Carbonate biomineralization and heavy metal remediation by calcifying fungi isolated from karstic caves

Dhami, Navdeep Kaur; Quirin, Marie Emmanuella Christelle

doi:10.1016/j.ecoleng.2017.03.007

Cited by 76 publications

(20 citation statements)

References 52 publications

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“…Based on the discovery of biomineralization, researchers have begun to develop new cementing materials. Biomineralization can also be used in the treatment of environmental pollution such as the removal or fixing of heavy metals [32,33] and the depletion of carbon dioxide [34][35][36][37][38].…”

Section: Introductionmentioning

confidence: 99%

Mechanism of Biomineralization Induced by Bacillus subtilis J2 and Characteristics of the Biominerals

et al. 2019

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Biomineralization induced by microorganisms has become a hot spot in the field of carbonate sedimentology; however, the mechanisms involved still need to be explored. In this study, the bacterium Bacillus subtilis J2 (GenBank MG575432) was used to induce the precipitation of calcium carbonate minerals at Mg/Ca molar ratios of 0, 3, 6, 9, and 12. Bacillus subtilis J2 bacteria released ammonia to increase pH, but the ammonia released only made the pH increase to 8.25. Carbonic anhydrase was also produced to catalyze the hydration of carbon dioxide, and this process released carbonate and bicarbonate ions that not only increased pH but also elevated carbonate supersaturation. The biominerals formed at a Mg/Ca molar ratio of 0 were spherulitic, elongated, dumbbell-shaped, and irregularly rhombohedral calcite; at a Mg/Ca molar ratio of 3, the biominerals were calcite and aragonite, the weight ratio of calcite decreased from 26.7% to 15.6%, and that of aragonite increased from 73.3% to 84.4% with increasing incubation time. At higher Mg/Ca molar ratios, the biominerals were aragonite, and the crystallinity and thermal stability of aragonite decreased with increasing Mg/Ca molar ratios. FTIR results showed that many organic functional groups were present on/within the biominerals, such as C–O–C, N–H, C=O, O–H, and C–H. HRTEM-SAED examination of the ultra-thin slices of B. subtilis J2 bacteria showed that nano-sized minerals with poor crystal structure had grown or been adsorbed on the EPS coating. The EPS of the B. subtilis J2 strain contained abundant glutamic acid and aspartic acid, which could be deprotonated in an alkaline condition to adsorb Ca2+ and Mg2+ ions; this made EPS act as the nucleation sites. This study may provide some references for further understanding of the mechanism of biomineralization induced by microorganisms.

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Section: Introductionmentioning

confidence: 99%

Mechanism of Biomineralization Induced by Bacillus subtilis J2 and Characteristics of the Biominerals

et al. 2019

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“…The potential for microbes to synthesize carbonates has recently emerged as a prospective technology, called as Microbially Induced Calcium Carbonate Precipitation (MICCP), for civil and environmental engineering applications ( Skinner and Jahren, 2004 ; Phillips et al, 2013 ; Zhu and Dittrich, 2016 ). Current usage of the technology includes remediation of heavy metal polluted sites, sequestration of CO 2 , and the construction of biocement ( Dhami et al, 2012 , 2014 , 2016 , 2017b ; Dejong et al, 2013 ; Zhu and Dittrich, 2016 ). Several breakthroughs have been made at laboratory and field scale in the creation and utilization of biomineralized carbonates ( De Muynck et al, 2010 ; Phillips et al, 2013 ; Dhami et al, 2017a ; Porter et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions

Dhami

Watkin

2018

Front. Microbiol.

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Natural mineral formations are a window into important processes leading to carbon storage and mineralized carbonate structures formed through abiotic and biotic processes. In the current study, we made an attempt to undertake a comprehensive approach to characterize the mineralogical, mechanical, and microbial properties of different kinds of speleothems from karstic caves; with an aim to understand the bio-geo-chemical processes in speleothem structures and their impact on nanomechanical properties. We also investigated the biomineralization abilities of speleothem surface associated microbial communities in vitro. Mineralogical profiling using techniques such as X-ray powder Diffraction (XRD) and Tescan Integrated Mineral Analyzer (TIMA) demonstrated that calcite was the dominant mineral in the majority of speleothems with Energy Dispersive X-ray Analysis (EDS) indicating a few variations in the elemental components. Differing proportions of polymorphs of calcium carbonate such as aragonite and vaterite were also recorded. Significant variations in trace metal content were recorded through Inductively Coupled Plasma Mass Spectrometer (ICP-MS). Scanning Electron Microscopy (SEM) analysis revealed differences in morphological features of the crystals which varied from triangular prismatic shapes to etched spiky forms. Microbial imprints and associations were seen in a few sections. Analysis of the associated microbial diversity showed significant differences between various speleothems at Phylum level; although Proteobacteria and Actinobacteria were found to be the predominant groups. Genus level microbial associations showed a relationship with the geochemistry, mineralogical composition, and metal content of the speleothems. The assessment of nanomechanical properties measured by Nanoindentation revealed that the speleothems with a dominance of calcite were stronger than the speleothems with mixed calcium carbonate polymorphs and silica content. The in vitro metabolic activity of the microbial communities associated with the surfaces of the speleothems resulted in calcium carbonate crystal precipitation. Firmicutes and Proteobacteria dominated these populations, in contrast to the populations seen in natural systems. The precipitation of calcium carbonate crystals in vitro indicated that microbial metabolic activity may also play an important role in the synthesis and dissociation of biominerals in the natural environment. Our study provides novel evidence of the close relationship between mineralogy, microbial ecology, geochemistry, and nanomechanical properties of natural formations.

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“…Previous studies suggest that caves support a considerable diversity of microbes (Bindschedler, Cailleau, & Verrecchia, 2016;Carmichael et al, 2015;Dhami, Quirin, & Mukherjee, 2017;Hathaway et al, 2014;Jiang et al, 2017;Ortiz et al, 2013;Vanderwolf, Malloch, McAlpine, & Forbes, 2013;Zhang et al, 2017). Ortiz et al (2013) investigated the bacterial diversity in Kartchner Caverns using 454pyrosequencing, and 1,994 OTUs were obtained from ten sample sites.…”

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confidence: 99%

Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

Zhang

Cai

2019

Journal of Biogeography

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Aim Previous studies primarily based on the culture method have revealed that caves host a high fungal diversity and that exogenous carbon sources influence fungal communities. Here, we assess the fungal diversity and distribution patterns in karst caves in Southwest China and reveal the major factors that shape the fungal communities. Location Southwest China. Methods Samples of air, rock, sediment and water were collected from eight caves in Southwest China. Using high‐throughput sequencing of the internal transcribed spacer 1 region of fungal rDNA, we examined the cave fungal communities in Southwest China and studied their correlations with potentially influential factors, such as substrate, cave, location and environmental variables. Results Approximately 10,000 fungal operational taxonomic units (OTUs) spanning 15 phyla were obtained. The highest diversity genus was Penicillium, while Mortierella had the highest relative abundance. Compared with air and rock samples, sediment and water samples harboured higher diversity and distinct communities. Substrate and cave were revealed to be the key determinants of the fungal communities in caves. Sample location and sampling distance from the entrance had more significant impacts on rock and sediment communities than on air and water assemblages. The fungal assemblages in air and water samples from the cave and outside cave environments were similar, while those of rock and sediment samples were significantly different. Main conclusions Our results indicate that sediment and water harboured higher fungal diversity than air and rock, and substrate and spatial variables are key determinants of fungal communities in caves.

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Carbonate biomineralization and heavy metal remediation by calcifying fungi isolated from karstic caves

Cited by 76 publications

References 52 publications

Mechanism of Biomineralization Induced by Bacillus subtilis J2 and Characteristics of the Biominerals

Mechanism of Biomineralization Induced by Bacillus subtilis J2 and Characteristics of the Biominerals

Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions

Substrate and spatial variables are major determinants of fungal community in karst caves in Southwest China

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