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Laboratory experiments on bacterial weathering of granite and its constituent minerals

Expérimentation en laboratoire de la météorisation du granite et de ses minéraux constituants
Wonsuh Song, Naoto Ogawa, Chiaki Takashima-Oguchi, Tamao Hatta et Yukinori Matsukura
p. 327-336

Résumés

Cette étude s’intéresse à la météorisation bactérienne du granite et de ses minéraux par Bacillus subtilis. Une expérimentation en laboratoire pendant 30 jours a permis de répondre aux interrogations suivantes : de quelles manières la bactérie ubiquiste Bacillus subtilis altère-t-elle le granite et ses minéraux (analyse d’images exoscopiques) ? Quels minéraux du granite sont les plus vulnérables dans un environnement bactérien (modèle rocheux et mono-minéral) ? Les résultats obtenus à la suite de plusieurs protocoles expérimentaux sont : 1) les bactéries augmentent la météorisation du granite et de ses minéraux par formation de puits à la surface des minéraux ; 2) les plagioclases sont les minéraux les plus fragiles lorsque le granite est au contact de bactéries. Dans le protocole mono-minéral, l’albite (groupe des plagioclases) est le plus vulnérable ; 3) le classement normalisé du rapport puit/surface et la densité de puits dans le protocole bactérien est en accord avec l’ordre traditionnel de météorisation des minéraux, indiquant que la météorisation bactérienne contribue largement au processus d’altération.

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Notes de la rédaction

Article soumis le 5 janvier 2010, accepté le 3 avril 2010

Texte intégral

This article is based on research supported by the JSPS KAKENHI (16300292; principal investigator: Y. Matsukura) and the Sasakawa Scientific Research Grant (held by W. Song) from the Japan Science Society. The manuscript was greatly improved by thoughtful and precious comments by the two anonymous referees. We deeply thank the referees.And we also thank Dr. Samuel Etienne for the French translation and his great support, Dr. T. Hattanji for his precise comments andkind support, and all the coordinators of this journal for their efforts.  

Introduction

1Processes of rock weathering are usually classified into three types: physical weathering (pressure release; wet-dry slaking; frost shattering and thermal expansion), chemical weathering (dissolution; hydrolysis; oxidation) and biological weathering (chelation by plants; microbial activities). Among various biological weathering agencies, the important role of microorganisms in rock weathering or mineral alteration has been highlighted previously (e.g., Ehrlich, 1981, p. 63; Viles, 1995; Uroz et al., 2009). In one of the first compilations of the weathering literature, E. Yatsu (1988, p. 285-399) highlighted that eighteen percent of the references dealt with biological weathering. A particular concentration of research has focused on iron-oxidising bacteria and sulphur-oxidising bacteria related to pyrite weathering. Bacterial weathering is a micrometer-scale phenomenon. It therefore tends to be underestimated in the literature, compared to physical weathering and chemical weathering. The long geological history and ubiquitousness of bacteria warrant additional research on the weathering effects of bacteria. Bacteria are ubiquitous in soils, sediments, and subsurface environments with concentrations ranging from 105 cells/cm3 to 109 cells/cm3 (Hicks and Fredrickson, 1989; Kampfer et al., 1991; Albrechtsen and Winding, 1992; Edwards et al., 1998). Bacteria exist even in extreme environments, such as boiling hot spring or deep ocean sediments (Bland and Rolls, 1998; Ingraham and Ingraham, 2000; Madigan et al., 2003).

2The assumption of this research is that ubiquitous bacteria must have affected rock weathering to some extent, given their ubiquitous presence in the terrestrial weathering environment. General methods for weathering studies include field observation and experimentation. The need for microscopy to observe micrometer-scale bacteria leads us to understake an experimental approach. Experiments involving bacterial weathering are typically laboratory based (e.g., Vandevivere et al., 1994; Fein et al., 1999; Maurice et al., 2001), or field based (e.g., Bennett et al., 1996; Rogers and Bennett, 2004). Laboratory experiments have the advantage of being able to control conditions. Laboratory experiments usually consist of a medium (liquid), bacteria and minerals. Thus, laboratory experiments analyse the interaction of water, microorganisms, and mineral surfaces. Most of previous experiments used powdered or small fragmented minerals and only showed SEM images that were taken after the experiment (Paciorek et al., 1981; Escobar et al., 1996; Kalinowski et al., 2000). Comparison of rock or mineral surface images taken before and after an experiment are important to create a more thorough understanding of entire process of bacterial weathering. In addition, many of these previous studies have been mainly concerned with a single mineral and bacteria interactions (Lee and Fein, 2000; Edwards and Rutenberg, 2001; Yu et al., 2001, Cruz et al., 2005). Few bacterial weathering studies have analysed a suite of minerals that compose a rock (Vuorinen et al., 1981; Puente et al., 2006). An experiment using a rock composed of several minerals combined with SEM images comparison and chemical analysis of media, can show selective weathering of composing minerals in the rock.

3Our previous study (Song et al., 2007) on bacterial granite weathering has focused only on an experiment using granite. In this paper, we consider albite, microcline, and quartz and also upgraded experimental methods to enable quantitative surface analysis. The purpose of this work is to investigate (i) how the ubiquitous soil bacterium Bacillus subtilis weathers granite and its constituent single minerals through image analysis of mineral surface and (ii) which mineral in granite that appears to be the most vulnerable to bacterial weathering by Bacillus subtilis.

Materials and methods

4Granite. Tab. 1 shows sampling point, normalised chemical composition, and bulk density of the specimens. Granite sampling point and preparation methods were same as that of Song et al. (2007). Ten test samples of granite were prepared (five for bacteria-bearing experiment and five for bacteria-free), 10.0 mm long, 10.0 mm wide, and 3.0 mm thick (fig. 1). The initial condition of the representative granite surfaces were coated with gold then observed with the aid SEM (Jeol, JSM-5600LV), prior to the start of the experiment. The images were acquired at 70 × magnification. It is a twice higher magnification than that of W. Song et al. (2007). The number 1 specimen (Gr1) was used for the bacteria-free experiment and the number 2 specimen (Gr2) was used in the bacteria-bearing experiment. The half of each granite surface (10.0 mm by 5.0 mm, yellow colored area in fig. 1) was analysed by SEM-EDS with 70 × magnification for chemical composition. Major element maps were obtained to approximate mineral distribution map with the SEM-EDS (Jeol, JSM-5600LV) overlay function. Fig. 1 shows the mineral distributions of the granite. Mineral area is calculated by using Adobe® Photoshop® 7.0.1 based on the overlaid element maps: plagioclase (Na-rich) 45-49%, quartz 28-35%, alkali feldspar 11-17%, and biotite 7-8%. Granite specimens were autoclaved at 121°C for 20 mn and dried in a desiccator for 1 h.

Fig. 1 –Mineral distribution of Gr1 and Gr2 analysed by SEM-EDS.
Fig. 1 – Distribution des minéraux dans les échantillons de granite (Gr1 et Gr2) analysés au MEB et à la micro-sonde.

Fig. 1 –Mineral distribution of Gr1 and Gr2 analysed by SEM-EDS.Fig. 1 – Distribution des minéraux dans les échantillons de granite (Gr1 et Gr2) analysés au MEB et à la micro-sonde.

10.0 × 5.0 mm area (yellow colored area) was analysed (Gr: granite). 1: quartz; 2: plagioclase; 3: K-feldspar; 4: biotite.
La zone colorée en jaune (10 x 5 mm) a été analysée (Gr : granite). 1 : quartz ; 2 : plagioclase ; 3 : feldspath alcalin ; 4 : biotite.

5Mineral preparation. Sampling points and bulk density for each mineral are shown in the tab. 1. Ten pieces of each mineral sample were prepared in a fashion similar to the granite rock fragments. However, only two samples from each mineral are a part of this experiment, one being subject to bacterial weathering (e.g., Ab2, Mc2, and Qtz2 in tab. 1). The other mineral is a control (e.g., Ab1, Mc1, and Qtz1 in tab. 1). SEM-EDS analyses of these minerals, normalised to 100%, are reported in tab. 1.

Tab. 1 – Sampling point, bulk density and chemical composition of the specimens.
Tab. 1 – Lieux d’échantillonnage, densité globale et composition chimique des échantillons.

Granite  

Albite

Microcline

Quartz

Sampling point

Aji, Kagawa, Japan

Itoigawa, Niigata, Japan

Nellore, Andhra Pradesh, India

Minas Gerais, Brazil

Gr1

Gr2

Ab1

Ab2

Mc1

Mc2

Qtz1

Qtz2

Na2O

6.0

7.2

14.1

14.5

6.2

6.5

0.4

0.3

MgO

0.6

0.7

0.3

0.4

0.1

0.2

0.4

0.2

Al2O3

19.4

16,0

15.3

18.5

20.7

20,0

4,0

3.1

SiO2

67.4

70.4

69.6

66.1

63.6

63.9

94.8

96,0

K2O

2.9

1.5

0.1

0,0

9.2

9.1

0,0

0,0

CaO

1.7

2.1

0.3

0.3

0.1

0.1

0,0

0.1

TiO2

0.2

0.2

0.1

0,0

0,0

0.1

0.1

0,0

MnO

0.1

0.1

0.1

0,0

0.1

0.1

0.1

0,0

FeO

1.6

1.7

0.2

0.1

0.1

0.1

0.1

0.2

Total

100,0

100,0

100,0

100,0

100,0

100,0

100,0

100,0

Bulk density (in g/cm³)

2.67

2.67

2.6

2.6

2.57

2.57

2.63

2.63

* Chemical composition was measured by using SEM-EDS. The values of the chemical composition are normalised.
* La composition chimique a été analysée à la micro-sonde (MEB). Les valeurs sont normalisées.

6Bacteria and medium. This experiment used the same species of bacteria (Bacillus subtilis strain 168) as W. Song et al. (2007). Bacillus subtilis is a gram-positive, aerobic bacterium that is commonly found in soil, groundwater, plants, air, and hay. These bacteria are shaped like a rice grain, with a width of 0.7-0.8 µm and a length of 1.5-2.0 µm. Bacillus subtilis was grown on the polypepton (Wako 394-00115) agar plate. Composition of the medium is shown in tab. 2. The medium (total volume of a each bottle is 500 ml) for the incubation of the strain 168 consisted of 0.1 M NaCl, 0.4% (w/v) glucose, and 0.1% (w/v) yeast extract (Difco 212750, Bacto TM Yeast Extract, Extract of Autolysed yeast cells). A more detailed explanation of the medium is described in W. Song et al. (2007). The net weight of bacteria is 8-10 mg per a bottle.

Tab. 2 – Composition of the medium.
Tab. 2 – Composition du médium expérimental.

Sample name

Medium   (in ml)

Innoculation (in mg)

Glucose (wt. in %)

Yeast extract (wt. in %)

Gr1

500

None

0.4

0.1

Gr2

500

10

0.4

0.1

Ab1

500

None

0.4

0.1

Ab2

500

8

0.4

0.1

Mc1

500

None

0.4

0.1

Mc2

500

8

0.4

0.1

Qtz1

500

None

0.4

0.1

Qtz2

500

8

0.4

0.1

Ctrl1

500

None

0.4

0.1

Ctrl2

500

8

0.4

0.1

7Experimental methods. The experimental setup is shown in fig. 2. Two holes in the silicone packing of the bottles were for input air by an air pump and for output. The air pump supplied air (500 cc/min) to the all bottles. The bottles were placed in an incubation room at 27°C. After 30 days, granite and mineral specimens were taken out of the bottle with autoclaved forceps, washed lightly with ultra-pure deionised water (milliQ), and dried at room temperature for a few days. The surfaces of the specimens were then observed by SEM to compare with images acquired before the experiment. Images were examined on the computer screen and on hardcopy (transparent films). Newly formed pits were counted manually. Defects and pits greater than a width of 5 µm can be identified at 70 × magnification. Thus, our methodology is to systematically ignore weathering pits less than 5 µm.

Fig. 2 –Contour of the experiment.
Fig. 2 – Aspect du protocole expérimental.

Fig. 2 –Contour of the experiment.Fig. 2 – Aspect du protocole expérimental.

Red circled granite and minerals are representatively observed before and after the experiment (Gr: granite; Ctrl: control; Ab: albite; Qtz: quartz; Mc: microcline).
Les échantillons de granite et les minéraux cerclés de rouge ont été observé avant et après l’expérimentation (Gr : granite ; Ctrl : contrôle ; Ab : albite ; Qtz : quartz ; Mc : microcline).

Results

8Granite (bacteria-free/bearing). After 30 days, pits were found on surfaces of both bacteria-bearing granite (Gr2) and bacteria-free granite (Gr1). However, the number, size and distribution of pits were very different in these two samples (Gr1 and Gr2). Comparing magnified images of a part of bacteria-free (Gr1) before and after the experiment, for example, reveals that the surface of plagioclase did not change substantially after the 30-day experiment (fig. 3).

Fig. 3 –Comparison of the Gr1 surface before and after the experiment
Fig. 3 – Comparaison de la surface de l’échantillon Gr1 avant et après l’expérimentation

Fig. 3 –Comparison of the Gr1 surface before and after the experimentFig. 3 – Comparaison de la surface de l’échantillon Gr1 avant et après l’expérimentation

(Pl: plagioclase; K-fs: alkali feldspar; Bt: biotite). Plagioclase did not change substantially after the 30-day experiment.
(Pl : plagioclase ; K-fs : feldspath alcalin ; Bt : biotite). Le plagioclase n’a subi aucune modification notable au terme des 30 jours d’expérimentation.

9In contrast, many pits were formed on a similar plagioclase surface for the bacterial-bearing sample (Gr2) (fig. 4). The SEM images of Gr2 after the experiment also shows many angular pits with bacteria (cocoon shaped materials with ca. 1 µm length). To assess the difference between Gr1 and Gr2 quantitatively, the total number and size of pits were compared. A different SEM using secondary electrons (Keyence, VE-9800) and Adobe® Photoshop® 7.0.1 were used in the calculation of pit area. Concerning the number and size of pits, tab. 3 summarises measured data on micrometer-scale pitting, both number and area. Tab. 3 includes specifies for each different mineral in the granite (Gr1 and Gr2). In the bacteria-free granite (Gr1), 52 of new and widened pits were found on the surface that is 10.0 mm long and 5.0 wide (tab. 3A). Twenty-one pits (40% of the pits) were observed in plagioclase, 9 in quartz (17% of the pits), 5 in biotite, and one pit was found in alkali feldspar. Nine pits were found on the grain boundaries between quartz and plagioclase. The total area of the newly formed pits on the Gr1, calculated by SEM (Keyence, VE-9800), is approximately 3573 µm2. Frequency distribution of pit area of the Gr1 is shown in fig. 5. Pit area which is under 100 µm2 is the largest, and among the pits plagioclase dominates over 20%. In bacteria-bearing granite (Gr2), 192 of new and widened pits were found after the experiment (tab. 3B). Among these pits, 137 pits were formed in plagioclase (71% of the pits), 9 in quartz (5% of the pits), and 13 in biotite (7% of the pits). Seven pits were found in alkali feldspar and 22 at the boundary of plagioclase and quartz (11% of the pits). Over 70% of the pits were formed in plagioclase. The total area of the pits is 16735 µm2. Frequency distribution of pit area of the Gr2 is wider than Gr1, however most of the pit area are under 100 µm2 (fig. 5). The number of pits Gr2 was 3.7 times as large as that on Gr1. The total area of pits on the bacterially weathered Gr2 was 4.7-times larger than that on the bacteria-free Gr1.

Fig. 4 – Comparison of the Gr2 surface before and after the experiment
Fig. 4 – Comparaison de la surface de l’échantillon Gr2 avant et après l’expérimentation

Fig. 4 – Comparison of the Gr2 surface before and after the experiment Fig. 4 – Comparaison de la surface de l’échantillon Gr2 avant et après l’expérimentation

Pl: plagioclase; Bt: biotite; Qtz: quartz
(Pl : plagioclase ; Bt : biotite ; Qtz : quartz)

Tab. 3 – Number, area and volume of the newly formed or widened pits, in Gr1 and Gr2.
Tab. 3 – Nombre, surface et volume des puits néoformés ou agrandis dans les échantillons Gr1 et Gr2.

(A)  Gr1 (bacteria-free)

Pit number

Pit number ratio (in %)

  Av. Area
(in
μm2)

Total pit area (in μm2)

Pl

21

40

88

1848.5

Qtz

9

17

53.9

484.8

Kfs

1

2

22.7

22.7

Bt

5

10

59.7

298.5

Pl-Kfs

2

4

99

197.9

Pl-Bt

0

0

0

0

Qtz-Pl

9

17

36

323.6

Qtz-Kfs

3

6

46.2

138.7

Qtz-Bt

1

2

174

174

Qtz-Pl-Kfs

1

2

83.9

83.9

Qtz-Pl-Bt

0

0

0

0

Total

52

100

3572.8

(B)  Gr2 (bacteria-bearing)

Pit number

Pit number
ratio (in %)

Av. Area
(in
μm2)

Total pit area
(in
μm2)

Pl

137

71

97.6

13376.1

Qtz

9

5

43.5

391.6

Kfs

7

4

106.8

747.8

Bt

13

7

76.6

995.3

Pl-Kfs

0

0

0

0

Pl-Bt

1

1

82.2

82.2

Qtz-Pl

22

11

43.4

955.9

Qtz-Kfs

2

1

46.7

93.5

Qtz-Bt

0

0

0

0

Qtz-Pl-Kfs

0

0

0

0

Qtz-Pl-Bt

1

1

92.3

92.3

Total

192

100

16734.7

Fig. 5 – Frequency distribution of pit area of the granites. Fig. 5 – Fréquence des puits observés sur les granites, classés selon leur taille.

Fig. 5 – Frequency distribution of pit area of the granites. Fig. 5 – Fréquence des puits observés sur les granites, classés selon leur taille.

1: other mineralspits formed in Qtz, Kfs, Bt, and mineral boundaries;2: plagioclase: pits formed in plagioclase.
1 : autres minéraux : puits formés dans le quartz (Qtz), les feldspaths alcalins (Kfs), la biotite (Bt) et aux frontières inter-minérales ; 2 : plagioclases : puits formés dans les plagioclases.

10Albite (bacteria-free/bearing). In bacteria-free specimen (Ab1), 19 pits were found after the experiment (tab. 4). Fifty-two new pits were found in the bacterially-weathered Ab2. Fig. 6 shows SEM image, both before and after, of Ab1 and Ab2. Arrows show newly formed pits after the experiment. However, bacteria were rarely seen on the mineral surfaces.

11Microcline (bacteria-free/bearing). Two pits were found in the bacteria-free specimen, Mc1 (tab. 4). The upper two images in fig. 6 show the surface of Mc1 before and after the experiment. Nothing has changed after the experiment. Most surface of the Mc1 was similar to the magnified images of fig. 7. Four pits were found in the bacterially-weathered Mc2. Fewer bacteria are seen on the surface of Mc2 compared to a similar surface area of the bacterially weathered granitic slab, Gr2. The lower two images in fig. 7 show the surface of Mc2 both before and after the experiment. With a magnification of 70 ×, micro-meter-scale materials were observed on the surface of Mc2.

Tab. 4 – Number of the newly formed pits.
Tab. 4 – Nombre de puits néoformés.

Number of the pits

Gr

Ab

Mc

Qtz

Bac-free

52

19

2

0

Bac-bearing

192

52

4

0

Fig. 6 –SEM Image comparison of Ab1 (upper, bacteria-free), and Ab2 (lower, bacteria-bearing).
Fig. 6 – Comparaison d’images MEB des échantillons d’albite : Ab1 (en haut, protocole sans bactérie), Ab2 (en bas, protocole bactérien).

Fig. 6 –SEM Image comparison of Ab1 (upper, bacteria-free), and Ab2 (lower, bacteria-bearing).Fig. 6 – Comparaison d’images MEB des échantillons d’albite : Ab1 (en haut, protocole sans bactérie), Ab2 (en bas, protocole bactérien).

Arrows show newly formed pits after the experiment.
Les flèches signalent les puits apparus durant l’expérimentation.

Fig. 7 – SEM image comparison of Mc1 (upper, bacteria-free), and Mc2 (lower, bacteria-bearing).
Fig. 7 – Comparaison d’images MEB des échantillons de microcline : Mc1 (en haut, protocole sans bactérie), Mc2 (en bas, protocole bactérien).

Fig. 7 – SEM image comparison of Mc1 (upper, bacteria-free), and Mc2 (lower, bacteria-bearing).Fig. 7 – Comparaison d’images MEB des échantillons de microcline : Mc1 (en haut, protocole sans bactérie), Mc2 (en bas, protocole bactérien).

12Quartz (bacteria-free/bearing). No pits were found in either bacteria-free or bacteria-bearing specimens (Qtz1, and Qtz2; tab. 4). The upper two images in fig. 8 show the surface of Qtz1, before and after the experiment. Nothing has changed after the experiment. The lower two images in fig. 8 show the surface of bacteria-bearing quartz (Qtz2). Again, we could detect no changes after the experiment except for a few bacteria present on the surface of Qtz2.

Fig. 8 – SEM image comparison of Qtz1 (upper, bacteria-free), and Qtz2 (lower, bacteria-bearing).
Fig. 8 – Comparaison d’images MEB des échantillons de quartz : Qtz1 (en haut, protocole sans bactérie), Qtz2 (en bas, protocole bactérien).

Fig. 8 – SEM image comparison of Qtz1 (upper, bacteria-free), and Qtz2 (lower, bacteria-bearing).Fig. 8 – Comparaison d’images MEB des échantillons de quartz : Qtz1 (en haut, protocole sans bactérie), Qtz2 (en bas, protocole bactérien).

Discussion

13An overall picture of the influence of bacteria on weathering a 10 mm by 5 mm slab of granite can be obtained in tab. 5. To construct tab. 5, the area of all pits on a mineral boundary was equally divided by the number of minerals and added to the each mineral area. The plagioclase occupies nearly half area (49% of Gr1, 45% of Gr2) of both granite specimens. Since areal ratio of each mineral is different, normalisation of the pit area provides more insight. Normalised pit-area ratio is calculated here as; normalised pit-area ratio (%) = total pit area (µm2) / mineral area (µm2). We also employed another parameter, pit density, that is defined as the number of pit per unit area, i.e., pit density (mm-2) = the number of pits / mineral area (mm-2). The results for granite specimens (Gr 1 and Gr2) are shown in tab. 6. The order of the both normalised pit-area ratio and pit density of minerals in the bacteria-bearing specimen (Gr2) is: plagioclase > biotite > alkali feldspar > quartz. Plagioclase has the highest normalised pit-area ratio or pit density in Gr2. Pit density of plagioclase (6.619 mm-2) is over 5.5 times higher than that of quartz (1.205 mm-2) in Gr2 (tab. 6). In contrast, the order of the normalised pit-area ratio of minerals in bacteria-free specimen (Gr1) is: biotite > plagioclase > quartz > alkali feldspar. The order of the pit density of minerals in Gr1 is: biotite > quartz > plagioclase > alkali feldspar. Plagioclase has the largest total pit area in each bacteria-free and bacteria-bearing condition (tab. 3). However, when it is arranged in the order of normalised pit ratio, biotite has the largest pit area ratio and pit density for bacteria-free granite (tab. 6). Plagioclase, thus, appears to be the most vulnerable to Bacillus subtilis in Gr2. This effect is also seen in the single mineral experiment where albite (plagioclase group) has the most pits after the experiment in bacteria-bearing circumstances (fig 4, lower images). The order of normalised pit-area ratio and pit density in bacteria-bearing granite are in accorded with the traditional weathering-series of S.S. Goldich (1938): plagioclase > biotite > alkali feldspar > quartz. Similar results are found in the single mineral experiments: albite > microcline > quartz.

14W.W. Barker et al. (1997) reported that feldspars are more susceptible to microbial attack than quartz because they contain ions that react strongly with microbially produced compounds, such as organic acids. When ample organic acids derived from bacteria, algae, fungi and lichens are present, the weathering sequence matches the Goldich model (Bland and Rolls, 1998). It suggests most of the early work on weathering sequences relied on data from samples taken from environments. The Goldich’s classic sequence of mineral susceptibility to weathering may vary with the nature of the biochemical environment (Wasklewicz, 1994). On the other hand, the weathering sequence for bacteria-free granite of the present research is different from the Goldich’s sequence, perhaps because of the lack of biological activity. The accordance of the bacterially-weathered with Goldich’s weathering sequence suggests that Goldich did not simply study chemical weathering. Goldich’s observations must have mixed purely chemical and biochemical reactions in his field sites.

Tab. 5 – Mineral area ratio and total pit area of the granite.
Tab. 5 – Proportion des différents minéraux et surface des puits dans le granite.

Gr1 (bacteria-free)

Gr2 (bacteria-bearing)

Mineral  area  ratio (in %)

Total pit area (in μm2)

Mineral  area  ratio (in %)

Total pit area (in μm2)

Pl

49,0

2137.3

45,0

13925.9

Qtz

27.7

831,0

35.4

947.1

Kfs

16.6

219,0

11.2

794.5

Bt

6.7

385.5

8.4

1067.1

Total

100,0

3572.8

100,0

16734.7

Tab. 6 – Normalised pit-area ratio and pit density for bacteria-free (Gr1) and bacteria-bearing granite (Gr2).
Tab. 6 – Proportion normalisée des surfaces de puits et densité de puits sur les granites pour les protocoles sans bactérie (Gr1) et bactérien (Gr2).

Normalised pit area ratio
(in %)

pit density
(in mm
-2)

Gr1

Gr2

Gr1

Gr2

Pl

0.0087

0.0619

1.095

6.619

Qtz

0.006

0.0054

1.143

1.205

Kfs

0.0026

0.0142

0.462

1.427

Bt

0.0115

0.0254

1.642

3.29

Whole analysed area

0.0289

0.1068

1.04

3.84

Conclusions

15The present research reveals that bacteria can play an important role in weathering of granite and its constituent minerals by making pits. Our quantitative analyses reveal that the area of the newly formed pits on the bacteria-bearing granite surface is 4.7 times larger than bacteria-free granite. Plagioclase or albite (plagioclase group) appears the most vulnerable mineral to weathering by Bacillus subtilis. The weathering sequences obtained in the present research are in accorded with the traditional Goldich’s weathering-series. Thus, we speculate that this classic weathering sequence is not just chemical weathering, but should be interpreted as a mixture of chemical and biochemical weathering.

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Annexe

Version française abrégée

Les processus de météorisation des roches sont habituellement classés en trois catégories : processus mécaniques, processus chimiques et processus biologiques. Parmi les différentes combinaisons de processus de biométéorisation, la place déterminante des micro-organismes a été de nombreuses fois soulignée (Ehrlich, 1981 ; Viles, 1995 ; Uroz et al., 2009). La météorisation bactérienne est un phénomène d’échelle microscopique et, de ce fait, tend à être sous-estimée dans la littérature. Pourtant, la longue histoire géologique des bactéries et leur caractère ubiquiste ne justifie pas un tel désintérêt. Cette étude s’intéresse à la météorisation bactérienne du granite et de ses minéraux par Bacillus subtilis. Le postulat de ce travail est que la météorisation bactérienne est incontournable dans les environnements météoriques terrestres. Les méthodes d’étude des actions bactériennes expérimentales prennent place en laboratoire (Vandevivere et al., 1994 ; Fein et al., 1999 ; Maurice et al., 2001) ou sur le terrain (Bennett et al., 1996 ; Rogers and Bennett, 2004). Les études en laboratoire offrent l’avantage du contrôle des conditions environnementales. Une expérimentation in vitro a permis de répondre aux interrogations suivantes : de quelles manières la bactérie ubiquiste Bacillus subtilis altère-t-elle le granite et ses minéraux (analyse d’images exoscopiques ; fig. 1) ? Quels minéraux du granite sont les plus vulnérables dans un environnement bactérien (modèle rocheux et mono-minéral) ? L’expérimentation (fig. 2) a pris place dans une chambre d’incubation à température contrôlée (27°C) : des fragments de granite ou des minéraux (protocole de préparation identique à celui décrit par Song et al., 2007 ; tab. 1) ont été placés avec des souches de Bacillus subtilis (souche n° 168) dans un médium liquide composé de 0,1 M de chlorure de sodium, 0,4 % de glucose et 0,1 % d’extrait de levure (volume total : 500 ml). L’immersion a duré 30 jours. Des répliquats de contrôle ont été immergés dans un médium identique mais dénué de bactéries. Des observations comparatives ont été effectuées à l’issue de l’expérimentation avec un microscope électronique à balayage Jeol JSM-5600-LV (fig. 3).

De nombreux puits ont été observés à la surface de la roche (fig. 4) ; leur nombre est 3,7 fois plus important dans les échantillons soumis au protocole bactérien que dans ceux soumis au protocole sans bactérie. Les puits ont une surface généralement inférieure à 100 µm² (fig. 5) ; cependant, leur surface totale est 4,7 fois plus importante dans le protocole bactérien. Les plagioclases sont les minéraux préférentiellement attaqués (71 % des puits), devant la biotite (7 %) et le quartz (5 %) ; 11 % des puits sont localisés à l’interface plagioclase-quartz. Dans le protocole mono-minéral (tab. 4), l’albite (fig. 6) montre la formation de 19 puits sans action bactérienne, mais 52 avec les bactéries. Pour le microcline, aucun changement n’a été détecté avant/après l’expérimentation dans le protocole sans bactérie, et 4 puits apparaissent en mode bactérien. Aucune modification n’apparaît pour le quartz, quel que soit le protocole. Un aperçu général des effets des bactéries sur la météorisation du granite ou de ses minéraux est résumé dans le tab. 5. Après normalisation des surfaces altérées en fonction de la proportion de chaque minéral, l’ordre de météorisation des minéraux est le suivant : biotite > plagioclase > quartz > feldspath alcalin, pour le protocole sans bactéries ; plagioclase > biotite > feldspath alcalin > quartz, pour le protocole bactérien. Cette dernière série est conforme avec celle de S.S. Goldich (1938), ce qui tend à prouver que les observations de ce dernier prennent en compte à la fois l’altération purement chimique et les effets de la bioaltération.

Les résultats obtenus à la suite des protocoles expérimentaux sont donc : 1) les bactéries augmentent la météorisation du granite et de ses minéraux par formation de puits à la surface des minéraux ; 2) les plagioclases sont les minéraux les plus fragiles lorsque le granite est au contact de bactéries. Dans le protocole mono-minéral, l’albite (groupe des plagioclases) est le plus vulnérable ; 3) le classement normalisé du rapport puits/surface et la densité de puits dans le protocole bactérien est en accord avec l’ordre traditionnel de météorisation des minéraux (série de Goldich), indiquant que, dans les milieux naturels, la météorisation bactérienne contribue largement au processus d’altération.

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Table des illustrations

Titre Fig. 1 –Mineral distribution of Gr1 and Gr2 analysed by SEM-EDS.Fig. 1 – Distribution des minéraux dans les échantillons de granite (Gr1 et Gr2) analysés au MEB et à la micro-sonde.
Légende 10.0 × 5.0 mm area (yellow colored area) was analysed (Gr: granite). 1: quartz; 2: plagioclase; 3: K-feldspar; 4: biotite.La zone colorée en jaune (10 x 5 mm) a été analysée (Gr : granite). 1 : quartz ; 2 : plagioclase ; 3 : feldspath alcalin ; 4 : biotite.
URL http://geomorphologie.revues.org/docannexe/image/8038/img-1.jpg
Fichier image/jpeg, 236k
Titre Fig. 2 –Contour of the experiment.Fig. 2 – Aspect du protocole expérimental.
Légende Red circled granite and minerals are representatively observed before and after the experiment (Gr: granite; Ctrl: control; Ab: albite; Qtz: quartz; Mc: microcline).Les échantillons de granite et les minéraux cerclés de rouge ont été observé avant et après l’expérimentation (Gr : granite ; Ctrl : contrôle ; Ab : albite ; Qtz : quartz ; Mc : microcline).
URL http://geomorphologie.revues.org/docannexe/image/8038/img-2.jpg
Fichier image/jpeg, 88k
Titre Fig. 3 –Comparison of the Gr1 surface before and after the experimentFig. 3 – Comparaison de la surface de l’échantillon Gr1 avant et après l’expérimentation
Légende (Pl: plagioclase; K-fs: alkali feldspar; Bt: biotite). Plagioclase did not change substantially after the 30-day experiment. (Pl : plagioclase ; K-fs : feldspath alcalin ; Bt : biotite). Le plagioclase n’a subi aucune modification notable au terme des 30 jours d’expérimentation.
URL http://geomorphologie.revues.org/docannexe/image/8038/img-3.jpg
Fichier image/jpeg, 108k
Titre Fig. 4 – Comparison of the Gr2 surface before and after the experiment Fig. 4 – Comparaison de la surface de l’échantillon Gr2 avant et après l’expérimentation
Légende Pl: plagioclase; Bt: biotite; Qtz: quartz(Pl : plagioclase ; Bt : biotite ; Qtz : quartz)
URL http://geomorphologie.revues.org/docannexe/image/8038/img-4.jpg
Fichier image/jpeg, 164k
Titre Fig. 5 – Frequency distribution of pit area of the granites. Fig. 5 – Fréquence des puits observés sur les granites, classés selon leur taille.
Légende 1: other mineralspits formed in Qtz, Kfs, Bt, and mineral boundaries;2: plagioclase: pits formed in plagioclase.1 : autres minéraux : puits formés dans le quartz (Qtz), les feldspaths alcalins (Kfs), la biotite (Bt) et aux frontières inter-minérales ; 2 : plagioclases : puits formés dans les plagioclases.
URL http://geomorphologie.revues.org/docannexe/image/8038/img-5.jpg
Fichier image/jpeg, 48k
Titre Fig. 6 –SEM Image comparison of Ab1 (upper, bacteria-free), and Ab2 (lower, bacteria-bearing).Fig. 6 – Comparaison d’images MEB des échantillons d’albite : Ab1 (en haut, protocole sans bactérie), Ab2 (en bas, protocole bactérien).
Légende Arrows show newly formed pits after the experiment. Les flèches signalent les puits apparus durant l’expérimentation.
URL http://geomorphologie.revues.org/docannexe/image/8038/img-6.jpg
Fichier image/jpeg, 128k
Titre Fig. 7 – SEM image comparison of Mc1 (upper, bacteria-free), and Mc2 (lower, bacteria-bearing).Fig. 7 – Comparaison d’images MEB des échantillons de microcline : Mc1 (en haut, protocole sans bactérie), Mc2 (en bas, protocole bactérien).
URL http://geomorphologie.revues.org/docannexe/image/8038/img-7.jpg
Fichier image/jpeg, 132k
Titre Fig. 8 – SEM image comparison of Qtz1 (upper, bacteria-free), and Qtz2 (lower, bacteria-bearing).Fig. 8 – Comparaison d’images MEB des échantillons de quartz : Qtz1 (en haut, protocole sans bactérie), Qtz2 (en bas, protocole bactérien).
URL http://geomorphologie.revues.org/docannexe/image/8038/img-8.jpg
Fichier image/jpeg, 200k
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Référence papier

Wonsuh Song, Naoto Ogawa, Chiaki Takashima-Oguchi, Tamao Hatta et Yukinori Matsukura, « Laboratory experiments on bacterial weathering of granite and its constituent minerals », Géomorphologie : relief, processus, environnement, vol. 16 - n° 4 | 2010, 327-336.

Référence électronique

Wonsuh Song, Naoto Ogawa, Chiaki Takashima-Oguchi, Tamao Hatta et Yukinori Matsukura, « Laboratory experiments on bacterial weathering of granite and its constituent minerals », Géomorphologie : relief, processus, environnement [En ligne], vol. 16 - n° 4 | 2010, mis en ligne le 01 décembre 2012, consulté le 24 juillet 2017. URL : http://geomorphologie.revues.org/8038 ; DOI : 10.4000/geomorphologie.8038

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Auteurs

Wonsuh Song

Graduate School of Life and Environmental Science - University of Tsukuba - Ibaraki 305-8572 - Japan (wonsuhs@gmail.com)

Naoto Ogawa

Faculty of Agriculture - Shizuoka University - Shizuoka 422-8529 - Japan

Chiaki Takashima-Oguchi

Geosphere Research Institute of Saitama University - Saitama 338-8570 - Japan

Tamao Hatta

Japan International Research Center for Agricultural Sciences - Ibaraki 305-8686 - Japan

Yukinori Matsukura

Graduate School of Life and Environmental Science - University of Tsukuba - Ibaraki 305-8572 – Japan

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Droits d’auteur

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