conference on practice improvement - stfm

The occurrence and significance of biogenic

opal in the regolith

Jonathan Clarke*

Department of Geology, CRC LEME, Australian National University, ACT 0200, Canberra, Australia

Received 23 November 2001; accepted 28 February 2002

Abstract

Biogenic opal produced by vascular plants, diatoms, and siliceous sponges have been found in soils and terrestrial sediments

of all continents except Antarctica since the middle of the 19th century. The opal particles range in size from fine silt to fine

sand. Almost all soils contain detectable opal up to levels of 2–3%, and a significant number contain values in excess of 5%.

Even higher values have been found from soils and sediments of all continents in a wide range of soil types. The most important

factor is poor soil drainage and seasonal to permanent water logging. This encourages the proliferation of silica producing

organisms. Such conditions have been found in the soils and aquatic sediments of the monsoonal tropics, tropical rain forests,

temperate forests, tropical savanna, tropical islands, semi-arid grasslands and savanna, and temperate woodland and grassland.

The presence of a volcanic substrate also appears favourable in some cases, but is not necessary. Biogenic opal preferentially

collects in the A horizon of soils and, to a lesser extent, in the B horizon. This preferential distribution facilitates identification

of palaeosols in stacked soil sequences. Biogenic opal is also a component of windblown dust, even in arid environments.

Biogenic opal is significant to regolith processes in a number of ways. Firstly, as in the case in marine environments, it is likely

to be important in silica cycling and storage because of its greater lability compared to quartz. Secondly, dissolution and

reprecipitation of opal A as opal CT or micro-quartz may play a role in cementation and silicification of regolith to form silica

hardpans and silcrete. Thirdly, the organisms that form biogenic opal can have considerable palaeoenvironmental significance

and be valuable in reconstructing regolith evolution. Finally, some forms of biogenic silica, in particular sponge spicules, can

present a health hazard. Their high abundance in some soils and sediments needs to be considered when assessing the health

implications of airborne dust.

D 2002 Elsevier Science B.V. All rights reserved.

Keywords: regolith; opal; phytolith; soil science; micropalaeontology

1. Introduction

There is an increasing awareness of the role of biota

in the regolith generally. Examples include the precip-

itation of iron and manganese (Skinner and Fitzpatrick,

1992) and interaction between bacteria and minerals

(McIntosh and Groat, 1997). Part of this role is the

deposition of biogenic silica in the form of opal.

Examples include phytoliths, diatoms, and siliceous

sponge spicules. Brewer et al. (1993) described phyto-

liths in Australian soils as ‘‘almost ubiquitous’’. In

contrast, the same authors describe diatoms as ‘‘have

been recorded’’ and sponge spicules as ‘‘rare’’ and

‘‘almost certainly inherited’’. Wilding et al. (1989)

0012-8252/02/$ - see front matter D 2002 Elsevier Science B.V. All rights reserved.

PII: S0012 -8252 (02 )00092 -2

* Fax: +61-2-6125-5544.

E-mail address: [email protected] (J. Clarke).

www.elsevier.com/locate/earscirev

Earth-Science Reviews 60 (2003) 175–194

regarded most soils as containing up to 3% biogenic

opal and cited examples where up to 20% was present.

These values mean that opal comprises a significant

part of the silica component of many soils and can com-

monly exceed the abundances of potassium, calcium,

magnesium, sodium and phosphate. However, bio-

genic silica is normally regarded as a minor component

and the potential role of organisms in the large-scale

deposition of silica in the regolith is largely ignored.

Despite this, there is considerable evidence that

opal from phytoliths, diatoms, sponge spicules, and

other organisms are often abundant in the regolith in

many localities. Widespread and common accumula-

tions >2% by grain abundance are known from every

continent except Antarctica in environments as

diverse as coastal and inland swamps, forests, grass-

lands, and flood plains. They are present in the

tropical, temperate, and semi arid regions.

Assessing the actual abundance of biogenic silica

in regolith materials is difficult. Most studies concen-

trate on one component, such as phytoliths, and do not

discuss the presence of other forms. Some authors

(e.g., Brewer, 1955) give actual percentages (Table 1),

others list proportions (Table 2) (e.g., Schwandes and

Collins, 1994) in opal grains per gram, still others

(e.g., Hart, 1992) as percentage of a particular size

fraction, such as silt, or (Clark et al., 1992a) as cm2

cm3. None of the works, to date, appears to have used

the various chemical techniques used in the study of

biogenic opal in marine sediments (see Muller and

Schneider, 1993 and references therein).

This paper reviews occurrences of biogenic opal in

the regolith and their potential importance to regolith

processes. Far from being of minor importance, I argue

that biogenic opal is a key constituent of the regolith.

2. Status of terrestrial biogenic opal research

For more than 150 years, biogenic silica has been

known to be a component of the regolith. The earliest

mention of biogenic opal in soils was in 1841 by the

German microscopist Ehrenherg (Piperno, 1988). A

few years later, Gregory (1855) reported spicules and

diatoms as well as phytoliths in soils. Early studies on

spicules were listed by Smithson (1959), while Oehler

Table 1

Abundances of opaline material in selected soils (representative only)

% Opal Forms Setting Locality Source

19 Spicules Flooded forest Central Amazonia Chauvel et al. (1996)

3.2 Phytoliths, spicules,

diatoms

Coastal swamps Dalmore, Victoria,

Australia

Baker (1959b)

2.1 Phytoliths, diatoms Forested hills Mt. Gellibrand,

Victoria, Australia

Baker (1959b)

24 Spicules, diatoms,

phytoliths

Alluvial plain Duntroon, ACT,

Australia

Brewer (1955)


phytoliths

Alluvial plain Deep Creek, NSW,

Australia

Brewer (1955)


phytoliths

Alluvial plain Doughboy Creek,

NSW, Australia

Brewer (1955)

43 Phytoliths Bamboo forested

slope

Reunion Island Meunier et al. (1999)

0.9 Phytoliths Forested plain Amazonia Kondo and Iwasa

(1981)

4.5 Phytoliths Swamp Northern Sydney,

Australia

Hart (1992)

20 Phytoliths Grassland Oregon, USA Hart (1992)

100 Phytoliths Basalt flow East Africa Hart (1992)

30–60 Phytoliths Volcanic slopes Japan Hart (1992)

48 Phytoliths, spicules,

diatoms

Seasonal

wetlands

Magela Creek,

NT, Australia

Clark et al. (1992b)

100 Phytoliths, spicules,

diatoms

Seasonal

wetlands

Magela Creek,

NT, Australia

Clark et al. (1992b)

J. Clarke / Earth-Science Reviews 60 (2003) 175–194176

(1979) provided a review of the significance, origin,

and biogeochemical cycling of silica in the terrestrial

environment. Much has been documented on the

taxonomy of biogenic opal in soils, and some detailed

palaeoenvironmental and palaeoecological studies

have been carried, most on local scales (e.g., Gasse,

1987; Volkmer-Ribeiro, 1992). However, much of this

work has been fragmentary and focused on specific

applications, such as palaeoenvironmental and ar-

chaeological analysis. There has been little integration

of data from soil science, palaeoenvironmental, palae-

ontological, sedimentological, and regolith studies.

3. Sources of biogenic silica in soils

3.1. Plant opal

Many groups of plants produce silt-sized opal

grains known as phytoliths (Fig. 1A). These form

structural elements and provide a defense against

herbivores (Lewin and Reimann, 1969). They are

extremely abundant in grasses, which can contain up

to 10% silica by weight (Lovering, 1959) and horse-

tails (Equisetum) can contain up to 16% dry weight of

biogenic opal (Lewin and Reimann, 1969). However,

phytoliths also occur in a wide range of other plant

groups (see Piperno, 1988) and it would be a mistake

to assume that they are abundant only in grasses and

horsetails. Phytoliths are found in most soils, includ-

ing those from temperate forests of North America

(Wilding and Drees, 1971), the savanna landscapes of

Kenya (Runge, 1999) and tropical forests of Amazo-

nia (Kondo and Iwasa, 1981) and Africa (Runge,

1999). They locally reach abundances of 43% in the

B-horizon of some soils on Reunion Island (Meunier

et al., 1999). They offer considerable potential for

palaeoenvironmental reconstruction, owing to differ-

ent morphologies derived from different plant com-

munities (Runge, 1999; Wilding and Drees, 1971).

Phytoliths are the most common form of biogenic

silica in most terrestrial environments. A much rarer

occurrence is tabashir, massive bodies of opal found

in bamboo (Jones et al., 1966). Phytoliths may be

confused with sponge spicules, especially in older

literature (see review in Hart and Humphreys, 1997).

Both have a rod- or needle-shaped morphologies,

however sponge spicules typically have a central

canal, absent in phytoliths. Some spicules are highly

complex and irregular in shape, especially those of the

lithistid sponges, common in Eocene marine sedi-

ments in southern Australia, these, along with gem-

mule bodies and microscleres lack a central canal, and

may be confused with phytoliths.

Table 2

Other selected abundances of opaline material in soils (non-compatible units)

Amount Units Forms Setting Locality Source

0.5–6 % silt

fraction

Phytoliths Tropical

forest soils

D. R. Congo Runge (1999)

>0.1–2 % sand

fraction

Phytoliths Tropical

forest soils

D. R. Congo Runge (1999)

14 % silt

fraction

Phytoliths Tropical

forest soils

Central African Republic Runge (1999)

1.65 % sand

fraction

Phytoliths Tropical

forest soils

Central African Republic Runge (1999)

500,000 Grains/gram Spicules Histsol Florida Schwandes and Collins

(1994)

4600 Grains/gram Spicules Entisol Florida Schwandes and Collins

(1994)

48,000 Grains/gram Spicules Spodsol Florida Schwandes and Collins

(1994)

9500 Grains/gram Spicules Mollisol Florida Schwandes and Collins

(1994)

23,000 Grains/gram Spicules Ultisol Florida Schwandes and Collins

(1994)

f 10,000 Grains cm2 cm3 Phytoliths,

spicules, diatoms

Black soils Magela Creek, Northern

Territory

Clark et al. (1992a)

J. Clarke / Earth-Science Reviews 60 (2003) 175–194 177

Fig. 1. Representative examples of opal secreting organisms showing the immense range in morphology. (A) Phytoliths (after Baker, 1959a). (B)

Marine and freshwater diatoms (after Braiser, 1980). (C) Marine and freshwater sponge spicules (after de Laubenfels, 1955). (D)

Silicoflagellates, (E) chrysomonads, (F) radiolaria, and (G) ebridians (all after Braiser, 1980). (H) Helizoans (after Moore, 1964).


Fig. 1 (continued).


3.2. Diatoms

Diatoms (Fig. 1B) are found in lakes, rivers, and

soils. They also occur subaerially on plant and rock

surfaces in moist environments (Patrick, 1977). Dia-

toms comprise the bulk of the 24% of siliceous

remains reported by Brewer (1955) from the A2

horizons of soils in Canberra, Australia. Compara-

tively pure accumulations of diatoms (diatomites) are

known only from lake and swamp basins, however

such sediments may form part of the regolith, espe-

cially where they occur in stable continental environ-

ments. Modern Australian examples include the

Holocene diatomites of the Swan coast plain of West-

ern Australia (Gibson, 1976) and the Neogene diatom-

ites of Victoria (Kenley, 1976) which are intimately

associated with lakes and sediments formed by Qua-

ternary basaltic volcanism and associated drainage

diversion. Miocene Bonnie Doon Diatomite from

New South Wales is not, however, associated with

volcanism (Taylor et al., 1990). All these deposits

contain varying amounts of clastic material and sponge

spicules in addition to the diatom frustrules. Secondary

silica mobilisation is common in the Victorian depos-

its, as they have been exposed to percolating ground-

water, forming opaline bands. Diatoms are known

from all continents. The expansion and contraction

of large lakes in low relief continental environments,

such as the modern lake Chad, can result in deposition

of diatomaceous sediments over large areas and then

expose them to pedogenic processes (Thiry, 1999).

3.3. Sponges

Siliceous sponges (Fig. 1C) are normally only a

minor component of marine and terrestrial ecosys-

tems. Their presence in sediments and soils (Smith-

son, 1959) are similarly normally minor. Under

conditions not fully understood they can, however,

proliferate and even dominate. Late Eocene spicular

marine and marginal marine sediments, locally with

up to 100% sponge spicules (Clarke, 1994a), form the

land surface over large areas of southern Australia.

The reasons for this proliferation during a narrow time

interval are not fully known, but probably related to a

unique confluence of runoff, turbidity, and nutrient

conditions (Gammon et al., 2000).

Freshwater sponges produce much smaller spicules

than marine sponges, typically silt rather than sand-

sized. Thus, they are often missed by those looking

only at the larger fraction. They are known not only

from lakes (Harrison, 1988) and rivers (Chauvel et al.,

1996) but also bogs (Volkmer-Ribeiro, 1992) and

waterlogged soils (Schwandes and Collins, 1994).

They have been reported as composing more than

20% of the silt fraction of the soil in parts of Amazonia

(Chauvel et al., 1996) and in numbers of more than one

million spicules to the gram (Schwandes and Collins,

1994). They have been found to date in the soils of all

continents except Antarctica.

Even though the presence of such spicules has been

taken to indicate high levels of dissolved silica (see

Turner, 1985), this need not be the case. Spicule-rich

Fig. 1 (continued).


sediments were reported from rivers in Amazonia by

Chauvel et al. (1996) that have extremely low dissolved

silica levels of 2.1 ppb. In comparison, Aston (1983)

gives an average global silicon value for river water of

13.1 ppm, while Wollast and Mackenzie (1983) say

5.42 ppm.

3.4. Other organisms (Figs. 1 D–G)

Many groups of regolith bacteria are known to

dissolve silicates (see review of Silverman, 1979)

through enzyme and organic acid secretion. Some,

such as Proteus mirabilis, also store the silica within

their cells and in slime layers (Tesic and Todorovic,

1958; Lauwers and Heinen, 1974) as monomeric

silica. The fate of such silica in the regolith is not

known but it may provide both a source of silica for

uptake by higher plants and, potentially, as a means of

silica cementation should the silica in the slime layers

and dead bacterial cells between regolith grains

undergo polymerisation. The abundance of bacterial

remains in hydrothermal and marine chert deposits

suggests that bacteria do play a role in silica deposi-

tion (Ferris, 1997). Shaw et al. (1990) reported that

desiccation of formerly floating colonies of the fila-

mentous cyanobacteria Chloriflexus provided a tem-

plate for silica deposition in a silica-depositing

alkaline saline pan in Botswana. Widespread silicifi-

cation of bacterial cells has been reported (Ferris,

1997) and strongly supports a bacterial role in the

deposition of silica in the regolith.

Radiolaria are significant siliceous organisms in

the pelagic realm (Braiser, 1980). Not found in

terrestrial aquatic environments, they are likewise rare

in the coastal sediments likely to be incorporated into

the terrestrial regolith. However, the Australian rego-

lith includes epicontinental sediments of Cretaceous

age, and these can include radiolarian-rich deposits.

An example is the radiolarian-bearing Darwin Mem-

ber of the Bathurst Island Formation of the Northern

Territory (Nott, 1994) which may be the source of

silica in siliceous bands in the weathering profile.

Helizoans are Protozoa with a siliceous test similar to

radiolaria but restricted to freshwater environments.

They are rarely preserved because their fragility

normally results in the rapid disintegration of the test

after death (Braiser, 1980). Heliozoans however have

occasionally been reported from Quaternary sedi-

ments and are thought to indicate swampy to lacus-

trine environments (Piperno, 1988; Moore, 1964).

Another group of Protozoa are the testate amobae

known as rhizopods (Charman, 2000). While some

rhizopods form tests (xenosomic tests) of cemented

grains from the local environment, others have very

weak siliceous tests. These are known as idiosomic

tests and are formed by the parent amobae during

reproduction. Rhizopods are found in lakes and peat-

lands and in recent research has demonstrated their

potential for palaeoecological studies. Their larger

scale significance to silica cycling is unclear, as they

are only weakly mineralised.

Silicoflagellates are also important silica depositing

organisms in pelagic marine environments. They are

not, however known from terrestrial environments,

nor are they, unlike diatoms and sponges, known at

present to be locally common enough in coastal sedi-

ments to become significant components of the rego-

lith as a result of sea level changes (Braiser, 1980).

Whether they, as radiolaria do, occur in significant

numbers in marine epicontinental deposits such as the

Cretaceous of the Australian regolith, is not known.

Chrysomonads are mostly non-marine Chrysophyte

algae related to silicoflagellates (Braiser, 1980). They

appear to be of minor importance in siliceous non-

marine sediments.

Ebridians are a small and comparatively minor

group of siliceous marine plankton allied to dinofla-

gellates (Braiser, 1980) and are not presently known

to form significant accumulations on their own. They

are common in some diatomite deposits (Bohaty and

Harwood, 2000). Some Ebridians produce external

siliceous scales or spines while all produce siliceous

resting cysts termed statosphores (Smol, 1987).

4. Spatial distribution in the regolith

4.1. Opal in the landscape

No detailed study has been carried on the spatial

distribution of biogenic opal in soils. However, fol-

lowing Hart’s (1992) analysis of the data of Stace et

al. (1968), detectable opal is common in many

Australian soils profiles. Stace et al. (1968) compiled

147 representative soil profiles from 43 soil groups.

Micromorphological data was provided for 85 of


Table 3

Abundance of biogenic opal in Australian soil profiles. After Stace et al. (1968)

Abundance Number

of profiles

Percentage

all profiles

Soil groups Fraction of profiles

in each soil group

Frequent (>5%) 12 14.1 Grey, brown and red clays 1/13

Solodized solonetz and sodic soils 2/4

Soloths 4/5

Krasnozems 1/2

Red podzolic 1/1

Yellow podzolic 1/3

Humic gleys 3/4

Common (2–5%) 14 16.5 Grey, brown and red clays 2/13

Prairie soils 1/4

Soloths 2/5

Red-brown earths 2/5

Non-calcic brown soils 1/1

Chocolate soils 1/2

Yellow earths 1/1

Yellow podzolic 1/3

Gleyed podzolic 1/1

Podzols 1/1

Humic gleys 1/4

Occasional (0.5–2%) 24 27.1 Siliceous sands 1/2

Earthy sands 1/1

Desert loams 1/5

Grey, brown and red clays 4/13

Chernozerms 1/2

Prairie soils 2/3


Solonized brown soils 1/6

Red-brown earths 3/5

Chocolate soils 1/2

Calcareous red earths 2/6

Red earths 1/4

Terra rossa soils 1/1

Brown podzolic 1/1

Lateritic podzolic 2/4

Humic gleys 1/5

Rare ( < 0.5% but easily seen 10 12.9 Grey, brown and red clays 1/13

under microscope) Solonized brown soils 1/6

Brown earths 1/1


Red earths 1/4

Euchrozems 1/1

Yellow podzolic 1/3

Lateritic podzolic 2/4

Humic gley 1/5

Very rare (hard to find under 21 24.7 Grey, brown and red calcareous soils 2/2

microscope) Desert loams 4/5

Grey, brown and red clays 5/13

Black earth 1/1




Red earths 2/4

Xanthrozems 1/1


profiles. Opal was detected in 81 of these (Table 3)

representing over 95% of soils studied. Just over

30% (26 examples) contained more than 2% opal,

and just over 56% (47 examples) contained more

than 0.5%.

Abundant (>2%) opal was found in soils from

western Australia, Victoria, New SouthWales, Queens-

land, South Australia, and the Australian Capital

Territory. All but three of these soils (88.5%) were

characterised by slow or impeded, drainage. In con-

trast, poor drainage was a feature of only 41.6%

profiles containing occasional opal grains. Profiles

with rare and very rare grains of biogenic opal were

poorly drained in only 30% and 33% of cases, respec-

tively.

These results indicate that there is a strong corre-

lation between the occurrence of high levels of bio-

genic opal in soils with poor drainage. Stace et al.

(1968) performed no soil petrography on alluvial or

organic-rich soils. Data on occurrences of exception-

ally high levels of biogenic opal indicate that they

often occur in such soils also. Examples include those

of the flood plains (Chauvel et al., 1996) and bogs

(Volkmer-Ribeiro, 1992) of Brazil, and the Magela

Creek flood plain of the Northern Territory of Aus-

tralia (Clark et al., 1992a,b) (Fig. 2). As post-organic-

rich soils, such as histosols are poorly drained, the

correlation with poor drainage and water logging,

noted by Brewer (1955), is thus probably much

stronger than these data indicate.

4.2. Opal in soil profiles

There have been many studies noting the pres-

ence of biogenic opal in soils, and the following

references provide an outline only. Biogenic opal is

normally preferentially concentrated in the A-hori-

zon of individual soil profiles (Oehler, 1979). It is

also present less commonly in the B-horizon, and

sometimes both (Simons et al., 2000). Accumulation

in the B-horizon is typically due to downward

movement resulting from bioturbation and percolat-

ing soil water (Hart and Humphreys, 1997; Boet-

tinger, 1994; Piperno, 1988). In some cases the

biogenic opal may be concentrated entirely in the

B-horizon (see Meunier et al., 1999; Schwandes and

Collins, 1994), but this is exceptional. Bobrova and

Bobrov (1997) and Bobrov and Bobrova (2001) re-

ported the concentration of phytoliths in illuvial and

eluvial horizons.

Because phytoliths are commonly perceived to be

concentrated in the A horizon of soils, increases in

their abundance within a profile have sometimes been

used as indicators of palaeosols in a succession (see

Dormaar and Lutwick, 1969). Care should be taken in

such interpretations, because of the downward move-

Abundance Number

of profiles

Percentage

all profiles

Soil groups Fraction of profiles

in each soil group

Krasnozems 1/2

Alpine humus soils 1/1

Absent 5 4.7 Siliceous sands 1/1



Undescribed Solonchalks

Alluvial soils

Lithosols

Red-brown hardpan soils

Redzinas

Wiesenboden

Calcareous sands

Grey-brown podzolic

Humus podzols

Peaty podzols

Neutral to alkaline peats

Acid peats

Table 3 (continued)


ment in such circumstances noted above by Simons et

al. 2000) and should only be carried out with good

soil stratigraphic control.

5. Composition and chemistry

Biogenic silica is formed mainly as amorphous

opaline silica (opal A), but plant opal is also known

to contain opal CT (Wilding and Drees, 1974).

Diagenesis of the opal in soils results in further

production of opal CT and eventually its stablisation

as quartz (Wilding et al., 1989). Studies of the

subsequent precipitation of dissolved silica from

biogenic opal are rare, but amorphous opal, opal

CT and quartz are all possible secondary phases,

with crystalline forms becoming more likely with

time.

Plant opal can contain significant amounts of Al,

Fe, Ti, Mn, P, Cu, N, and C (Wilding et al., 1989).

The Al is known to play a key role in the surface

chemistry of plant opal, influencing dissolution and

interaction with organic acids (Bartoli, 1985). Much

or all of the Al is chemisorbed on the surface,

rendering the plant opal as reactive in the soil as iron

and aluminium hydroxides and allophanes. Nitrogen,

phosphorous, and carbon may be the result of inclu-

sion of lignin and cellulose during formation of the

phytoliths. Trace element composition of other forms

of biogenic opal, such as spicules and diatoms, is not

known.

Biogenic opal also shows high delta O18 values.

Diatoms typically show approximate values of + 29

to + 32 relative to SMOW, and phytoliths values of

+ 36 to + 39 (Wilding et al., 1989). This strongly

suggests that the isotopic value of regolith opal, at

Fig. 2. An opal factory (1): wetlands of Kakadu National Park, Australia contain up to 100% opal. Open water billabongs (A) and seasonal grass

and sedge wetlands (B) have the highest opal productivity. Paperbark wetlands (C) are less productive. Biogenic opal is visible as pale streaks in

the black soils of the seasonal wetlands (D). All photographs courtesy of R. Wasson.


least in its particulate or dispersed form, can be used

to demonstrate biological origin. Webb and Long-

staffe (1997) argued that progressive depletion

reflected increasing values of evapotranspiration.

Bombin and Muehlenbachs (1980) earlier noted that

the oxygen isotope values varied according to both

temperature and humidity. This makes the use of these

isotopes as direct palaeoclimatic indicators problem-

atic, although they certainly appear to have potential

as evapotranspiration indicators. It is not known

whether these signatures persist through diagenesis

of the opal. Webb and Longstaffe also reported

extreme depletion in deuterium (� 125), the reasons

for which were not known at the date of publication.

This contrasts with the study of Fredlund (1993), who

found deuterium values consist with that of the waters

that supported plant growth, allowing for the usual

levels of biological fractionation. Carbon isotope

ratios of phytoliths were reported by Fredlund as

reflecting the C3/C4 ratio within the source vegeta-

tion. As is the case with oxygen isotopes, it is not yet

known whether these hydrogen and carbon survive

diagenesis.

As noted by Oehler (1979), non-crystalline forms

of silica are much more soluble than crystalline forms.

Wilding et al. (1989) said that amorphous silica was

more soluble than quartz by a factor of 10 or more.

Biogenic opal showed a great range in solubility.

Generally, those remains containing less organic car-

bon were more soluble than those that still contained

significant organic matter. In addition, some types of

biogenic opal are more soluble than others. Wilding

and Drees (1974) found that forest opal was 10–15

times more soluble than grass opal, owing to its

greater surface area. In sediments, biogenic opal is

more labile than quartz. Kosters and Bailey (1983)

identified sponge spicules as among the most chemi-

cally mobile silica sources in sediments from the

Mississippi Delta.

Once silica has been dissolved from biogenic opal

grains, it can then be re-precipitated lower in the soil

profile. Alexandre et al. (1997) described incipient

cementation of soil particles in the lower part of a soil

profile by opal remobilised from phytoliths and other

organisms. Dissolution and cementation of silica in

soils can occur quite rapidly under favourable con-

ditions, as shown by Breese (1960) in studies of

aeolian dust.

6. Biogeochemical cycling of silica in the regolith

Organisms play a vital role in both the dissolution

(Silverman, 1979) and deposition (Oehler, 1979) of

silica in the regolith. Ambivalent results were reported

in early studies cited by Jones and Handreck (1967)

on the effect of growing plants in silicon-free sub-

strates. Some studies showed no ill effect whereas

others did. One of the main functions of biogenic opal

in plants is in improving pest resistance, thus under

field conditions improved silicon availability to plants

is desirable. A more recent work cited in Epstein

(1999) shows that silicon-deprived plants are structur-

ally weaker, have various abnormalities, and are more

susceptible to biotic and abiotic stress. Results from

experimental studies in silicon-free media replicate

studies of plant pathologies found in silicon-poor

soils, especially lateritic and bauxitic soils of tropical

regions. In Epstein’s words, ‘‘the evidence is over-

whelming that silicon should be included among the

elements having a major bearing on plant life

(Epstein, 1999). Because of its greater chemical

mobility than crystalline silica phases, biogenic opal

plays a major role in the cycling of silica in soils

(Alexandre et al., 1997), just as it does in aquatic

environments (Konhauser et al., 1992).

As pointed out by Heinen and Oehler (1979), the

cycling of silica through the biosphere has evolved

through time. Silica bacteria may have been present

since the Precambrian. Marine sponges are known

since just before the end of the Neoproterozoic (Braiser

et al., 1997) and have formed strandline accumulations

since the Carboniferous (Carlson, 1994). Sponges have

been reported from freshwater environments of at least

Carboniferous age (De Laubenfels, 1955) and probably

form a significant source of silica in coals throughout

geological history (Davis et al., 1984). Equisetum, the

single modern representative of the Equisetales, a

dominant component of land vegetation from the

Devonian through to Permian, contains abundant silica

(Lewin and Reimann, 1969). If these values of silica

content reflect a characteristic of the taxon as a whole,

evolution of these plants would have significantly

increased the rates of silica cycling in the regolith.

Rates of silica cycling would have increased still

further with the evolution of grasses and their ecolog-

ical dominance from the Oligocene onwards (Braiser,

1980). Although diatoms may have appeared in the


Jurassic, they are common in terrestrial environments

only from the Miocene (Braiser, 1980).

Thus, the pattern rate of silica cycling and the

potential for accumulations of biogenic silica in the

regolith has increased markedly with time. Major

increases would have occurred in the Mid to late

Palaeozoic and near to the Paleogene–Neogene boun-

dary.

Alexandre et al. (1997) reported that 92% of the

biogenic silica in the soil is recycled by plants and is

the main source of this nutrient. Only the remaining

8% accumulates in the soil. Konhauser et al. (1992),

in a study of the seasonally flooded forests of the

Amazon basin reported that diatoms played a key role

in silica exchange between the dissolved and precipi-

tated state, with the precipitated silica being stored as

gel coatings on wood. The significance of sponges in

silica cycling is not known, but the abundance of

siliceous spicules in some soils in the flooded forests

of the Amazon (19%) indicates that they, along with

diatoms, are likely to be significant in at least some

water logged environments.

7. Application to understanding and study of

regolith processes

7.1. Setting of exceptionally opal-rich environments

Although small values of opal are fairly ubiquitous

in many soils and sediments significant quantities

(e.g., >5%) occur less commonly. Apart from the

unusual stranded Eocene sediments of southern Aus-

tralia, examples are non-marine. Examples reviewed in

this paper include the Magela Creek flood plain,

(Northern Territory, Australia; Clark et al., 1992a,b),

Amazonia (Chauvel et al., 1996), Bungendore (NSW)

and Duntroon (ACT; both Brewer, 1955) (Fig. 3). The

Okavango Delta has abundant dissolution and precip-

itation of silica (Shaw et al., 1990; Shaw and Nash,

1998), and high levels of opal productivity. Peat

formed from grasses and sedges contain up to 30%

phytoliths, along with minor diatoms and sponge

spicules (McCarthy et al., 1989).

These opal-depositing environments differ in many

respects. With respect to vegetation, Amazonia con-

sists of flooded tropical rainforest, Bungendore and

Duntroon formerly temperate eucalypt woodland,

Magela Creek monsoon grassland, woodland, and

wetland, and the Okavango Delta seasonally to per-

manently flooded arid wetland. With respect to water

chemistry, Magela Creek and Amazonia waters are

acidic, the Okavango region strongly alkaline, and the

NSW and ACT examples near neutral. The Okavango

waters are also comparatively saline whereas the

others are dilute.

The common feature in all of these environments is

seasonal to permanent flooding. Under such condi-

tions the diatoms and sponge bloom in sufficient

quantities so as to make a significant component of

the sediment. The sponges and diatoms may be

epiphytic (Chauvel et al., 1996; Konhauser et al.,

1992; Clark et al., 1992b), or planktonic (Volkmer-

Ribeiro, 1992). Furthermore, in many wetlands the

plant taxa include those with high phytolith produc-

tion, such as grasses and sedges (Clark et al.,

1992a,b). This association of poor drainage and high

levels of opal reinforces the conclusions drawn above

from a review of soil micromorphology in Stace et al.

(1968) discussed above.

Under ideal conditions, these environments can

produce sediments as rich in biogenic silica as those

of the marine realm. Magela Creek forms part of the

East Alligator River drainage system in the Northern

Territory of Australia. The black alluvial soils, typi-

cally between 30 cm and 2 m thick, can average up to

35% biogenic opal over lateral distances of several km

and up to 48% in a single soil core. The mineral

fraction of individual beds within the black soils can

be composed entirely of biogenic opal (Clark et al.,

1992a,b).

Other unusually opal-rich environments are found

on volcanic soils in Africa, Japan (see references in

Hart, 1992) and Reunion (Meunier et al., 1999). The

high levels of opal in these soils may reflect unusually

rapid release and uptake of silica into plants as a result

of the fast weathering of soils derived from the

weathering of volcanic debris and rocks, especially

those low in silica.

Although high rainfall encourages water logging

and thus potentially high productivity of opal, it is not

necessary for it. Water logged soils and aquatic envi-

ronments occur in arid and semi arid environments,

provided there is sufficient water. More critical is

salinity, but provided it is not excessive, these environ-

ments are potentially highly productive, even in dry


environments. Examples discussed in this paper

include Lake Chad and the Okavango Delta.

7.2. Dust

Most dust contains a small proportion of opal, this

being almost entirely of biogenic origin. Australian

windblown dusts (Baker, 1960) contain phytoliths,

sponge spicules, and diatoms. Drees et al. (1993)

reported that the main type of biogenic opal in dusts

from Niger is sponge spicules. These dusts have been

deflated from the Sahara or Sahel regions of Africa,

not the most obvious habitat for freshwater sponges.

Jones and Beavers (1963) and Wilding and Drees

(1968) used the presence of sponge spicules in soils

from ridge tops to indicate contributions from wind-

blown materials. Given the ubiquity of spicules and

spicule-like structures in many soils, this criterion

may prove to be of doubtful value. However, recog-

nising windblown components to soils is important to

the regolith geology of many areas (Greene, in press),

such as eastern Australia, where dryland soil salinity

is believed to be the result of accession of aeolian

material and potential tools in its recognition should

not be ignored. In addition, Wilding and Drees

(1974) suggested the clay-sized quartz particles in

some soil profiles that have been attributed to aeolian

accession may, in fact, be due to the recrystallisation

of phytoliths.

7.3. Palaeoenvironmental reconstruction

Opal-forming organisms are highly sensitive to

environmental variations and, properly interpreted,

Fig. 3. An opal factory (2): soils of the Canberra region contain significant amounts of opal. (A) Podzolic soils in gently undulating landscapes

north of Duntroon, Canberra, Australia contain up to 22% biogenic opal. (B) Alluvial soils at Barrack Flat, Queanbeyan, contain up to 7% opal

(Angela Harrison, unpublished data). (C) Soils at Deep Creek, east of Bungendore, ACT, Australia reportedly contain 11% biogenic opal (D).

Some 2% biogenic opal has been reported from Doughboy Creek, east of Bungendore.


can be a useful guide in environmental reconstruction.

Both phytoliths and diatoms have been widely used in

palaeoenvironmental interpretation. Sponge spicules

have been used less because of difficulties in taxo-

nomic identification, but are good indicators of per-

manently waterlogged conditions and, where taxa are

recognisable, of marine influence.

Beavers and Stephen (1958) showed that phytoliths

in the soils of Illinois varied according to vegetation

type. Such patterns can be used to reconstruct ancient

vegetation patterns. One such example is the report of

Barboni et al. (1999), which provides an example of

phytoliths in the environmental reconstruction of

archaeologically significant regions in Ethiopia.

Because phytoliths are commonly perceived to be

concentrated in the A horizon of soils (Oehler,

1979), increases in their abundance within a profile

have sometimes been used as indicators of palaeosols

in a succession (Dormaar and Lutwick, 1969). As

noted above, care should be taken in such interpreta-

tions as exceptions are known. Piperno (1988) gave

an extensive review of the use of phytoliths in palae-

oenvironmental reconstruction and archaeology, with

the collection edited by Meunier and Colin (2001)

providing a summary of the state of the art.

The use of diatoms to reconstruct lacustrine sedi-

mentary environments is well known (Smol, 1987).

However, diatoms can be used even in arid and semi-

arid regions, as illustrated by the study of Gasse

(1987) from sub-Saharan Africa. In this example,

the diatoms live in a wide range of environments,

including former mega-Lake Chad, dilute swamps,

and small hypersaline lakes, fed by groundwater

discharge or ephemeral streams.

Harrison (1988) reviews the use of sponge spicules

from a Canadian lake. Sponge gemmules are also

valuable in reconstructing environments and have

been found in diverse environments such as bogs of

the Puget Lowland, Washington (Turner, 1985) and

the flood plain forests of Amazonia (Junk, 1984).

Piperno (1988) provides one of the few examples

of using a wide range of siliceous organisms in

environmental reconstruction. She was able to extract

a diverse assemblage of phytoliths, diatoms, sponge

spicules, and helizoans from a series of terrestrial

sediment cores from Panama. Piperno was able to

identify moist tropical forest, marine swamp, fresh-

water swamp and cropland vegetation and therefore

reconstruct an environmental and floral history of the

last 11,300 years. The record closely matched that

obtained from palynology and indicates the potential

utility of siliceous remains to document palaeoenvir-

onments in sediments that might not preserve organic

microfossils. Similarly, Clark et al. (1992a,b) used

palynology, diatom taxonomy, and distribution of

phytoliths and sponge spicules to determine the Hol-

ocene evolution of the Magela Creek floodplain in the

Northern Territory of Australia. These authors were

able to demonstrate how the environment evolved

from a mangrove swamp to seasonal freshwater wet-

land. Opal production was a clear indication of wet-

land development. However, very high levels of opal

productivity (>8% for bulk soil composites) were

associated with grass and sedge wetlands, rather than

wooded wetlands or mangroves. Sponges were the

main source of opal in the mangrove environment.

Despite these studies, the use of biogenic, opal,

apart from phytoliths, as a tool in regolith geology is

in its infancy. Most studies using siliceous remains

have concentrated on the Quaternary, rather than the

much longer time necessary in many regolith studies

as illustrated by Ollier and Pain (1996). Some work

has been done on siliceous remains in older sedi-

ments, such as that of Folk (1964) on Cainozoic

phytoliths. Marine sponge spicules have been impor-

tant in understanding Eocene environments of south-

ern Australia (Clarke, 1994a,b; Gammon et al., 2000).

Phytolith geochemistry is another possible but

poorly explored avenue for palaeoclimatic research.

Webb and Longstaffe (1997) indicated that increasing

enrichment in O18 reflected increasing degrees of

evapotranspiration. More needs to be known about

the range of O18 values of different taxa before this

can be routinely applied.

7.4. Silcretes siliceous hardpans, and hardsetting soils

Silcretes are silica-rich duricrusts found in many

parts of the globe (Thiry, 1999). They are enigmatic

features in that, unlike other duricrusts such as cal-

cretes, bauxites, and ferricretes, there are few known

modern analogues. Silcrete appears to form by a range

of different processes in a diverse range of landscape

contexts and eras (Thiry, 1999; Alley, 1996; Firman,

1994; Ollier, 1991), matched only by the diversity of

opinions as to its formative conditions. An important


series of observations, however is that it commonly

appears to have formed on former valley slopes and

floors, often, although not always, in quartz-rich

colluvium or alluvium. Importantly, to distinguish

silcretes from siliceous hardpans (see below), there

is also silicification of the host material, as well as

silica cementation. Once formed, such silcretes typi-

cally form inverted relief (Ollier and Pain, 1996).

Such silcretes need not have extended across the

entire landscape, but rather have formed in selected

localities by the lateral migration of silica-rich

groundwater.

The greater lability of biogenic opal compared to

other forms of silica means that it is a prime source of

silica for precipitation in the regolith. Several authors

have suggested a connection between silcretes and

biogenic opal. Gunn and Galloway (1978) raised the

possibility that biogenic silica leached from marine

organisms was an important component in some

Australian silcretes developed on Cretaceous marine

shales. Oehler (1979) similarly suggested that bio-

genic opal may play a role in silcrete formation,

postulating that dissolution of the siliceous remains

of terrestrial organisms may have contributed to the

formation of silcretes. Thiry (1999) noted silica dep-

osition by diatoms in the regolith during pluvial

highstands of Lake Chad (see also Gasse, 1987).

Few examples of recognisable biogenic silica remains

have been noted from silcretes, however. One exam-

ple is that of Clarke (1994b), which noted that almost

all the silcretes present in the Kambalda and Norse-

man regions of WA were developed on Eocene

spicular marine sediments, such as the Princess Royal

Spongolite and Pallinup Siltstone. The formation of

silcrete has largely obliterated the spicules and they

are preserved only as ghosts. These marine spicules

are quite large, typically 1–5 mm in length and 100

Am in diameter. It is likely that the smaller freshwater

spicules (100–300 Am in length and 3–10 Am across)

originally present in a silcreted sediment would be

completely destroyed or rendered unrecognisable, as

would the even more delicate diatoms and phytoliths.

Therefore, the remains of siliceous microfossils may

have been originally much more common in what are

now silcreted surficial sediments. A possible addi-

tional link between biogenic opal and silcretes is the

high levels of titanium found in many silcretes (Thiry,

1999) and the observation than phytoliths are com-

monly also enriched in this element (Wilding et al.,

1989). Much more work must be done to elucidate

this relationship, as detrital Ti from insoluble residules

or adsorbed Ti on clays and iron oxides are alter-

natives to a biological origin.

Clearly, the accumulation of biogenic silica in the

regolith alone is not the key to silcrete formation. As

the literature reviewed in this paper has shown, such

accumulations are not uncommon. Modern analogies

for silcrete are, however, difficult to find. What

remains unanswered is what conditions facilitate the

large-scale cementation and replacement by silica in

the regolith. If biogenic opal indeed plays a role in

this, it is through the stablisation of that opal as quartz.

It is possible however that accumulation of biogenic

silica, followed by major shifts in physical and chem-

ical hydrology associated with the Cainozoic climate

changes, may have been a factor.

Siliceous hardpans (Wright, 1983) are also com-

mon in many parts of inland Australia and also from

the Paris Basin (Thiry, 1999). They consist of silica-

cemented alluvium and colluvium. Other cementing

agents, including iron oxides, carbonate, and clay are

also present (Bettenay and Churchwood, 1974). Typ-

ically, they contain less silica and more iron and

carbonate than silcretes. Hardpans may form a con-

tinuum with silcretes, or represent an early stage in

silcrete development. Unlike silcretes, they are often

less indurated, lacking in silicification, and appear

more likely related to contemporary or near-contem-

porary landscape processes (Milnes et al., 1991) in

arid and semi-arid environments. Also, hardpans form

through siliceous cementation, rather than whole-scale

silicification. Despite this, their genesis and relation-

ship to silcrete is still obscure. Nor can they always be

related to overlying soil profiles (Wright, 1983).

However, the presence of common mobile silica from

biogenic opal would clearly be a favourable precursor

to their formation. As for silcretes, the fact that

biogenic opal is more common that hardpans suggests

that the key question is not the presence of opal in the

soil, but what factors encourage its stablisation in the

regolith as a quartz cement.

Hardsetting soils (Greene, in press) may be an early

precursor to hardpans. Hardsetting occurs through

cyclic wetting and drying of the soils. Slaking of soils

aggregates under conditions of rapid wetting, and/or

dispersion of the clay fraction alone. However, in some


cases, cementation of the subsoil can also occur as a

result release of soluble silica during wetting and

reprecipitation as the soil dries (Chartres et al.,

1990). The presence of potentially labile silica in the

form of biogenic opal may facilitate this process.

Another possible link is the relationship sometimes

noted between some silcretes and volcanic rocks,

especially basalts (see Ollier, 1991). In the past this

was normally attributed to silica released during

hydrothermal alteration or rapid weathering. While a

hydrothermal origin is ruled out by modern workers

(Taylor and Eggleton, 2001), the exceptionally high

levels of biogenic opal found in soils developed on

some volcanic rocks (Meunier et al., 1999, and

references in Hart, 1992) suggest that it is the organ-

isms that are responsible for this association.

7.5. Health

The size, geometry and composition of biogenic

silica bodies in the regolith is a potential health issue.

The large marine spicules of the Eocene of WA can

cause contact dermatitis among geologists logging

percussion and air core holes in the palaeovalley fills

of the area. The irritation caused by the spicules is

increased by the hypersaline waters which often satu-

rates these deposits. The numbers of open pits through

the Eocene cover is also increasing, although no

effects among mine waters are as yet reported. Sponge

spicules in soils of southwestern Western Australia,

probably also Eocene in age, have been linked to hoof

disease in horses (Carroll, 1932). Stone et al. (1970)

mentioned similar contact dermatitis amongst agricul-

tural workers in areas of freshwater spicule-rich soil of

New York, as did miners of freshwater spiculites in

Brazil (Volkmer-Ribeiro, 1992).

Although respirable dust (must with a median

aerodynamic diameter of 10 Am and less) is normally

regarded as an urban problem, it is also a major health

issue in rural areas (Clausnitzer and Singer, 1996). The

lower size limit of freshwater sponge spicules ( < 5 Amacross and some less than 3 Am) places them within the

definition of hazardous mineral fibre (Skinner et al.,

1988). Some of the cellular damage caused by fibrous

materials is from fibre penetration. Many sponge

spicules have sharper terminations than non-biogenic

mineral fibres, which greatly increases their penetra-

tion potential. Other cellular damage is caused by

mineral reactivity, however the biological reactivity

of opal is unknown. The presence of spicules in

windblown dust raises the possibility that they may

present a respirable silica hazard in dust-affected areas.

Silicified root hair cells (Piperno, 1988) also have a

high aspect ratio, are sharp, and potentially fall into the

hazardous size range. Most are probably too large to

pose a cancer risk, although respiratory irritation has

been reportedly caused by them (Parry et al., 1984).

8. Conclusions

Biogenic opal in soils was first recognised in the

1840s. The potential importance of silica-secreting

plants in the formation of silcretes was suggested in

the 1950s. Despite periodic reviews in the 1970s and

1980s, and considerable research of aspects of bio-

genic silica in soils and terrestrial sediments since

then, regolith science is not much closer to under-

standing the larger scale significance of biogenic opal

than we were 50 years ago.

What is known is that juvenile biogenic opal is

present in most soils in at least trace amounts and

common (up to 2–3% in the A horizons many soils on

all continents except Antarctica. Phytoliths, sponges,

and diatoms largely produce the opal. Furthermore, in

a significant number of cases, it can be present in large

amounts comprising more than 10% of the mineral

fraction, and in some examples 100%. There is a

strong correlation between poorly drained or at least

seasonally water logged conditions, and abundant

biogenic opal. In some cases, volcanic substrates are

also conducive to abundant soil opal. Biogenic opal

may play an important role in the cycling of silica in

soils and aquatic sediments, in the genesis of the

siliceous cements of hardpans, and silcretes, and may

be significant in environmental health.

A number of approaches for future research appear

promising. The first is taxonomy; what opal-secreting

organisms are present in the regolith, in what numbers,

and how can they be recognised from their remains.

The second is the ecological limits and roles repre-

sented by each organism, which requires both drainage

basin and catena studies. Thirdly, we need to know the

stratigraphic distribution of these remains especially

through the Cainozoic. These studies will enable a

better understanding of the both the regolith signifi-


cance of biogenic opal in a wide range of environments

and also constrain the conditions under which they

may become the dominant part. Fourthly, we need to

identify the possible geochemical signatures of bio-

genic opal in mature regolith profiles. Fifthly, research

is needed into the physical, chemical, and biological

conditions necessary to convert labile opal into stable

quartz, leading to the formation of silica cements,

hardpans, and silcretes. Sixthly, the role of opal in

nutrient cycling needs better documentation. Finally,

the potential health hazards of biogenic opal in respi-

rable dusts would also be a fruitful research area.

Study of the importance of opal producing organ-

isms in the regolith is clearly a multidisciplinary

process. After more than 160 years, the importance

of biogenic opal in the regolith is surely an idea whose

time has come.

Acknowledgements

I would like to thank Doreen Bowdery, Robin

Clark, Tony Eggleton, John Field, Dianne Hart, Megan

Kilby, Ian Roach, and Bob Wasson for their help and

suggestions in preparing this paper. Graham Taylor

and J. Meunier made several helpful and encouraging

comments in their reviews of the manuscript. The

paper is published with the permission of CRC LEME.

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Jonathan Clarke graduated with a BSc

(Hons.) from the University of Tasmania

and completed his PhD degree at Flinders

University in South Australia. He worked

for 10 years at WMC Resources Ltd. in

mineral exploration and research before

joining the geology department at the

Centre for Landscape, Environment, and

Mineral Exploration at the Australian

National University. His past research inter-

ests have included Cambrian reef, platform,

and slope carbonates, cool water carbonate deposition, coal geology,

modern sediments on the Australian shelf, evolution of the Great

Australian Bight, and regolith geology in Western Australia. Other

current research interests include the history of aridity of the

Atacama Desert, Eocene carbonate, clastic, and biosiliceous sed-

imentation in the Eucla Basin, and terrestrial Mars analogues.


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