria.
Another well known example of natural cementation is the precipitation of silica dioxide, which
fills in the pores and glues the soil particles together.
It is also known as natural soil calcification due to
the deposition of calcium carbonate from upward
flow of groundwater, enhanced evapotranspiration
from soil, or formation of calcium carbonate within
zones of elevated carbonate alkalinity formed by
microbial decay of organic matter (Mozley and
Davis 2005).
Kucharski et al. (2005) applied for a patent on
microbial biocementation for the formation of high
strength cement in a permeable material using the
combination of this material with biomass of ureaseproducing microorganism, urea, and soluble calcium
salts. Microorganisms provide fast urea hydrolysis,
increase the pH during hydrolysis of urea to ammonia,
and form calcite in soil or rocks. The cement produced
has a compressive strength up to 5MPa. The materials,
treated by biocementation, may be conglomerate,
breccia, sandstone, siltstone, shale, limestone, gypsum, peat, lignite, sand, soil, clay, sediments, and
sawdust. The urease-producing microorganisms are
from genera Bacillus, Sporosarcina, Sporolactobacillus, Clostridium and Desulfotomaculum.

3.2 Laboratory tests and applications

Some laboratory tests on dike reinforcement using
biocementation were carried out in Netherlands (http:
//www.geodelft.com/files/bacteriabuildbiodikes.pdf).
Biomass of aerobic bacteria has been introduced into
soil to achieve cementation due to the bacteria-mediated production of calcium carbonate connecting the
sand grains together with the formation of sandstone.
Similarly, a cemented soil matrix within initially
loose, collapsible sand was formed using microbialinduced calcite precipitation due to amendment of the
biomass of aerobic bacteria Bacillus pasteurii and a

145

liquid growth medium with urea and a dissolved calcium salt. Cemented sand, assessed by shear wave
velocity and undrained compression triaxial tests,
exhibits a less brittle shear behavior with a higher
initial shear stiffness and ultimate shear capacity than
untreated loose specimens. Precipitated calcite is
formed through particleparticle contacts. This has
been confirmed by X-ray compositional mapping in
which the observed cement bonds comprise of calcite
(DeJong et al. 2006).
This method of microbial cementation could be
used for the following civil and environmental
engineering applications (Kucharski et al. 2005):

Enhancing stability for retaining walls, embankments, and dams;

Reinforcing or stabilizing soil to facilitate the
stability of tunnels or underground constructions;
Increasing the bearing capacity of piled or nonpiled foundations;
Reducing the liquefaction potential of soil;
Treating pavement surface;
Strengthening tailings dams to prevent erosion
and slope failure;
Constructing a permeable reactive barriers in
mining and environmental engineering;
Binding of the dust particles on exposed surfaces
to reduce dust levels;
Increasing the resistance to petroleum borehole
degradation during drilling and extraction;
Increasing the resistance of offshore structures to
erosion of sediment within or beneath gravity
foundations and pipelines;
Stabilising pollutants from soil by the binding;
Controlling erosion in coastal area and rivers;
Creating water filters and bore hole filters;
Immobilising bacterial cells into a cemented
active biofilter.

However, successful field applications of biocementation have not been reported so far.
The study on the biocementation of sand with
enrichment culture of iron-reducing bacteria, fine
particles of iron ore, and cellulose as electron donor
has demonstrated that solution of Fe2+ (700 mg Fe2+/
L), formed from iron ore particles, can produce
significant cementation effect for sand after oxidation
of Fe2+ by air. The unconfined shear strength of the
sand has increased from zero to 140 kPa (Ivanov and
Chu, unpublished data).

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3.3 Comparison of soil biocementation

with mechanical compaction and chemical
grouting of soil
Modification of the physical properties of soil can be
achieved using mechanical compaction, chemical
grouting, or biocementation. Shallow mechanical
compaction of soil is accomplished by rolling or
vibrating. Deep compaction of soil is performed by
vibrocompaction or dynamic compaction which
involves tamping the ground by repeated dropping a
heavy weight. However, most of the compaction
techniques are only effective or economically viable
to a depth less than 10 m (Indraratna and Chu 2005).
Another major disadvantage of dynamic compaction
is that it is not applicable for clayey soils and recent
municipal landfills.
Chemical grouting injects chemical grout into soil
or rock to enhance their mechanical properties by
changing their physical properties. To increase soil
stability and strength, some chemical suspended
substances (particulate grout) or dissolved substances
(chemical grout) must be added. For soil slope
stability and erosion control, only the top layer of
soil is needed to be treated. To diminish soil
permeability and increase its mechanical strength,
an injection of additives into soil is used. Grouting
fluids comprise of typically cement, bentonite, silicate (sodium silicate solution with cement, bentonite,
or chemical additives such as calcium chloride,
sodium aluminate, phosphoric and some other acids),
lignosulfonates (waste by-product of paper mills),
pozzolanic-based materials, thermoplastic polymers,
organic polymers, a solution of monomers polymerizing in situ, a mixture of ferrous sulfate combined
with calcium hydroxide (Karol 2003). The market
share of two major commercial products, silicates and
acrylic-based grouts, is from 85% to 90% in the
United States (Karol 2003). The pressure injections
of grouting fluids are most effective in sandy soils
and cracked rocks with filtration rates from 0.5 to
80 m/day. After injection of the suspension into soil,
a cylinder of strengthened soil or rock with a
diameter 0.31 m (depending on filtration rate) is
formed around the injector or injection well. Injectors
or injecting wells are arranged by the chess cells
order to ensure full fixation of soil on defined area.
Distance between the injectors must be approximately 1.5 times smaller than radius of the fixed soil

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column formed by one injector. The grout must have

a proper hardening time that matches the method of
injection. This will ensure that the grout does not
harden before it reaches the areas required, or harden
too slowly so the grout will spread too thinly.
There are several ways of injection in chemical
grouting, which can be used also for microbial
grouting. In low pressure grouting, a low-viscosity
grout is injected into soil at low pressure and fills the
voids without the changes of soil volume. In jet
grouting, the grouting injects at high pressure and flow
of high velocity mixes the grout and soil (Karol 2003).
The grout can be performed using stage-down or
stage-up methods, grout port, and vibrating beam. In
the stage-down method, a borehole is drilled to the full
depth and grout is injected as the drill is withdrawn. In
the stage-up method, the grout is injected starting at
the top of the borehole and continuing to the desired
depth. The grout port method uses a slotted injection
pipe and a double packer to inject the grout at specific
intervals. In the vibrating beam method, a beam is
vibrated into the soil to the desired depth, and then
grout is injected as the beam is withdrawn. Horizontal
grout curtains are constructed by horizontal overlapping of the grout injection zones, or using grout holes
installed using horizontal drilling methods. Vertical
microbial grout curtains could also be designed as
barriers to groundwater flow (Karol 2003).
Technologies for the microbial grouting could be
similar to those used in chemical grouting. Depth of
penetration depends on the size of used microorganisms. The typical size of unicellular bacteria is from 1
to 3 lm, but the length of microbial cellular filaments
can be up to 100 lm, which can be an obstacle in
penetration of filamentous microorganisms into soil.
The specificity of microbial grouting is that such
optimal for microbial activity conditions as optimal
pH, salinity, oxidation-reduction potential, concentrations of nutrients, and content of water must be
provided for.
An advantage of microbial grouting over chemical
one is that the microbial grouts may be non-toxic,
whereas many chemical grouts, especially those based
on acrylamides, lignosulfonates, and polyurethane,
are toxic and environmentally harmful. Another
advantage of microbial grouting over chemical one
is the lower cost of reagents. The evaluated costs of
the raw materials for the chemical soil grouting are in
the range from $2 to $72 per m3 of soil (Table 2). The

Rev Environ Sci Biotechnol (2008) 7:139153

147

Table 2 Approximate cost of raw materials for chemical

grouting
Cost of
additives
($/m3)

Material

Price
($/kg)

Amount of
additives
required
(kg/m3)

LignosulphitesLignosulphonates

0.10.3

2060

218

Sodium silicate
formulations

0.61.8

1040

672

Phenoplasts

0.51.5

510

2.515

Acrylates

1.03.0

510

530

Acrylamides

1.03.0

510

530

Polyurethanes

5.010.0

15

550

chemical grouts, especially those based on acrylates,

acrylamides, and polyurethanes are most expensive.
The costs of the raw materials for the microbial
grouting could be in the range from $0.5 to $9.0 per
m3 of soil in cases when the waste materials are used
as the source of carbon for microbial growth
(Table 3). It should be pointed out that the evaluated
costs given in the Tables 2 and 3 are raw material
costs at the market prices only and the cost of
placement is not included. As pointed out by Karol
(2003), the cost of placement of grouts can be a major
part of the total cost of chemical grouting. However,
assuming that the costs of placement involved in the
chemical grouting is comparable to microbial grouting, then the cost comparisons shown in the Tables 2
and 3 are relevant.

3.4 Limitation of soil biocementation

A disadvantage of soil bioclogging and biocementation
in comparison with chemical grouting is that the

microbial process is usually slower. Another disadvantage is that the microbial process is more complex
than the chemical one because the microbial activity
depends on many environmental factors such as
temperature, pH, concentrations of donors and acceptors of electrons, concentrations and diffusion rates of
nutrients and metabolites. The design of microbial
applications in bioclogging and biocementation must
take into account not only soil conditions and grouting
medium content but also microbiological, ecological
and geotechnical engineering aspects of the process.
Design of bioclogging and biocementation requires
data of the biological processes (growth, biosynthesis,
biodegradation, bioreduction, biooxidation, and specific enzymatic activities), chemical reactions
accompanied with formation of insoluble compounds,
and physico-chemical processes such as precipitation,
crystallization, and adhesion. Specific geotechnical
parameters of soil must be used as process optimization
criteria. Design of bioclogging and biocementation
processes is not shown in this review because there are
no related papers yet. Due to the complexity, none of
the bioclogging or biocementation processes have been
tested in large-scale construction or land reclamation
project yet.

3.5 Summary
Different possible microbial processes that can lead
potentially to biocementation are summarized in
Table 4. These include binding of the soil particles
with sulphides of metals produced by sulphatereducing bacteria; binding of the particles with
carbonates of metals produced due to hydrolysis of
urea; and binding of the particles with ferrous and
ferric salts and hydroxides, produced due to activity
of iron-reducing bacteria.

Table 3 Approximate cost of raw materials for microbial grouting

Materials

Molasses + microorganisms
Homogenized food-processing wastes + microorganisms
Iron ore + organic wastes + microorganisms
Organic wastes (agricultural, horticultural, food-processing wastes)
Calcium chloride + urea + microorganisms

Price ($/kg)

Amount of additives
required (kg/m3)

Cost of additives
(m3 of soil)

0.10.2

520

0.54.0

0.050.1

1020

0.52.0
1.04.0

0.10.2

1020

0.050.1

1020

0.52.0

0.20.3

2030

4.09.0

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Rev Environ Sci Biotechnol (2008) 7:139153

Table 4 Possible microbial processes that can lead potentially to biocementation

Physiological
group of
microorganisms

Mechanism of biocementation

Essential conditions for

biocementation

Sulphatereducing
bacteria

Production of undissolved sulphides of metals

Anaerobic conditions; presence Enhance stability for

of sulphate and carbon source
slopes and dams
in soil

Ammonifying
bacteria

Formation of undissolved carbonates of metals in Presence of urea and dissolved

soil due to increase of pH and release of CO2
metal salt

Potential geotechnical
applications

Mitigate liquefaction
potential of sand
Enhance stability for
retaining walls,
embankments, and dams;
Increase bearing capacity
of foundations

Iron-reducing
bacteria

Production of ferrous solution and precipitation

of undissolved ferrous and ferric salts and
hydroxides in soil

Anaerobic conditions changed

for aerobic conditions;
presence of ferric minerals

Density soil on reclaimed

land sites and prevent
soil avalanching
Reduce liquefaction
potential of soil

4 Screening of microorganisms suitable for soil

bioclogging and biocementation
The group of chemotrophic prokaryotes is most
suitable for the soil bioclogging and biocementation
because of their smallest cell size, typically from 0.5
to 2 lm, ability to grow inside soil, and big
physiological diversity. Phototrophic prokaryotes,
mainly cyanobacteria, grow on soil surface only
because light penetrates only a few millimeters into
soil. These bacteria can produce rigid crust on surface
of soil or sediment, which diminishes soil infiltration
rate and improves slope stability. Cyanobacteria can
also create millimeter-scale laminated carbonate
build-ups called stromatolites, which are formed in
shallow marine environment, due to the sequence of
sedimentation, growth of biofilm, production of a
layer of exopolymers, and lithification of sediments
by the precipitation of microcrystalline carbonate
(Reid et al. 2000; Buffle and van Leeuwen 2002).
Selection of the groups of chemotrophic bacteria
for bioclogging and biocementation using modern
phylogenetic classification of prokaryotes is impossible because it is based mainly on the comparisons of
the gene of 16S rRNA (Bergeys Manual of Systematic Bacteriology 2001, 2005). This classification has
weak connection with physiological grouping of
chemotrophic prokaryotes and cannot be used as a
practical tool in the ecological design of bioclogging

123

or biocementation. Physiological classification of

chemotrophic prokaryotes, originally proposed by
the authors as shown in Table 5, can be used in
ecological design of bioclogging and biocementation.
This classification is based on two features: (1)
relation to oxygen connected with the type of energy
generation and (2) type of cell wall. The four periods
(columns) as shown in Table 5 are as follows: (1)
fermenting anaerobes; (2) anaerobic respiring prokaryotes that produce energy by anaerobic oxidation
of chemical substances using such electron acceptors
3+
as nitrate (NO3 ), nitrite (NO2 ), ferric (Fe ), sulphate
2(SO4 ), sulphur (S), or carbon dioxide (CO2); (3)
microaerophilic and facultative anaerobic prokaryotes; (4) aerobes. Three parallel lines in the periodic
table of chemotrophic prokaryotes show evolutionary
origin of microbial group: (1) prokaryotes of aquatic
origin, cells with Gram-negative type of cell wall that
were evolutionary adapted to the environments with
stable osmotic pressure; (2) prokaryotes of terrestrial
origin, cells with Gram-positive type cell wall that
were evolutionary adapted to the environments with
changeable osmotic pressure; (3) Archaea originated
from the environments with extreme temperature,
salinity, pH, or redox potential. There are total 12
physiological groups in the periodic table of chemotrophic prokaryotes.
Archaea could be excluded from the consideration
of being used as bioagents for soil bioclogging and

Rev Environ Sci Biotechnol (2008) 7:139153

149

Table 5 The periodic table of physiological classification of chemotrophic prokaryotes for the screening of the physiological groups
suitable for soil bioclogging and biocementation
Ecology of origin

Prokaryotes of aquatic origin

Prokaryotes of terrestrial origin

Relation to oxygen and type of energy generation

Anaerobic
fermenting
prokaryotes

Anaerobic
respirating
prokaryotes

Facultative anaerobic and

microaerophilic prokaryotes

Aerobic
respirating
prokaryotes

Bacteroides

Desulfobacter

Escherichia

Pseudomonas

Prevotella
Ruminobacter

Geobacter
Wolinella

Clostridium

Desulfotomaculum

Microthrix

Desulfitobacterium

Nocardia

Peptococcus
Eubacterium
Prokaryotes originating from extreme Desulfurococcus
environments (Archaea)
Thermosphaera
Pyrodictium

Bacillus infernus
Methanobacterium

Shewanella
Beggiatoa

Streptococcus
Metallosphaera

Acinetobacter
Nitrosomonas
Bacillus
Arthrobacter
Streptomyces
Picrophilus

Thermococcus

Acidianus

Ferroplasma

Haloarcula

Haloferax

Sulfolobus

Selected examples of conventional genera are shown in the cells

biocemenetation, because all of them are living in

extreme environments that are not compatible with
the majority of the construction or land reclamation
site conditions.
Anaerobic fermenting bacteria may be involved in
cementation of soil particles under the presence of
calcium, magnesium, or ferrous ions. This cementation can be due to the increase in pH caused by
ammonification (release of ammonia) and carbon
dioxide production in soil added with urea or waste
protein (Bachmeier et al. 2002; Castanier et al. 1999;
Hammes and Verstraete 2002; Kucharski et al. 2005;
Stocks-Fischer and Galinat 1999). The insoluble
carbonates and hydroxides of metals will be precipitating at high pH thus binding the soil particles and
clogging soil. However, if carbohydrates are added to
soil, fermenting anaerobic bacteria can diminish the
pH due to formation of organic acids during fermentation of carbohydrates. This could be potentially
used in bioclogging and biocementation to precipitate
silicates from colloidal silica suspension. It is known
that stability of colloidal silica suspension is reduced
at acidic pH and inorganic acids are added in this type
of chemical grouting (Karol 2003). From other point
of view, organic acids produced in fermentation can
dissolve carbonates and hydroxides binding soil
particles or plugging soil pores. Anaerobic bacteria
cannot clog soil pores by the synthesis of extracellular polymers because they are not able to produce
big quantity of slime (Atmaca et al. 1996) due to

their low efficiency of biological energy production

in fermentation.
Organic acids, hydrogen, and alcohols, which are
produced by anaerobic fermenting bacteria from
polysaccharides and monosaccharides, can be used
as donors of electrons by anaerobic respiring bacteria.
One example is the group of iron-reducing bacteria,
which are using products of fermentation as electron
donors to produce dissolved Fe(II) ions by reduction
of insoluble Fe(III) compounds (Lovley et al. 2004;
Weber et al. 2006). Microbial reduction of Fe(III) is
used in environmental biotechnology for treatment of
groundwater and wastewater (Fredrickson and Gorby
1996; Ivanov et al. 2004, 2005; Stabnikov and Ivanov
2006) and could be used hypothetically for soil
cementation because iron-reducing bacteria could
produce Fe2+ in situ from cheap sources of Fe(III)
and products of anaerobic fermentation of organic
wastes (Ivanov et al. 2004, 2005; Stabnikov and
Ivanov 2006). Ions of ferrous can be oxidized
chemically or biologically. Products of this oxidation
are insoluble ferric hydroxides and ferric carbonates,
which could clog the soil pores and bind the soil
particles altogether.
Another example of anaerobic respiring bacteria,
which could be used in bioclogging and biocementation, is sulphate-reducing bacteria. These bacteria
produce dihydrogen sulphide using organic acids,
hydrogen, or alcohols as electron donors and sulphate
as electron acceptor. Sulphide reacts with iron and

123

150

other metal cations to form insoluble suphides of

metals, which clogs the soil pores and binds the soil
particles. However, the soil compaction created by the
formation of sulphides is unstable because they can be
chemically or biologically oxidized to sulphuric acid
or sulphates under aerobic conditions. There is a case
where a thousand houses built on excavated nonweathered mudstone sediments were damaged by
microbially induced heaves of foundations (Yamanaka et al. 2002). The mechanisms of this damage
were identified as: (1) sulphate-reducing bacteria in
the mudstone reduced sulphate to hydrogen sulphide;
(2) the mudstone sediments under the houses became
permeable to air due to gradual drying; (3) dihydrogen
sulfide was oxidized by sulphide-oxidizing bacteria to
sulphuric acid; and (4) acid dissolved calcium
carbonate binding the particles of mudstone sediments. Additional negative impact of activity of
sulphate-reducing bacteria is the increased corrosion
and release of toxic and bad smelling dihydrogen
sulphide.
Denitrification process, which is bioreduction of
nitrate (NO3 ) and nitrite (NO2 ) to nitrogen gas, is not
applicable to the soil bioclogging or biocementation,
because bacteria produce big volume of dinitrogen
gas during denitrification and the cost of nitrate as
electron acceptor is not affordable for large-scale
construction and land reclamation projects.
Facultative anaerobic bacteria could be considered
as the most suitable bioagents for soil bioclogging and
biocementation because many species are able to
produce big quantity of exopolysaccharides, which
usually promote formation of cell aggregates, and can
grow under either aerobic or anaerobic conditions. Last
property of facultative anaerobic bacteria is most
essential for biotreatment of soil in situ where supply
of oxygen is limited by the soil porosity and both
aerobic and anaerobic microzones co-exist in soil.
There are, for example, bacteria from genera Alcaligenes, Enterobacter, Staphylococcus, Streptococcus,
Rhodococcus, corynebacteria (Gordonia, Nocardioides), gliding bacteria (Myxococcus, Flexibacter,
Cytophaga) and oligotrophic bacteria (Caulobacter)
(Wingender et al. 1999; Jones et al. 2004; Ivanov and
Tay 2006b).
Microaerophilic bacteria could be used for the
biobinding of soil particles because many strains of
microaerophilic bacteria are combined in filaments
(Beccari and Ramadori 1996; Seviour and Blackall

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2007) or joined by sheathes (Mulder and Deinema

1992) and these filamentous structures can also bind
the soil particles. The filamentous bacteria from the
genera Beggiatoa, Haliscomenobacter, Microthrix,
Nocardia, Sphaerotilus, and Thiothrix are common in
aerobic tanks of wastewater treatment plants (Beccari
and Ramadori 1996; Seviour and Blackall 2007) and
can be probably used for biobinding of soil particles.
Aerobic bacteria could be suitable for soil bioclogging, biocementation, and biobinding of soil particles
because many species are able to produce big quantity
of slime, form chains and filaments, increase pH,
and oxidize different organic and inorganic substances. Cells of many Actinomycetes, a group of
Gram-positive bacteria, typical soil inhabitants, form
particles-binding mycelium and produce particlesbinding slime in soil (Wu et al. 1997; Jones et al.
2004; Dworkin et al. 2006). These bacteria are most
prospective for the aerobic soil bioclogging, biocementation, and biobinding. The examples of direct
involvement of both facultative anaerobic and aerobic
bacteria may be the cementation of soil particles under
presence of calcium, magnesium, or ferrous ions due
to increase of pH caused by ammonification and
carbon dioxide production in soil with added urea
(Kucharski et al. 2005). The insoluble carbonates and
hydroxides of metals are precipitating at high pH thus
binding the soil particles and clogging the soil pores.
Such bacterial groups as gliding bacteria, oligotrophic
bacteria, and nitrifying bacteria could be most active
in the formation of polysaccharides, which are
binding the soil particles. Aerobic sulphide-, sulphur-, and ammoniumoxidizing bacteria produce
sulphuric or nitric acids could hypothetically compact
the soil particles due to dissolution of minerals,
change of zeta-potential of colloid particles and
precipitation of colloidal silica at low pH.
The use of anaerobic bacteria can be complicated by
the presence of oxygen in the upper layer of soil and
sensitivity of anaerobic bacteria to oxygen. Alternatively, if aerobic bacteria are used for soil clogging or
cementation, a major technological problem is the air
supply into soil. If the rate of oxygen supply into soil by
aeration and diffusion is not sufficient, there will be
formation of anaerobic layer or zones, where aerobic
bacteria will not be active. Therefore, from the
technological and biological points of view, the most
suitable physiological groups for the soil bioclogging
and biocementation in situ are facultative anaerobic

Rev Environ Sci Biotechnol (2008) 7:139153

bacteria, which are active under both aerobic and

anaerobic conditions. Depending on the site conditions
of a real soil treatment project, a technique to alter the
anaerobic and aerobic conditions in situ can be implemented to ensure the sequence of anaerobic and
aerobic biogeochemical processes and facilitate soil
bioclogging or biocementation.
Another assumption from the general consideration
of physiological diversity of prokaryotes is that the
most suitable bacteria for soil bioclogging or biocementation are bacteria with Gram-positive type of cell
wall because these bacteria are most resistant to the
changes of osmotic pressure, which is the typical
condition for soil on construction or reclamation sites.
Another important aspect in the screening of
microorganisms suitable for soil bioclogging and
biocementation is biosafety. To diminish the risk of
pathogenic bacteria accumulation and release during
bioclogging and biocementation, the following selective conditions can be used:

an application of carbon sources, which are used

in nature by saprophytic microorganisms, such as
cellulose, cellulose-containing agricultural waste,
vegetable-processing waste, molasses;
the conditions that are suitable for the growth of
autolithotrophic bacteria. Carbon dioxide is used
as a carbon source and inorganic substances
(NH+4 , Fe2+, S) are used as electron donor;
the conditions that are suitable for application of
bacteria able for anaerobic respiration with SO24
or Fe3+ as electron acceptors;
an application of solution with low concentration
of carbon source for preferable growth of oligotrophic microorganisms in soil.

The problem of biosafety can be solved also by the

selection of safe bacterial strain. The biomass of this
safe strain can be produced in bioreactor and used as a
starter culture for bioclogging or biocementation.
There are known similar applications of starter cultures
to start up the large-scale non-aseptic environmental
processes for faster start-up and increased biosafety
(Ivanov et al. 2006b; Ivanov and Tay 2006a).

5 Conclusions
(1)

Bioclogging and biocementation of soils could

be used in geotechnical engineering to improve

151

(2)

(3)

the mechanical properties of soil in situ. These

methods can replace the more energy demanding mechanical compaction methods or the
expensive and environmentally unfriendly
chemical grouting methods. However, to adopt
the microbial method effectively, an integration
of engineering, microbiological, and ecological
studies and design consideration are required.
The most suitable microorganisms for soil
bioclogging or biocementation for large scale
construction and environmental problems are
facultative anaerobic and microaerophilic bacteria.
There are several laboratory-scale studies and
field tests on bioclogging and biocementation of
soil. However, the industrial-scale applications
of microorganisms in geotechnical engineering
have yet to be demonstrated.

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