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The role of molecular biology in geotechnical engineering
Le rôle de la biologie moléculaire en géotechnique
Stewart D.I. , Fuller S.J.
School of Civil Engineering, University of Leeds, Leeds, UK
Burke I.T., Whittleston R.A., Lockwood C.L.
School of Earth and Environment, University of Leeds, Leeds, UK
Baker A.
School of Biology, University of Leeds, Leeds, UK.
ABSTRACT: This paper reviews techniques from molecular biology for characterising microbial populations that are accessible to
Geotechnical or Geo-Environmental Engineers. With reference to data from contaminated land studies, it discusses which techniques
it might be appropriate to use in an engineering context, how the data generated can be visualised and interpreted, and the dangers of
over interpretation. Finally it reports on the capabilities of the latest high throughput next-generation sequencing platforms, and
speculates on what engineering developments may result from this technological advance.
RÉSUMÉ:
Ce document passe en revue les techniques de la biologie moléculaire pour la caractérisation des populations microbiennes
qui sont accessibles aux ingénieurs géotechniques ou géo-environnementaux. En faisant référence aux données provenant d'études de
terres contaminées, il aborde les techniques qu’il pourrait être approprié d'utiliser dans un contexte d'ingénierie, la manière dont les
données générées peuvent être visualisées et interprétées, et les dangers d’une sur-interprétation. Enfin, il rend compte de la capacité
des plateformes les plus récentes de séquençage à haut débit de prochaine génération, et s'interroge les développements techniques
qu’il pourrait résulter de cette avancée technologique.
KEYWORDS: Geo-environment, Molecular Biology, DNA, rRNA, 16S gene sequencing
1 INTRODUCTION
In recent years Geotechnical and Geo-Environmental Engineers
have started to exploit soil microorganisms, nature’s catalysts,
to deliver sustainable engineering solutions to big problems
facing society. Such microorganisms obtain energy from cata-
lysing thermodynamically favourable chemical reactions
between natural soil constituents, but in the process can also
catalyse chemical reactions that are of engineering interest. To
date approaches such as monitored natural attenuation and
active bioremediation have become well-established for the
treatment of soils contaminated with petroleum hydrocarbons
and organic solvents. However this field is about to expand
rapidly, with techniques such as the reductive precipitation of
contaminant metals and radionuclides, microbial induced calcite
precipitation to improve soil strength, bacterially mediated
phosphate recovery from waste streams and bacterially
enhanced carbon capture likely to emerge from a research
setting and into engineering practice in the near future.
What all these applications have in common is that they
involve managing populations of microorganisms to bring about
chemical transformations within an engineering context. Thus,
if engineers are to manage these populations effectively, they
need to characterise microbial populations to identify whether
the necessary organisms are present, or better still to determine
the genetic potential of the population to perform particular
chemical transformations. In the near future engineers seeking
better process control might wish to identify which metabolic
pathways are active under particular conditions in order to
predict which chemical transformations are about to occur.
To be able to quantify the contributions of microorganisms
to a process, and ultimately to control that contribution, it is
necessary to first know what organisms are present, secondly
how this population changes with the conditions, and thirdly
which organisms and conditions are the most important for
achieving the desired outcome. Traditional microbiology
methods involve culturing, identifying and enumerating the
microorganisms present. However these suffer from a number
of disadvantages; not all microorganisms can be cultured, the
culture conditions selected can favour some species over others,
and identification requires a high level of expertise in microbial
taxonomy. In contrast methods based on nucleic acids, DNA
and RNA the genetic material of all organisms, have become
quick, simple and relatively cheap. A modest investment of a
few thousand pounds can equip a laboratory for such analyses.
With the exception of some viruses the genome of all organ-
isms is made up of DNA, Watson and Crick’s famous double
helix, in which two strands that run anti-parallel to one another
are held together by H-bonds between complementary bases; A
(adenine) always bonds with T (thymine), and G (guanine) with
C (cytosine). This complementary base pairing allows each
strand to provide the information for synthesis of its comple-
mentary strand during DNA replication. In the cell this process
is carried out by enzymes called polymerases using building
blocks called deoxynucleotide triphosphates (dNTPs) and is
essential for cells to replicate. The DNA contains all the genes
necessary to specify all structures and functions of the cell. As
some processes (such as synthesising proteins) are fundamental
to all cells, some genes are very similar in all organisms. Others
play much more specialised roles and their presence can be used
to infer the presence of specific organisms (see section 4).
Fundamental to all the methods to be discussed is the ability to
amplify and determine the sequence of specific sections of
DNA from environmental samples. This allows inferences to be
drawn about the presence or absence of organisms or to gain
insights into the populations present and their dynamics.
2 THE POLYMERASE CHAIN REACTION (PCR)
The polymerase chain reaction (PCR) is a technique for
replicating a selected section of a DNA fragment. It starts with
one or two copies of the target section, and increases that by
several orders of magnitude. PCR involves repeatedly heating
and cooling the DNA using a piece of equipment known as a
thermocycler. There are usually three discrete temperature
