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Sansupa C, Suphaphimol N, Nonthijun P, Ronsuek T, Yimklan S, Semakul N, Khrueraya T, Suwannarach N, Purahong W, Disayathanoowat T. Life on the wall: the diversity and activity of microbes on 13th - century AD. Lan Na mural painting. Front Microbiol 2023; 14:1220901. [PMID: 37779706 PMCID: PMC10540211 DOI: 10.3389/fmicb.2023.1220901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/31/2023] [Indexed: 10/03/2023] Open
Abstract
Diverse microorganisms from the three domains of life (Archaea, Bacteria, and Eukaryota) cause deterioration in mural paintings worldwide; however, few studies have simultaneously targeted these three domains. This study aims to survey the microbiome and its potential for biodeterioration on unpreserved Lan Na mural paintings in Sean Khan temple, Chiang Mai, Thailand. The overview of the archaeal, bacterial, and fungal communities was reported by Illumina sequencing, whereas the potential for deterioration was revealed by culturable techniques and a literature search. The abundant microbes reported in this study were also found in other ancient mural paintings worldwide. Halococcus, a salt-tolerant archaeon, as well as the eubacterial genus Crossiella dominated the prokaryotic community. On the other hand, the main fungal group was the genus Candida (Ascomycota). However, a low number of fungi and bacteria were isolated. Most of the isolates showed the ability to survive in the drought conditions of mural paintings but could not perform discoloration activities. The deterioration activity mainly affected calcium compounds, which are the main components of painting substrates. Aspergillus and several bacterial isolates could dissolve calcium compounds, but only Trichaptum species could induce crystal formation. These results suggest that deterioration of painting substrate should be taken into consideration in addition to deterioration of color in mural paintings. For the Lan Na painting in Sean Khan temple, the plaster is the prime target for biodeterioration, and thus we suggest that the preservation effort should focus on this component of the mural painting.
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Affiliation(s)
- Chakriya Sansupa
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Nattaphon Suphaphimol
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Paradha Nonthijun
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Teewararat Ronsuek
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Saranphong Yimklan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Natthawat Semakul
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | | | - Nakarin Suwannarach
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Witoon Purahong
- Department of Soil Ecology, UFZ-Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Terd Disayathanoowat
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
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Ciplak ES, Bilecen K, Akoglu KG, Guchan NS. Use of bacterial binder in repair mortar for micro-crack remediation. Appl Microbiol Biotechnol 2023; 107:3113-3127. [PMID: 37014395 DOI: 10.1007/s00253-023-12507-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/24/2023] [Accepted: 03/28/2023] [Indexed: 04/05/2023]
Abstract
Micro-cracks are one of the types of stone deterioration which can propagate and lead to surface detachments and larger cracks in the long run. The present study developed a sustainable and environmentally friendly infill material-biological mortar (BM), as an alternative to conventional approaches. Using a biomineralization approach, this BM was explicitly designed for healing micro-cracks (less than 2 mm) in historic travertines. To this end, the mortar was prepared using a calcifying Bacillus sp. isolated from thermal spring water resources in Pamukkale Travertines (Denizli), stone powder gathered from travertine quarries in the vicinity, and a triggering solution specifically designed to set off calcium carbonate precipitation reaction. After setup, BM was applied to micro-cracks of artificially aged test stones for testing. Scanning electron microscopy revealed calcium carbonate-coated Bacillus sp. bodies in the BM matrix, optical microscopy showed secondary calcite minerals throughout the BM applied micro-cracks, and stereomicroscopy and nanoindentation analyses demonstrated bonding of BM with stone due to microbial calcification activities. Furthermore, BM and original material contact showed a continuous and coherent structure in all samples. Within this context, BM could be considered a promising and alternative approach for the remediation of micro-cracks of historic stones. KEY POINTS: A binder was produced by the MICP of Bacillus sp. Pamukkale. Physical, mineralogical, and nanomechanical characterization demonstrated microbial calcite precipitates in BM. A significant bond was determined between the grains and matrix of BM due to Bacillus sp. calcite production activities.
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Affiliation(s)
- Elif Sirt Ciplak
- Graduate Program in Conservation of Cultural Heritage, Faculty of Architecture, METU, 06800, Ankara, Turkey.
| | - Kivanc Bilecen
- Department of Molecular Biology and Genetics, Konya Food and Agriculture University, 42080, Konya, Turkey
| | | | - Neriman Sahin Guchan
- Graduate Program in Conservation of Cultural Heritage, Faculty of Architecture, METU, 06800, Ankara, Turkey
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3
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Ropiness in Bread—A Re-Emerging Spoilage Phenomenon. Foods 2022; 11:foods11193021. [PMID: 36230100 PMCID: PMC9564316 DOI: 10.3390/foods11193021] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
As bread is a very important staple food, its spoilage threatens global food security. Ropy bread spoilage manifests in sticky and stringy degradation of the crumb, slime formation, discoloration, and an odor reminiscent of rotting fruit. Increasing consumer demand for preservative-free products and global warming may increase the occurrence of ropy spoilage. Bacillus amyloliquefaciens, B. subtilis, B. licheniformis, the B. cereus group, B. pumilus, B. sonorensis, Cytobacillus firmus, Niallia circulans, Paenibacillus polymyxa, and Priestia megaterium were reported to cause ropiness in bread. Process hygiene does not prevent ropy spoilage, as contamination of flour with these Bacillus species is unavoidable due to their occurrence as a part of the endophytic commensal microbiota of wheat and the formation of heat-stable endospores that are not inactivated during processing, baking, or storage. To date, the underlying mechanisms behind ropy bread spoilage remain unclear, high-throughput screening tools to identify rope-forming bacteria are missing, and only a limited number of strategies to reduce rope spoilage were described. This review provides a current overview on (i) routes of entry of Bacillus endospores into bread, (ii) bacterial species implicated in rope spoilage, (iii) factors influencing rope development, and (iv) methods used to assess bacterial rope-forming potential. Finally, we pinpoint key gaps in knowledge and related challenges, as well as future research questions.
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Ekprasert J, Pongtharangkul T, Chainakun P, Fongkaew I, Khanthasombat K, Kamngam R, Boonsuan W, Ditta ZM, Seemakram W, Boonlue S. Kinetic model of a newly-isolated Lysinibacillus sp. strain YL and elastic properties of its biogenic CaCO 3 towards biocement application. Biotechnol J 2021; 17:e2100124. [PMID: 34592060 DOI: 10.1002/biot.202100124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND Biocement, calcifying bacteria-incorporated cement, offers an environmentally-friendly way to increase the cement lifespan. This work aimed to investigate the potential use of Lysinibacillus sp. strain YL towards biocement application in both theoretical and experimental ways. METHODS AND RESULTS Strain YL was grown using calcium acetate (Ca(C2 H3 O2 )2 ), calcium chloride (CaCl2 ) and calcium nitrate (Ca(NO3 )2 ). Maximum bacterial growth of ~0.09 hr-1 and the highest amount of CaCO3 precipitation of ~8.0 g/L were obtained when using Ca(C2 H3 O2 )2 . The SEM and XRD results confirmed that biogenic CaCO3 were calcites. The bulk, Young's and shear moduli of biogenic CaCO3 calculated via the VRH approximation were ~1.5-2.3 times larger than those of ordinary Portland cement. The Poisson's ratio was 0.382 and negative in some directions, suggesting its ductility and auxetic behaviors. The new model was developed to explain the growth kinetic of strain YL in the presence of Ca(C2 H3 O2 )2 , whose concentration was optimized for biocement experiments. Strain YL could increase the compressive strength of cement up to ~50% higher than that of the uninoculated cement. CONCLUSION Strain YL is a promising candidate for biocement applications. This work represents the trials of experiments and models allowing quantitatively comparison with large-scale production in the future.
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Affiliation(s)
- Jindarat Ekprasert
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | | | - Poemwai Chainakun
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Ittipon Fongkaew
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.,Center of Excellence in Advanced Functional Materials, School of Physics, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Kamonwan Khanthasombat
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Rungtiwa Kamngam
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Wachiraya Boonsuan
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Zerlinda Mara Ditta
- Biological Science Program, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Wasan Seemakram
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Sophon Boonlue
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
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Ramdas VM, Lalloo R, Lekha P, Mgangira M, Muniyasamy S, Mukaratirwa S, Ramchuran S. Understanding the mechanism of interaction of candidate soil stabilizing prototypes by using microscopy and spectroscopy techniques. Microsc Res Tech 2021; 84:2652-2665. [PMID: 34014009 DOI: 10.1002/jemt.23815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 11/06/2022]
Abstract
Globally, there is a high demand for bio-based soil stabilizers required for improving the strength properties of weak in situ soil. Microbes and microbial components such as Bacillus spp. have gained interest as soil stabilizers due to their production of spores, bio-enzymes, and bio-polymers. However, the current approach for any microlevel assessment of bio-additives and in situ soil improvement is limited. This paper provides data for microstructural evaluation of stabilized soil material for the postulation of the mode of action. In this study, the microbonding effect (i.e., bio-based cementation, bio-clogging, and soil particle bio-coating) is successfully observed within the various stabilizing prototypes, obtained from a novel Bacillus spp. using advanced methods, namely field emission gun-scanning electron microscopy and Fourier transform-infrared spectroscopy. The results show that treated soil versus untreated soil properties are altered by the bio-additive/s stabilizing effect. These indicator tests provide data for further bio-stabilizer product prototype development and processes (i.e., improved products in terms of strength and moisture susceptibility). The use of microscopy and spectroscopy was sufficient for the preliminary selection of suitable candidates for soil stabilization.
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Affiliation(s)
- Veshara Malapermal Ramdas
- School of Life Sciences, University of KwaZulu Natal, Durban, South Africa.,Council for Scientific and Industrial Research (CSIR), Chemicals Cluster, Pretoria, South Africa
| | - Rajesh Lalloo
- Council for Scientific and Industrial Research (CSIR), Chemicals Cluster, Pretoria, South Africa
| | - Prabashni Lekha
- Council for Scientific and Industrial Research (CSIR), Biorefinery Industry Development Facility, Durban, South Africa
| | - Martin Mgangira
- Council for Scientific and Industrial Research (CSIR), Smart Mobility Transport Infrastructure Engineering, Pretoria, South Africa
| | - Sudhakar Muniyasamy
- Council for Scientific and Industrial Research (CSIR), Chemicals Cluster, Pretoria, South Africa
| | - Samson Mukaratirwa
- School of Life Sciences, University of KwaZulu Natal, Durban, South Africa
| | - Santosh Ramchuran
- School of Life Sciences, University of KwaZulu Natal, Durban, South Africa.,Council for Scientific and Industrial Research (CSIR), Chemicals Cluster, Pretoria, South Africa
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Muras A, Romero M, Mayer C, Otero A. Biotechnological applications of Bacillus licheniformis. Crit Rev Biotechnol 2021; 41:609-627. [PMID: 33593221 DOI: 10.1080/07388551.2021.1873239] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bacillus licheniformis is a Gram positive spore-forming bacterial species of high biotechnological interest with numerous present and potential uses, including the production of bioactive compounds that are applied in a wide range of fields, such as aquaculture, agriculture, food, biomedicine, and pharmaceutical industries. Its use as an expression vector for the production of enzymes and other bioproducts is also gaining interest due to the availability of novel genetic manipulation tools. Furthermore, besides its widespread use as a probiotic, other biotechnological applications of B. licheniformis strains include: bioflocculation, biomineralization, biofuel production, bioremediation, and anti-biofilm activity. Although authorities have approved the use of B. licheniformis as a feed additive worldwide due to the absence of toxigenic potential, some probiotics containing this bacterium are considered unsafe due to the possible transference of antibiotic resistance genes. The wide variability in biological activities and genetic characteristics of this species makes it necessary to establish an exact protocol for describing the novel strains, in order to evaluate its biotechnological potential.
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Affiliation(s)
- Andrea Muras
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Manuel Romero
- School of Life Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK
| | - Celia Mayer
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Ana Otero
- Departmento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía-CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Yi D, Zhang H, Zhang W, Zong Y, Zhao K. Fabrication of patterned calcium carbonate materials through template-assisted microbially induced calcium carbonate precipitation. RSC Adv 2021; 11:28643-28650. [PMID: 35478572 PMCID: PMC9038093 DOI: 10.1039/d1ra04072c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
Patterned calcium carbonate materials with controlled morphologies have broad applications in both environmental and engineering fields. However, how to fabricate such materials through environmental-friendly methods under ambient conditions is still challenging. Here, we report a green approach for fabricating patterned calcium carbonate materials. This eco-friendly approach is based on template-assisted microbially induced calcium carbonate precipitation. As a proof of concept, by varying the templates and optimizing fabrication parameters, different patterned calcium carbonate materials were obtained. The optimized parameters include CCa2+ = 80 mM, Ti = 15 °C, and templates made of small-sized CaCO3 particles with a concentration of 1.5 mg mL−1, under which better and more sharp patterns were obtained. Materials with periodic patterns were also fabricated through a periodic template, showing good scalability of this approach. The results of this study could mean great potential in applications where spatially controlled calcium carbonate depositions with user-designed patterns are needed. A simple and green approach based on template-assisted microbially induced calcium carbonate precipitation for the fabrication of patterned calcium carbonate materials was demonstrated.![]()
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Affiliation(s)
- Dewei Yi
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Hong Zhang
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Wenchao Zhang
- School of Chemistry and Life Science, Suzhou University of Science and Technology, Suzhou 215009, P. R. China
| | - Yiwu Zong
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
| | - Kun Zhao
- Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, P. R. China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. China
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8
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Han L, Li J, Xue Q, Chen Z, Zhou Y, Poon CS. Bacterial-induced mineralization (BIM) for soil solidification and heavy metal stabilization: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 746:140967. [PMID: 32763598 DOI: 10.1016/j.scitotenv.2020.140967] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/12/2020] [Accepted: 07/12/2020] [Indexed: 06/11/2023]
Abstract
Solidification and stabilization (S/S) treatment via cement is common and effective for improving soil strength and stabilizing heavy metals in contaminated soils, but has certain drawbacks, such as high fossil energy consumption, big carbon footprint, poor chemical compatibility, and ambiguous long-term stability. This paper innovatively proposes bacterial-induced mineralization (BIM) as an eco-friendly and efficient S/S method. In the BIM-S/S treatment, life activities of bacteria produce minerals to cement the soil particles and fix the heavy metals. This review firstly summarizes the basic theories of BIM technology followed by the evaluation on remediation effects and long-term stability in terms of soil solidification and heavy metal stabilization. Then the factors in BIM-S/S application are reviewed. Emphasis is put on the comparison of the BIM-S/S effect with that of cement-based-S/S technology. It is concluded that BIM-S/S technology is promising with outstanding performance in sustainability. On the other hand, current limitations and deficiencies with this technology are identified finally, hereby the directions for future research are pointed to make a major advancement in the BIM-S/S technology.
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Affiliation(s)
- Lijun Han
- State Key Laboratory of Geomechanics and Geotechnical Engineering, Institute of Rock and Soil Mechanics, Chinese Academy of Sciences, Wuhan 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiangshan Li
- State Key Laboratory of Geomechanics and Geotechnical Engineering, Institute of Rock and Soil Mechanics, Chinese Academy of Sciences, Wuhan 430071, China; IRSM-CAS/HK PolyU Joint Laboratory on Solid Waste Science, Wuhan 430071, China.
| | - Qiang Xue
- State Key Laboratory of Geomechanics and Geotechnical Engineering, Institute of Rock and Soil Mechanics, Chinese Academy of Sciences, Wuhan 430071, China.
| | - Zhen Chen
- State Key Laboratory of Geomechanics and Geotechnical Engineering, Institute of Rock and Soil Mechanics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yaoyu Zhou
- College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Chi Sun Poon
- IRSM-CAS/HK PolyU Joint Laboratory on Solid Waste Science, Wuhan 430071, China; Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
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Ekprasert J, Fongkaew I, Chainakun P, Kamngam R, Boonsuan W. Investigating mechanical properties and biocement application of CaCO 3 precipitated by a newly-isolated Lysinibacillus sp. WH using artificial neural networks. Sci Rep 2020; 10:16137. [PMID: 32999379 PMCID: PMC7527966 DOI: 10.1038/s41598-020-73217-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
A newly-isolated Lysinibacillus sp. strain WH could precipitate CaCO3 using calcium acetate (Ca(C2H3O2)2), calcium chloride (CaCl2) and calcium nitrate (Ca(NO3)2) via non-ureolytic processes. We developed an algorithm to determine CaCO3 crystal structures by fitting the simulated XRD spectra to the experimental data using the artificial neural networks (ANNs). The biogenic CaCO3 crystals when using CaCl2 and Ca(NO3)2 are trigonal calcites with space group R3c, while those when using Ca(C2H3O2)2 are hexagonal vaterites with space group P6522. Their elastic properties are derived from the Voigt–Reuss–Hill (VRH) approximation. The bulk, Young's, and shear moduli of biogenic calcite are 77.812, 88.197, and 33.645 GPa, respectively, while those of vaterite are 67.082, 68.644, 25.818 GPa, respectively. Their Poisson’s ratios are ~ 0.3–0.33, suggesting the ductility behavior of our crystals. These elastic values are comparable to those found in limestone cement, but are significantly larger than those of Portland cement. Based on the biocement experiment, the maximum increase in the compressive strength of Portland cement (27.4%) was found when Ca(NO3)2 was used. An increased strength of 26.1% was also found when Ca(C2H3O2)2 was used, implying the transformation of less-durable vaterite to higher-durable calcite. CaCO3 produced by strain WH has a potential to strengthen Portland cement-based materials.
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Affiliation(s)
- Jindarat Ekprasert
- Department of Microbiology, Faculty of Science, Khon Kaen University, 123 Mitraparp Road, Muang, Khon Kaen, 40002, Thailand.
| | - Ittipon Fongkaew
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Poemwai Chainakun
- School of Physics, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Rungtiwa Kamngam
- Department of Microbiology, Faculty of Science, Khon Kaen University, 123 Mitraparp Road, Muang, Khon Kaen, 40002, Thailand
| | - Wachiraya Boonsuan
- Department of Microbiology, Faculty of Science, Khon Kaen University, 123 Mitraparp Road, Muang, Khon Kaen, 40002, Thailand
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10
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Park S, Cho YJ, Jung DY, Jo KN, Lee EJ, Lee JS. Microbial Diversity in Moonmilk of Baeg-nyong Cave, Korean CZO. Front Microbiol 2020; 11:613. [PMID: 32390967 PMCID: PMC7190796 DOI: 10.3389/fmicb.2020.00613] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
The Baeg-nyong cave is a limestone cave which has been nominated as the first critical zone observatory (CZO) in South Korea. Moonmilk is a well-known speleothem composed of various carbonate minerals. To characterize moonmilk from the Baeg-nyong cave, we performed mineralogical analyses and applied high-throughput 16S rRNA gene sequencing to analyze the microbial communities, including bacteria and fungi, of dry and wet moonmilk samples. The results showed that the dry and wet moonmilk samples had different and atypical crystal structures, although they were predominantly composed of CaCO3. Furthermore, metagenomic data revealed that the dry and wet moonmilk samples collected from an oligotrophic environment had completely different bacterial communities when compared to the outside soil, and there was a difference in bacterial communities even between dry and wet moonmilk specimens. Fungal communities, however, did not differ significantly between dry and wet moonmilk samples. This study is the first metagenomic analysis of two different types of moonmilk with different physical properties and the first report on the microbial diversity of moonmilk from a cave in the first CZO in South Korea.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
| | - Yong-Joon Cho
- School of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Da-yea Jung
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
- Division of Geology and Geophysics, College of Natural Sciences, Chuncheon, South Korea
| | - Kyung-nam Jo
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
- Division of Geology and Geophysics, College of Natural Sciences, Chuncheon, South Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
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11
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Taha TH, Elnouby MS, Abu-Saied MA, Alamri S. Tested functionalization of alginate-immobilized ureolytic bacteria for improvement of soil biocementation and maximizing water retention. RSC Adv 2020; 10:21350-21359. [PMID: 35518771 PMCID: PMC9054386 DOI: 10.1039/d0ra01734e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 03/16/2020] [Indexed: 11/24/2022] Open
Abstract
The future expected water scarcity in the world invites the scientists to figure out sustainable solutions for agriculture needs. One of suggested solutions could be the improvement of soil stability and increasing its water retention ability. The current proposal is concerning by the improvement of soil stability through biocementation process. While, water retention ability was enhanced through the amendment of tested soils with alginate hydrogel. An ureolytic bacterial isolate showed a detectable ability to dissociate urea and act as a nucleation site for calcium carbonate precipitation. The bacterium was identified as Bacillus sp. after comparing with other strains in GenBank. The mechanical properties of three tested soil types (sand, calcareous, and clay) were improved after the biocementation by calcium carbonate from 119.8, 45.9, and 5 (N) to 187.5, 423.9, and 337.2, respectively. The Energy-dispersive X-ray spectroscopy (EDX) analysis confirmed the appearance of carbon element in samples containing bacterial-immobilized beads and free bacterial cells indicating calcium carbonate formation. The water uptake measurements investigated the ability of alginate beads to retain water with a percentage of 55%. The overall results prove the capability of Bacillus sp. strain combined with alginate hydrogel to improve the soil stability and water retention ability. An ureolytic bacteria that forming calcite and enhance soil stability was isolated. Water retention of soils was increased by addition of hydrogel polymer.![]()
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Affiliation(s)
- Tarek H. Taha
- Environmental Biotechnology Department
- Genetic Engineering and Biotechnology Research Institute (GEBRI)
- City of Scientific Research and Technological Applications (SRTA-City)
- New Borg El-Arab City
- Egypt
| | - Mohamed S. Elnouby
- Composite and Nanostructured Materials Research Department
- Advanced Technology and New Materials Research Institute
- City of Scientific Research and Technological Applications (SRTA-City)
- New Borg El-Arab City
- Egypt
| | - M. A. Abu-Saied
- Polymer Materials Research Department
- Advanced Technology and New Materials Research Institute
- City of Scientific Research and Technological Applications (SRTA-City)
- New Borg El-Arab City
- Egypt
| | - Saad Alamri
- Department of Biology
- College of Science
- King Khalid University
- Abha
- Saudi Arabia
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Tepe M, Arslan Ş, Koralay T, Mercan Doğan N. Precipitation and characterization of CaCO3 of Bacillus amyloliquefaciens U17 strain producing urease and carbonic anhydrase. ACTA ACUST UNITED AC 2019; 43:198-208. [PMID: 31320818 PMCID: PMC6620036 DOI: 10.3906/biy-1901-56] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In the present study, the properties of calcium carbonate mineralization and urease and carbonic anhydrase activities of Bacillus amyloliquefaciens U17 isolated from calcareous soil of Denizli (Turkey) were analyzed. CaCO3 was produced in all growth phases. Strain U17 showed 0.615 ± 0.092 µmol/min/mg urease enzyme activity in calcium mineralization medium and 1.315 ± 0.021 µmol/min/mg urease enzyme activity in Luria-Bertani medium supplemented with urea, whereas it showed 36.03 ± 5.48 nmol/min/mg carbonic anhydrase enzyme activity in CaCO3 precipitation medium and 28.82 ± 3.31 nmol/min/mg carbonic anhydrase enzyme activity in Luria-Bertani medium supplemented with urea. The urease B protein expression level of strain U17 was detected by western blotting for the first time. The produced CaCO3 crystals were analyzed by X-ray diffraction, X-ray fluorescence, confocal RAMAN spectrophotometer, scanning electron microscopy, and electron probe microanalyzer for the evaluation of their morphological and elemental properties. Rhombohedral vaterite and layered calcite crystals were clearly detected and verified by mineralogical analyses. All these results showed that strain U17 can be used in many engineering and geological applications due to its CaCO3 precipitation ability.
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Affiliation(s)
- Merve Tepe
- Department of Biology, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Şevki Arslan
- Department of Biology, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
| | - Tamer Koralay
- Department of Geology, Faculty of Engineering, Pamukkale University, Denizli, Turkey
| | - Nazime Mercan Doğan
- Department of Biology, Faculty of Science and Arts, Pamukkale University, Denizli, Turkey
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Abdel-Aleem H, Dishisha T, Saafan A, AbouKhadra AA, Gaber Y. Biocementation of soil by calcite/aragonite precipitation usingPseudomonas azotoformansandCitrobacter freundiiderived enzymes. RSC Adv 2019; 9:17601-17611. [PMID: 35520555 PMCID: PMC9064560 DOI: 10.1039/c9ra02247c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 05/28/2019] [Indexed: 11/21/2022] Open
Abstract
Microbial geotechnology is the use of microorganisms and/or their derivatives to alter engineering properties of soil for improving its stability, strength and stiffness.
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Affiliation(s)
- Heba Abdel-Aleem
- Department of Microbiology and Immunology
- Faculty of Pharmacy
- Beni-Suef University
- Beni-Suef
- Egypt
| | - Tarek Dishisha
- Department of Microbiology and Immunology
- Faculty of Pharmacy
- Beni-Suef University
- Beni-Suef
- Egypt
| | - Amal Saafan
- Department of Pharmaceutical Microbiology
- Faculty of Pharmacy
- Menoufia University
- Shebeen El-kom
- Egypt
| | | | - Yasser Gaber
- Department of Microbiology and Immunology
- Faculty of Pharmacy
- Beni-Suef University
- Beni-Suef
- Egypt
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14
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Song W, Ogunbanwo F, Steinsbø M, Fernø MA, Kovscek AR. Mechanisms of multiphase reactive flow using biogenically calcite-functionalized micromodels. LAB ON A CHIP 2018; 18:3881-3891. [PMID: 30462124 DOI: 10.1039/c8lc00793d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Dissolution of carbonate minerals in porous media is important to many instances of subsurface flow, including geological carbon dioxide (CO2) sequestration, karst formation, and crude-oil reservoir stimulation and acidizing. Of particular interest, geological CO2 storage in deep carbonate reservoirs presents a significant long-term opportunity to mitigate atmospheric carbon emissions. The reactivity of carbonate reservoirs, however, may negatively impact storage formation integrity and hence jeopardize sequestered CO2 storage security. In this work, we develop a novel biogenically calcite-functionalized microvisual device to study the fundamental pore-scale reactive transport dynamics in carbonate formations. Importantly, we discover a new microscale mechanism that dictates the overall behavior of the reactive transport phenomenon, where the reaction product, CO2, due to carbonate rock dissolution forms a separate, protective phase that engulfs the carbonate rock grain and reduces further dissolution. The presence of the separate, protective CO2 phase determines overall dissolution patterns in the storage reservoir and leads to formation of preferential leakage paths. We scale these results using nondimensional numbers to demonstrate their influence on industrial CO2 storage security, safety, and capacity.
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Affiliation(s)
- Wen Song
- Department of Energy Resources Engineering, Stanford University, Stanford, CA 94305, USA.
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15
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Zhang W, Ju Y, Zong Y, Qi H, Zhao K. In Situ Real-Time Study on Dynamics of Microbially Induced Calcium Carbonate Precipitation at a Single-Cell Level. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9266-9276. [PMID: 30036465 DOI: 10.1021/acs.est.8b02660] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ureolytic microbially induced calcium carbonate precipitation (MICP) is a promising green technique for addressing a variety of environmental and architectural concerns. However, the dynamics of MICP especially at the microscopic level remains relatively unexplored. In this work, by applying a bacterial tracking technique, the growth dynamics of micrometer-sized calcium carbonate precipitates induced by Sporosarcina pasteurii were studied at a single-cell resolution. The growth of micrometer-scale precipitates and the occurrence and dissolution of many unstable submicrometer calcium carbonate particles were observed in the precipitation process. More interestingly, we observed that micrometer-sized precipitated crystals did not grow on negatively charged cell surfaces nor on other tested polystyrene microspheres with different negatively charged surface modifications, indicating that a negatively charged surface was not a sufficient property for nucleating the growth of precipitates in the MICP process under the conditions used in this study. Our observations imply that the frequently cited model of bacterial cell surfaces as nucleation sites for precipitates during MICP is oversimplified. In addition, additional growth of calcium carbonates was observed on old precipitates collected from previous runs. The presence of bacterial cells was also shown to affect both morphologies and crystalline structures of precipitates, and both calcite and vaterite precipitates were found when cells physically coexisted with precipitates. This study provides new insights into the regulation of MICP through dynamic control of precipitation.
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Affiliation(s)
- Wenchao Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Ying Ju
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Yiwu Zong
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Hao Qi
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
| | - Kun Zhao
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology , Tianjin University , Tianjin 300072 , China
- Collaborative Innovation Centre of Chemical Science and Engineering , Tianjin University , Tianjin 300072 , China
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16
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Aoki M, Noma T, Yonemitsu H, Araki N, Yamaguchi T, Hayashi K. A Low-Tech Bioreactor System for the Enrichment and Production of Ureolytic Microbes. Pol J Microbiol 2018; 67:59-65. [PMID: 30015425 DOI: 10.5604/01.3001.0011.6144] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2017] [Indexed: 11/13/2022] Open
Abstract
Ureolysis-driven microbially induced carbonate precipitation (MICP) has recently received attention for its potential biotechnological applications. However, information on the enrichment and production of ureolytic microbes by using bioreactor systems is limited. Here, we report a low-tech down-flow hanging sponge (DHS) bioreactor system for the enrichment and production of ureolytic microbes. Using this bioreactor system and a yeast extract-based medium containing 0.17 M urea, ureolytic microbes with high potential urease activity (> 10 μmol urea hydrolyzed per min per ml of enrichment culture) were repeatedly enriched under non-sterile conditions. In addition, the ureolytic enrichment obtained in this study showed in vitro calcium carbonate precipitation. Fluorescence in situ hybridization analysis showed the existence of bacteria of the phylum Firmicutes in the bioreactor system. Our data demonstrate that this DHS bioreactor system is a useful system for the enrichment and production of ureolytic microbes for MICP applications.
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Affiliation(s)
- Masataka Aoki
- Department of Civil Engineering, National Institute of Technology, Wakayama College,Gobo, Wakayama,Japan
| | - Takuya Noma
- Department of Civil Engineering, National Institute of Technology, Wakayama College,Gobo, Wakayama,Japan
| | - Hiroshi Yonemitsu
- Department of Applied Chemistry and Biochemistry, National Institute of Technology, Wakayama College,Gobo, Wakayama,Japan
| | - Nobuo Araki
- Department of Civil Engineering, National Institute of Technology, Nagaoka College,Nagaoka, Niigata,Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology,Nagaoka, Niigata,Japan
| | - Kazuyuki Hayashi
- Department of Civil Engineering, National Institute of Technology, Wakayama College,Gobo, Wakayama,Japan
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17
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Dhami NK, Mukherjee A, Watkin ELJ. Microbial Diversity and Mineralogical-Mechanical Properties of Calcitic Cave Speleothems in Natural and in Vitro Biomineralization Conditions. Front Microbiol 2018; 9:40. [PMID: 29472898 PMCID: PMC5810276 DOI: 10.3389/fmicb.2018.00040] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 01/09/2018] [Indexed: 11/17/2022] Open
Abstract
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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Affiliation(s)
- Navdeep K. Dhami
- Biologically Activated Materials Laboratory, Department of Civil Engineering, Curtin University, Perth, WA, Australia
| | - Abhijit Mukherjee
- Biologically Activated Materials Laboratory, Department of Civil Engineering, Curtin University, Perth, WA, Australia
| | - Elizabeth L. J. Watkin
- School of Biomedical Sciences, Curtin Health Innovation Research Institute-Biosciences, Curtin University, Perth, WA, Australia
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Dade-Robertson M, Keren-Paz A, Zhang M, Kolodkin-Gal I. Architects of nature: growing buildings with bacterial biofilms. Microb Biotechnol 2017; 10:1157-1163. [PMID: 28815998 PMCID: PMC5609236 DOI: 10.1111/1751-7915.12833] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/18/2017] [Accepted: 07/18/2017] [Indexed: 12/22/2022] Open
Abstract
In his text 'On Architecture', Vitruvius suggested that architecture is an imitation of nature. Here we discuss what happens when we begin using nature in architecture. We describe recent developments in the study of biofilm structure, and propose combining modern architecture and synthetic microbiology to develop sustainable construction approaches. Recently, Kolodkin-Gal laboratory and others revealed a role for precipitation of calcium carbonate in the maturation and assembly of bacterial communities with complex structures. Importantly, they demonstrated that different secreted organic materials shape the calcium carbonate crystals formed by the bacterial cells. This provides a proof-of-concept for a potential use of bacteria in designing rigid construction materials and altering crystal morphology and function. In this study, we discuss how these recent discoveries may change the current strategies of architecture and construction. We believe that biofilm communities enhanced by synthetic circuits may be used to construct buildings and to sequester carbon dioxide in the process.
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Affiliation(s)
- Martyn Dade-Robertson
- Faculty of Humanities and Social Sciences, School of Architecture, Planning and Landscape, Newcastle University, Newcastle upon Tyne, UK
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Meng Zhang
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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19
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Song X, Mei J, Zhang X, Wang L, Singh G, Xing MMQ, Qiu X. Flexible and highly interconnected, multi-scale patterned chitosan porous membrane produced in situ from mussel shell to accelerate wound healing. Biomater Sci 2017; 5:1101-1111. [DOI: 10.1039/c7bm00095b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mussel shell-derived dressing for full-thickness wound healing. The mussel shell-derived, in situ formed flexible membrane dressing promotes wound healing processes.
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Affiliation(s)
- Xiaoping Song
- Department of Anatomy
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering
- Southern Medical University
- Guangdong
- China
| | - Jie Mei
- Department of Anatomy
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering
- Southern Medical University
- Guangdong
- China
| | - Xingying Zhang
- Department of Mechanical and Manitoba Institute of Child Health
- University of Manitoba
- Winnipeg
- Canada
| | - Leyu Wang
- Department of Anatomy
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering
- Southern Medical University
- Guangdong
- China
| | - Gurankit Singh
- Department of Mechanical and Manitoba Institute of Child Health
- University of Manitoba
- Winnipeg
- Canada
| | - Malcolm M. Q. Xing
- Department of Mechanical and Manitoba Institute of Child Health
- University of Manitoba
- Winnipeg
- Canada
| | - Xiaozhong Qiu
- Department of Anatomy
- Guangdong Provincial Key Laboratory of Construction and Detection in Tissue Engineering
- Southern Medical University
- Guangdong
- China
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20
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Heidari Nonakaran S, Pazhouhandeh M, Keyvani A, Abdollahipour FZ, Shirzad A. Isolation and identification of Pseudomonas azotoformans for induced calcite precipitation. World J Microbiol Biotechnol 2015; 31:1993-2001. [DOI: 10.1007/s11274-015-1948-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 09/14/2015] [Indexed: 11/24/2022]
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