1) The document summarizes a paper about calcium carbonate precipitation and limestone formation from a microbiological perspective. 2) It describes different pathways by which heterotrophic bacteria can produce calcium carbonates, including passive precipitation through nitrogen and sulfur cycles, and active precipitation through cell membrane exchanges. 3) It discusses experiments showing bacterial involvement in carbonate crystallization under both nutrient-rich and nutrient-poor conditions, and how this affects crystal structure formation.

1. GEOL533 - Carbonates and Evaporites
Assignment 1 - Paper Presentation
Ca - Carbonate Production By Heterotrophic Bacteria
by
Omar Atef Radwan
PhD Student

2. Castanier, S., Le Métayer-Levrel, G., & Perthuisot, J. P. (1999).
Ca-carbonates precipitation and limestone genesis—the
microbiogeologist point of view. Sedimentary Geology, 126(1), 9-23.
Title: Ca-carbonates precipitation and limestone genesis—the
microbiogeologist point of view
Authors: Castanier, Sabine; Le Métayer-Levrel, Gaële;
Perthuisot, Jean Pierre
Affiliation: Universite de Nantes, Laboratoire de Biogéologie,
Nantes, France
Journal: Sedimentary Geology
Received: 9 March 1998
Accepted: 3 March 1999
DOI: 10.1016/S0037-0738(99)00028-7
Pages: 15
References: 38
Citation Count: 288 Cited by in Scopus
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3. Objectives
Objective I:
Investigation of the metabolic pathways of bacterial Ca-carbonate formation
Objective II:
Investigation of the modes and conditions of bacterial Ca-carbonate formation
Objective III:
Evaluation of bacterial carbonate productivity
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4. Outline
1. Introduction
2. Pathways of bacterial Ca-carbonate formation
2.1. Autotrophic pathways
2.2. Heterotrophic pathways
2.2.1. Passive precipitation
2.2.2. Active precipitation
3. Relationships between bacteria, minerals and environmental conditions
3.1. In situ experiments with eutrophication
3.2. Observations of karstic helictite
4. Heterotrophic bacterial productivity and geological implications
5. Conclusions
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5. Definitions
• Bacteria: single celled microbes
• Autotrophic organisms use an inorganic carbon compound for their sole
carbon source (i.e. produce their own food).
• Heterotrophic organisms use organic carbon compounds for their carbon
source (i.e. rely on other organisms for food).
• Aerobiosis (i.e. in the presence of gaseous or dissolved oxygen).
• Microaerophily (i.e. in the presence of very low amounts of oxygen).
• Anaerobiosis (i.e. in the absence of oxygen).
• Metabolism: all chemical reactions involved in maintaining the living state
of the cells and the organism.
• Eutrophic: rich in nutrients
• Oligotrophic: low levels of nutrients
5
Introduction

6. Biologically controlled
mineralization
• Caused by cellular
activities that
specifically direct the
formation of minerals
Biologically influenced
mineralization
• Caused by the
presence of cell
surface organic matter
Biologically
induced mineralization
• Caused by chemical
modification of the
environment by
biological activity that
results in
supersaturation and
the precipitation of
minerals
Introduction
6
MICP

7. Pathways of bacterial Ca-carbonate formation
Bacterial calcium-
carbonate production
Autotrophic
pathways
Heterotrophic
pathways
Passive
precipitation
Nitrogen cycle
Sulphur cycle
Active
precipitation
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8. Pathways of bacterial Ca-carbonate formation
Autotrophic pathways
• Three metabolic
pathways
• use CO2 as carbon
source to produce
organic matter
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9. Pathways of bacterial Ca-carbonate formation
Passive precipitation
• or passive carbonatogenesis
• operates by producing
carbonate and bicarbonate
ions
• Two metabolic cycles can be
involved:
• the nitrogen cycle
• the sulphur cycle
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10. Passive precipitation
• or passive carbonatogenesis
• operates by producing
carbonate and bicarbonate
ions
• Two metabolic cycles can be
involved:
• the nitrogen cycle
• the sulphur cycle
Pathways of bacterial Ca-carbonate formation
10

11. Pathways of bacterial Ca-carbonate formation
Active precipitation
• or active carbonatogenesis
• independent of the other previously mentioned metabolic pathways
• The carbonate particles are produced by ionic exchanges through the
cell membrane following still poorly known mechanisms.
• The active carbonatogenesis seems to start first and to be followed by
the passive one which induces the growth of initially produced
particles.
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12. Relationships between bacteria, minerals and
environmental conditions
• In most cases, the primary bacterial origin of carbonate is blurred by
subsequent diagenesis.
• Observations of recently formed or unmodified carbonate bacterial grains
could give information on their original nutritional microenvironment and
possibly on metabolic pathways of bacterial carbonatogenesis.
Exp-1: (Castanier, 1987)
The solid products of bacterial carbonatogenesis were first studied in
eutrophicated karstic originated waters from a natural pool situated at
Les Cugnes near Les Eyzies.
Exp-2: (Le Métayer-Levrel, 1996; Le Métayer-Levrel et al., 1997)
Bacterial calcite from a helictite of Clamouse Cave, formed in an
oligotrophic environment, was also investigated.
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13. Exp-1
The first solid products are
probably amorphous and
perhaps hydrated at the
beginning. They appear on the
surface of the bacterial bodies
as patches or stripes that
extend and coalesce until
forming a rigid coating (cocoon)
(Fig. 4).
Relationships between bacteria, minerals and
environmental conditions
13

14. Relationships between bacteria, minerals and
environmental conditions
Exp-1
In other cases, solid particles
formed inside the cellular body,
are excreted from the cell
(excretates). All these tiny
particles, including more or less
calcified bacterial cells, assemble
into biomineral aggregates which
often display `precrystalline' or
rather `procrystalline' structures
(Fig. 5).
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15. Relationships between bacteria, minerals and
environmental conditions
Exp-1
the calcified bacterial
cells tend to arrange
themselves into nearly
crystalline structures
(Fig. 5, 5)
and sometimes into
fibroradial or dendritic
fabrics (Fig. 6).
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16. Exp-1
The primary aggregates grow and
form secondary biocrystalline
assemblages or build-ups which
progressively display more
crystalline structures with growth
(Fig. 7). Tetrahedral assemblages are
often observed.
This phase should correspond to the
passive carbonatogenesis.
Relationships between bacteria, minerals and
environmental conditions
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17. Relationships between bacteria, minerals and
environmental conditions
Exp-2
Two micro-organisms are present
(Fig. 8):
The first one exhibits chains of
spheres budding or ellipsoids ca.
0.5 to 1 μm in diameter.
The second organism exhibits
more or less anastomosed
ribbons 1 μm wide, wearing very
numerous finger-shaped
refringent, strongly calcified
excrescences 0.1 to 0.3 μm wide.
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18. • These observations and experiments show that in both nutritional
conditions bacteria play a major role in crystallization, both in supplying
carbonate matter and in its physical structure.
• After eutrophication, bacterial activity is very high at the beginning and
early solid products, as well as biomineral aggregates, have poorly
defined crystal structure which is overwhelmed by biological luxuriant
processes.
• On the contrary, in oligotrophic conditions, bacterial production rate is
low so that the crystallographic rules soon overcome the biological
primary disorder.
Relationships between bacteria, minerals and
environmental conditions
18

19. Heterotrophic bacterial productivity
production of solid carbonate
depends essentially upon the
strains in the bacterial
population, the environmental
conditions (temperature,
salinity, etc.), the quality and
quantity of available nutrients,
and time.
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20. Heterotrophic bacterial productivity
• The most critical geological question is whether extensive thicknesses of
limestone and early carbonate cements are formed primarily by biotic
or abiotic means. Therefore, it is necessary to compare the efficiency of
heterotrophic bacterial carbonatogenesis and inorganic precipitation.
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21. Heterotrophic bacterial productivity
As a comparison, with the
present-day composition of
seawater, and assuming a
mean oceanic evaporation rate
of 150 mm y−1, such a physical
process would produce a
CaCO3 layer 15 μm thick, i.e.
15 m in one million years.
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22. • Such considerations, when applied to real examples from the geological
record, suggest that heterotrophic bacterial carbonatogenesis much
more likely accounts for extensive apparently abiotic (azoic) limestone
formation than any other process.
Heterotrophic bacterial productivity
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23. • The environmental conditions of heterotrophic bacterial metabolic
pathways are diverse (aerobiosis, anaerobiosis, microaerophily).
• Observations of recently formed or unmodified carbonate bacterial
grains could give information on their original nutritional
microenvironment and possibly on metabolic pathways of bacterial
carbonatogenesis.
Conclusions
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24. • The yield of heterotrophic bacterial carbonatogenesis and the scale of
solid carbonate production by heterotrophic bacteria are potentially
much higher than autotrophic or chemical sedimentation in marine,
paralic or aqueous continental environments.
• Bacterial heterotrophic carbonatogenesis is neither restricted to
particular taxonomic groups of bacteria nor to specific environments so
that it probably has been a ubiquitous phenomenon since Precambrian
times. It just requires organic matter enrichment.
Conclusions
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25. Further Reading
• Keyword: Microbially induced calcite precipitation (MICP)
• Recent Review: Anbu, P., Kang, C. H., Shin, Y. J., & So, J. S.
(2016). Formations of calcium carbonate minerals by
bacteria and its multiple applications. SpringerPlus,5(1), 1.
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