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Martinez-Moreno MF, Povedano-Priego C, Mumford AD, Morales-Hidalgo M, Mijnendonckx K, Jroundi F, Ojeda JJ, Merroun ML. Microbial responses to elevated temperature: Evaluating bentonite mineralogy and copper canister corrosion within the long-term stability of deep geological repositories of nuclear waste. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170149. [PMID: 38242445 DOI: 10.1016/j.scitotenv.2024.170149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/21/2024]
Abstract
Deep Geological Repositories (DGRs) consist of radioactive waste contained in corrosion-resistant canisters, surrounded by compacted bentonite clay, and buried few hundred meters in a stable geological formation. The effects of bentonite microbial communities on the long-term stability of the repository should be assessed. This study explores the impact of harsh conditions (60 °C, highly-compacted bentonite, low water activity), and acetate:lactate:sulfate addition, on the evolution of microbial communities, and their effect on the bentonite mineralogy, and corrosion of copper material under anoxic conditions. No bentonite illitization was observed in the treatments, confirming its mineralogical stability as an effective barrier for future DGR. Anoxic incubation at 60 °C reduced the microbial diversity, with Pseudomonas as the dominant genus. Culture-dependent methods showed survival and viability at 60 °C of moderate-thermophilic aerobic bacterial isolates (e.g., Aeribacillus). Despite the low presence of sulfate-reducing bacteria in the bentonite blocks, we proved their survival at 30 °C but not at 60 °C. Copper disk's surface remained visually unaltered. However, in the acetate:lactate:sulfate-treated samples, sulfide/sulfate signals were detected, along with microbial-related compounds. These findings offer new insights into the impact of high temperatures (60 °C) on the biogeochemical processes at the compacted bentonite/Cu canister interface post-repository closure.
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Affiliation(s)
| | | | - Adam D Mumford
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Mar Morales-Hidalgo
- Faculty of Sciences, Department of Microbiology, University of Granada, Granada, Spain
| | | | - Fadwa Jroundi
- Faculty of Sciences, Department of Microbiology, University of Granada, Granada, Spain
| | - Jesus J Ojeda
- Department of Chemical Engineering, Faculty of Science and Engineering, Swansea University, Swansea, United Kingdom
| | - Mohamed L Merroun
- Faculty of Sciences, Department of Microbiology, University of Granada, Granada, Spain
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2
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Lücking G, Albrecht K, Märtlbauer E, Schauer K. Draft genome sequences of two thermophilic, spore-forming Aeribacillus pallidus strains isolated from dairy products. Microbiol Resour Announc 2024; 13:e0089623. [PMID: 38088573 DOI: 10.1128/mra.00896-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The presence of thermophilic spore-forming bacteria is challenging in industrial food processing. The presented genome sequences of Aeribacillus pallidus, isolated from raw milk and cocoa powder, provide insights into how to prevent damage to minimally processed foods and products with extended shelf life, such as milk products.
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Affiliation(s)
- Genia Lücking
- Chair of Microbial Ecology, TUM School of Life Sciences, Technical University of Munich , Freising, Germany
| | - Klement Albrecht
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians University of Munich , Oberschleiβheim, Germany
| | - Erwin Märtlbauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians University of Munich , Oberschleiβheim, Germany
| | - Kristina Schauer
- Department of Veterinary Sciences, Faculty of Veterinary Medicine, Ludwig-Maximilians University of Munich , Oberschleiβheim, Germany
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin , Dublin, Ireland
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3
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Nguyen TP, Koyama M, Nakasaki K. Effects of oxygen supply rate on organic matter decomposition and microbial communities during composting in a controlled lab-scale composting system. WASTE MANAGEMENT (NEW YORK, N.Y.) 2022; 153:275-282. [PMID: 36150273 DOI: 10.1016/j.wasman.2022.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/02/2022] [Accepted: 09/06/2022] [Indexed: 06/16/2023]
Abstract
The study aimed to elucidate the effect of oxygen supply rate (OSR) on the composting of model organic waste independently from other factors by using a controlled laboratory-scale reactor system. Four OSRs, 96.2, 24.2, 13.7, and 3.45 mL-O2/min/kg-WS (wet solid), were tested. The delay of organic matter degradation was observed temporarily in the early stage of composting with 13.7 mL-O2/min/kg-WS and severe oxygen deficiency was observed in lower OSR, indicating that the critical OSR existed around this value. Composting with 3.45 mL-O2/min/kg-WS resulted in constantly low CO2 evolution rate and remarkably low degree of organic matter degradation. Under deficient oxygen, all enzymes measured, such as phosphatases, esterases, lipases, proteases, and sugar degrading enzymes, showed lower activities. High-throughput sequencing revealed Caldibacillus and Ureibacillus became dominant in the later stages of the oxygen deficiency composting, while Geobacillus was the most dominant microorganism throughout composting with OSR higher than 13.7 mL-O2/min/kg-WS.
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Affiliation(s)
- Thien-Phuc Nguyen
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Mitsuhiko Koyama
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Kiyohiko Nakasaki
- School of Environment and Society, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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Bacterial communities in home-made Doushen with and without chili pepper. Food Res Int 2022; 156:111321. [PMID: 35651075 DOI: 10.1016/j.foodres.2022.111321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/24/2022]
Abstract
Doushen is a traditional Chinese fermented soybean product prepared with sterilizated soybeans under open conditions. However, little is known on the bacterial community and their influence on the flavor of Doushen. In the present study, Doushen samples with and without chili pepper were collected to reveal the bacterial community and assess a correlation between bacterial community and VFCs in the two kinds of Doushen samples. We identified four phyla and 97 bacterial genera in the two kinds of Doushen samples. In addition, a total of 17 significantly different OTUs were detected by LEfSe (Line Discriminant Analysis (LDA) Effect Size). Results of Principal coordinates analysis (PCoA), unweighted pair-group method (UPGMA) and functional and phenotypes prediction showed that bacterial communities in the two kinds of Doushen were significantly different. Spearman correlation analysis showed that all the dominant genera, except Clostridium Sensu stricto 1, were significantly correlated with the characteristic VFCs. This study provides a theoretical basis for improving the flavour quality of traditional homemade Doushen.
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Effect of hydrothermal treatment on organic matter degradation, phytotoxicity, and microbial communities in model food waste composting. J Biosci Bioeng 2022; 133:382-389. [PMID: 35115228 DOI: 10.1016/j.jbiosc.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 01/17/2023]
Abstract
Hydrothermal treatment (HTT) as a pretreatment method for compost raw material has multiple benefits such as enhanced solubility of organic material, improved bioaugmentation, and reduced biohazard by killing harmful microorganisms. In this study, we pretreated food waste via HTT at 180 °C for 30 min to investigate its effect on food waste composting. HTT generated 8.98 mg/g-dry solid (g-ds) of 5-hydroxymethylfurfural and 4.32 mg/g-ds furfural. These furan compounds were completely decomposed in the early stage of composting, subsequently the organic matter in the food waste started to be degraded. The HTT-pretreated experiment demonstrated less organic matter degradation during composting as well as lower compost phytotoxicity compared to the non-HTT-pretreated experiment, where the conversion of carbon was 25.2% and the germination index value was 55%. HTT probably denatured part of the organic matter and making it more difficult to decompose, thereby preventing the rapid release of high concentrations of phytotoxic compounds such as organic acids and ammonium ions during composting. High-throughput microbial community analysis revealed that only Firmicutes appeared in the HTT-pretreated experiment, however, other bacterial groups also appeared in the non-HTT-pretreated experiment. This was possibly influenced by furan compounds and the changes of easily degradable organic matter to hardly degradable. Bacillus and Lysinibacillus were dominant in both composting experiments during vigorous organic matter degradation, suggesting that these bacterial groups were the main contributors to food waste composting. This study suggests that HTT is advantageous for the pretreatment of easily degradable food waste, as compost with less phytotoxicity was produced.
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Loakasikarn T, Kubota Y, Koyama M, Nakasaki K. Effect of seeding materials on organic matter degradation and microbial community succession during model organic waste composting. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Effect of Carbon Sources in Carotenoid Production from Haloarcula sp. M1, Halolamina sp. M3 and Halorubrum sp. M5, Halophilic Archaea Isolated from Sonora Saltern, Mexico. Microorganisms 2021; 9:microorganisms9051096. [PMID: 34065163 PMCID: PMC8160830 DOI: 10.3390/microorganisms9051096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 04/29/2021] [Accepted: 05/11/2021] [Indexed: 12/25/2022] Open
Abstract
The isolation and molecular and chemo-taxonomic identification of seventeen halophilic archaea from the Santa Bárbara saltern, Sonora, México, were performed. Eight strains were selected based on pigmentation. Molecular identification revealed that the strains belonged to the Haloarcula, Halolamina and Halorubrum genera. Neutral lipids (quinones) were identified in all strains. Glycolipid S-DGD was found only in Halolamina sp. strain M3; polar phospholipids 2,3-O-phytanyl-sn-glycerol-1-phosphoryl-3-sn-glycerol (PG), 2,3-di-O-phytanyl-sn-glycero-1-phospho-3′-sn-glycerol-1′-methyl phosphate (PGP-Me) and sodium salt 1-(3-sn-phosphatidyl)-rac-glycerol were found in all the strains; and one unidentified glyco-phospholipid in strains M1, M3 and M4. Strains M1, M3 and M5 were selected for further studies based on carotenoid production. The effect of glucose and succinic and glutamic acid on carotenoid production was assessed. In particular, carotenoid production and growth significantly improved in the presence of glucose in strains Haloarcula sp. M1 and Halorubrum sp. M5 but not in Halolamina sp. M3. Glutamic and succinic acid had no effect on carotenoid production, and even was negative for Halorubrum sp. M5. Growth was increased by glutamic and succinic acid on Haloarcula sp. M1 but not in the other strains. This work describes for first time the presence of halophilic archaea in the Santa Bárbara saltern and highlights the differences in the effect of carbon sources on the growth and carotenoid production of haloarchaea.
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Papale M, Romano I, Finore I, Lo Giudice A, Piccolo A, Cangemi S, Di Meo V, Nicolaus B, Poli A. Prokaryotic Diversity of the Composting Thermophilic Phase: The Case of Ground Coffee Compost. Microorganisms 2021; 9:microorganisms9020218. [PMID: 33494462 PMCID: PMC7911569 DOI: 10.3390/microorganisms9020218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 01/22/2023] Open
Abstract
Waste biomass coming from a local coffee company, which supplied burnt ground coffee after an incorrect roasting process, was employed as a starting material in the composting plant of the Experimental Station of the University of Naples Federico II at Castel Volturno (CE). The direct molecular characterization of compost using 13C-NMR spectra, which was acquired through cross-polarization magic-angle spinning, showed a hydrophobicity index of 2.7% and an alkyl/hydroxyalkyl index of 0.7%. Compost samples that were collected during the early "active thermophilic phase" (when the composting temperature was 63 °C) were analyzed for the prokaryotic community composition and activities. Two complementary approaches, i.e., genomic and predictive metabolic analysis of the 16S rRNA V3-V4 amplicon and culture-dependent analysis, were combined to identify the main microbial factors that characterized the composting process. The whole microbial community was dominated by Firmicutes. The predictive analysis of the metabolic functionality of the community highlighted the potential degradation of peptidoglycan and the ability of metal chelation, with both functions being extremely useful for the revitalization and fertilization of agricultural soils. Finally, three biotechnologically relevant Firmicutes members, i.e., Geobacillus thermodenitrificans subsp. calidus, Aeribacillus pallidus, and Ureibacillus terrenus (strains CAF1, CAF2, and CAF5, respectively) were isolated from the "active thermophilic phase" of the coffee composting. All strains were thermophiles growing at the optimal temperature of 60 °C. Our findings contribute to the current knowledge on thermophilic composting microbiology and valorize burnt ground coffee as waste material with biotechnological potentialities.
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Affiliation(s)
- Maria Papale
- Institute of Polar Sciences, National Research Council of Italy, Spianata San Raineri 86, 98122 Messina, Sicilia, Italy; (M.P.); (A.L.G.)
| | - Ida Romano
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
| | - Ilaria Finore
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
| | - Angelina Lo Giudice
- Institute of Polar Sciences, National Research Council of Italy, Spianata San Raineri 86, 98122 Messina, Sicilia, Italy; (M.P.); (A.L.G.)
| | - Alessandro Piccolo
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agro-alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055 Portici, Naples, Italy; (A.P.); (S.C.)
| | - Silvana Cangemi
- Centro Interdipartimentale di Ricerca sulla Risonanza Magnetica Nucleare per l’Ambiente, l’Agro-alimentare ed i Nuovi Materiali (CERMANU), Università di Napoli Federico II, Via Università 100, 80055 Portici, Naples, Italy; (A.P.); (S.C.)
| | - Vincenzo Di Meo
- Dipartimento di Agraria, Università Federico II, Via Università 100, 80055 Portici, Naples, Italy;
| | - Barbara Nicolaus
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
| | - Annarita Poli
- Institute of Biomolecular Chemistry, National Research Council of Italy, Via Campi Flegrei 34, 80078 Pozzuoli, Naples, Italy; (I.R.); (I.F.); (B.N.)
- Correspondence: ; Tel.: +39-081-867-5311
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9
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Bin Hudari MS, Vogt C, Richnow HH. Effect of Temperature on Acetate Mineralization Kinetics and Microbial Community Composition in a Hydrocarbon-Affected Microbial Community During a Shift From Oxic to Sulfidogenic Conditions. Front Microbiol 2021; 11:606565. [PMID: 33391229 PMCID: PMC7773710 DOI: 10.3389/fmicb.2020.606565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/23/2020] [Indexed: 01/04/2023] Open
Abstract
Aquifer thermal energy storage (ATES) allows for the seasonal storage and extraction of heat in the subsurface thus reducing reliance on fossil fuels and supporting decarbonization of the heating and cooling sector. However, the impacts of higher temperatures toward biodiversity and ecosystem services in the subsurface environment remain unclear. Here, we conducted a laboratory microcosm study comprising a hydrocarbon-degrading microbial community from a sulfidic hydrocarbon-contaminated aquifer spiked with 13C-labeled acetate and incubated at temperatures between 12 and 80°C to evaluate (i) the extent and rates of acetate mineralization and (ii) the resultant temperature-induced shifts in the microbial community structure. We observed biphasic mineralization curves at 12, 25, 38, and 45°C, arising from immediate and fast aerobic mineralization due to an initial oxygen exposure, followed by slower mineralization at sulfidogenic conditions. At 60°C and several replicates at 45°C, acetate was only aerobically mineralized. At 80°C, no mineralization was observed within 178 days. Rates of acetate mineralization coupled to sulfate reduction at 25 and 38°C were six times faster than at 12°C. Distinct microbial communities developed in oxic and strictly anoxic phases of mineralization as well as at different temperatures. Members of the Alphaproteobacteria were dominant in the oxic mineralization phase at 12–38°C, succeeded by a more diverse community in the anoxic phase composed of Deltaproteobacteria, Clostridia, Spirochaetia, Gammaproteobacteria and Anaerolinea, with varying abundances dependent on the temperature. In the oxic phases at 45 and 60°C, phylotypes affiliated to spore-forming Bacilli developed. In conclusion, temperatures up to 38°C allowed aerobic and anaerobic acetate mineralization albeit at varying rates, while mineralization occurred mainly aerobically between 45 and 60°C; thermophilic sulfate reducers being active at temperatures > 45°C were not detected. Hence, temperature may affect dissolved organic carbon mineralization rates in ATES while the variability in the microbial community composition during the transition from micro-oxic to sulfidogenic conditions highlights the crucial role of electron acceptor availability when combining ATES with bioremediation.
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Affiliation(s)
| | - Carsten Vogt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Hans Hermann Richnow
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research, Leipzig, Germany
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Li J, Zhang B, Liu G, Liu Y, Yang H, Yang R, Huang Y, Li S, Chen T, Zhang W, Zhang G. Radiobacillus deserti gen. nov., sp. nov., a UV-resistant bacterium isolated from desert soil. Int J Syst Evol Microbiol 2020; 70:6338-6347. [PMID: 33118923 DOI: 10.1099/ijsem.0.004536] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, rod-shaped, non-motile, endospore-forming and UV-resistant bacterial strain, designated strain TKL69T, was isolated from sandy soil sampled in the Taklimakan Desert. The strain grew at 20-50 °C, pH 6-9 and with 0-12 % (w/v) NaCl. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. The only respiratory quinone was MK-7. The cell-wall peptidoglycan was meso-diaminopimelic acid. Diphosphatidyl glycerol, two unidentified aminophospholipids and one unidentified phospholipid were identified as the major polar lipids. Genomic DNA analysis revealed a G+C content of 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain TKL69T has the highest similarity to Salinibacillus xinjiangensis CGMCC 1.12331T (96.9 %) but belongs to an independent taxon separated from other genera of the family Bacillaceae. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain TKL69T represents a novel species of a new genus, for which the name Radiobacillus gen. nov., sp. nov. is proposed, with the type strain being Radiobacillus deserti TKL69T (=JCM 33497T=CICC 24779T).
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Affiliation(s)
- Juan Li
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Binglin Zhang
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Yang Liu
- University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Hui Yang
- Key Laboratory of Microbial Resources Exploition and Application, Gansu Province, Lanzhou 730000, PR China
| | - Ruiqi Yang
- School of Geography and Environmental Engineering, Lanzhou City University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Yixuan Huang
- School of Environmental and Municipal, Lanzhou Jiaotong University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Shiweng Li
- School of Environmental and Municipal, Lanzhou Jiaotong University, Lanzhou 730070, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Sciences, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
| | - Wei Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China.,Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, PR China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Gansu Province, Lanzhou 730000, PR China
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Talamantes-Becerra B, Carling J, Kilian A, Georges A. Discovery of thermophilic Bacillales using reduced-representation genotyping for identification. BMC Microbiol 2020; 20:114. [PMID: 32404118 PMCID: PMC7222431 DOI: 10.1186/s12866-020-01800-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 04/23/2020] [Indexed: 12/25/2022] Open
Abstract
Background This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across the bacterial genomes. Isolates were obtained from compost, hot water systems, and artesian bores of the Great Artesian Basin. Genomic DNA was double-digested with two combinations of restriction enzymes followed by PCR amplification, using a commercial provider of DArTseq™, Diversity Arrays Technology Pty Ltd. (Canberra, Australia). The resulting fragments which formed a reduced-representation of approximately 2.3% of the genome were sequenced. The sequence tags obtained were aligned against all available RefSeq bacterial genome assemblies by BLASTn to identify the nearest reference genome. Results Based on the preliminary identifications, a total of 99 bacterial isolates were identified to species level, from which 8 isolates were selected for whole-genome sequencing to assess the identification results. Novel species and strains were discovered within this set of isolates. The preliminary identifications obtained by reduced-representation genotyping, as well as identifications obtained by BLASTn alignment of the 16S rRNA gene sequence, were compared with those derived from the whole-genome sequence data, using the same RefSeq sequence database for the three methods. Identifications obtained with reduced-representation sequencing agreed with the identifications provided by whole-genome sequencing in 100% of cases. The identifications produced by BLASTn alignment of 16S rRNA gene sequence to the same database differed from those provided by whole-genome sequencing in 37.5% of cases, and produced ambiguous identifications in 50% of cases. Conclusions Previously, this method has been successfully demonstrated for use in bacterial identification for medical microbiology. This study demonstrates the first successful use of DArTseq™ for preliminary identification of thermophilic bacterial isolates, providing results in complete agreement with those obtained from whole-genome sequencing of the same isolates. The growing database of bacterial genome sequences provides an excellent resource for alignment of reduced-representation sequence data for identification purposes, and as the available sequenced genomes continue to grow, the technique will become more effective.
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Affiliation(s)
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, Canberra, ACT, 2617, Australia
| | - Arthur Georges
- Institute of Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
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Joulak I, Finore I, Nicolaus B, Leone L, Moriello AS, Attia H, Poli A, Azabou S. Evaluation of the production of exopolysaccharides by newly isolated Halomonas strains from Tunisian hypersaline environments. Int J Biol Macromol 2019; 138:658-666. [DOI: 10.1016/j.ijbiomac.2019.07.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Revised: 07/17/2019] [Accepted: 07/21/2019] [Indexed: 01/01/2023]
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13
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Multidisciplinary involvement and potential of thermophiles. Folia Microbiol (Praha) 2018; 64:389-406. [PMID: 30386965 DOI: 10.1007/s12223-018-0662-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/25/2018] [Indexed: 12/15/2022]
Abstract
The full biotechnological exploitation of thermostable enzymes in industrial processes is necessary for their commercial interest and industrious value. The heat-tolerant and heat-resistant enzymes are a key for efficient and cost-effective translation of substrates into useful products for commercial applications. The thermophilic, hyperthermophilic, and microorganisms adapted to extreme temperatures (i.e., low-temperature lovers or psychrophiles) are a rich source of thermostable enzymes with broad-ranging thermal properties, which have structural and functional stability to underpin a variety of technologies. These enzymes are under scrutiny for their great biotechnological potential. Temperature is one of the most critical parameters that shape microorganisms and their biomolecules for stability under harsh environmental conditions. This review describes in detail the sources of thermophiles and thermostable enzymes from prokaryotes and eukaryotes (microbial cell factories). Furthermore, the review critically examines perspectives to improve modern biocatalysts, its production and performance aiming to increase their value for biotechnology through higher standards, specificity, resistance, lowing costs, etc. These thermostable and thermally adapted extremophilic enzymes have been used in a wide range of industries that span all six enzyme classes. Thus, in particular, target of this review paper is to show the possibility of both high-value-low-volume (e.g., fine-chemical synthesis) and low-value-high-volume by-products (e.g., fuels) by minimizing changes to current industrial processes.
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