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6 Cherts and siliceous sediments

6.1 Introduction

Chert is a general term for fine-grained siliceous sediment, of inorganic, biochemical,

biogenic, volcanic and hydrothermal origin. It is a dense, very hard rock, which splinters

with conchoidal fracture when struck.

Specific names are given to the following varieties of chert:

Flint is given to chert and particularly chert nodules occurring in the Cretaceous chalks;

Jasper refers to red variety of chert containing finely disseminated hematite;

Porcelanite refers to fine-grained siliceous rock with a texture and fracture similar to

unglazed porcelain. This term is used also more specifically for an opaline claystone

composed largely of opal-CT.

Cherts in the stratigraphic record are divided into bedded cherts and nodular cherts.

Bedded cherts could be of volcanic origin or biogenic origin. The modern equivalents of

many ancient bedded cherts are the radiolarian and diatom oozes that cover large areas of

deep-ocean floors. Most bedded cherts are primary marine accumulations, whereas

nodular cherts occurring mainly within limestones and less commonly in mudstones and

evaporites are of diagenetic origin. Some of the siliceous sediments could be deposited in

lakes; others may form soils (silecretes).

6.2 Chert petrology

Bedded and nodular cherts consist of three types of quartz: microquartz, megaquartz and

chalcedonic quartz.

Microquartz consists of equant quartz crystals of only a few microns in size (Fig. 6.1a, b,

c).

Fig. 6.1a: Photomicrograph showing microquartz, chalcedonic quartz and megaquartz,

plane polarized light. Note the brown color and pore-filling nature of the chalcedonic

quartz, whereas the microquartz and megaquartz are light brown-colored or colorless.

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Fig. 6.1b: Same as 6.1b but under crossed polars. Note the microqurtz in circular to

elliptical areas consisting of very fine quartz crystals (characterized by pin-point

extinction) that replace original calcite grains. Megaquartz is seen in the upper right part

of the photo as coarse equant quartz which contains inclusions of high birefrengent

calcite, indicating also the replacement origin of megaquartz to calcite grains. The

chalcedonic quartz occurs as filling pore spaces between replaced calcite grains in form

of radial fibrous crystals.

Fig. 6.1c: Chert rock fragments consisting of microquartz that is characterized by pin-

point extinction, XPL.

Megaquartz crystals are larger, attaining 500 µm or more in size; the crystals have unit

extinction and commonly possess good crystal shapes and terminations (Fig. 6.1a, b).

Megaquartz could be called drusy quartz because it occurs as filling pore spaces with

increasing size from walls of the pores towards their centers.

Chalcedonic quartz is a fibrous variety with crystals varying in length from a few tens to

hundreds of microns. They usually occur in radiating arrangement (Fig. 6.1a, b), forming

wedge-shaped, mammillated and spherulitic growth structures (Fig. 6.2).

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Fig. 6.2: Photomicrograph of chalcedonic quartz in spherulitic growth structure, crossed

polars.

Radiolarians (marine zooplankton with a range of Cambrian to Recent), diatoms (marine

and non-marine phytoplanktons, Triassic to Recent) and siliceous sponges (marine and

non-marine, Cambrian to Recent) are composed of opaline silica. This is an isotropic

amorphous variety, containing up to 10% water.

Radiolarians and diatoms have disc-shaped, elongate and spherical tests with spines and

surface ornamentation (Fig. 6.3). They range in size from a few tens to hundreds of

microns. Sponge spicules have a similar size and a Y-shape, giving circular and elongate

sections in thin sections.

Fig. 6.3: Scanning electron microscope micrographs of radiolarians, illustrating variety of

shapes. All are from Upper Cretaceous of Cyprus and between 200 and 300 µm across.

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6.3 Bedded cherts

6.3.1 Siliceous oozes and bedded cherts

Radiolarian and diatom oozes are accumulating on the floors at the present time. They

occur especially where there is high organic productivity in near-surface water produced

by upwelling currents rich with nutrients.

The siliceous oozes preferentially accumulate in abyssal plains where depths exceed the

carbonate compensational depth (CCD) around 4500 m in central Pacific. But they could

from at shallower depths where surface water is fertile and there is a paucity of

calcareous plankton and terrigenous detrital material.

The depth at which silica itself dissolves rapidly, the opal compensational depth (OCD),

is around 6000 m.

Ancient bedded cherts commonly occur in mountainous belts and other zones of folded

rocks, many have been deposited in deep-water basins. The uniform rhythmic bedding,

which is a characteristic feature of these cherts, is generally on the scale of several

centimeters, with millimeter-thick beds or partings of shale between.

Other chert beds are massive with no internal sedimentary structure. Some chert beds

show graded bedding, parallel small-scale cross-lamination, and basal scour structures.

All such features indicate deposition by turbidity currents derived from some nearby

topographic high where siliceous sediment were first deposited, then slided downslope as

turbidity currents.

Many bedded cherts consist of poorly preserved radiolarian tests, consisting of micro- or

megaquartz-filled moulds contained in a matrix of microqurtaz (Fig. 6.4a, b).

Fig. 6.4a: Photomicrograph of chert showing spherical radiolarian skeleton and their long

thin spines set in a reddish matrix consisting of fine-grained iron oxide, plane polarized.

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Fig. 6.4b: Same as 6.4b but under crossed polars. Note the spherical radiolarian skeleton

and their long thin spines that are now composed of fine crystalline quartz (microquartz)

which replaced the original opal.

Fine clastic and carbonate sediment may be present in some cherts (Fig. 6.5a, b), and

with an increasing concentration the cherts pass into siliceous shales and limestones.

Fig. 6.5a: Photomicrograph for sediment consisting of terrigenous quartz grains,

carbonate grains including an endopunctate brachiopod shell, echinoderm plates

impregnated with iron oxide, and silicified (chertified) ooids, plane polarized light.

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Fig. 6.5b: Same as 6.5a but under crossed polarized light.

Some bedded cherts are associated with volcanic rocks, others are not.

Where there is a volcanic association, the cherts are deposited within or above billow

lavas. Lava flows and volcaniclastic sediments may be intercalated, as well as horizons of

black shales and pelagic limestones. In some cases ultramafic rocks and dyke complexes

also are present, so that the whole igneous sedimentary assemblage constitutes an

ophiolite suite, generally accepted as a fragment of the oceanic crust and overlying

sediments. The chert may be derived from devitrification of volcanic ash or biogenic

silica.

Bedded cherts are common in the Precambrian banded iron formations. Although there

were no siliceous organisms at that time, the source of silica was volcanic material and

hydrothermal fluids. Probably, the sea water during the early Precambrian had higher

concentration of silica than in the Phanerozoic and a lower pH to promote primary silica

precipitation.

Siliceous sediments rich in diatoms are called diatomites that could be ancient such as the

Miocene deposits of Mediterranean region, and modern, such as the diatomite of the

Azraq lake in Jordan.

6.3.2 The origin of chert

There are two alternative views for the formation of chert:

1- that the cherts are entirely biogenic in origin, unrelated to any igneous activity;

2- that the cherts are a product of submarine volcanism, either directly through inorganic

precipitation of silica derived from subaqueous magmas and hydrothermal activity, or

indirectly through plankton blooms induced by submarine volcanism.

According to plate tectonics theory, sea floor volcanic activities are restricted to oceanic

ridges and localized “hot spots” which could not give rise to regionally extensive cherts.

Also radiolarian cherts are not related to volcanic activity but are of biogenic origin as

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living radiolarians indicate. Therefore, the second view of chert formation is rejected as

applied to Phanareozoic cherts, but not to the Precambrian ones.

Cores collected during deep-sea drilling permitted detailed studies of how the siliceous

oozes are transformed into cherts during diagenesis.

From the biogenic amorphous opal, present in the siliceous oozes, that is also called

opal-A, the first diagenetic stage is the development of crystalline opal, identified by X-

ray diffraction (Fig. 6.6) and referred to as opal-CT.

Fig. 6.6: Schematic changes in silica mineralogy with increasing diagenesis, and X-ray

diffraction patterns for opal-A, opal-CT and quartz showing increasing crystallinity.

This opal-CT consists of an interlayering of cristobalite and tridymite, hence the name.

Also it is called disordered cristobalite, alpha-cristobalite or lussatite. The disordered

nature of opal-CT results from the small crystal size and incorporation of cations into the

crystal lattice.

Opal-CT replaces radiolarian and diatom skeletons and is precipitated as bladed crystals

lining cavities and forming microspherules (5-10µm diameter) called lepispheres (Fig.

6.7).

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Fig. 6.7: Lepispheres of opal-CT growing in voids in silicified Eocene chalk from

Arabian Sea. Sample is from 630 m below sea floor. Prismatic crystals are clinoptilolite

(a zeolite mineral), scanning electron micrograph.

Further diagenesis results in the metastable opal-CT being converted to quartz chert,

mostly an equant mosaic of microquartz crystals but also chalcedonic quartz.

This recrystallization of opal-CT to quartz obliterates the structure of many diatom and

radiolarian tests.

The driving forces behind chert formation from biogenic opal-A are the solubility

differences and the chemical conditions. Biogenic silica has a solubility of 120-140 ppm,

cristobalite of 25-30 ppm, and quartz of 6-10 ppm in the pH ranges of marine sediment

pore water (Fig. 6.8).

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Fig. 6.8: The solubility of quartz and amorphous silica at 25 ºC. At pH values less than 9,

the silica is in solution as undissolved orthosilicic acid (H4SiO4); above pH 9, this

dissociates into H3SiO42-

4 and H2SiO42-

. H2SiO42-

When the metastable opal-A dissolves the solution is saturated with respect to opal-CT

and quartz. The precipitation of opal-CT in preference to quartz probably results from the

more internally structured nature of quartz, which would require slow precipitation from

less concentrated solutions. Temperature also is involved; with the rise in temperature, as

through increasing burial depth, the rate of transformation of opal-CT to quartz increases

substantially.

The formation of chert from opal-A has been referred to as a “maturation” process.

The maturation of siliceous sediments leads to a decrease in porosity. The diatomites may

have porosities of 50-90%, porcelanites (metastable precursor to chert) up to 30%, and

cherts less than 10% (Fig. 6.9).

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Fig. 6.9: Porosity reduction with depth for a) diatomaceous oozes to opal-CT porcelanite

to quartzose chert, compared with b) deep-sea terrigenous sediment, where porosity loss

is gradual rather than stepwise.

6.4 Nodualr chert

Nodular cherts occur predominantly in carbonate host rocks. They are small to large,

susbspherical to irregular nodules, commonly concentrated along particular bedding

planes; they may coalesce to form near continuous layers, where they resemble bedded

cherts.

Nodualr cherts are common in shelf limestones and also in pelagic limestones (Fig. 6.10)

and many have developed in burrow fills and nucleated around fossils.

Fig. 6.10: Chert nodules (flint) in Cretaceous chalk of Yorkshire, England. Sutured

stylolites are present in the chalk.

Origin of nodular chert is mainly biogenic, similar to bedded cherts. It was proposed that

chert nodules were directly precipitated from seawater to blobs of silica gel on the sea

floor that hardened into chert nodules. This origin is now not accepted, since there is

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clear evidence that they originate through replacement and thus are diagenetic not

primary direct precipitation. For example, inside the nodules, originally calcareous grains

such as ooids and skeletal debris are preserved in the nodules (Fig. 6.11).

Fig. 6.11: Silicified oolite. Ooids have been replaced by microquartz and are enclosed in

booth of microquartz and megaquartz mosaic (lower part of photo), crossed polars.

Also bedding structures such as lamination may be preserved in the nodules. The

diagenetic processes involved in chert-nodule formation are similar to those operating in

bedded chert. Biogenic silica disseminated in the sediments dissolves and it is re-

precipitated in the form of opal-CT at nodule growth points. Pore spaces are first filled

with opal-CT lepispheres and then carbonate-skeletal and matrix replacement by opal-CT

follows. Maturation of the opal-CT to microquartz and chalcedonic quartz takes place

from the nodule center outwards.

It can be shown in thin sections that the microquartz has formed by replacement of

carbonate and that the megaquartz and chalcedonic quartz are dominantly pore filling

(Fig. 6.11).

6.5 Non-marine siliceous sediments and cherts

Biogenic and inorganic siliceous sediments can form in lakes and ephemeral water bodies

and in soil.

Diatoms, which can occur in great abundances in lakes, form diatomaceous earths or

diatomites, such as the Azraq Lake in NE Jordan.

Inorganic precipitation of silica can take place where there are great fluctuations in pH.

Quartz starts to dissolve when pH reaches 9 and then with increasing pH, the solubility

increases dramatically (Fig. 6.8). This increase of pH takes place in some lakes through

photosynthesis of phytoplankton, and the lake becomes supersaturated with respect to

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amorphous silica. Evaporation of lake water and the decrease in pH cause silica to be

precipitated as a gel of cristobalite, which would give rise to chert upon maturation.

Silica also may be precipitated from hot springs through evaporation and rapid cooling of

spring water to form sinter. Silicification of microbes may take place by impregnation of

organic tissues, as what could have happened in the Precambrian, and in the oldest

Devonian preserved land plant that is also a hot spring deposit.

Chert can be precipitated in some soils, where silcrete is deposited. Silcretes mostly form

under arid/semi-arid climates, where ground waters are alkaline with pH above 9, but

they can form also in humid areas. Silcrete usually consists of microquartz cement

between sand grains, and microquartz mosaic where they have formed within fine-

grained sediments. Megaquartz and chalcedonic or fibrous quartz occur within vugs.

There may be small canals and tubes from the decay of rootlets.