ionic pumps or channels, probably coupled with carbonate ion production. Active
precipitation would be independent of specific metabolic pathways.
More recently, Dupraz et al. (2009) introduced the term biologically influenced
mineralization, distinguished from biologically induced, to refer to passive mineralization of organic matter. While in “biologically induced” precipitation, microbial activities generate biogeochemical conditions that facilitate precipitation,
and mineralization results from the interactions between biological activity and
the environment, in biologically influenced mineralization, external, environmental
parameters, rather than microbial activities are responsible for creating the
conditions (e.g., increased alkalinity) for mineral precipitation and the presence
of living organisms is not required. An organic matrix (biogenic or abiogenic in
origin) is, however, involved in biologically influenced mineralization, influencing
the morphology and composition of the crystals through interactions between the
mineral and the organic matter (serving as template for precipitation). While both
types of precipitation typically occur outside of cells, “biologically influenced”
precipitation is a passive process, resulting from interactions between extracellular
biopolymers and the geochemical environment.
Moreover, Dupraz et al. (2009) propose the use of the term organomineralization
sensu lato (s.l.) as an umbrella term encompassing biologically influenced and
biologically induced mineralization. The organomineralization process can be
intrinsically (microbial metabolism) or extrinsically driven (e.g., degassing,
evaporation).
Microbial precipitation of CaCO 3 occurs by organomineralization s.l. through
these two major processes: microbiologically induced (active) and microbiologically influenced precipitation (passive). In the geochemical environment near
cells, however, both processes occur in spatial and temporal proximity and it is
difficult to separate these effects in situ (Weiner and Dove 2003).
Dupraz et al. (2009) proposed that the term biomineral should be used in a
restrictive definition for the product of selective uptake of elements, which are
incorporated into functional structures under strict biological control. Biominerals
are consequently strictly referred as the product of biologically controlled mineralization, which becomes synonymous of biomineralization, while biologically
induced minerals are excluded.
For a review on definitions and mechanisms of mineralization, see Dupraz et al.
(2009).
The terminology from Dupraz et al. (2009) has the advantage to reconsider in a
clear view the debated role of bacteria in CaCO 3 mineralization (active vs. passive
mineralization requires an active role from bacteria, living and metabolic active
cells, independently from the mechanism used to favor precipitation (a specific
metabolic pathway, pump, or cell surface properties)). In this sense, the active role
of bacteria in CCP is expanded and encompasses any activity fostering CCP by
living cells. Urea hydrolysis, sulfate reduction, and denitrification (Sect. 5.3.1) are
three examples of metabolic pathways driving this type of precipitation process,
while they were considered linked to a passive role by other authors (Castanier et al.
1999). On the contrary, influenced mineralization requires a passive role from
5 Molecular Basis of Bacterial Calcium Carbonate Precipitation
117
precipitation would be independent of specific metabolic pathways.
More recently, Dupraz et al. (2009) introduced the term biologically influenced
mineralization, distinguished from biologically induced, to refer to passive mineralization of organic matter. While in “biologically induced” precipitation, microbial activities generate biogeochemical conditions that facilitate precipitation,
and mineralization results from the interactions between biological activity and
the environment, in biologically influenced mineralization, external, environmental
parameters, rather than microbial activities are responsible for creating the
conditions (e.g., increased alkalinity) for mineral precipitation and the presence
of living organisms is not required. An organic matrix (biogenic or abiogenic in
origin) is, however, involved in biologically influenced mineralization, influencing
the morphology and composition of the crystals through interactions between the
mineral and the organic matter (serving as template for precipitation). While both
types of precipitation typically occur outside of cells, “biologically influenced”
precipitation is a passive process, resulting from interactions between extracellular
biopolymers and the geochemical environment.
Moreover, Dupraz et al. (2009) propose the use of the term organomineralization
sensu lato (s.l.) as an umbrella term encompassing biologically influenced and
biologically induced mineralization. The organomineralization process can be
intrinsically (microbial metabolism) or extrinsically driven (e.g., degassing,
evaporation).
Microbial precipitation of CaCO 3 occurs by organomineralization s.l. through
these two major processes: microbiologically induced (active) and microbiologically influenced precipitation (passive). In the geochemical environment near
cells, however, both processes occur in spatial and temporal proximity and it is
difficult to separate these effects in situ (Weiner and Dove 2003).
Dupraz et al. (2009) proposed that the term biomineral should be used in a
restrictive definition for the product of selective uptake of elements, which are
incorporated into functional structures under strict biological control. Biominerals
are consequently strictly referred as the product of biologically controlled mineralization, which becomes synonymous of biomineralization, while biologically
induced minerals are excluded.
For a review on definitions and mechanisms of mineralization, see Dupraz et al.
(2009).
The terminology from Dupraz et al. (2009) has the advantage to reconsider in a
clear view the debated role of bacteria in CaCO 3 mineralization (active vs. passive
mineralization requires an active role from bacteria, living and metabolic active
cells, independently from the mechanism used to favor precipitation (a specific
metabolic pathway, pump, or cell surface properties)). In this sense, the active role
of bacteria in CCP is expanded and encompasses any activity fostering CCP by
living cells. Urea hydrolysis, sulfate reduction, and denitrification (Sect. 5.3.1) are
three examples of metabolic pathways driving this type of precipitation process,
while they were considered linked to a passive role by other authors (Castanier et al.
1999). On the contrary, influenced mineralization requires a passive role from
5 Molecular Basis of Bacterial Calcium Carbonate Precipitation
117