Bergaya F. Handbook of Clay Science

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Handbook of Clay Science

Edited by F. Bergaya, B.K.G. Theng and G. Lagaly

Developments in Clay Science, Vol. 1

477

Chapter 9

CLAYS, MICROORGANISMS, AND BIOMINERALIZATION

K. TAZAKI

Department of Earth Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192,

Japan

Clays and microorganisms are ubiquitous on the Earth’s surface and, more often

than not, are closely associated with one ano ther. Indeed, microorganisms in soil

tend to gather at or near clay surfaces as these are enriched in ions, water, and

organic matter relative to the bulk soil (Theng and Orchard, 1995). In other eco-

systems the mineral–microbe interaction is reﬂected in the widespread occurrence of

colorful microbial mats in river, hot springs, ponds, lakes, deep sea ﬂoor, and geo-

thermal areas (Tazaki, 1999). The mineral component in these biomineral assem-

blages variously consists of carbonates, Fe–Mn oxides, hydrated phosphates, and

sulfides as well as layer silicates (clay minerals). The type of assemblage formed is

dependent on a number of biogeochemical factors, such as temperature, pH, redox

potential (Eh), dissolved oxygen (DO) concentration, electrical conductivity (EC),

and element supply (Tazaki, 1997a, 1997b). For example, the formation of intra- and

extra-cellular magnetite by Fe(III)-reducing bacteria requires a suitable comb ination

of Eh and pH together with a favourable rate of supply of Fe(II) and Fe(III) ions to

the grow ing crystal (Mann et al., 1990; Schwertmann and Fitzpatrick, 1992). The

bioformation of magnetite (and siderite) plays an important role in the cycling of

iron an d carbon as well as in carbon sequestration in natural environments (Roh

et al., 2003). Biogenic iron-rich minerals may also serve as physical indicators of

previous biological activities in modern and ancient geological settings.

‘Biomineralization’ is the process by which living organisms convert ions in so-

lution into solid minerals. The process is the result of cellular activities that allow for

certain physicochemical changes to oc cur (Simkiss and Wilbur, 1989). The number

of minerals of biological origin currently exceeds 250. The most numerous biogenic

minerals in terms of anion type are phosphates, followed by oxides, and carbonates.

All the major groups of microorganisms have members that are capable of forming

minerals. Here we focus on the ability of various bacteria to accumulate metallic ions

from their external aquatic environments, and mediate the crystallization and pre-

cipitation of clay minerals (Tazaki et al., 200 2 ). Such minerals were referred to as

‘bio-clays’ (Tazaki and Ishida, 1996; Tazaki and Asada, 2003) although according to

DOI: 10.1016/S1572-4352(05)01014-7

the proposed definitions for ‘clay’ and ‘clay mineral’ (Guggenheim and Martin,

1995, see Chapter 1), they should strictly be called ‘bio-clay minerals’.

9.1. EXPERIMENTAL ASPECTS

The study of biomineralization is a multi-disciplinary science involving geology,

mineralogy, microbiology, and chemistry. Both ﬁeld observations and laboratory

measurements are required for an understanding of the underlying mechanisms.

9.1.1. Field Investigation

A. Geology

An appreciation of the geological environment in which bio-clays are formed is

fundamental to their investigation. This is because microorganisms in microbial mats

metabolize and use materials from the surrounding air, water, sedimen ts, and rocks.

For this reason, it is essential to record details not only of the mats but also of the

terrain, basement petrology, soils, and hydrology. Depending on the situation, sam-

ples are taken of sediments, rocks, water, and other materials. Appropriate sampling

and handling methods must be followed in collecting microbial mats.

B. Water Chemistry

Since microorganisms in microbial mats take in ions (into their cells) from the

external solution, knowledge of the chemistry of the surrounding water is important

in identifying the microbial species in question. Water temperature, pH, Eh, DO, and

EC are measured in the ﬁeld. Seasonal changes in these parameters should be taken

into consideration.

C. Microbial Mats

The following information should be recorded: colour of mat; exposure to solar

radiation; volume and ﬂow rate of surrounding water; sedim ent and rock type;

thickness, hardness, and any other physical characteristics of mat. In addition,

photographs of the location and physical background are taken.

9.1.2. Laboratory Work

A. Sample Preparation

(a) Thin sections. Optical microscopy examination of thin sections is required to

determine the spatial relationship between microorganisms and clay minerals in

microbial mats. However, the preparation of thin sections can be problematic be-

cause microbial mats contain water and are often fragile. Breakage may be prevented

by coating the samples with a resin. The following steps are commonly taken: drying

in air at room temperature; embedding in cyanobond; coating with epoxy or

Chapter 9: Clays, Microorganisms, and Biomineralization478

polyester resin; thin section preparation is completed in the same way as for ordinary

rock and mineral preparation.

(b) Ultra-thin sections. Ultra-thin section s (80–100 nm in thickness) are used to

observe the inner micro-texture of cells, and the distribution of minute mineral

grains. The procedure for preparing ultra-thin sections is as follows: ﬁxing with

glutaraldehyde or a similar ﬁxative (to preserve micro-texture); dehydration (to

substitute water for a water-soluble synthetic resin); coating with a synthetic resin;

cutting with an ultra-microtome; dyeing or coating (to increase contrast in Trans-

mission Electron Microscopy (TEM) image).

B. Optical Microscopy

(a) Bright ﬁeld image. Observation by a bright ﬁeld image in transmitted light is a

standard ﬁrst step in laboratory studies of microbial mats. This method is usually

used in conjunction with stereoscopic and differential interference imagery distri-

bution. Form, color, and texture of microorganisms and minerals, ranging in size

from a few to several hundred microns, can be obse rved at the level of magniﬁcation

of an optical microscope.

(b) Polarizing microscope image. Observation by a polarizing microscope with

plane-polarized light, crossed Nicols, and conoscopic illumination is essential in

identifying the minerals present in microbial mats.

(UV) radiation, some minerals and microorganisms in microbial mats show ﬂuo-

rescence and epiﬂuorescence, which can be observed by means of a ﬂuorescence and

epiﬂuorescence microscope. For example, the chlorophyll of bacteria exhibits red

ﬂuorescence. In some instances, ﬂuorescence is observed before and after dyeing to

help distinguish microorganisms from minerals. Nucleic acids (DNA and RNA) can

combine with certain ﬂuorescing dyes. Thus, DNA stained with 4

,6-diamidino-2-

phenylindole (DAPI) displays blue ﬂuorescence when exposed to UV rays. Similarly,

the RNA in cells can be specifically stained with acridine orange (AO), causing it to

ﬂuoresce on exposure to light at a wavelength of 436 or 490 nm. Indian ink, ru-

thenium red, and vinegar are used to indicate the existence of S-layers or extracel-

lular polymers around microbial cells.

C. X-ray Diffraction (XRD)

X-ray diffraction (XRD) remains the single, most useful method of identifying and

quantifying clay minerals (Brindley, 1980; Moore and Reynolds, 1997). For XRD

analysis of microbial mats, either a powdered sample of the mat or a piece of dry,

intact mat is placed on a non-refracting glass slide.

9.1. Experimental Aspects 479

D. X-ray Fluorescence Spectroscopy (XRF)

When an element is bombarded by hard X-rays, it emits X-rays at a wavelength

characteristic of the element. The elements present in microbial mats can thus be

determined qualitatively and quantitatively by XRF.

E. Scanning Electron Microscopy (SEM)

Microbial mats must be dried under high-vacuum conditions before observation by

SEM. Where this is a problem, other methods such as freeze-drying or observation

under low-vacuum conditions can be used.

F. Transmission Electron Microscopy (TEM)

Since micr obial mats contain very ﬁne mineral grains that are scarcely visible under

an optical microscope, TEM is a very useful instrumental method of investigation.

TEM images can be divided into bright-ﬁeld (high-resolution images, crystal lattice

images) and dark-ﬁeld images. Electr on diffraction patterns of selected areas (of

mineral grains) can also be obtained from a TEM image.

G. Energy Dispersive X-ray Spectrometry (EDX)

EDX allows qualitative and quantitative analysis to be made of elements that are

associated with speciﬁc sites/structures within the SEM or TEM image of the sample.

H. Microorganism Culture Methods

Field environmental conditions may be simulated by supplying water and sediments,

collected from the ﬁeld, to living microbial mats in the laboratory. This ‘‘natural’’

culture method also helps preserve the integrity of the mats. Other environmental

parameters, such as pH, temperature, light, and partial pressur e of oxygen can be

controlled or modiﬁed during culture in the laboratory. However, problems can arise

when microbial mats are cultured by such methods over a long period.

Alternatively, we may separate a particular species of microorganism from a

microbial mat, and culture it in an artiﬁcial medium . This approach is especially

useful for studying the behaviour and properties of individual microorganisms.

The applications of these experimental methods and instrumental techniques to

characterizing microbial mats and bio-clays from various localities are summarized

below.

9.2. BIOFORMATION OF X-RAY AMORPHO US LAYER SILICATES

9.2.1. Microbial Mats in Ponds

Red-brownish microbial mats, in solid or colloidal form, are found at various lo-

cations in Japan: over a cut cliff in the Omma Formation of sandstone, and in drains

and settling ponds near the Kakuma campus of Kanazawa University (Tazaki,

Chapter 9: Clays, Microorganisms, and Biomineralization480

1997a, 1997b; Yoshizu and Tazaki, 1997). The pH of the water ﬂowing through the

Omma Formation into settling ponds ranges from weakly acidic to neutral (pH

6.4–7.1). The values of Eh (40 to 80 mV) and DO (6.3–9.7 mg/L) are subjected to

seasonal variations. The fresh water chemistry is as follows: Mn 1.03 ppm; Fe

2.50–10.00 ppm; Ca 76.00 ppm; K 18.00 ppm; pH 6.5–6.8; temperature 12–20 1 C.

Optical and ﬂuorescence microscopy revealed the presence of bacillus, spiral, and

ﬁlamentous microbes associated with holdfast (Fig. 9.1A). SEM showed a doughnut-

shaped structure with a capsule of Siderocapsa sp. in the centre (Figs. 9.1B, C). EDX

analysis indicated that this structure was mainly composed of Al, Si, Ca, and Fe

probably in layer silicate structures (Fig. 9.1D ).

XRD patterns showed strong peaks for crystalline calcite (0.3 nm) and illite to-

gether with large amounts of X-ray amorphous (short-range order) layer silicates

and/or organic matter. Natural culturing gave rise to Fe- and Mn-rich structures

after ageing for 2 months. SEM of the holdfasts on the cover glass of slides showed

successive formation of mixtures of layer silicates and hydrated Fe/Mn oxides. TEM

also showed the doughnut-shaped holdfast with a hole in its center, containing

coccus-type bacteria (arrows) (Fig. 9.2A). A close-up photograph of the bacteria

revealed dense granular materials on the cell wall (Fig. 9.2B).

9.2.2. Microbial Mats in Hot Springs

The coccus and bacillus-type bacteria in microbial mats collected from hot springs

(pH 6.8, 39 1C) in Laugarvatn, Iceland, indicated the incipient formation of granular

layer silicates on the cell wall. TEM of an ultra-thin section of the cells clearly

showed a distinct cell wall (a), surface array (b), capsule (c), and plasma membrane

(d), covered by layer silicates of high density (Figs. 9.3A, B)(Tazaki and Ishida,

1996).

The XRD pa ttern of the bulk microbial mats showed a broad, diff use band

centering at 0.3–0.4 nm (Figs. 9.3A

). The TEM and EDX of thin-sections re-

vealed the remains of bacterial cells with accumulation of Si, Al, and Fe.

9.3. BIOFORMATION OF HALLOYSITE, KAOLINITE AND IMOGOLITE

9.3.1. Bio-Halloysite from Feldspar in Kutani Glaze

Bio-weathering of K-feldspar was investigated using aqueous suspensions of Kutani

glaze (‘‘Kutani’’ is a distinctive ceramic ware from Kanazawa Prefecture, Japan).

After 3 years standing in a brightly lit room, green microbial mats (Fig. 9.4A)

formed in the container together with (solid) precipitates composed mainly of

K-feldspar.

The pH of the water was 9.0–9.4 and the EC was 0.38–0.65 mS/cm. Major oxide

analysis of the K-feldspar by XRF yield ed the following composition: SiO

69.03,

9.3. Bioformation of Halloysite, Kaolinite and Imogolite 481

Fig. 9.1. Optical (A), SEM (B, C), and EDX (D) micrographs of the holdfasts and bacilli

(arrows) on the slide cover glass showing successive formation of mixtures of layer silicates

and Fe/Mn oxides. (From Tazaki, 1997a.)

Chapter 9: Clays, Microorganisms, and Biomineralization482

Fig. 9.2. TEM micrographs of clay ﬁlms attached to doughnut-shaped holdfasts with bacilli

and coccus bacteria (A, arrows), and of coccus bacteria with granular coating of X-ray

amorphous materials (B). (From Tazaki, 1997a.)

9.3. Bioformation of Halloysite, Kaolinite and Imogolite 483

Fig. 9.3. TEM micrographs (ultra-thin section) of X-ray amorphous layer silicates. The

spherules with high concentrations of Fe and Ca show internal cell structures: a, cell wall; b,

surface array; c, capsule; d, plasma membrane.

XRD patterns of A and B samples indicating presence of X-ray amorphous materials (A

(From Tazaki and Ishida, 1996.)

Chapter 9: Clays, Microorganisms, and Biomineralization484

17.37, Fe

0.06, CaO 0.89, MgO 0.06, K

O 8.94, Na

O 3.33, loss on ignition

0.31 where the numb ers denote wt% (Ueshima and Tazaki, 1997).

Optical microscopy of the green microbial mats showed chains of microbial cells

with a capsule of ﬁne- and coarse-grained particles surrounded by a sheath of

Fig. 9.4. Green microbial colonies in Kutani glaze solution (A) and optical micrographs of a

green cyanobacterial colony (B) and K

-feldspar particles (arrow in C) on the sheath (arrow

in C) of cyanobacteria surrounding capsule. (From Ueshima and Tazaki, 1997.)

9.3. Bioformation of Halloysite, Kaolinite and Imogolite 485