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ESS102H1 Lecture Notes - Ferroplasma, Geomicrobiology, Deinococcus Radiodurans

Earth Sciences
Course Code
John Ferris

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General Principles
1.0 Introduction
The field of aqueous microbial geochemistry is highly interdisciplinary with
scientific roots not only in biology, but also geology and physical chemistry. A major
objective is to understand the central role of microbial processes in regulating the
chemical composition of natural and contaminated aqueous systems including
groundwaters, lakes and rivers, estuaries, and oceans. Even broader associations exist in
terms of bioremediation, global elemental cycling, environmental change, and even
possibilities for life beyond Earth.
As an interdisciplinary science, aqueous microbial geochemistry is challenging in
that it demands acquisition and application of a broad range of scientific knowledge. For
individuals new to the field, the learning curve may appear to be frightfully steep;
however, there are many common threads between different scientific disciplines and
aqueous geochemistry, few of which are stronger or more compelling than the
fundamental characteristics of natural waters. These are defined in physical, chemical,
and biological terms that are not always used commonly across disciplines.
One should not be surprised that lexicon is a confounding issue for
interdisciplinary science. Natural philosophy has always been disguised by the passion
of ardent observers, so much the better to obfuscate the obvious and lay claim to
otherwise common scientific principles. For this reason, this chapter is focused on
providing a modicum of terminology that usefully serves physical and biological
scientists alike.
1.1 Chemical Speciation and Fractionation
Natural waters, whether they are pristine or contaminated, are not simple aqueous
solutions. At first blush, it is easy to acknowledge that a wide range of dissolved and
solid materials are likely present in a water sample. Moreover, dissolved and solid
concentrations are apt to be quite different depending on the provenance and
environmental quality of the water sample. These simple considerations raise a number
of problematic issues that relate to how dissolved and solid materials in natural waters are
distinguished in a consistent manner across scientific disciplines.
The different physicochemical forms adopted by an individual element or its
compounds in aqueous solution are referred to as species. In this context, substances
that differ in isotopic composition, molecular conformation, oxidation state, or in the
nature of their ionic or covalently bound substituents, can be regarded as distinct
chemical species. Further to this concept, the term speciation is used to indicate the
specific distribution of chemical species that are present in a given sample. The physical
activity of identifying and measuring different chemical species is speciation analysis. In
conjunction with use of speciation to describe chemical species distributions,

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fractionation is the classification of materials according to physical (e.g., size, solubility)
or chemical (e.g., bonding, reactivity) properties.
There is no perfect way to distinguish precisely between dissolved and particulate
fractions in a water sample. This is because the size distributions of aqueous components
vary in a continuous manner from ions and molecules in the 10-10 to 10-9 m range to
bacteria and algae in the 10-6 to 10-3 m range. Materials between 10-9 and 10-7 m are
defined as colloids; however, use of the term nanoparticle has grown in popularity to
describe a wide variety of colloidal materials. In natural waters, colloids are
characterized by extreme diversity including organic macromolecules, biological debris,
clay minerals, iron and manganese oxides, and even viruses.
The most common approach in water analysis to separate dissolved and
particulate fractions is to filter samples through membrane filters with pore sizes of 0.2 to
0.5 µm. Constituents of the dissolved fraction1 must be small enough to survive
filtration, whereas the particulate solid fraction is retained by the filter. There are some
obvious problems with this operation definition of dissolved and particulate fractions,
especially in relation to the fractionation of colloidal particles; however, aggregation of
colloids to form larger agglomerates and adherence to other particles like bacteria cells or
algae enhances the fractionation efficiency of membrane filtration. Alternatively,
filtration can be done using filters with nanometer-size pores or centrifugation can be
used to sediment the particulate materials.
1.2 Concentrations
Concentration is a term that refers to the quantity of a substance in a water
sample. A number of different ways are used to express concentrations depending
foremost on the field of application. Because of the interdisciplinary nature of physical
biogeochemistry, all methods used to report concentrations are apt to be encountered.
An especially common approach to expressing concentrations is based on
reporting the quantity of a substance in a fixed quantity of solution. In this context, the
quantities used are typically weight and/or volume. These different measurement
possibilities give rise to several concentration scales including weight per weight (w/w),
volume per volume (v/v), and weight per volume (w/v). The corresponding
concentration values are reported generally in “parts per” format. For example,
concentrated solutions are often specified in terms of parts per hundred, which is
equivalent to percentage. In more dilute solutions, parts per thousand (ppt) or parts per
million (ppm) are used, whereas parts per billion (ppb) is applied to describe
concentrations in extremely dilute solutions.
Mole concentrations are expressed in terms of molality m (mol kg-1 of solvent) or
molarity M (mol L-1 of solution). Molarity is the most commonly used mole
1 Total dissolved solids (TDS) is another term commonly used in reference to the dissolved fraction of a
water sample.

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concentration scale, whereas molality is used almost exclusively to describe the
physicochemical properties of solutions because it is based on a temperature-independent
mass rather than a volume. An important point to recognize about molarity is that the
volume of solvent and the volume of a solution are different. The former quantity can be
determined from the molarity only if the densities of both the solution and pure solvent
are known.
One essential chemical criterion that must be respected for any solution is the
principle of electroneutrality. This can be evaluated by first converting molar
concentrations of ions to electrical charge equivalent concentrations. In general, the
conversion of molar concentrations to equivalent concentrations is expressed by
eq/L = z*M
where z is the absolute charge of the ion under consideration .
Example 1.1
A solution contains 0.1 mM Fe3+.
The oxidation state of ferric iron corresponds to a molar charge concentration of 3
equivalents (eq)/mole (or 3 meq/mmole) so the equivalent concentration of the solution is
0.1 mM = 0.1 mmole/L * 3 meq/mmole = 0.3 meq/L Fe3+
For electroneutrality to be respected, the summed equivalent concentrations of
positively charged cations and negatively charged anions in solution must be equal (i.e.,
charge balance).
0eq/L eq/L
eq/L eq/L
The concept of charge balance is a useful way to evaluate whether a chemical analysis of
a water sample is reasonably complete. This can be expressed in terms of a charge
balance error (CBE)
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