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Miralles-Robledillo JM, Martínez-Espinosa RM, Pire C. Transcriptomic profiling of haloarchaeal denitrification through RNA-Seq analysis. Appl Environ Microbiol 2024; 90:e0057124. [PMID: 38814058 DOI: 10.1128/aem.00571-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Denitrification, a crucial biochemical pathway prevalent among haloarchaea in hypersaline ecosystems, has garnered considerable attention in recent years due to its ecological implications. Nevertheless, the underlying molecular mechanisms and genetic regulation governing this respiration/detoxification process in haloarchaea remain largely unexplored. In this study, RNA-sequencing was used to compare the transcriptomes of the haloarchaeon Haloferax mediterranei under oxic and denitrifying conditions, shedding light on the intricate metabolic alterations occurring within the cell, such as the accurate control of the metal homeostasis. Furthermore, the investigation identifies several genes encoding transcriptional regulators and potential accessory proteins with putative roles in denitrification. Among these are bacterioopsin-like transcriptional activators, proteins harboring a domain of unknown function (DUF2249), and cyanoglobin. In addition, the study delves into the genetic regulation of denitrification, finding a regulatory motif within promoter regions that activates numerous denitrification-related genes. This research serves as a starting point for future molecular biology studies in haloarchaea, offering a promising avenue to unravel the intricate mechanisms governing haloarchaeal denitrification, a pathway of paramount ecological importance.IMPORTANCEDenitrification, a fundamental process within the nitrogen cycle, has been subject to extensive investigation due to its close association with anthropogenic activities, and its contribution to the global warming issue, mainly through the release of N2O emissions. Although our comprehension of denitrification and its implications is generally well established, most studies have been conducted in non-extreme environments with mesophilic microorganisms. Consequently, there is a significant knowledge gap concerning extremophilic denitrifiers, particularly those inhabiting hypersaline environments. The significance of this research was to delve into the process of haloarchaeal denitrification, utilizing the complete denitrifier haloarchaeon Haloferax mediterranei as a model organism. This research led to the analysis of the metabolic state of this microorganism under denitrifying conditions and the identification of regulatory signals and genes encoding proteins potentially involved in this pathway, serving as a valuable resource for future molecular studies.
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Affiliation(s)
- Jose María Miralles-Robledillo
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
| | - Carmen Pire
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, Universitat d'Alacant, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
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2
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Arthi R, Parameswari E, Dhevagi P, Janaki P, Parimaladevi R. Microbial alchemists: unveiling the hidden potentials of halophilic organisms for soil restoration. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024:10.1007/s11356-024-33949-9. [PMID: 38877191 DOI: 10.1007/s11356-024-33949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Salinity, resulting from various contaminants, is a major concern to global crop cultivation. Soil salinity results in increased osmotic stress, oxidative stress, specific ion toxicity, nutrient deficiency in plants, groundwater contamination, and negative impacts on biogeochemical cycles. Leaching, the prevailing remediation method, is expensive, energy-intensive, demands more fresh water, and also causes nutrient loss which leads to infertile cropland and eutrophication of water bodies. Moreover, in soils co-contaminated with persistent organic pollutants, heavy metals, and textile dyes, leaching techniques may not be effective. It promotes the adoption of microbial remediation as an effective and eco-friendly method. Common microbes such as Pseudomonas, Trichoderma, and Bacillus often struggle to survive in high-saline conditions due to osmotic stress, ion imbalance, and protein denaturation. Halophiles, capable of withstanding high-saline conditions, exhibit a remarkable ability to utilize a broad spectrum of organic pollutants as carbon sources and restore the polluted environment. Furthermore, halophiles can enhance plant growth under stress conditions and produce vital bio-enzymes. Halophilic microorganisms can contribute to increasing soil microbial diversity, pollutant degradation, stabilizing soil structure, participating in nutrient dynamics, bio-geochemical cycles, enhancing soil fertility, and crop growth. This review provides an in-depth analysis of pollutant degradation, salt-tolerating mechanisms, and plant-soil-microbe interaction and offers a holistic perspective on their potential for soil restoration.
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Affiliation(s)
- Ravichandran Arthi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Periyasamy Dhevagi
- Department of Environmental Science, Tamil Nadu Agricultural University, Coimbatore, India
| | - Ponnusamy Janaki
- Nammazhvar Organic Farming Research Centre, Tamil Nadu Agricultural University, Coimbatore, India
| | - Rathinasamy Parimaladevi
- Department of Bioenergy, Agrl. Engineering College & Research Institute, Tamil Nadu Agricultural University, Coimbatore, India
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Lee J, Um S, Kim EH, Kim SH. Genomic and Metabolomic Analyses of Nocardiopsis maritima YSL2 as the Mycorrhizosphere Bacterium of Suaeda maritima (L.) Dumort. JOURNAL OF NATURAL PRODUCTS 2024; 87:733-742. [PMID: 38573876 DOI: 10.1021/acs.jnatprod.3c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Nine bacteria were isolated from the episphere of Suaeda maritima (L.) Dumort. Among them, the bacterial strain YSL2 displayed the highest antimicrobial activity on agar plates and exhibited significant novelty compared with other bacteria based on 16S rRNA analysis. Consequently, Nocardiopsis maritima YSL2T was subjected to phenotypic characterization and whole-genome sequencing. Phylogenetic analysis revealed its close association with Nocardiopsis aegyptia SNG49T. Furthermore, genomic analysis of strain YSL2T revealed the presence of various gene clusters, indicating its potential for producing antimicrobial secondary metabolites. Upon cultivation on a large scale, maritiamides A and B (1 and 2) were isolated and characterized as cyclic hexapeptides based on nuclear magnetic resonance, ultraviolet, infrared, and mass spectrometric data. The absolute configurations of the amino acid residues in the maritiamides were determined through chiral derivatization, utilizing FDAA and GITC. Maritiamides 1 and 2 exhibited promising antibacterial activities against Staphylococcus epidermidis and weakly inhibited the growth of Escherichia coli and Pseudomonas fluorescens.
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Affiliation(s)
- Jaeyoun Lee
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, South Korea
| | - Soohyun Um
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, South Korea
| | - Eun-Hee Kim
- Ochang Center, Korea Basic Science Institute, 162 Yeongudanji-Ro, Ochang-Eup, Cheongju-Si, Chungcheongbuk-Do 28119, South Korea
| | - Seung Hyun Kim
- College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon 21983, South Korea
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4
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Lee KC, Archer SDJ, Kansour MK, Al-Mailem DM. Bioremediation of oily hypersaline soil via autochthonous bioaugmentation with halophilic bacteria and archaea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 922:171279. [PMID: 38428597 DOI: 10.1016/j.scitotenv.2024.171279] [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: 12/27/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
Kuwaiti hypersaline soil samples were contaminated with 5 % (w/w) weathered Kuwaiti light crude oil and bioaugmented with autochthonous halophilic hydrocarbonoclastic archaeal and bacterial strains, two each, individually and as consortia. Residual oil contents were determined, and microbial communities were analyzed by culture-dependent and culture-independent approaches initially and seasonally for one year. After one year of the bioremediation process, the mean oil degradation rate was similar across all treated soils including the controlled unbioaugmented one. Oil hydrocarbons were drastically reduced in all soil samples with values ranging from 82.7 % to 93 %. During the bioremediation process, the number of culturable oil-degrading bacteria increased to a range of 142 to 344 CFUx104 g-1 after 12 months of bioaugmentation. Although culture-independent analysis showed a high proportion of inoculants initially, none could be cultured throughout the bioremediation procedure. Within a year, microbial communities changed continually, and 33 species of halotolerant/halophilic hydrocarbonoclastic bacteria were isolated and identified belonged mainly to the three major bacterial phyla Actinobacteria, Proteobacteria, and Firmicutes. The archaeal phylum Halobacterota represented <1 % of the microbial community's relative abundance, which explains why none of its members were cultured. Improving the biodegradability of an already balanced environment by autochthonous bioaugmentation is more involved than just adding the proper oil degraders. This study emphasizes the possibility of a relatively large resistant population, a greater diversity of oil-degrading microorganisms, and the highly selective impacts of oil contamination on hypersaline soil bacterial communities.
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Affiliation(s)
- Kevin C Lee
- School of Science, Faculty of Health and Environmental Science, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Stephen D J Archer
- AgResearch Limited, Grasslands Research Centre, Palmerston North 4442, New Zealand.
| | - Mayada K Kansour
- Microbiology Program, Department of Biological Sciences, Faculty of Science, Kuwait University, P. O. Box 5969, Safat 13060, Kuwait.
| | - Dina M Al-Mailem
- Microbiology Program, Department of Biological Sciences, Faculty of Science, Kuwait University, P. O. Box 5969, Safat 13060, Kuwait.
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Belykh E, Maystrenko T, Velegzhaninov I, Tavleeva M, Rasova E, Rybak A. Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review. Microorganisms 2024; 12:733. [PMID: 38674676 PMCID: PMC11051952 DOI: 10.3390/microorganisms12040733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 03/28/2024] [Accepted: 04/01/2024] [Indexed: 04/28/2024] Open
Abstract
Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.
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Affiliation(s)
- Elena Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Tatiana Maystrenko
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Ilya Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Marina Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
- Department of Biology, Institute of Natural Sciences, Pitirim Sorokin Syktyvkar State University, 55 Oktyabrsky Prospekt, Syktyvkar 167001, Russia
| | - Elena Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
| | - Anna Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28 Kommunisticheskaya St., Syktyvkar 167982, Russia (I.V.); (E.R.)
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Shokri S, Bonakdarpour B, Abdollahzadeh Sharghi E. How high salt shock affects performance and membrane fouling characteristics of a halophilic membrane bioreactor used for treating hypersaline wastewater. CHEMOSPHERE 2024; 354:141716. [PMID: 38490610 DOI: 10.1016/j.chemosphere.2024.141716] [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: 11/05/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/17/2024]
Abstract
In the present study, the effect of short-term salt shocks (13% and 20%) on the performance of a halophilic MBR bioreactor used to treat a hypersaline (5% salt) synthetic wastewater was considered. 13% and 20% salt shocks resulted in a transient and permanent decrease in chemical oxygen demand removal efficiency, respectively which could be correlated with soluble microbial products (SMP) concentration and specific oxygen uptake rate values of the halophilic population. DNA leakage tests suggested that both 13% and 20% short-term salt shocks resulted in some cell structural damage. During both 13% and 20% salt shocks mixed liquor SMP, extracellular polymeric substances (EPS), zeta potential and endogenous respiration increased while relative hydrophobicity, EPSp/EPSc and exogenous respiration decreased; in both cases, however, the pre-shock values for these parameters were restored after the removal of the salt shock. 13% salt shock resulted in a transient increase in the membrane fouling rate and a permanent rise in total membrane resistance (Rt). On the other hand, both membrane fouling rate and Rt increased during 20% salt shock. Membrane fouling rate initially reduced after the 20% salt shock removal but after 5 days a "TMP jump" occurred. The latter was caused by the higher steady state SMPc and SMPp concentrations after removal of 20% salt shock compared to pre-shock values. This might have either resulted in a decrease in critical flux or an increase in local flux above critical flux in some parts of the membrane. The contribution of cake layer resistance to overall membrane resistance increased after the 13% and 20% salt shocks. The findings of the present study reveal the robustness of halophilic MBRs against salt shocks in the treatment of hypersaline wastewater. However, in cases of very high salt shocks, appropriate membrane fouling reduction strategies should be carried out during its operation.
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Affiliation(s)
- Sousan Shokri
- Department of Chemical Engineering, Amirkabir University of Technology, Tehran, Iran
| | - Babak Bonakdarpour
- Department of Chemical Engineering, Amirkabir University of Technology, Tehran, Iran.
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Zhang J, Yan X, Park H, Scrutton NS, Chen T, Chen GQ. Nonsterile microbial production of chemicals based on Halomonas spp. Curr Opin Biotechnol 2024; 85:103064. [PMID: 38262074 DOI: 10.1016/j.copbio.2023.103064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/09/2023] [Accepted: 12/30/2023] [Indexed: 01/25/2024]
Abstract
The use of extremophile organisms such as Halomomas spp. can eliminate the need for fermentation sterilization, significantly reducing process costs. Microbial fermentation is considered a pivotal strategy to reduce reliance on fossil fuel resources; however, sustainable processes continue to incur higher costs than their chemical industry counterparts. Most organisms require equipment sterilization to prevent contamination, a practice that introduces complexity and financial strain. Fermentations involving extremophile organisms can eliminate the sterilization process, relying instead on conditions that are conductive solely to the growth of the desired organism. This review discusses current challenges in pilot- and industrial-scale bioproduction when using the extremophile bacteria Halomomas spp. under nonsterile conditions.
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Affiliation(s)
- Jing Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China
| | - Xu Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Helen Park
- School of Life Sciences, Tsinghua University, Beijing 100084, China; EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC Synthetic Biology Research Centre, SYNBIOCHEM, Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, The University of Manchester, Manchester, UK
| | - Tao Chen
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin 300072, China.
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China; MOE Key Lab for Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing 100084, China.
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8
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Ashcroft E, Munoz-Munoz J. A review of the principles and biotechnological applications of glycoside hydrolases from extreme environments. Int J Biol Macromol 2024; 259:129227. [PMID: 38185295 DOI: 10.1016/j.ijbiomac.2024.129227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/27/2023] [Accepted: 01/02/2024] [Indexed: 01/09/2024]
Abstract
It is apparent that Biocatalysts are shaping the future by providing a more sustainable approach to established chemical processes. Industrial processes rely heavily on the use of toxic compounds and high energy or pH reactions, factors that both contributes to the worsening climate crisis. Enzymes found in bacterial systems and other microorganisms, from the glaciers of the Arctic to the sandy deserts of Abu Dhabi, provide key tools and understanding as to how we can progress in the biotechnology sector. These extremophilic bacteria harness the adaptive enzymes capable of withstanding harsh reaction conditions in terms of stability and reactivity. Carbohydrate-active enzymes, including glycoside hydrolases or carbohydrate esterases, are extremely beneficial for the presence and future of biocatalysis. Their involvement in the industry spans from laundry detergents to paper and pulp treatment by degrading oligo/polysaccharides into their monomeric products in almost all detrimental environments. This includes exceedingly high temperatures, pHs or even in the absence of water. In this review, we discuss the structure and function of different glycoside hydrolases from extremophiles, and how they can be applied to industrial-scale reactions to replace the use of harsh chemicals, reduce waste, or decrease energy consumption.
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Affiliation(s)
- Ellie Ashcroft
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
| | - Jose Munoz-Munoz
- Microbial Enzymology Lab, Department of Applied Sciences, Ellison Building A, Northumbria University, Newcastle Upon Tyne NE1 8ST, United Kingdom.
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Yao H, Liu S, Liu T, Ren D, Zhou Z, Yang Q, Mao J. Microbial-derived salt-tolerant proteases and their applications in high-salt traditional soybean fermented foods: a review. BIORESOUR BIOPROCESS 2023; 10:82. [PMID: 38647906 PMCID: PMC10992980 DOI: 10.1186/s40643-023-00704-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/31/2023] [Indexed: 04/25/2024] Open
Abstract
Different microorganisms can produce different proteases, which can adapt to different industrial requirements such as pH, temperature, and pressure. Salt-tolerant proteases (STPs) from microorganisms exhibit higher salt tolerance, wider adaptability, and more efficient catalytic ability under extreme conditions compared to conventional proteases. These unique enzymes hold great promise for applications in various industries including food, medicine, environmental protection, agriculture, detergents, dyes, and others. Scientific studies on microbial-derived STPs have been widely reported, but there has been little systematic review of microbial-derived STPs and their application in high-salt conventional soybean fermentable foods. This review presents the STP-producing microbial species and their selection methods, and summarizes and analyzes the salt tolerance mechanisms of the microorganisms. It also outlines various techniques for the isolation and purification of STPs from microorganisms and discusses the salt tolerance mechanisms of STPs. Furthermore, this review demonstrates the contribution of modern biotechnology in the screening of novel microbial-derived STPs and their improvement in salt tolerance. It highlights the potential applications and commercial value of salt-tolerant microorganisms and STPs in high-salt traditional soy fermented foods. The review ends with concluding remarks on the challenges and future directions for microbial-derived STPs. This review provides valuable insights into the separation, purification, performance enhancement, and application of microbial-derived STPs in traditional fermented foods.
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Affiliation(s)
- Hongli Yao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Department of Biology and Food Engineering, Bozhou University, Bozhou, 236800, Anhui, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Tiantian Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Dongliang Ren
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhilei Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Qilin Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China.
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China.
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10
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Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
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Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
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Nwankwo C, Hou J, Cui HL. Extracellular proteases from halophiles: diversity and application challenges. Appl Microbiol Biotechnol 2023; 107:5923-5934. [PMID: 37566160 DOI: 10.1007/s00253-023-12721-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/26/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023]
Abstract
Halophilic extracellular proteases offer promising application in various fields. Information on these prominent proteins including the synthesizing organisms, biochemical properties, domain organisation, purification, and application challenges has never been covered in recent reviews. Although extracellular proteases from bacteria pioneered the study of proteases in halophiles, progress is being made in proteases from halophilic archaea. Recent advances in extracellular proteases from archaea revealed that archaeal proteases are more robust and applicable. Extracellular proteases are composed of domains that determine their mechanisms of action. The intriguing domain structure of halophilic extracellular proteases consists of N-terminal domain, catalytic domain, and C-terminal extension. The role of C-terminal domains varies among different organisms. A high diversity of C-terminal domains would endow the proteases with diverse functions. With the development of genomics, culture-independent methods involving heterologous expression, affinity chromatography, and in vitro refolding are deployed with few challenges on purification and presenting novel research opportunities. Halophilic extracellular proteases have demonstrated remarkable potentials in industries such as detergent, leather, peptide synthesis, and biodegradation, with desirable properties and ability to withstand harsh industrial processes. KEY POINTS: • Halophilic extracellular proteases have robust properties suitable for applications. • A high diversity of C-terminal domains may endow proteases with diverse properties. • Novel protease extraction methods present novel application opportunities.
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Affiliation(s)
- Chidiebele Nwankwo
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China
- Natural Sciences Unit, School of General Studies, University of Nigeria, Nsukka, 410002, Enugu State, Nigeria
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria, Nsukka, 410002, Enugu State, Nigeria
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China.
| | - Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Jingkou District, Zhenjiang, 212013, Jiangsu, People's Republic of China.
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12
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Feng Y, Cui J, Xu B, Jiang Y, Fu C, Tan L. A Potentially Practicable Halotolerant Yeast Meyerozyma guilliermondii A4 for Decolorizing and Detoxifying Azo Dyes and Its Possible Halotolerance Mechanisms. J Fungi (Basel) 2023; 9:851. [PMID: 37623622 PMCID: PMC10456123 DOI: 10.3390/jof9080851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
In this study, a halotolerant yeast that is capable of efficiently decolorizing and detoxifying azo dyes was isolated, identified and characterized for coping with the treatment of azo-dye-containing wastewaters. A characterization of the yeast, including the optimization of its metabolism and growth conditions, its detoxification effectiveness and the degradation pathway of the target azo dye, as well as a determination of the key activities of the enzyme, was performed. Finally, the possible halotolerance mechanisms of the yeast were proposed through a comparative transcriptome analysis. The results show that a halotolerant yeast, A4, which could decolorize various azo dyes, was isolated from a marine environment and was identified as Meyerozyma guilliermondii. Its optimal conditions for dye decolorization were ≥1.0 g/L of sucrose, ≥0.2 g/L of (NH4)2SO4, 0.06 g/L of yeast extract, pH 6.0, a temperature of 35 °C and a rotation speed of ≥160 rpm. The yeast, A4, degraded and detoxified ARB through a series of steps, relying on the key enzymes that might be involved in the degradation of azo dye and aromatic compounds. The halotolerance of the yeast, A4, was mainly related to the regulation of the cell wall components and the excessive uptake of Na+/K+ and/or compatible organic solutes into the cells under different salinity conditions. The up-regulation of genes encoding Ca2+-ATPase and casein kinase II as well as the enrichment of KEGG pathways associated with proteasome and ribosome might also be responsible for its halotolerance.
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Affiliation(s)
- Yue Feng
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian 116081, China; (Y.F.); (J.C.); (Y.J.); (C.F.)
| | - Jingru Cui
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian 116081, China; (Y.F.); (J.C.); (Y.J.); (C.F.)
| | - Bingwen Xu
- Dalian Center for Certification and Food and Drug Control, Dalian 116037, China;
| | - Yifan Jiang
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian 116081, China; (Y.F.); (J.C.); (Y.J.); (C.F.)
| | - Chunqing Fu
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian 116081, China; (Y.F.); (J.C.); (Y.J.); (C.F.)
| | - Liang Tan
- Key Laboratory of Plant Biotechnology of Liaoning Province, School of Life Science, Liaoning Normal University, Dalian 116081, China; (Y.F.); (J.C.); (Y.J.); (C.F.)
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13
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Ji C, Huang J, Zhang X, Yang G, Xing S, Fu W, Hao Z, Chen B, Zhang X. Response of soil fungal community to chromium contamination in agricultural soils with different physicochemical properties. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 879:163244. [PMID: 37004770 DOI: 10.1016/j.scitotenv.2023.163244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/30/2023] [Accepted: 03/30/2023] [Indexed: 05/17/2023]
Abstract
Chromium (Cr) contamination has been of great concern in agricultural soil health due to its persistence, toxicity and bioaccumulation. Fungi, as an essential regulator of soil remediation and biochemical processes, had an unclear response to Cr contamination. In this study, the composition, diversity and interaction mechanisms of fungal communities in agricultural soils from ten different provinces of China were investigated in order to elucidate the fungal community response to varying soil properties and Cr concentrations. The results showed that high concentrations of Cr led to substantial alterations in the fungal community composition. The complex soil properties had a far greater impact on the fungal community structure than the single factor of Cr concentration, with soil available phosphorus (AP) and pH being most influential. Function predictions based on FUNGuild indicated that high concentrations of Cr have a significant impact on certain functional groups of fungi, including mycorrhizal fungi and plant saprotroph. The fungal community tended to resist Cr stress by enhancing interactions and clustering among network modules, while generating new keystone taxa. This study allowed insights into the response of soil fungal community to Cr contamination in different agricultural soils from different provinces and provided a theoretical basis for soil Cr ecological risk assessment and the development of bioremediation techniques for Cr-contaminated soils.
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Affiliation(s)
- Chuning Ji
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Jiu Huang
- School of Environment Science and Spatial Information, China University of Mining and Technology, Xuzhou, Jiangsu 221116, China
| | - Xuemeng Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; RDFZ Chaoyang School, Beijing 100028, China
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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14
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Najjari A, Boussetta A, Youssef N, Linares-Pastén JA, Mahjoubi M, Belloum R, Sghaier H, Cherif A, Ouzari HI. Physiological and genomic insights into abiotic stress of halophilic archaeon Natrinema altunense 4.1R isolated from a saline ecosystem of Tunisian desert. Genetica 2023; 151:133-152. [PMID: 36795306 PMCID: PMC9995536 DOI: 10.1007/s10709-023-00182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023]
Abstract
Halophilic archaea are polyextremophiles with the ability to withstand fluctuations in salinity, high levels of ultraviolet radiation, and oxidative stress, allowing them to survive in a wide range of environments and making them an excellent model for astrobiological research. Natrinema altunense 4.1R is a halophilic archaeon isolated from the endorheic saline lake systems, Sebkhas, located in arid and semi-arid regions of Tunisia. It is an ecosystem characterized by periodic flooding from subsurface groundwater and fluctuating salinities. Here, we assess the physiological responses and genomic characterization of N. altunense 4.1R to UV-C radiation, as well as osmotic and oxidative stresses. Results showed that the 4.1R strain is able to survive up to 36% of salinity, up to 180 J/m2 to UV-C radiation, and at 50 mM of H2O2, a resistance profile similar to Halobacterium salinarum, a strain often used as UV-C resistant model. In order to understand the genetic determinants of N. altunense 4.1R survival strategy, we sequenced and analyzed its genome. Results showed multiple gene copies of osmotic stress, oxidative stress, and DNA repair response mechanisms supporting its survivability at extreme salinities and radiations. Indeed, the 3D molecular structures of seven proteins related to responses to UV-C radiation (excinucleases UvrA, UvrB, and UvrC, and photolyase), saline stress (trehalose-6-phosphate synthase OtsA and trehalose-phosphatase OtsB), and oxidative stress (superoxide dismutase SOD) were constructed by homology modeling. This study extends the abiotic stress range for the species N. altunense and adds to the repertoire of UV and oxidative stress resistance genes generally known from haloarchaeon.
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Affiliation(s)
- Afef Najjari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Ayoub Boussetta
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, USA
| | - Javier A Linares-Pastén
- Department of Biotechnology, Faculty of Engineering, Lunds Tekniska Högskola (LTH), Lund University, P. O. Box 124, 22100, Lund, Sweden.
| | - Mouna Mahjoubi
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Rahma Belloum
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
| | - Haitham Sghaier
- Laboratory "Energy and Matter for Development of Nuclear Sciences" (LR16CNSTN02), National Center for Nuclear Sciences and Technology (CNSTN), Ariana, Tunisia
| | - Ameur Cherif
- University of Manouba, ISBST, LR11-ES31 BVBGR, Biotechpole Sidi Thabet, 2020, Ariana, Tunisia
| | - Hadda Imene Ouzari
- Faculté des Sciences de Tunis, LR03ES03 Laboratoire de Microbiologie et Biomolécules Actives, Université Tunis El Manar, 2092, Tunis, Tunisie
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15
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Lopez MF, Martínez FL, Rajal VB, Irazusta VP. Biotechnological potential of microorganisms isolated from the salar del hombre muerto, Argentina. AN ACAD BRAS CIENC 2023; 95:e20211199. [PMID: 36790270 DOI: 10.1590/0001-3765202320211199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 06/27/2022] [Indexed: 02/12/2023] Open
Abstract
Bacterial strains were isolated from soil and aqueous solution samples from the Salar del Hombre Muerto, Argentina. A total of 141 strains were characterized and the tolerance to sodium chloride was evaluated. We performed a screening to search for molecules of biotechnological interest: carotenoids (11%), emulsifiers (95%), and exopolysaccharides (6%), and to assess the production of enzymes, including proteolytic (39%), lipolytic (26%), hemolytic (50%), and catalase activities (99%); 25 bacterial strains were selected for further studies. Some of them produced biofilms, but only Bacillus sp. HA120b showed that ability in all the conditions assayed. Although 21 strains were able to form emulsions, the emulsifying index Kocuria sp. M9 and Bacillus sp. V3a cultures were greater than 50% and, emulsions were more stable when the bacteria grew in higher salt concentrations. Only pigmented Kocuria sp. M9 showed lipolytic activity on olive oil medium and was able to produce biofilms when cultured without and with 4 M of NaCl. Yellow pigments, lipase activity, and biosurfactant production were observed for Micrococcus sp. SX120. Summarizing, we found that the selected bacteria produced highly interesting molecules with diverse industrial applications and, many of them are functional in the presence of high salt concentrations.
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Affiliation(s)
- Marta Florencia Lopez
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina.,Facultad de Ingeniería, Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina
| | - Fabiana Lilian Martínez
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina
| | - Verónica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina.,Facultad de Ingeniería, Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina.,Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 637551, Singapore
| | - Verónica Patricia Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina.,Facultad de Ciencias Naturales, Universidad Nacional de Salta (UNSa), Salta, 4400, Argentina
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16
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Ibrahim IM, Fedonenko YP, Sigida EN, Kokoulin MS, Grinev VS, Mokrushin IG, Burygin GL, Zakharevich AM, Shirokov AA, Konnova SA. Structural characterization and physicochemical properties of the exopolysaccharide produced by the moderately halophilic bacterium Chromohalobacter salexigens, strain 3EQS1. Extremophiles 2023; 27:4. [PMID: 36715826 DOI: 10.1007/s00792-023-01289-0] [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: 08/08/2022] [Accepted: 01/15/2023] [Indexed: 01/31/2023]
Abstract
A strain, 3EQS1, was isolated from a salt sample taken from Lake Qarun (Fayoum Province, Egypt). On the basis of physiological, biochemical, and phylogenetic analyses, the strain was classified as Chromohalobacter salexigens. By 72 h of growth at 25 °C, strain 3EQS1 produced large amounts (15.1 g L-1) of exopolysaccharide (EPS) in a liquid mineral medium (initial pH 8.0) containing 10% sucrose and 10% NaCl. The EPS was precipitated from the cell-free culture medium with chilled ethanol and was purified by gel-permeation and anion-exchange chromatography. The molecular mass of the EPS was 0.9 × 106 Da. Chemical analyses, Fourier transform infrared spectroscopy, and nuclear magnetic resonance spectroscopy showed that the EPS was a linear β-D-(2 → 6)-linked fructan (levan). In aqueous solution, the EPS tended to form supramolecular aggregates with a critical aggregation concentration of 240 µg mL-1. The EPS had high emulsifying activity (E24, %) against kerosene (31.2 ± 0.4%), sunflower oil (76.9 ± 1.3%), and crude oil (98.9 ± 0.8%), and it also had surfactant properties. A 0.1% (w/v) aqueous EPS solution reduced the surface tension of water by 11.9%. The levan of C. salexigens 3EQS1 may be useful in various biotechnological processes.
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Affiliation(s)
- Ibrahim M Ibrahim
- Department of Agricultural Microbiology, Faculty of Agriculture, Fayoum University, Fayoum, 63514, Egypt.,Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov, 410012, Russia
| | - Yuliya P Fedonenko
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, 410049, Russia.
| | - Elena N Sigida
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Maxim S Kokoulin
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of Russian Academy of Sciences, 159 Prospekt 100 let Vladivostoku, Vladivostok, 690022, Russia
| | - Vyacheslav S Grinev
- Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov, 410012, Russia.,Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | | | - Gennady L Burygin
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Andrey M Zakharevich
- Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov, 410012, Russia
| | - Alexander A Shirokov
- Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov, 410012, Russia.,Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, 410049, Russia
| | - Svetlana A Konnova
- Chernyshevsky Saratov State University, 83 Ulitsa Astrakhanskaya, Saratov, 410012, Russia.,Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 13 Prospekt Entuziastov, Saratov, 410049, Russia
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17
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Liu S, Liu X, Shi Y, Zhuang S, Chen Q. RETRACTED: The adaptive mechanism of halophilic Brachybacterium muris in response to salt stress and its mitigation of copper toxicity in hydroponic plants. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120124. [PMID: 36089137 DOI: 10.1016/j.envpol.2022.120124] [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: 06/07/2022] [Revised: 08/27/2022] [Accepted: 09/03/2022] [Indexed: 06/15/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Authors who have indicated that there are significant errors with the scientific data upon which this study is based. Specifically, the authors have subsequently discovered that the 16S rDNA sequencing of Brachybacterium muris may not be reliable because of the limited identification methods from a few years ago. The authors are now repeating their experiments to reconfirm their data. The Authors take full responsibility for these errors and offer their sincere apologies.
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Affiliation(s)
- Siyu Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiayu Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Ying Shi
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China.
| | - Shulin Zhuang
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qihe Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Future Food Laboratory, Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 310000, China.
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18
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Passante EK, Dechant LE, Paradis CJ, McLellan SL. Halophilic bacteria in a Lake Michigan drainage basin as potential biological indicators of chloride-impacted freshwaters. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157458. [PMID: 35863571 DOI: 10.1016/j.scitotenv.2022.157458] [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: 05/13/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
There are few biological indicators for freshwater systems subjected to high chloride levels. Freshwater systems receive many forms of chloride such as road salts (e.g., NaCl, CaCl2, MgCl2), fertilizers (e.g., KCl), and year-round water softener pollution. The goal our study was to investigate Halomonadaceae populations as prospective biological indicators of chloride-impacted freshwaters. The bacterial family Halomonadaceae are halophiles that generally require the presence of salt to survive, which make them an attractive candidate in determining chloride impaired areas. Field sediment surveys assessed how salt tolerant and halophilic bacteria abundance corresponded to chloride and conductivity measurements. Colony forming unit (CFU) counts on modified M9 6% NaCl plates (w/v) at urbanized sites compared to the rural sites had highest counts during winter and spring when chloride concentrations were also highest. Select isolates identified as Halomonadaceae through 16S rRNA sequencing were kept as active cultures to determine the NaCl concentration and temperature preference that resulted in the isolates optimal growth. Isolates tested under 5 °C (cold) grew optimally in 2 % NaCl (w/v), whereas under 18 °C (warm), isolates showed optimal growth at 6 % NaCl. The majority of isolates had maximum growth in the warmer temperature, however, select isolates grew better in the cold temperature. Culture-independent methods were used and identified Halomonadaceae were widespread and permeant members of the microbial community in a Lake Michigan drainage basin. Quantitative polymerase chain reaction (qPCR) targeting Halomonadaceae genera demonstrated that abundance varied by site, but overall were present throughout the year. However, community sequencing revealed there were a large relative proportion of specific Halomonadaceae populations present in winter versus summer. Methods targeting salt tolerant bacteria and specific members of Halomonadaceae appears to be a promising approach to assess chloride-impacted areas to better understand the long-term ecological impacts as we continue to salinize freshwater resources.
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Affiliation(s)
- Elexius K Passante
- School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | - Leah E Dechant
- Department of Geosciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | - Charles J Paradis
- Department of Geosciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA
| | - Sandra L McLellan
- School of Freshwater Sciences, University of Wisconsin Milwaukee, Milwaukee, WI, USA.
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19
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Biswas J, Jana SK, Mandal S. Biotechnological impacts of Halomonas: a promising cell factory for industrially relevant biomolecules. Biotechnol Genet Eng Rev 2022:1-30. [PMID: 36253947 DOI: 10.1080/02648725.2022.2131961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
Abstract
Extremophiles are the most fascinating life forms for their special adaptations and ability to offer unique extremozymes or bioactive molecules. Halophiles, the natural inhabitants of hypersaline environments, are one among them. Halomonas are the common genus of halophilic bacteria. To support growth in unusual environments, Halomonas produces various hydrolytic enzymes, compatible solutes, biopolymers like extracellular polysaccharides (EPS) and polyhydroxy alkaloates (PHA), antibiotics, biosurfactants, pigments, etc. Many of such molecules are being produced in large-scale bioreactors for commercial use. However, the prospect of the remaining bioactive molecules with industrial relevance is far from their application. Furthermore, the genetic engineering of the respective gene clusters could open up a new path to bio-prospect these molecules by overproducing their products through heterologous expression. The present survey on Halomonas highlights their ecological diversity, application potential of the their various industrially relevant biomolecules and impact of these biomolecules on respective fields.
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Affiliation(s)
- Jhuma Biswas
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Santosh Kumar Jana
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, Kolkata, India
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20
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Wu JH, McGenity TJ, Rettberg P, Simões MF, Li WJ, Antunes A. The archaeal class Halobacteria and astrobiology: Knowledge gaps and research opportunities. Front Microbiol 2022; 13:1023625. [PMID: 36312929 PMCID: PMC9608585 DOI: 10.3389/fmicb.2022.1023625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 09/07/2022] [Indexed: 09/19/2023] Open
Abstract
Water bodies on Mars and the icy moons of the outer solar system are now recognized as likely being associated with high levels of salt. Therefore, the study of high salinity environments and their inhabitants has become increasingly relevant for Astrobiology. Members of the archaeal class Halobacteria are the most successful microbial group living in hypersaline conditions and are recognized as key model organisms for exposure experiments. Despite this, data for the class is uneven across taxa and widely dispersed across the literature, which has made it difficult to properly assess the potential for species of Halobacteria to survive under the polyextreme conditions found beyond Earth. Here we provide an overview of published data on astrobiology-linked exposure experiments performed with members of the Halobacteria, identifying clear knowledge gaps and research opportunities.
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Affiliation(s)
- Jia-Hui Wu
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Terry J. McGenity
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Petra Rettberg
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Marta F. Simões
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau SAR, China
- China National Space Administration (CNSA), Macau Center for Space Exploration and Science, Taipa, Macau SAR, China
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21
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Molecular Characterization and Biocompatibility of Exopolysaccharide Produced by Moderately Halophilic Bacterium Virgibacillus dokdonensis from the Saltern of Kumta Coast. Polymers (Basel) 2022; 14:polym14193986. [PMID: 36235941 PMCID: PMC9570845 DOI: 10.3390/polym14193986] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/09/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
The use of natural polysaccharides as biomaterials is gaining importance in tissue engineering due to their inherent biocompatibility. In this direction, the present study aims to explore the structure and biocompatibility of the EPS produced by Virgibacillus dokdonensis VITP14. This marine bacterium produces 17.3 g/L of EPS at 96 h of fermentation. The EPS was purified using ion exchange and gel permeation chromatographic methods. The porous web-like structure and elemental composition (C, O, Na, Mg, P, S) of the EPS were inferred from SEM and EDX analysis. AFM analysis revealed spike-like lumps with a surface roughness of 84.85 nm. The zeta potential value of −10 mV indicates the anionic nature of the EPS. Initial molecular characterization showed that the EPS is a heteropolysaccharide composed of glucose (25.8%), ribose (18.6%), fructose (31.5%), and xylose (24%), which are the monosaccharide units in the HPLC analysis. The FTIR spectrum indicates the presence of functional groups/bonds typical of EPSs (O-H, C-H, C-O-H, C-O, S=O, and P=O). The polymer has an average molecular weight of 555 kDa. Further, NMR analysis revealed the monomer composition, the existence of two α- and six β-glycosidic linkages, and the branched repeating unit as → 1)[α-D-Xylp-(1 → 2)-α-D-Glcp-(1 → 6)-β-D-Glcp-(1 → 5)]-β-D-Frup-(2 → 2)[β-D-Xylp-(1 → 4)]-β-D-Xylp-(1 → 6)-β-D-Fruf-(2 → 4)-β-D-Ribp-(1 →. The EPS is thermally stable till 251.4 °C. X-ray diffraction analysis confirmed the semicrystalline (54.2%) nature of the EPS. Further, the EPS exhibits significant water solubility (76.5%), water-holding capacity (266.8%), emulsifying index (66.8%), hemocompatibility (erythrocyte protection > 87%), and cytocompatibility (cell viability > 80% on RAW264.7 and keratinocyte HaCaT cells) at higher concentrations and prolongs coagulation time in APTT and PT tests. Our research unveils the significant biocompatibility of VITP14 EPS for synthesizing a variety of biomaterials.
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Zhang X, Chen B, Yin R, Xing S, Fu W, Wu H, Hao Z, Ma Y, Zhang X. Long-term nickel contamination increased soil fungal diversity and altered fungal community structure and co-occurrence patterns in agricultural soils. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129113. [PMID: 35580502 DOI: 10.1016/j.jhazmat.2022.129113] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 04/23/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Nickel (Ni) contamination imposes deleterious effects on the stability of soil ecosystem. Soil fungal community as a crucial moderator of soil remediation and biochemical processes has attracted more and more research interests. In the present study, soil fungal community composition and diversity under long-term Ni contamination were investigated and fungal interaction networks were built to reveal fungal co-occurrence patterns. The results showed that moderate Ni contamination significantly increased fungal diversity and altered fungal community structure. Functional predictions based on FUNGuild suggested that the relative abundance of arbuscular mycorrhizal fungi (AMF) significantly increased at moderate Ni contamination level. Ni contamination strengthened fungal interactions. Keystone taxa at different Ni contamination levels, such as Penicillium at light contamination, were identified, which might have ecological significance in maintaining the stability of fungal community to Ni stress. The present study provided a deeper insight into the effect of long-term Ni contamination on fungal community composition and co-occurrence patterns, and was helpful to further explore ecological risk of Ni contamination in cultivated field.
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Affiliation(s)
- Xuemeng Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baodong Chen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongbin Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuping Xing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Fu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhipeng Hao
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yibing Ma
- Macau Environmental Research Institute, Macau University of Science and Technology, Macau 999078, China
| | - Xin Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Menasria T, Monteoliva-Sánchez M, Benhadj M, Benammar L, Boukoucha M, Aguilera M. Unraveling the enzymatic and antibacterial potential of rare halophilic actinomycetes from Algerian hypersaline wetland ecosystems. J Basic Microbiol 2022; 62:1202-1215. [PMID: 35945171 DOI: 10.1002/jobm.202200085] [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: 02/12/2022] [Revised: 06/18/2022] [Accepted: 07/10/2022] [Indexed: 11/07/2022]
Abstract
The study aimed to isolate rare halophilic actinomycetes from hypersaline soils of Algerian inland Wetland Ecosystems "Sebkhas-Chotts" located in arid and hot hyperarid lands with international importance under the Ramsar Convention and to explore their enzyme-producing and antibacterial abilities. The halophilic actinomycetes were selectively isolated using agar-rich media supplemented with 5, 10, and 15% (W/V) of total salts. Thirty-one isolates were obtained and 16S rRNA gene sequencing analysis revealed the presence of members affiliated to rare halophilic actinobacterial genera (Actinopolyspora and Nocardiopsis) accounting for 74.19% (23 isolates out of 31) and 25.8% (8 isolates), respectively. Both phylotypes are alkalitolerant and halophilic thermotolerant actinomycetes displaying significant hydrolytic activities relative to (amylase, asparaginase, cellulase, esterase, glutaminase, inulinase, protease, pectinase, xylanase), and over 96% of tested isolates exhibited all common enzymes, mainly active at 10% of growing salt. In addition, high antibacterial activity was observed against Bacillus cereus, Bacillus subtilis, Micrococcus luteus, and Staphylococcus aureus. The findings showed that saline wetlands ecosystems represent a rich reservoir for the isolation of significant rare halophilic actinomycetes with potential adaptive features and valuable sources for novel bioactive metabolites and biocatalysts of biotechnological interest.
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Affiliation(s)
- Taha Menasria
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa, Algeria.,Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
| | | | - Mabrouka Benhadj
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa, Algeria
| | - Leyla Benammar
- Department of Microbiology and Biochemistry, Faculty of Natural and Life Sciences University of Batna, Batna, Algeria
| | - Mourad Boukoucha
- Department of Applied Biology, Faculty of Exact Sciences and Natural and Life Sciences, University of Larbi Tebessi, Tebessa, Algeria
| | - Margarita Aguilera
- Department of Microbiology, Faculty of Pharmacy, University of Granada, Granada, Spain
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Microbial Diversity and Adaptation under Salt-Affected Soils: A Review. SUSTAINABILITY 2022. [DOI: 10.3390/su14159280] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The salinization of soil is responsible for the reduction in the growth and development of plants. As the global population increases day by day, there is a decrease in the cultivation of farmland due to the salinization of soil, which threatens food security. Salt-affected soils occur all over the world, especially in arid and semi-arid regions. The total area of global salt-affected soil is 1 billion ha, and in India, an area of nearly 6.74 million ha−1 is salt-stressed, out of which 2.95 million ha−1 are saline soil (including coastal) and 3.78 million ha−1 are alkali soil. The rectification and management of salt-stressed soils require specific approaches for sustainable crop production. Remediating salt-affected soil by chemical, physical and biological methods with available resources is recommended for agricultural purposes. Bioremediation is an eco-friendly approach compared to chemical and physical methods. The role of microorganisms has been documented by many workers for the bioremediation of such problematic soils. Halophilic Bacteria, Arbuscular mycorrhizal fungi, Cyanobacteria, plant growth-promoting rhizobacteria and microbial inoculation have been found to be effective for plant growth promotion under salt-stress conditions. The microbial mediated approaches can be adopted for the mitigation of salt-affected soil and help increase crop productivity. A microbial product consisting of beneficial halophiles maintains and enhances the soil health and the yield of the crop in salt-affected soil. This review will focus on the remediation of salt-affected soil by using microorganisms and their mechanisms in the soil and interaction with the plants.
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Krawczyk KT, Locht C, Kowalewicz-Kulbat M. Halophilic Archaea Halorhabdus Rudnickae and Natrinema Salaciae Activate Human Dendritic Cells and Orient T Helper Cell Responses. Front Immunol 2022; 13:833635. [PMID: 35720372 PMCID: PMC9204267 DOI: 10.3389/fimmu.2022.833635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 04/28/2022] [Indexed: 12/03/2022] Open
Abstract
Halophilic archaea are procaryotic organisms distinct from bacteria, known to thrive in hypersaline environments, including salt lakes, salterns, brines and salty food. They have also been identified in the human microbiome. The biological significance of halophiles for human health has rarely been examined. The interactions between halophilic archaea and human dendritic cells (DCs) and T cells have not been identified so far. Here, we show for the first time that the halophilic archaea Halorhabdus rudnickae and Natrinema salaciae activate human monocyte-derived DCs, induce DC maturation, cytokine production and autologous T cell activation. In vitro both strains induced DC up-regulation of the cell-surface receptors CD86, CD80 and CD83, and cytokine production, including IL-12p40, IL-10 and TNF-α, but not IL-23 and IL-12p70. Furthermore, autologous CD4+ T cells produced significantly higher amounts of IFN-γ and IL-13, but not IL-17A when co-cultured with halophile-stimulated DCs in comparison to T cells co-cultured with unstimulated DCs. IFN-γ was almost exclusively produced by naïve T cells, while IL-13 was produced by both naïve and memory CD4+ T cells. Our findings thus show that halophilic archaea are recognized by human DCs and are able to induce a balanced cytokine response. The immunomodulatory functions of halophilic archaea and their potential ability to re-establish the immune balance may perhaps participate in the beneficial effects of halotherapies.
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Affiliation(s)
- Krzysztof T Krawczyk
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Camille Locht
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Magdalena Kowalewicz-Kulbat
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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Tourova TP, Sokolova DS, Semenova EM, Ershov AP, Grouzdev DS, Nazina TN. Genomic and Physiological Characterization of Halophilic Bacteria of the Genera Halomonas and Marinobacter from Petroleum Reservoirs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722300038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Márquez-Villa JM, Mateos-Díaz JC, Rodríguez-González JA, Camacho-Ruíz RM. Optimization of Lipopeptide Biosurfactant Production by Salibacterium sp. 4CTb in Batch Stirred-Tank Bioreactors. Microorganisms 2022; 10:microorganisms10050983. [PMID: 35630427 PMCID: PMC9145298 DOI: 10.3390/microorganisms10050983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/25/2022] [Accepted: 04/30/2022] [Indexed: 02/05/2023] Open
Abstract
Halophilic microorganisms are potentially capable as platforms to produce low-cost biosurfactants. However, the robustness of bioprocesses is still a challenge and, therefore, it is essential to understand the effects of microbiological culture conditions through bioreactor engineering. Based on a design of experiments (DOE) and a response surface methodology (RSM) tailored and taken from the literature, the present work focuses on the evaluation of a composite central design (CCD) under batch cultures in stirred-tank bioreactors with the halophilic bacteria Salibacterium sp. 4CTb in order to determine the operative conditions that favor mass transfer and optimize the production of a lipopeptide. The results obtained showed profiles highlighting the most favorable culture conditions, which lead to an emulsification index (E24%) higher than 70%. Moreover, through the behavior of dissolved oxygen (DO), it was possible to experimentally evaluate the higher volumetric coefficient of mass transfer in the presence of lipopeptide (kLa = 31 1/h) as a key criterion for the synthesis of the biosurfactant on further cell expansion.
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Martínez GM, Pire C, Martínez-Espinosa RM. Hypersaline environments as natural sources of microbes with potential applications in biotechnology: the case of solar evaporation systems to produce salt in Alicante County (Spain). CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100136. [PMID: 35909606 PMCID: PMC9325878 DOI: 10.1016/j.crmicr.2022.100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/14/2022] [Accepted: 04/24/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Guillermo Martínez Martínez
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Carmen Pire
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, Alicante, E-03080 Spain
- Corresponding author.
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Zhang T, Zhang X, Li Y, Yang N, Qiao L, Miao Z, Xing J, Zhu D. Study of osmoadaptation mechanisms of halophilic Halomonas alkaliphila XH26 under salt stress by transcriptome and ectoine analysis. Extremophiles 2022; 26:14. [PMID: 35229247 DOI: 10.1007/s00792-022-01256-1] [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: 04/07/2021] [Accepted: 01/04/2022] [Indexed: 11/04/2022]
Abstract
Halophilic bacteria such as the genus Halomonas are promising candidates in diverse industrial, agricultural and biomedical applications. Here, we successfully isolated a halophilic Halomonas alkaliphila strain XH26 from Xiaochaidan Salt Lake, and studied its osmoadaptation strategies using transcriptome and ectoine analysis. Divergent mechanisms were involved in osmoadaptation at different salinities in H. alkaliphila XH26. At moderate salinity (6% NaCl), increased transcriptions of ABC transporters related to iron (III), phosphate, phosphonate, monosaccharide and oligosaccharide import were observed. At high salinity (15% NaCl), transcriptions of flagellum assembly and cell motility were significantly inhibited. The transcriptional levels of ABC transporter genes related to iron (III) and iron3+-hydroxamate import, glycine betaine and putrescine uptake, and cytochrome biogenesis and assembly were significantly up-regulated. Ectoine synthesis and accumulation was significantly increased under salt stress, and the increased transcriptional expressions of ectoine synthesis genes ectB and ectC may play a key role in high salinity induced osmoadaptation. At extreme high salinity (18% NaCl), 5-hydroxyectoine and ectoine worked together to maintain cell survival. Together these results give valuable insights into the osmoadaptation mechanisms of H. alkaliphila XH26, and provide useful information for further engineering this specific strain for increased ectoine synthesis and related applications.
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Affiliation(s)
- Tiantian Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Xin Zhang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Yongzhen Li
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Ning Yang
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Lijuan Qiao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Zengqiang Miao
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China
| | - Jiangwa Xing
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China.
| | - Derui Zhu
- Research Centre of Basic Medical Sciences, Medical College, Qinghai University, Xining, 810016, People's Republic of China.
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Recent Antimicrobial Responses of Halophilic Microbes in Clinical Pathogens. Microorganisms 2022; 10:microorganisms10020417. [PMID: 35208871 PMCID: PMC8874722 DOI: 10.3390/microorganisms10020417] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 01/27/2023] Open
Abstract
Microbial pathogens that cause severe infections and are resistant to drugs are simultaneously becoming more active. This urgently calls for novel effective antibiotics. Organisms from extreme environments are known to synthesize novel bioprospecting molecules for biomedical applications due to their peculiar characteristics of growth and physiological conditions. Antimicrobial developments from hypersaline environments, such as lagoons, estuaries, and salterns, accommodate several halophilic microbes. Salinity is a distinctive environmental factor that continuously promotes the metabolic adaptation and flexibility of halophilic microbes for their survival at minimum nutritional requirements. A genetic adaptation to extreme solar radiation, ionic strength, and desiccation makes them promising candidates for drug discovery. More microbiota identified via sequencing and ‘omics’ approaches signify the hypersaline environments where compounds are produced. Microbial genera such as Bacillus, Actinobacteria, Halorubrum and Aspergillus are producing a substantial number of antimicrobial compounds. Several strategies were applied for producing novel antimicrobials from halophiles including a consortia approach. Promising results indicate that halophilic microbes can be utilised as prolific sources of bioactive metabolites with pharmaceutical potentialto expand natural product research towards diverse phylogenetic microbial groups which inhabit salterns. The present study reviews interesting antimicrobial compounds retrieved from microbial sources of various saltern environments, with a discussion of their potency in providing novel drugs against clinically drug-resistant microbes.
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Production of Polyhydroxyalkanoates in Unsterilized Hyper-Saline Medium by Halophiles Using Waste Silkworm Excrement as Carbon Source. Molecules 2021; 26:molecules26237122. [PMID: 34885704 PMCID: PMC8659123 DOI: 10.3390/molecules26237122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/20/2021] [Accepted: 11/21/2021] [Indexed: 12/03/2022] Open
Abstract
The chlorophyll ethanol-extracted silkworm excrement was hardly biologically reused or fermented by most microorganisms. However, partial extremely environmental halophiles were reported to be able to utilize a variety of inexpensive carbon sources to accumulate polyhydroxyalkanoates. In this study, by using the nile red staining and gas chromatography assays, two endogenous haloarchaea strains: Haloarcula hispanica A85 and Natrinema altunense A112 of silkworm excrement were shown to accumulate poly(3-hydroxybutyrate) up to 0.23 g/L and 0.08 g/L, respectively, when using the silkworm excrement as the sole carbon source. The PHA production of two haloarchaea showed no significant decreases in the silkworm excrement medium without being sterilized compared to that of the sterilized medium. Meanwhile, the CFU experiments revealed that there were more than 60% target PHAs producing haloarchaea cells at the time of the highest PHAs production, and the addition of 0.5% glucose into the open fermentation medium can largely increase both the ratio of target haloarchaea cells (to nearly 100%) and the production of PHAs. In conclusion, our study demonstrated the feasibility of using endogenous haloarchaea to utilize waste silkworm excrement, effectively. The introduce of halophiles could provide a potential way for open fermentation to further lower the cost of the production of PHAs.
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Lach J, Jęcz P, Strapagiel D, Matera-Witkiewicz A, Stączek P. The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools. Genes (Basel) 2021; 12:genes12111756. [PMID: 34828362 PMCID: PMC8619533 DOI: 10.3390/genes12111756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/18/2021] [Accepted: 10/30/2021] [Indexed: 02/06/2023] Open
Abstract
Halophiles, the salt-loving organisms, have been investigated for at least a hundred years. They are found in all three domains of life, namely Archaea, Bacteria, and Eukarya, and occur in saline and hypersaline environments worldwide. They are already a valuable source of various biomolecules for biotechnological, pharmaceutical, cosmetological and industrial applications. In the present era of multidrug-resistant bacteria, cancer expansion, and extreme environmental pollution, the demand for new, effective compounds is higher and more urgent than ever before. Thus, the unique metabolism of halophilic microorganisms, their low nutritional requirements and their ability to adapt to harsh conditions (high salinity, high pressure and UV radiation, low oxygen concentration, hydrophobic conditions, extreme temperatures and pH, toxic compounds and heavy metals) make them promising candidates as a fruitful source of bioactive compounds. The main aim of this review is to highlight the nucleic acid sequencing experimental strategies used in halophile studies in concert with the presentation of recent examples of bioproducts and functions discovered in silico in the halophile's genomes. We point out methodological gaps and solutions based on in silico methods that are helpful in the identification of valuable bioproducts synthesized by halophiles. We also show the potential of an increasing number of publicly available genomic and metagenomic data for halophilic organisms that can be analysed to identify such new bioproducts and their producers.
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Affiliation(s)
- Jakub Lach
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
- Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz, 93-338 Lodz, Poland;
- Correspondence:
| | - Paulina Jęcz
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Environmental Protection, University of Lodz, 93-338 Lodz, Poland;
| | - Agnieszka Matera-Witkiewicz
- Screening Laboratory of Biological Activity Tests and Collection of Biological Material, Faculty of Pharmacy, Wroclaw Medical University, 50-368 Wroclaw, Poland;
| | - Paweł Stączek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, 93-338 Lodz, Poland; (P.J.); (P.S.)
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Martínez FL, Rajal VB, Irazusta VP. Genomic characterization and proteomic analysis of the halotolerant Micrococcus luteus SA211 in response to the presence of lithium. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147290. [PMID: 33940405 DOI: 10.1016/j.scitotenv.2021.147290] [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: 02/18/2021] [Revised: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Micrococcus luteus SA211, isolated from the Salar del Hombre Muerto in Argentina, developed responses that allowed its survival and growth in presence of high concentrations of lithium chloride (LiCl). In this research, analysis of total genome sequencing and a comparative proteomic approach were performed to investigate the responses of this bacterium to the presence of Li. Through proteomic analysis, we found differentially synthesized proteins in growth media without LiCl (DM) and with 10 (D10) and 30 g/L LiCl (D30). Bi-dimensional separation of total protein extracts allowed the identification of 17 over-synthesized spots when growth occurred in D30, five in D10, and six in both media with added LiCl. The results obtained showed different metabolic pathways involved in the ability of M. luteus SA211 to interact with Li. These pathways include defense against oxidative stress, pigment and protein synthesis, energy production, and osmolytes biosynthesis and uptake. Furthermore, mono-dimensional gel electrophoresis revealed differential protein synthesis at equivalent NaCl and LiCl concentrations, suggesting that this strain would be able to develop different responses depending on the nature of the ion. Moreover, the percentage of proteins with acidic pI predicted and observed was highlighted, indicating an adaptation to saline environments. To the best of our knowledge, this is the first report showing the relationship between protein synthesis and genome sequence analysis in response to Li, showing the great biotechnological potential that native microorganisms present, especially those isolated from extreme environments.
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Affiliation(s)
- Fabiana Lilian Martínez
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Argentina
| | - Verónica Beatriz Rajal
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Argentina; Facultad de Ingeniería, UNSa, Argentina; Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
| | - Verónica Patricia Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Salta (UNSa), Argentina; Facultad de Ciencias Naturales, UNSa, Argentina.
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Marsh WS, Heise BW, Krzmarzick MJ, Murdoch RW, Fathepure BZ. Isolation and characterization of a halophilic Modicisalibacter sp. strain Wilcox from produced water. Sci Rep 2021; 11:6943. [PMID: 33767228 PMCID: PMC7994583 DOI: 10.1038/s41598-021-86196-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
We report the isolation a halophilic bacterium that degrades both aromatic and aliphatic hydrocarbons as the sole sources of carbon at high salinity from produced water. Phylogenetic analysis of 16S rRNA-gene sequences shows the isolate is a close relative of Modicisalibacter tunisiensis isolated from an oil-field water in Tunisia. We designate our isolate as Modicisalibacter sp. strain Wilcox. Genome analysis of strain Wilcox revealed the presence of a repertoire of genes involved in the metabolism of aliphatic and aromatic hydrocarbons. Laboratory culture studies corroborated the predicted hydrocarbon degradation potential. The strain degraded benzene, toluene, ethylbenzene, and xylenes at salinities ranging from 0.016 to 4.0 M NaCl, with optimal degradation at 1 M NaCl. Also, the strain degraded phenol, benzoate, biphenyl and phenylacetate as the sole sources of carbon at 2.5 M NaCl. Among aliphatic compounds, the strain degraded n-decane and n-hexadecane as the sole sources of carbon at 2.5 M NaCl. Genome analysis also predicted the presence of many heavy metal resistance genes including genes for metal efflux pumps, transport proteins, and enzymatic detoxification. Overall, due to its ability to degrade many hydrocarbons and withstand high salt and heavy metals, strain Wilcox may prove useful for remediation of produced waters.
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Affiliation(s)
- William S Marsh
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Brenden W Heise
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Mark J Krzmarzick
- Civil and Environmental Engineering, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, 37996, USA
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | - Babu Z Fathepure
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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Abou Khalil C, Prince VL, Prince RC, Greer CW, Lee K, Zhang B, Boufadel MC. Occurrence and biodegradation of hydrocarbons at high salinities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143165. [PMID: 33131842 DOI: 10.1016/j.scitotenv.2020.143165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.
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Affiliation(s)
- Charbel Abou Khalil
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | | | | | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC H4P 2R2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Michel C Boufadel
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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Bioremediation of Diesel Contaminated Marine Water by Bacteria: A Review and Bibliometric Analysis. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2021. [DOI: 10.3390/jmse9020155] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oil pollution can cause tremendous harm and risk to the water ecosystem and organisms due to the relatively recalcitrant hydrocarbon compounds. The current chemical method used to treat the ecosystem polluted with diesel is incompetent and expensive for a large-scale treatment. Thus, bioremediation technique seems urgent and requires more attention to solve the existing environmental problems. Biological agents, including microorganisms, carry out the biodegradation process where organic pollutants are mineralized into water, carbon dioxide, and less toxic compounds. Hydrocarbon-degrading bacteria are ubiquitous in the nature and often exploited for their specialty to bioremediate the oil-polluted area. The capability of these bacteria to utilize hydrocarbon compounds as a carbon source is the main reason behind their species exploitation. Recently, microbial remediation by halophilic bacteria has received many positive feedbacks as an efficient pollutant degrader. These halophilic bacteria are also considered as suitable candidates for bioremediation in hypersaline environments. However, only a few microbial species have been isolated with limited available information on the biodegradation of organic pollutants by halophilic bacteria. The fundamental aspect for successful bioremediation includes selecting appropriate microbes with a high capability of pollutant degradation. Therefore, high salinity bacteria are remarkable microbes for diesel degradation. This paper provides an updated overview of diesel hydrocarbon degradation, the effects of oil spills on the environment and living organisms, and the potential role of high salinity bacteria to decontaminate the organic pollutants in the water environment.
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Wang Y, Xu B, Ning S, Shi S, Tan L. Magnetically stimulated azo dye biodegradation by a newly isolated osmo-tolerant Candida tropicalis A1 and transcriptomic responses. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111791. [PMID: 33360211 DOI: 10.1016/j.ecoenv.2020.111791] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
A recently isolated osmo-tolerant yeast Candida tropicalis A1, which could decolorize various azo dyes under high-salinity conditions, was systematically characterized in the present study. Stimulating dye-decolorization effectiveness and osmo-tolerance of the yeast by static magnetic field (SMF) was investigated and transcriptomic responses of the yeast to SMF was analyzed to propose possible mechanisms. The results demonstrated that the yeast A1 effectively decolorized (≥ 97.50% within 12 h) and detoxified (from high toxicity to low toxicity within 24 h) 70 mg/L Acid Red B (ARB) under the optimized conditions through a series of steps including naphthalene-amidine bond cleavage, reductive or oxidative deamination/desulfurization, open-loop of hydroxy-substituted naphthalene or benzene and TCA cycle. Moreover, dye decolorization performance and osmo-tolerance of the yeast A1 were further improved by 24.6 mT SMF. Genes encoding high-affinity hexose/glucose transporter proteins and NADH-ubiquinone oxidoreductase were up-regulated by 24.6 mT SMF, which might be responsible for the increase of dye decolorization. Significant up-regulation of glycerol-3-phosphate dehydrogenase and cell wall protein RHD3 suggested that osmo-tolerance was enhanced by 24.6 mT SMF through promoting production and intracellular accumulation of glycerol as compatible solute, as well as regulation of cell wall component. In conclusion, 24.6 mT SMF led to the up-regulation of related genes resulting in enhanced dye biodegradation efficiency and osmo-tolerance of the yeast A1.
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Affiliation(s)
- Yumeng Wang
- School of Life Sciences, Liaoning Normal University, Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China
| | - Bingwen Xu
- Institute of Agricultural Products and Aquatic Products Inspection and Testing, Dalian Center for Certification and Food and Drug Control, Dalian 116037, PR China
| | - Shuxiang Ning
- School of Life Sciences, Liaoning Normal University, Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China
| | - Shengnan Shi
- School of Life Sciences, Liaoning Normal University, Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China
| | - Liang Tan
- School of Life Sciences, Liaoning Normal University, Key Laboratory of Plant Biotechnology of Liaoning Province, Dalian, Liaoning 116081, PR China.
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Torregrosa-Crespo J, Pire C, Richardson DJ, Martínez-Espinosa RM. Exploring the Molecular Machinery of Denitrification in Haloferax mediterranei Through Proteomics. Front Microbiol 2020; 11:605859. [PMID: 33363526 PMCID: PMC7754194 DOI: 10.3389/fmicb.2020.605859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/16/2020] [Indexed: 12/02/2022] Open
Abstract
Many proteins and enzymes involved in denitrification in haloarchaea can be inferred to be located between the cytoplasmic membrane and the S-layer, based on the presence of a Tat signal sequence and the orientation of the active site that some of these enzymes have. The membrane fraction of the haloarchaeon Haloferax mediterranei (R-4), grown under anaerobic conditions in the presence of nitrate, was solubilized to identify the respiratory proteins associated or anchored to it. Using Triton X-100, CHAPS, and n-Octyl-β-d-glucopyranoside at different concentrations we found the best conditions for isolating membrane proteins in micelles, in which enzymatic activity and stability were maintained. Then, they were subjected to purification using two chromatographic steps followed by the analysis of the eluents by NANO-ESI Chip-HPLC-MS/MS. The results showed that the four main enzymes of denitrification (nitrate, nitrite, nitric oxide, and nitrous oxide reductases) in H. mediterranei were identified and they were co-purified thanks to the micelles made with Triton X-100 (20% w/v for membrane solubilisation and 0.2% w/v in the buffers used during purification). In addition, several accessory proteins involved in electron transfer processes during anaerobic respiration as well as proteins supporting ATP synthesis, redox balancing and oxygen sensing were detected. This is the first characterization of anaerobic membrane proteome of haloarchaea under denitrifying conditions using liquid chromatography-mass spectrometry. It provides new information for a better understanding of the anaerobic respiration in haloarchaea.
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Affiliation(s)
- Javier Torregrosa-Crespo
- División de Bioquímica y Biología Molecular, Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Carmen Pire
- División de Bioquímica y Biología Molecular, Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain.,Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Rosa María Martínez-Espinosa
- División de Bioquímica y Biología Molecular, Departamento de Agroquímica y Bioquímica, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain.,Multidisciplinary Institute for Environmental Studies "Ramón Margalef", University of Alicante, Alicante, Spain
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Kaminsky LM, Esker PD, Bell TH. Abiotic conditions outweigh microbial origin during bacterial assembly in soils. Environ Microbiol 2020; 23:358-371. [PMID: 33185966 DOI: 10.1111/1462-2920.15322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 11/30/2022]
Abstract
Understanding the processes guiding microbial community assembly in soils is essential for predicting microbiome structure and function following soil disturbance events like agricultural soil fumigation. However, assembly outcomes are complex and variable, being affected by both selective abiotic forces and by the history of colonizing microorganisms. To untangle the interactions between these factors, we conducted a controlled microcosm study tracking bacterial assembly in cleared soils over 7 weeks. We used mesh bags to connect five unsterilized source soils, differing in land use history (forested, agricultural, or fallow), with four sterile recipient soil treatments, differing in abiotic conditions (no soil additives, salt addition, urea addition, or mixed salt/urea addition). We found that 59%-96% of bacterial colonizers after 1 week were Firmicutes, but by 7 weeks Actinobacteria and Bacteroidetes were also dominant. Salt and nitrogen additions reshaped bacterial assembly by constraining alpha diversity by up to half and biomass accumulation by up to an order of magnitude. Within-treatment dispersion was significantly lower for salt and nutrient addition microcosms, suggesting deterministic selective pressures. In contrast, source soil origin had little impact on assembly trajectories. These results suggest that abiotic conditions can overshadow microbial source history in shaping community assembly outcomes.
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Affiliation(s)
- Laura M Kaminsky
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA
| | - Paul D Esker
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.,Graduate Faculty in International Agriculture and Development, The Pennsylvania State University, University Park, PA, USA
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, USA.,Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, USA
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40
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Oyewusi HA, Abdul Wahab R, Edbeib MF, Mohamad MAN, Abdul Hamid AA, Kaya Y, Huyop F. Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1840437] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
- Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ekiti State, Nigeria
| | - Roswanira Abdul Wahab
- Faculty of Science, Department of Chemistry, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
| | - Mohamed Faraj Edbeib
- Faculty of Medical Technology, Department of Medical Laboratories, Baniwalid University, Baniwalid, Libya
| | - Mohd Azrul Naim Mohamad
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
| | - Azzmer Azzar Abdul Hamid
- Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia (IIUM), Kuantan Pahang, Malaysia
| | - Yilmaz Kaya
- Agriculture Faculty, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
| | - Fahrul Huyop
- Faculty of Science, Department of Biosciences, Universiti Teknologi Malaysia, UTM Johor Bahru, Johor, Malaysia
- Agriculture Faculty, Department of Agricultural Biotechnology, Ondokuz Mayis University, Samsun, Turkey
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41
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Oyewusi HA, Huyop F, Wahab RA. Molecular docking and molecular dynamics simulation of Bacillus thuringiensis dehalogenase against haloacids, haloacetates and chlorpyrifos. J Biomol Struct Dyn 2020; 40:1979-1994. [PMID: 33094694 DOI: 10.1080/07391102.2020.1835727] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The high dependency and surplus use of agrochemical products have liberated enormous quantities of toxic halogenated pollutants into the environment and threaten the well-being of humankind. Herein, this study performed molecular docking, molecular dynamic (MD) simulations, molecular mechanics-Poisson Boltzmann Surface Area (MM-PBSA) calculations on the DehH2 from Bacillus thuringiensis, to identify the order of which the enzyme degrades different substrates, haloacids, haloacetate and chlorpyrifos. The study discovered that the DehH2 favored the degradation of haloacids and haloacetates (-3.3 - 4.6 kcal/mol) and formed three hydrogen bonds with Asp125, Arg201 and Lys202. Despite the inconclusive molecular docking result, chlorpyrifos was consistently shown to be the least favored substrate of the DehH2 in MD simulations and MM-PBSA calculations. Results of MD simulations revealed the DehH2-haloacid- (RMSD 0.15 - 0.25 nm) and DehH2-haloacetates (RMSF 0.05 - 0.25 nm) were more stable, with the DehH2-L-2CP complex being the most stable while the least was the DehH2-chlorpyrifos (RMSD 0.295 nm; RMSF 0.05 - 0.59 nm). The Molecular Mechanics Poisson-Boltzmann Surface Area calculations showed the DehH2-L-2CP complex (-24.27 kcal/mol) having the lowest binding energy followed by DehH2-MCA (-22.78 kcal/mol), DehH2-D-2CP (-21.82 kcal/mol), DehH2-3CP (-21.11 kcal/mol), DehH2-2,2-DCP (-18.34 kcal/mol), DehH2-2,3-DCP (-8.34 kcal/mol), DehH2-TCA (-7.62 kcal/mol), while chlorpyrifos was unable to spontaneously bind to DehH2 (+127.16 kcal/mol). In a nutshell, the findings of this study offer valuable insights into the rational tailoring of the DehH2 for expanding its substrate specificity and catalytic activity in the near future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Habeebat Adekilekun Oyewusi
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Biochemistry, School of Science and Computer Studies, Federal Polytechnic Ado Ekiti, Ado Ekiti PMB, Ekiti State, Nigeria
| | - Fahrul Huyop
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
| | - Roswanira Abdul Wahab
- Enzyme Technology and Green Synthesis Research Group, Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia.,Department of Chemistry, Faculty of Science, Universiti Teknologi Malaysia, Johor, Malaysia
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Lavrentyeva EV, Banzaraktsaeva TG, Radnagurueva AA, Buryukhaev SP, Dambaev VB, Baturina OA, Kozyreva LP, Barkhutova DD. Microbial Community of Umkhei Thermal Lake (Baikal Rift Zone) in the Groundwater Discharge Zone. CONTEMP PROBL ECOL+ 2020. [DOI: 10.1134/s1995425519060088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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43
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Study on the osmoregulation of "Halomonas socia" NY-011 and the degradation of organic pollutants in the saline environment. Extremophiles 2020; 24:843-861. [PMID: 32930883 DOI: 10.1007/s00792-020-01199-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
"Halomonas socia" NY-011, a new species of moderately halophilic bacteria isolated and identified in our laboratory, can grow in high concentrations of salt ranging from 0.5 to 25%. In this study, the whole genome of NY-011 was sequenced and a detailed analysis of the genomic features was provided. Especially, a series of genes related to salt tolerance and involved in xenobiotics biodegradation were annotated by COG, GO and KEGG analyses. Subsequently, RNA-Seq-based transcriptome analysis was applied to explore the osmotic regulation of NY-011 subjected to high salt stress for different times (0 h, 1 h, 3 h, 6 h, 11 h, 15 h). And we found that the genes related to osmoregulation including excluding Na+ and accumulating K+ as well as the synthesis of compatible solutes (alanine, glutamate, ectoine, hydroxyectoine and glycine betaine) were up-regulated, while the genes involved in the degradation of organic compounds were basically down-regulated during the whole process. Specifically, the expression trend of genes related to osmoregulation increased firstly then dropped, which was almost opposite to that of degrading organic pollutants genes. With the prolongation of osmotic up-shock, NY-011 survived and gradually adapted to osmotic stress, the above-mentioned two classes of genes slowly returned to normal expression level. Then, the scanning electron microscope (SEM) and transmission electron microscope (TEM) were also utilized to observe morphological properties of NY-011 under hypersaline stress, and our findings showed that the cell length of NY-011 became longer under osmotic stress, at the same time, polyhydroxyalkanoates (PHAs) were synthesized in the cells. Besides, physiological experiments confirmed that NY-011 could degrade organic compounds in a high salt environment. These data not only provide valuable insights into the mechanism of osmotic regulation of NY-011; but also make it possible for NY-011 to be exploited for biotechnological applications such as degrading organic pollutants in a hypersaline environment.
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Process Optimization of Palm Oil Mill Effluent-Based Biosurfactant of Halomonas meridiana BK-AB4 Originated from Bledug Kuwu Mud Volcano in Central Java for Microbial Enhanced Oil Recovery. Processes (Basel) 2020. [DOI: 10.3390/pr8060716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Biosurfactants are one of the microbial bioproducts that are in most demand from microbial-enhanced oil recovery (MEOR). The production of biosurfactant is still a relatively high cost. Therefore, this study aims to reduce production costs by utilizing palm oil mill effluent (POME) as the main carbon source. This work examines the optimal conditions of biosurfactant production by Halomonas meridiana BK-AB4 isolated from the Bledug Kuwu mud volcano in Central Java Indonesia and studies it for EOR applications. The biosurfactant production stage was optimized by varying POME concentration, incubation time, NaCl concentration, and pH to obtain the maximum oil displacement area (ODA) values. A response surface methodology (RSM) and a central composite design (CCD) were used to identify the influence of each variable and to trace the relationship between variables. Optimum biosurfactant production was found at a POME concentration (v/v) of 16%, incubation (h) of 112, NaCl concentration (w/v) of 4.7%, pH of 6.5, with an oil displacement area of 3.642 cm. The LC-MS and FTIR analysis revealed the functional groups of carboxylic acid or esters, which indicated that the biosurfactant produced belonged to the fatty acid class. The lowest IFT value was obtained at the second and seventh-day observations at a concentration of 500 mg/L, i.e., 0.03 mN/m and 0.06 mN/m. The critical micelle concentration (CMC) of biosurfactant was about 350 mg/L with a surface tension value of about 54.16 mN/m. The highest emulsification activity (E24 = 76%) in light crude oil (naphthenic–naphthenic) and could reduce the interfacial tension between oil and water up to 0.18 mN/m. The imbibition experiment with biosurfactant results in 23.89% additional oil recovery for 60 h of observation, with the highest increase in oil recovery occurring at the 18th hour, which is 2.72%. Therefore, this bacterium and its biosurfactant show potential, and the bacterium are suitable for use in MEOR applications.
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Alternative Bioremediation Agents against Haloacids, Haloacetates and Chlorpyrifos Using Novel Halogen-Degrading Bacterial Isolates from the Hypersaline Lake Tuz. Catalysts 2020. [DOI: 10.3390/catal10060651] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The indiscriminate use of chemical pesticides alongside the expansion of large-scale industries globally can critically jeopardize marine ecology and the well-being of mankind. This is because the agricultural runoffs and industrial effluents eventually enter waterways before flowing into highly saline environments i.e., oceans. Herein, the study assessed two novel bacterial isolates, Bacillus subtilis strain H1 and Bacillus thuringiensis strain H2 from the hypersaline Lake Tuz in Turkey to degrade recalcitrant haloalkanoic acids, haloacetates and chlorpyrifos, and consequently, identify their optimal pollutant concentrations, pH and temperature alongside salt-tolerance thresholds. Bacillus strains H1 and H2 optimally degraded 2,2-dichloropropionic acid (2,2-DCP) under similar incubation conditions (pH 8.0, 30 °C), except the latter preferred a higher concentration of pollutants as well as salinity at 30 mM and 35%, respectively, while strain H1 grew well on 20 mM at <30%. While both isolates could degrade all substrates used, the dehalogenase gene from strain H1 could not be amplified. Capacity of the H2 bacterial isolate to degrade 2,2-DCP was affirmed by the detection of the 795 bp putative halotolerant dehalogenase gene after a successful polymerase chain reaction (PCR) amplification. Hence, the findings envisage the potential of both isolates as bio-degraders of recalcitrant halogenated compounds and those of the same chemical family as chlorpyrifos, in saline environments.
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46
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Torregrosa-Crespo J, Pire C, Bergaust L, Martínez-Espinosa RM. Haloferax mediterranei, an Archaeal Model for Denitrification in Saline Systems, Characterized Through Integrated Physiological and Transcriptional Analyses. Front Microbiol 2020; 11:768. [PMID: 32390995 PMCID: PMC7188791 DOI: 10.3389/fmicb.2020.00768] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 03/31/2020] [Indexed: 11/13/2022] Open
Abstract
Haloferax mediterranei (R4) belongs to the group of halophilic archaea, one of the predominant microbial populations in hypersaline environments. In these ecosystems, the low availability of oxygen pushes the microbial inhabitants toward anaerobic pathways and the presence of N-oxyanions favor denitrification. In a recent study comparing three Haloferax species carrying dissimilatory N-oxide reductases, H. mediterranei showed promise as a future model for archaeal denitrification. This work further explores the respiratory physiology of this haloarchaeon when challenged with ranges of nitrite and nitrate concentrations and at neutral or sub-neutral pH during the transition to anoxia. Moreover, to begin to understand the transcriptional regulation of N-oxide reductases, detailed gas kinetics was combined with gene expression analyses at high resolution. The results show that H. mediterranei has an expression pattern similar to that observed in the bacterial Domain, well-coordinated at low concentrations of N-oxyanions. However, it could only sustain a few generations of exponential anaerobic growth, apparently requiring micro-oxic conditions for de novo synthesis of denitrification enzymes. This is the first integrated study within this field of knowledge in haloarchaea and Archaea in general, and it sheds lights on denitrification in salty environments.
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Affiliation(s)
- Javier Torregrosa-Crespo
- Department of Agrochemistry and Biochemistry, Faculty of Science, University of Alicante, Alicante, Spain
| | - Carmen Pire
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Linda Bergaust
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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47
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Mitra R, Xu T, Xiang H, Han J. Current developments on polyhydroxyalkanoates synthesis by using halophiles as a promising cell factory. Microb Cell Fact 2020; 19:86. [PMID: 32264891 PMCID: PMC7137286 DOI: 10.1186/s12934-020-01342-z] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 03/26/2020] [Indexed: 11/17/2022] Open
Abstract
Plastic pollution is a severe threat to our environment which necessitates implementation of bioplastics to realize sustainable development for a green world. Polyhydroxyalkanoates (PHA) represent one of the potential candidates for these bioplastics. However, a major challenge faced by PHA is the high production cost which limits its commercial application. Halophiles are considered to be a promising cell factory for PHA synthesis due to its several unique characteristics including high salinity requirement preventing microbial contamination, high intracellular osmotic pressure allowing easy cell lysis for PHA recovery, and capability to utilize wide spectrum of low-cost substrates. Optimization of fermentation parameters has made it plausible to achieve large-scale production at low cost by using halophiles. Further deeper insights into halophiles have revealed the existence of diversified and even novel PHA synthetic pathways within different halophilic species that greatly affects PHA type. Thus, precise metabolic engineering of halophiles with the help of advanced tools and strategies have led to more efficient microbial cell factory for PHA production. This review is an endeavour to summarize the various research achievements in these areas which will help the readers to understand the current developments as well as the future efforts in PHA research.
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Affiliation(s)
- Ruchira Mitra
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,International College, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Tong Xu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. .,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. .,College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
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48
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Sharma AK, Kikani BA, Singh SP. Biochemical, thermodynamic and structural characteristics of a biotechnologically compatible alkaline protease from a haloalkaliphilic, Nocardiopsis dassonvillei OK-18. Int J Biol Macromol 2020; 153:680-696. [PMID: 32145232 DOI: 10.1016/j.ijbiomac.2020.03.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 02/27/2020] [Accepted: 03/02/2020] [Indexed: 01/02/2023]
Abstract
This report describes purification strategies, biochemical properties and thermodynamic analysis of an alkaline serine protease from a marine actinomycete, Nocardiopsis dassonvillei strain OK-18. The solvent tolerance, broad thermal-pH stability, favourable kinetics and thermodynamics suggest stability of the enzymatic reaction. The enzyme was active in the range of pH 7-12 and 37-90 °C, optimally at pH 9 and 70 °C. The deactivation rate constant (Kd), half-life (t½), enthalpy (ΔH*), entropy (ΔS*), activation energy (E) and change in free energy (ΔG*) suggested stability and spontaneity of the reaction. β-Sheets as revealed by the Circular dichroism (CD) spectroscopy, were the major elements in the secondary structure of the enzyme, while Fourier-transform infrared spectroscopy (FTIR) indicated the presence of amide I and amide II. Based on the liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QToF-MS) analysis, the amino acid sequence had only 38% similarity with other proteases of Nocardiopsis strains, suggesting its novelty. The Ramachandran Plot revealed the location of the amino acid residues in the most favored region. The blood de-staining, gelatin hydrolysis, silver recovery and deproteinization of crab shells established the biotechnological potential of the enzyme.
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Affiliation(s)
- Amit K Sharma
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India
| | - Bhavtosh A Kikani
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360 005, Gujarat, India.
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Varrella S, Tangherlini M, Corinaldesi C. Deep Hypersaline Anoxic Basins as Untapped Reservoir of Polyextremophilic Prokaryotes of Biotechnological Interest. Mar Drugs 2020; 18:md18020091. [PMID: 32019162 PMCID: PMC7074082 DOI: 10.3390/md18020091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 12/18/2022] Open
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are considered to be among the most extreme ecosystems on our planet, allowing only the life of polyextremophilic organisms. DHABs’ prokaryotes exhibit extraordinary metabolic capabilities, representing a hot topic for microbiologists and biotechnologists. These are a source of enzymes and new secondary metabolites with valuable applications in different biotechnological fields. Here, we review the current knowledge on prokaryotic diversity in DHABs, highlighting the biotechnological applications of identified taxa and isolated species. The discovery of new species and molecules from these ecosystems is expanding our understanding of life limits and is expected to have a strong impact on biotechnological applications.
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Affiliation(s)
- Stefano Varrella
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy;
| | | | - Cinzia Corinaldesi
- Department of Materials, Environmental Sciences and Urban Planning, Polytechnic University of Marche, 60131 Ancona, Italy;
- Correspondence:
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50
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Ruginescu R, Purcărea C, Dorador C, Lavin P, Cojoc R, Neagu S, Lucaci I, Enache M. Exploring the hydrolytic potential of cultured halophilic bacteria isolated from the Atacama Desert. FEMS Microbiol Lett 2019; 366:5613365. [DOI: 10.1093/femsle/fnz224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 10/31/2019] [Indexed: 01/23/2023] Open
Abstract
ABSTRACTConsidering that most industrial processes are carried out under harsh physicochemical conditions, which would inactivate enzymes from commonly isolated mesophilic organisms, current studies are geared toward the identification of extremophilic microorganisms producing enzymes resistant to extreme salt concentrations, temperature and pH. Among the extremophiles, halophilic microorganisms are an important source of salt-tolerant enzymes that can be used in varying biotechnological applications. In this context, the aim of the present work was to isolate and identify halophiles producing hydrolases from the Atacama Desert, one of the harshest environments on Earth. Isolates were recovered from halite samples and screened for the presence of seven different hydrolase activities (amylase, caseinase, gelatinase, lipase, pectinase, cellulase and inulinase) using agar plate-based assays. From a total of 23 halophilic bacterial isolates, most showed lipolytic (19 strains) and pectinolytic (11 strains) activities. The molecular identification of eight selected isolates showed a strong similarity to members of the Halomonas and Idiomarina genera. Therefore, the present study represents a preliminary, but essential, step to identify novel biological sources of extremozymes in an environment once thought to be devoid of life.
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Affiliation(s)
- Robert Ruginescu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Cristina Purcărea
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, 601 Angamos Av., Antofagasta, 1240000, Chile
| | - Paris Lavin
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, 601 Angamos Av., Antofagasta, 1240000, Chile
| | - Roxana Cojoc
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Simona Neagu
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Ioana Lucaci
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
| | - Mădălin Enache
- Department of Microbiology, Institute of Biology Bucharest of the Romanian Academy, 296 Splaiul Independentei, Bucharest, 060031, Romania
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