Geology Reference
In-Depth Information
phosphatic functional groups. These charged groups
play a key role in the heterogeneous nucleation of
a new solid phase, as demonstrated by in vitro
studies of calcium carbonate precipitation in the
presence of amino acids (Jimenez-Lopez et al.
2003). Nonetheless, organic macromolecules play
a dual role in the nucleation process. They can act
as inhibitors or as promoters for mineral crystalliza-
tion (Rodriguez-Navarro et al. 2007). Typically,
crystallization inhibition occurs due to binding of
counter-ions (i.e. metal ions), thus reducing the
effective ion concentration in solution (i.e. reducing
supersaturation). This reportedly occurs in bacterial
biofilms due to the presence of EPS (Decho 2000;
Arp et al. 2001; Dupraz & Visscher 2005). EPS dis-
plays a random distribution of charged functional
groups which bind metals in a disordered array. The
disordered arrangement of bonded ions prevents
crystal nucleation (Arp et al. 2001). On the other
hand, if a periodic, ordered arrangement of the func-
tional groups in the organic matrix occurs, for
instance on the bacterial cell membrane (Schultze-
Lam et al. 1996), or on altered EPS subjected to
reorganization of acidic sites (Duprazz & Visscher
2005), stereochemical coupling between the organic
substrate and the newly-formed solid phase can
occur. The latter effect promotes heterogeneous
nucleation of a crystalline phase. Thus a biotically
induced or mediated mineral is formed on the
cell surface.
The resulting alkalinization around the bacteria
cells induces CO
22
generation:
HCO
3
þ OH
! CO
2
3
þ H
2
O
(2)
In the presence of Ca ions, CaCO
3
precipitates on
the cell surface according to the reaction:
Ca
2þ
þ CO
2
3
! CaCO
3
#
(3)
In the presence of SO
22
ions, gypsum nucleation on
the cell surface can also occur.
Additional details regarding different bacterial
metabolic pathways resulting in supersaturation
with respect to a particular mineral phases can be
found in Ehrlich (2002).
Myxobacteria
Myxobacteria are Gram-negative heterotrophic
bacteria whose cells are long rods with lengths of
3-12 mm and diameters of 0.7 - 1.2 mm (Fig. 1a).
On solid surfaces they display gliding motility,
which is necessary for their swarming and fruiting
body (Fig. 1b, c) development (Kaiser 2003).
Although phylogenetically they belong to the delta
subdivision of the Proteobacteria in the order
Myxobacterales (Shimkets & Woese 1992), they
do not share many of the phenotypic features
shown by the other members of this subdivision,
such as Bdellovibrio or Desulfovibrio. The charac-
teristics that define the order Myxobacterales are
thoroughly described by Shimkets et al. (2005).
Myxobacteria are very common in nature, par-
ticularly in topsoil rich in organic material. Within
a pH range of between 5 and 8, and in aerated
surface layers, all soils appear to contain some
myxobacteria (Dawid 2000). They are also able to
colonize other habitats, especially those rich in
microbial life, such as plant rhizosphere, dung,
decaying plant material, and bark from both living
and dead trees (Reichenbach 1993). Myxobacteria
are easily washed from soil into water where they
can survive and multiply, consequently they are
common
Metabolic pathways leading to mineral
precipitation
The main metabolic activities resulting in mineral
precipitation are: (a) oxygenic photosynthesis (e.g.
cyanobacteria); (b) ammonification by protein
degradation (e.g. soil bacteria such as Myxococcus
or Bacillus); (c) ammonia oxidation (e.g. nitrifying
bacteria); (d) iron (or manganese) oxidation (e.g.
iron-oxidizing bacteria such as Gallionella ferrugi-
nea); (e) sulphur oxidation by sulphur oxidizing
bacteria; and (f ) sulphur reduction by sulphate redu-
cing bacteria (for details see Nealson & Stahl 1997).
Detailed description of these metabolic pathways
falls outside the scope of this review. However, a
representative example of the complex reactions
leading to mineral precipitation is described below.
Thompson & Ferris (1990) proposed the follow-
ing metabolic pathway for calcium carbonate pre-
cipitation by the cyanobacterium Synechococcus.
The bacterium converts intracellular HCO
3
2
photo-
synthetically into reduced carbon (CH
2
O):
in
fresh
water
(Hook
1977),
and
in
marine environments (Iizuka et al. 2003).
Myxobacteria produce a large variety of active
compounds, such as enzymes and antibiotics,
which have great biotechnological applications
(Reichenbach & H ¨fle 1999; H¨fle & Reichenbach
2005). For example, myxobacteria are known to
produce antibacterial, antifungal, antiviral, and, to
a lesser extent, insecticidal compounds.
Myxobacteria form large communities known as
swarms that feed on a variety of macromolecules
(i.e. proteins, starch, lipids, nucleic acids and even
cellulose) because they produce numerous extra-
cellular hydrolytic enzymes. They can also degrade
HCO
3
þ H
2
O ! (CH
2
O) þ O
2
þ OH
(1)
Intracellular OH
2
ions are then exchanged for extra-
cellular bicarbonate ions across the cell membrane.
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