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Keywords: Studies on the formation and stability of vaterite by bacteria in experimental systems are of great importance for
Biomineralization understanding the mechanism by which microbes contribute to carbonate mineralization. In this study, mi-
Vaterite neralization experiments using Lysinibacillus sp. strain GW-2 were carried out for 72 h under shaking conditions
Stability and aging experiments using biotic and chemically synthesized vaterite were performed for 60 days in distilled
Aging
water and air. Our results indicate that Lysinibacillus sp. strain GW-2 can induce the formation of vaterite with
Lysinibacillus sp.
spherical morphology from an amorphous calcium carbonate precursor. Biogenic vaterite was more stable than
chemically synthesized vaterite in distilled water, perhaps due to organic matter secreted by bacteria that en-
wrapped the vaterite and prevented it from transforming into more stable phases. Infrared spectrophotometry of
biogenic and chemically synthesized vaterite confirmed the presence of organic matter in biogenic vaterite.
⁎
Corresponding author.
E-mail address: fchli@njau.edu.cn (F.-C. Li).
http://dx.doi.org/10.1016/j.jsb.2017.09.008
Received 3 August 2017; Received in revised form 21 September 2017; Accepted 23 September 2017
1047-8477/ © 2017 Elsevier Inc. All rights reserved.
Please cite this article as: Lv, J.J., Journal of Structural Biology (2017), http://dx.doi.org/10.1016/j.jsb.2017.09.008
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
9.0 either the GW-2 strain or the chemical method was placed into an
Erlenmeyer flask with distilled water and incubated at 30 °C. Samples
were taken every 10 days for a total of 60 days. Aging tests were also
8.5 carried out in dry conditions on slide glass in air at 30 °C for 60 days.
The plate counting method was used to count the number of bac-
teria in each sample. An electronic balance accurate to 1/10,000 was
used to weigh the precipitate. pH was measured with a pH meter (pHS-
7.5
3C, Yoke Instrument, Shanghai, China). An X-ray diffractometer (D/
max-B III, Rigaku, Beijing, China) with Cu-Kα radiation was used to
identify the mineral composition of the precipitates with an error
7.0 of < 5%. Each sample was scanned continuously at 2° (2θ) min−1from
10° to 60° (2θ) at 35 kV and 20 mA in 0.01° (2θ) steps. Qualitative
0 10 20 30 40 50 60 70 80 identification of mineral phases was performed using Jade 5.0. The
precipitates were analyzed using a Tensor 27 Fourier transform infrared
Time(h)
spectrophotometer (FT-IR) (Bruker, Ettlingen, Germany). The spectro-
Fig. 2. Temporal curve of pH value in the medium. meter was set to scan at 1 cm−1 resolution with a scan range of
4000–400 cm−1. An EVO18 scanning electron microscope (Carl Zeiss,
bacterial cells are short and rod-like in shape and contain spores in the Oberkochen, Germany) equipped with an energy dispersive detector
center ranging in size from 0.7–1.1 × 0.4–0.7 µm (Fig. 1). Gram was used to image minerals at the Nanjing Institute of Geography and
staining showed that strain GW-2 is Gram-positive. A comprehensive Limnology, Chinese Academy of Sciences, China. The dried samples
phylogenetic analysis of 16S rRNA gene sequences showed that strain were coated with 8 nm of gold before scanning electron microscopy
GW-2 belonged to Lysinibacillus sp. (Li and Guo, 2013). (SEM) imaging. Transmission electron microscopy (TEM) was per-
formed using a Tecnai G2 F20 electron microscope (FEI Co., Hillsboro,
2.2. Method of biomineralization experiments OR, USA) equipped with an energy dispersive spectrometer to analyze
the chemical composition and microstructure of the minerals. Samples
Four colonies growing on solid media were selected for inoculation were prepared by dispersing and settling the mineral powder with clear
of 300 ml of liquid media (without calcium acetate to avoid CaCO3 alcohol on a Cu grid.
precipitation) and a seed culture was obtained after incubation for 24 h
at 28 °C on a rotary shaker. The cell density of the seed culture was 2.6. Characterization of organic matters in vaterite
1.03 × 107 cfu/ml. Erlenmeyer flasks were filled with 90 ml of B4 li-
quid media and 10 ml of seed culture and incubated at 28 °C on a rotary Biogenic and abiotic vaterite were ground with an agate mortar. A
shaker. Samples were taken after inoculation for less than 5 min, after 5 ml centrifuge tube filled with 30 mg vaterite powder and 2 ml of a
every hour for the first 18 h, and every 8 h between 18 and 72 h after solution of dichloromethane and methanol at a ratio of 93:7 was placed
inoculation. The last sample was taken 72 h after inoculation. Abiotic in an ultrasonic generator at 4 °C for 30 min. The clear fluid was then
experiments were also performed under shaking conditions. Liquid and collected by centrifugation. A small amount of the clear fluid was re-
solid phases of samples were separated by centrifugation. moved with a capillary and dripped onto dried KBr powder. Once the
organic solvent was completely volatilized, the KBr powder was sub-
2.3. Synthetic method of abiotic vaterite jected to compression treatment and analyzed using the FT-IR (Qian
et al., 2017).
A 250 ml conical bottle containing the composite solution, 10 g L-
Asparagine powder, and 1 g CaCl2 powder was placed on an ultrasonic 3. Results
shaker for 20 min at 45 °C and 1 g Na2CO3 powder was slowly added.
The precipitated product was immediately centrifuged and placed in a 3.1. Changes of pH value
thermostatic oven at 35 °C to obtain abiotic vaterite.
The pH of the culture decreased slightly during the initial growth
2.4. Method of aging experiment stage, after which pH gradually increased. The maximum and minimum
pH values were 8.81 and 6.98, respectively. In abiotic experiments, pH
For aging experiments, a certain amount of vaterite induced by remained unchanged at 7.40 (Fig. 2).
2
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
20
able to continue exponential growth (Zhu et al., 2014). The initial
density of bacterial cells was 1.03 × 107 cfu/ml and the density
7
5
As shown in Fig. 4, although CaCO 3 began to precipitate after
8 h, only a small amount of precipitate formed before 16 h of in-
0
cubation. Precipitation then progressed rapidly between 16 and
0 10 20 30 40 50 60 70 80 18 h, after which the amount of precipitate increased slowly to a
Time(h) maximum of 99 mg per 100 ml culture media. In contrast to bac-
terial experiments, no mineral precipitation occurred in abiotic
Fig. 3. Growth curve of GW-2 strain in B4 liquid medium.
experiments.
3.2. 2Change of bacterial density As shown by X-ray diffraction, neither biogenic nor chemically
synthesized vaterite underwent any phase transformations in air
As shown in Fig. 3, after incubation, bacterial growth occurred after 60 days. Similarly, biogenic vaterite aged in distilled water for
throughout the lag (< 4 h), exponential (4–16 h), stationary 60 days did not transform (Fig. 8a) and its morphology remained
3000 V
V V
2500
16h V V V
Intensity (counts)
2000
1500
32h
1000
500
72h
0
10 20 30 40 50 60
2ș (°)
3
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
100 16h
90
874.04
1082.35
80
1402.07
70
60
50
100 32h
1088.51 744.69
80
60
875.56
40 1463.39
20
100 72h
744.30
1087.94
90
80 874.20
1438.42
70
spherical (Fig. 9a, b). However, almost all of the chemically syn- according to the following reactions: CaCO3:CO2(aq) + H2O →
thesized vaterite in distilled water was transformed into calcite HCO3− +
(aq) + H ; HCO3
−
(aq) → CO3(aq) + H ;CO3(aq) + Ca
2− + 2− 2+
→ CaCO3(s).
after 10 days (Fig. 8b) and its morphology changed from spherical Alternatively, two processes result in an increase in pH value (Li et al.,
to rhombohedral with a round pit in the center (Fig. 9c, d). 2013). As bacteria degrade organic matter into ammonia, NH4+ and
OH−are simultaneously produced according to the reactions R-
−
4. Discussion NH2 + H2O → NH3 + R-OH and NH3 + H2O → NH4+ (aq) + OH . Simi-
larly, when bacterial cells autolyse, nitrogen-containing molecules release
4.1. The increase of pH value is prerequisite condition for the precipitation ammonia. As the bacteria in this study began to reproduce logarithmically,
of vaterite these two processes likely dominated, resulting in an increase in pH.
Overall, the alkaline environment resulting from these processes allowed for
The pH of the culture decreased slightly during the initial growth carbonate precipitation.
stage, after which pH gradually increased. The maximum and minimum
pH values were 8.81 and 6.98, respectively (Fig. 2). In abiotic experi- 4.2. The rapid growth of bacteria ensured the precipitation and stabilization
ments, pH remained unchanged at 7.40. It is well known that an al- of vaterite
kaline environment is a prerequisite for carbonate precipitation. In this
study, although pH decreased slightly during the initial stage of the Figs. 2 and 3 showed that when bacterial growth went into sta-
experiment from 8.0 to 6.98, the media was still alkaline enough for tionary phase (16 h), precipitants began to form. Further studies con-
carbonate precipitation. As the incubation time increased, the pH value firmed that the precipitants were vaterite which has the highest nu-
also gradually increased. After 16 h, vaterite began to precipitate at pH cleation barrier (ΔGN∗) among the three anhydrous polymorphs of
7.77. Correlation analysis showed that there was a significant positive calcium carbonate. According to homogeneous/ heterogeneous nu-
correlation between the amount of precipitate and the pH value (cor- cleation theory, energy higher than the nucleation barrier is one of the
relation coefficient 0.87, P < 0.01) (Fig. 10). These results confirm necessary conditions for generation of a new nucleus. Here, the nu-
that an increase in alkalinity is favorable for the formation of vaterite cleation barrier is determined by ΔGN∗ = 16π rSL2Ω3/3(kTInS)2, where
(Rodrigue-Navarro et al., 2007; Fernández-Remolar et al., 2012). rSL is the interfacial energy (J/m2), Ω is the volume of the base unit, k is
In this experimental system, four processes may have affected the pH the Boltzmann constant, T is the thermodynamic temperature, and S is
value. First, bacteria secrete low-molecular-weight organic acids during the the supersaturation of the solution (Cui et al., 2007). It is obvious that
process of metabolism. At the initial stage of the experiment in this study, both reducing rSL and increasing S can reduce the ΔGN∗ value of the
this process likely dominated, leading to a slight reduction in pH value. At nucleation of calcium carbonate. Previous results have shown that
this stage, the lower alkalinity was not conducive to carbonate precipitation. bacterial cells (Costerton, 1995; Guo et al., 2013; Zhang et al., 2017)
Also leading to a reduction in pH is the process by which CO2 produced by and excreted EPS by bacteria are both likely to become effective mi-
bacterial respiration dissolves in water and then forms a precipitate neral nucleation sites (Schultze-Lam et al., 1996; Aloisi et al., 2006). As
4
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
5
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
a
V V C V
60d V V
1250
1000 30d
Intensity (Counts)
750
20d
500
10d
250
0d
0
10 20 30 40 50 60
2ș(°)
5000
C
b
4000
Intensity (Counts)
3000
2000
10d C C C C CC C
1000
V V
V V V
0d V
0
10 20 30 40 50 60
2ș(°)
Fig. 8. X-ray diffraction patterns of a) biogenic and b) abiotic vaterite from aging experiments.
solid impurities in the biomineralization system, bacteria can reduce 4.3. ACC is a precursor of vaterite
the interfacial energy (rSL) by serving as a kind of nucleation site. The
rapid growth of bacteria led to an increase in CO32− content and bac- In X-ray diffraction experiments, several diffraction peaks belonging
terial density in the system, which increased the supersaturation of the to vaterite were observed after 16 h of incubation, whereas in FT-IR
solution (S) and reduced the interfacial energy (rSL). During the middle analysis of samples collected at the same time point, absorption peaks
and late stages of experiments under shaking condition, the extreme around 1083, 875, and 1490–1420 cm−1 corresponded to ACC vibra-
supersaturation of CaCO3 and enough nucleation sites favor vaterite tions sample (Weng, 2010). TEM and selected area electron diffraction
formation because the increased supersaturation and reduce interfacial (SAED) experiments confirmed that samples taken after 16 h of in-
energy may decrease the nucleation energy barrier of vaterite. cubation were composed mainly of poorly crystallized vaterite and
ACC, whereas samples taken after 72 h of incubation contained well-
6
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
120 distilled water for 60 days (Fig. 9). While, the chemically synthesized
vaterite transformed into calcite, and their spherule-like morphology
became rhombohedron-like in the distilled water for 10 days.
Biofilms are multicellular communities that were so far thought
to be held together solely by a self-produced organic extracellular
Precipitate amount (mg)
4.4. Organic matters prevented vaterite from aging In conclusion, our discussion about experimental results suggests
the following: the Lysinibacillus sp. strain GW-2 could induce the for-
Usually, vaterite might transform into stable phases in certain mation of vaterite with spherule-like morphology under shaking con-
conditions after the formation. There are two instances in which va- dition. SAED patterns indicate that ACC might be precursor of vaterite.
terite transformed into calcite within 20–25 h at room temperature The aging experiments indicate that biogenic vaterite is more stable
(Kralj et al., 1997) and into aragonite within 1 h at 60 °C (Ogino et al., than the abiotic vaterite in the distilled water. The possible reason for
1987). However, the results of this paper show that vaterite retains stability of biogenic vaterite is that some bacterial secretion (for in-
steady in the experimental system until the end of the biominerlization stance, polysaccharides and proteins) were enwrapped by vaterite or
experiment (72 h). Moreover, XRD patterns indicate that vaterite enwrapped vaterite, and they might restrain vaterite from transforming
transformation had not occurred in air even for 300 days and in into more stable phases.
7
J.-J. Lv et al. Journal of Structural Biology xxx (xxxx) xxx–xxx
100 16h
98 P1 P2 P3 P4 P5 P6
96
2851.59
94
1464.96
1637.51 1061.42
92 2921.22
90
88
86
72h
95
90
2851.92
1466.50 1123.05
85 2923.39 1617.79
1653.95
80
3434.52
75
Fig. 11. FTIR patterns of extracts from biotic vaterite of the 16th and 72nd hour.
Table 1
Absorption peaks of extract from biotic vaterite of the 16th and 72nd hour by infrared spectrum detection(Weng, 2010; Qian et al., 2017).
Types of organic group Absorption peaks (cm−1) Vibration characteristics of groups Peak area in Fig. 11
Acknowledgments Cui, F.-Z., Feng, Q.-L., Tang, R.-K., Ouyang, J.-M., Wang, A.-H., Wang, K., 2007.
Biomineralization. Tsinghua University Press, Beijing (In Chinese).
Fernández-Remolar, D.C., Preston, L.J., Sánchez-Román, M., Izawa, M.R.M., Huang, L.,
This work was supported by the National Natural Science Southam, G., Banerjee, N.R., Osinski, G.R., Flemming, R., Gómez-Ortíz, D.,
Foundation of China (grant Nos: 41673083 and 41172308), the Key Ballesteros, O.P., Rodríguez, N., Amils, R., Darby Dyar, M., 2012. Carbonate pre-
cipitation under bulk acidic conditions as a potential biosignature for searching life
Research Program of the Chinese Academy of Sciences (Grant No: on Mars. Earth Planet. Sci. Lett. 351, 13–26.
KZZD-EW-04-02) and by Open Project of the State Key Laboratory of Grasby, S.E., 2003. Naturally precipitating vaterite (μ-CaCO3) spheres: unusual carbo-
Loess and Quaternary Geology, CAS (grant No: SKLLQG1309). The nates formed in an extreme environment. Geochim. Cosmochim. Acta 67,
1659–1666.
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Guo, W.-W., Ma, H., Li, F.-C., Jin, Z.-D., Li, J., Ma, F., Wang, C., 2013. Citrobacter sp.
Nanjing Institute of Geography and Limnology, Chinese Academy of strain GW-M mediates the coexistence of carbonate minerals with various morphol-
Sciences for SEM observation. ogies. Geomicrobiol. J. 30, 74757.
Kim, V.T., Nele, D.B., Willem, D.M., Willy, V., 2010. Use of bacteria to repair cracks in
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