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Moopantakath J, Imchen M, Anju VT, Busi S, Dyavaiah M, Martínez-Espinosa RM, Kumavath R. Bioactive molecules from haloarchaea: Scope and prospects for industrial and therapeutic applications. Front Microbiol 2023; 14:1113540. [PMID: 37065149 PMCID: PMC10102575 DOI: 10.3389/fmicb.2023.1113540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Marine environments and salty inland ecosystems encompass various environmental conditions, such as extremes of temperature, salinity, pH, pressure, altitude, dry conditions, and nutrient scarcity. The extremely halophilic archaea (also called haloarchaea) are a group of microorganisms requiring high salt concentrations (2–6 M NaCl) for optimal growth. Haloarchaea have different metabolic adaptations to withstand these extreme conditions. Among the adaptations, several vesicles, granules, primary and secondary metabolites are produced that are highly significant in biotechnology, such as carotenoids, halocins, enzymes, and granules of polyhydroxyalkanoates (PHAs). Among halophilic enzymes, reductases play a significant role in the textile industry and the degradation of hydrocarbon compounds. Enzymes like dehydrogenases, glycosyl hydrolases, lipases, esterases, and proteases can also be used in several industrial procedures. More recently, several studies stated that carotenoids, gas vacuoles, and liposomes produced by haloarchaea have specific applications in medicine and pharmacy. Additionally, the production of biodegradable and biocompatible polymers by haloarchaea to store carbon makes them potent candidates to be used as cell factories in the industrial production of bioplastics. Furthermore, some haloarchaeal species can synthesize nanoparticles during heavy metal detoxification, thus shedding light on a new approach to producing nanoparticles on a large scale. Recent studies also highlight that exopolysaccharides from haloarchaea can bind the SARS-CoV-2 spike protein. This review explores the potential of haloarchaea in the industry and biotechnology as cellular factories to upscale the production of diverse bioactive compounds.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - V. T. Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Rosa María Martínez-Espinosa
- Biochemistry, Molecular Biology, Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Alicante, Spain
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Alicante, Spain
- Rosa María Martínez-Espinosa,
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- *Correspondence: Ranjith Kumavath, ,
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Nishikawa Y, Kogawa M, Hosokawa M, Wagatsuma R, Mineta K, Takahashi K, Ide K, Yura K, Behzad H, Gojobori T, Takeyama H. Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater. ISME COMMUNICATIONS 2022; 2:92. [PMID: 37938694 PMCID: PMC9723564 DOI: 10.1038/s43705-022-00179-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 04/26/2023]
Abstract
Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1-25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.
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Affiliation(s)
- Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Masato Kogawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
| | - Ryota Wagatsuma
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Katsuhiko Mineta
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kai Takahashi
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Keigo Ide
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
| | - Kei Yura
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan.
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169-8555, Japan.
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Baeshen M, Alkaladi A, Alhejen A, Bataweel N, Abdelkader H, Suliman abuzahrah S. Exploring the Taxonomic and Functional Diversity of Marine Benthic Micro-Eukaryotes Along the Red Sea Coast of Jeddah City. Saudi J Biol Sci 2022; 29:103342. [PMID: 35846388 PMCID: PMC9278075 DOI: 10.1016/j.sjbs.2022.103342] [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: 12/15/2021] [Revised: 05/07/2022] [Accepted: 06/10/2022] [Indexed: 11/16/2022] Open
Abstract
Backgrounds Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential. Methods Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples. Results Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c). Conclusion Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.
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Alma'abadi A, Behzad H, Alarawi M, Conchouso D, Saito Y, Hosokawa M, Nishikawa Y, Kogawa M, Takeyama H, Mineta K, Gojobori T. Identification of Lipolytic Enzymes Using High-Throughput Single-cell Screening and Sorting of a Metagenomic Library. N Biotechnol 2022; 70:102-108. [PMID: 35636700 DOI: 10.1016/j.nbt.2022.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/19/2022] [Accepted: 05/24/2022] [Indexed: 11/19/2022]
Abstract
The demand for novel, robust microbial biocatalysts for use in industrial and pharmaceutical applications continues to increase rapidly. As a result, there is a need to develop advanced tools and technologies to exploit the vast metabolic potential of unculturable microorganisms found in various environments. Single-cell and functional metagenomics studies can explore the enzymatic potential of entire microbial communities in a given environment without the need to culture the microorganisms. This approach has contributed substantially to the discovery of unique microbial genes for industrial and medical applications. Functional metagenomics involves the extraction of microbial DNA directly from environmental samples, constructing expression libraries comprising the entire microbial genome, and screening of the libraries for the presence of desired phenotypes. In this study, lipolytic enzymes from the Red Sea were targeted. A high-throughput single-cell microfluidic platform combined with a laser-based fluorescent screening bioassay was employed to discover new genes encoding lipolytic enzymes. Analysis of the metagenomic library led to the identification of three microbial genes encoding lipases based on their functional similarity and sequence homology to known lipases. The results demonstrated that microfluidics is a robust technology that can be used for screening in functional metagenomics. The results also indicate that the Red Sea is a promising, under-investigated source of new genes and gene products.
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Affiliation(s)
- Amani Alma'abadi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, National Center of Biotechnology, P.O Box 6086, Riyadh 11442, Saudi Arabia
| | - Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - David Conchouso
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Puebla 72453, Mexico
| | - Yoshimoto Saito
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Marine Open Innovation (MaOI) Institute, 9-25, Hinodecho, Shimizu-ku, Shizuoka 424-0922, Japan
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
| | - Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
| | - Masato Kogawa
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan; Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-0072, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia; Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Behzad H, Ohyanagi H, Alharbi B, Ibarra M, Alarawi M, Saito Y, Duarte CM, Bajic V, Mineta K, Gojobori T. A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota. BMC Genomics 2022; 23:277. [PMID: 35392799 PMCID: PMC8991508 DOI: 10.1186/s12864-022-08485-w] [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: 04/20/2021] [Accepted: 03/21/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters. RESULTS We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month. CONCLUSION Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.
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Affiliation(s)
- Hayedeh Behzad
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Hajime Ohyanagi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Badr Alharbi
- National Centre for Environmental Technology, King Abdulaziz City for Science and Technology, Riyadh, 11442, Saudi Arabia
| | - Martin Ibarra
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yoshimoto Saito
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Marine Open Innovation (MaOI) Institute, Shizuoka, 424-0922, Japan
| | - Carlos M Duarte
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia. .,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Wang Y, Bao G. Diversity of prokaryotic microorganisms in alkaline saline soil of the Qarhan Salt Lake area in the Qinghai-Tibet Plateau. Sci Rep 2022; 12:3365. [PMID: 35233041 PMCID: PMC8888737 DOI: 10.1038/s41598-022-07311-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/14/2022] [Indexed: 12/20/2022] Open
Abstract
The composition of microbial communities varies considerably across ecological environments, particularly in extreme environments, where unique microorganisms are typically used as the indicators of environmental conditions. However, the ecological reasons for the differences in microbial communities remain largely unknown. Herein, we analyzed taxonomic and functional community profiles via high-throughput sequencing to determine the alkaline saline soil bacterial and archaeal communities in the Qarhan Salt Lake area in the Qinghai–Tibet Plateau. The results showed that Betaproteobacteria (Proteobacteria) and Halobacteria (Euryarchaeota) were the most abundant in the soils of this area, which are common in high salinity environments. Accordingly, microbes that can adapt to local extremes typically have unique metabolic pathways and functions, such as chemoheterotrophy, aerobic chemoheterotrophy, nitrogen fixation, ureolysis, nitrate reduction, fermentation, dark hydrogen oxidation, and methanogenesis. Methanogenesis pathways include hydrogenotrophic methanogenesis, CO2 reduction with H2, and formate methanogenesis. Thus, prokaryotic microorganisms in high salinity environments are indispensable in nitrogen and carbon cycling via particular metabolic pathways.
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Affiliation(s)
- Yaqiong Wang
- School of Ecology, Environment and Resources, Qinghai Minzu University, Bayi Road, Xining, 810007, Qinghai, China. .,Qinghai Provincial Key Laboratory of High-Value Utilization of Characteristic Economic Plants, Xining, 810007, China. .,Qinghai Provincial Biotechnology and Analytical Test Key Laboratory, Tibetan Plateau Juema Research Centre, Xining, 810007, China.
| | - Guoyuan Bao
- School of Ecology, Environment and Resources, Qinghai Minzu University, Bayi Road, Xining, 810007, Qinghai, China
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Renn D, Shepard L, Vancea A, Karan R, Arold ST, Rueping M. Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. Front Microbiol 2021; 12:732856. [PMID: 34777282 PMCID: PMC8578733 DOI: 10.3389/fmicb.2021.732856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.
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Affiliation(s)
- Dominik Renn
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Organic Chemistry, RWTH Aachen, Aachen, Germany
| | - Lera Shepard
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ram Karan
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging (ExMI), University Clinic, RWTH Aachen, Aachen, Germany
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8
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Fatani S, Saito Y, Alarawi M, Gojobori T, Mineta K. Genome sequencing and identification of cellulase genes in Bacillus paralicheniformis strains from the Red Sea. BMC Microbiol 2021; 21:254. [PMID: 34548024 PMCID: PMC8456639 DOI: 10.1186/s12866-021-02316-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 09/08/2021] [Indexed: 11/23/2022] Open
Abstract
Background Cellulolytic microorganisms are considered a key player in the degradation of plant biomass in various environments. These microorganisms can be isolated from various environments, such as soils, the insect gut, the mammalian rumen and oceans. The Red Sea exhibits a unique environment in terms of presenting a high seawater temperature, high salinity, low nutrient levels and high biodiversity. However, there is little information regarding cellulase genes in the Red Sea environment. This study aimed to examine whether the Red Sea can be a resource for the bioprospecting of microbial cellulases by isolating cellulase-producing microorganisms from the Red Sea environment and characterizing cellulase genes. Results Three bacterial strains were successfully isolated from the plankton fraction and the surface of seagrass. The isolated strains were identified as Bacillus paralicheniformis and showed strong cellulase activity. These results suggested that these three isolates secreted active cellulases. By whole genome sequencing, we found 10 cellulase genes from the three isolates. We compared the expression of these cellulase genes under cellulase-inducing and non-inducing conditions and found that most of the cellulase genes were generally upregulated during cellulolysis in the isolates. Our operon structure analysis also showed that cellulase genes form operons with genes involved in various kinds of cellular reactions, such as protein metabolism, which suggests the existence of crosstalk between cellulolysis and other metabolic pathways in the bacterial isolates. These results suggest that multiple cellulases are playing important roles in cellulolysis. Conclusions Our study reports the isolation and characterization of cellulase-producing bacteria from the Red Sea. Our whole-genome sequencing classified our three isolates as Bacillus paralicheniformis, and we revealed the presence of ten cellulase orthologues in each of three isolates’ genomes. Our comparative expression analysis also identified that most of the cellulase genes were upregulated under the inducing conditions in general. Although cellulases have been roughly classified into three enzyme groups of beta-glucosidase, endo-β-1,4-glucanase and exoglucanase, these findings suggest the importance to consider microbial cellulolysis as a more complex reaction with various kinds of cellulase enzymes. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02316-w.
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Affiliation(s)
- Siham Fatani
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yoshimoto Saito
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Open Innovation Institute (MaOI), Shizuoka, Japan
| | - Mohammed Alarawi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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9
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Wambua S, Gourlé H, de Villiers EP, Karlsson-Lindsjö O, Wambiji N, Macdonald A, Bongcam-Rudloff E, de Villiers S. Cross-Sectional Variations in Structure and Function of Coral Reef Microbiome With Local Anthropogenic Impacts on the Kenyan Coast of the Indian Ocean. Front Microbiol 2021; 12:673128. [PMID: 34248882 PMCID: PMC8260691 DOI: 10.3389/fmicb.2021.673128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
Coral reefs face an increased number of environmental threats from anthropomorphic climate change and pollution from agriculture, industries and sewage. Because environmental changes lead to their compositional and functional shifts, coral reef microbial communities can serve as indicators of ecosystem impacts through development of rapid and inexpensive molecular monitoring tools. Little is known about coral reef microbial communities of the Western Indian Ocean (WIO). We compared taxonomic and functional diversity of microbial communities inhabiting near-coral seawater and sediments from Kenyan reefs exposed to varying impacts of human activities. Over 19,000 species (bacterial, viral and archaeal combined) and 4,500 clusters of orthologous groups of proteins (COGs) were annotated. The coral reefs showed variations in the relative abundances of ecologically significant taxa, especially copiotrophic bacteria and coliphages, corresponding to the magnitude of the neighboring human impacts in the respective sites. Furthermore, the near-coral seawater and sediment metagenomes had an overrepresentation of COGs for functions related to adaptation to diverse environments. Malindi and Mombasa marine parks, the coral reef sites closest to densely populated settlements were significantly enriched with genes for functions suggestive of mitigation of environment perturbations including the capacity to reduce intracellular levels of environmental contaminants and repair of DNA damage. Our study is the first metagenomic assessment of WIO coral reef microbial diversity which provides a much-needed baseline for the region, and points to a potential area for future research toward establishing indicators of environmental perturbations.
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Affiliation(s)
- Sammy Wambua
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, Kenya.,Department of Biological Sciences, Pwani University, Kilifi, Kenya
| | - Hadrien Gourlé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Etienne P de Villiers
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.,Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Oskar Karlsson-Lindsjö
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nina Wambiji
- Kenya Marine and Fisheries Research Institute, Mombasa, Kenya
| | - Angus Macdonald
- School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Erik Bongcam-Rudloff
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Santie de Villiers
- Pwani University Bioscience Research Centre (PUBReC), Pwani University, Kilifi, Kenya.,Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
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10
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Conchouso D, Al-Ma'abadi A, Behzad H, Alarawi M, Hosokawa M, Nishikawa Y, Takeyama H, Mineta K, Gojobori T. Integration of Droplet Microfluidic Tools for Single-Cell Functional Metagenomics: An Engineering Head Start. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 19:504-518. [PMID: 34952209 PMCID: PMC8864243 DOI: 10.1016/j.gpb.2021.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 02/09/2021] [Accepted: 03/09/2021] [Indexed: 11/25/2022]
Abstract
Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput. However, their adoption in laboratories studying “-omics” sciences is still irrelevant due to the complex and multidisciplinary nature of the field. To facilitate their use, here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput. First, a device encapsulating single cells in droplets at a rate of ∼250 Hz is described considering droplet size and cell growth. Then, we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers (i.e., 405, 488, 561, and 637 nm) in a single platform to make it compatible with different fluorescence-emitting biosensors. For this sorter, both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz. Then, a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz. Finally, we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools. Because of the overall integration and the technical details presented here, our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability (>50,000 cells/day) for mining and bioprospecting metagenomic data
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Affiliation(s)
- David Conchouso
- Department of Industrial and Mechanical Engineering, Universidad de las Américas Puebla, Puebla 72810, Mexico; Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Amani Al-Ma'abadi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Hayedeh Behzad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Mohammed Alarawi
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Masahito Hosokawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan
| | - Yohei Nishikawa
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Haruko Takeyama
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo 162-0041, Japan; Department of Life Science and Medical Bioscience, Waseda University, Tokyo 162-8480, Japan; Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo 169-8555, Japan; Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, Tokyo 169-0072, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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11
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El-Hossary EM, Abdel-Halim M, Ibrahim ES, Pimentel-Elardo SM, Nodwell JR, Handoussa H, Abdelwahab MF, Holzgrabe U, Abdelmohsen UR. Natural Products Repertoire of the Red Sea. Mar Drugs 2020; 18:md18090457. [PMID: 32899763 PMCID: PMC7551641 DOI: 10.3390/md18090457] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
Marine natural products have achieved great success as an important source of new lead compounds for drug discovery. The Red Sea provides enormous diversity on the biological scale in all domains of life including micro- and macro-organisms. In this review, which covers the literature to the end of 2019, we summarize the diversity of bioactive secondary metabolites derived from Red Sea micro- and macro-organisms, and discuss their biological potential whenever applicable. Moreover, the diversity of the Red Sea organisms is highlighted as well as their genomic potential. This review is a comprehensive study that compares the natural products recovered from the Red Sea in terms of ecological role and pharmacological activities.
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Affiliation(s)
- Ebaa M. El-Hossary
- National Centre for Radiation Research & Technology, Egyptian Atomic Energy Authority, Ahmed El-Zomor St. 3, El-Zohoor Dist., Nasr City, Cairo 11765, Egypt;
| | - Mohammad Abdel-Halim
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Eslam S. Ibrahim
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt;
- Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2/Bau D15, 97080 Würzburg, Germany
| | - Sheila Marie Pimentel-Elardo
- Department of Biochemistry, University of Toronto, MaRS Centre West, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (S.M.P.-E.); (J.R.N.)
| | - Justin R. Nodwell
- Department of Biochemistry, University of Toronto, MaRS Centre West, 661 University Avenue, Toronto, ON M5G 1M1, Canada; (S.M.P.-E.); (J.R.N.)
| | - Heba Handoussa
- Department of Pharmaceutical Biology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Miada F. Abdelwahab
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
| | - Ulrike Holzgrabe
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
- Correspondence: (U.H.); (U.R.A.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt;
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, P.O. Box 61111 New Minia City, Minia 61519, Egypt
- Correspondence: (U.H.); (U.R.A.)
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12
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Cycil LM, DasSarma S, Pecher W, McDonald R, AbdulSalam M, Hasan F. Metagenomic Insights Into the Diversity of Halophilic Microorganisms Indigenous to the Karak Salt Mine, Pakistan. Front Microbiol 2020; 11:1567. [PMID: 32793134 PMCID: PMC7386132 DOI: 10.3389/fmicb.2020.01567] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 06/16/2020] [Indexed: 11/13/2022] Open
Abstract
Hypersaline regions are terrestrial analogs of the Earth’s primitive ecosystem and extraterrestrial environment. The salt range in Pakistan is considered among a few of the ancient salt deposits in the subcontinent. Karak salt mine is situated at the Northwest end in Pakistan. Despite the fact that halophiles initiated the formation of terrestrial ecosystems, their products and identities remain hidden. Some preliminary studies limited to culture-dependent isolations have been reported. Characterizing the microbiome that spans over centuries of ecosystem development is crucial, given their role in shaping landscape succession and biogeochemical cycles. Here, we used metagenomics techniques to explore the microbial diversity of the Karak salt mine. We used 16S rRNA Illumina amplicon sequencing to characterize the halophilic communities entrapped in Karak mine. The results were interpreted using Illumina Basespace, QIIME, and Cytoscape. Cultures were isolated at 16–25% salinity. Metagenomics data was consistent with our preliminary culturing data, indicating remarkable species to strain-level diversity of unique halophiles. A total of 107,099 (brine) and 122,679 (salt) reads were obtained. 16S rRNA based sequencing revealed a microbiome with bacteria (66% brine and 72% salt) dominated by Bacteroidetes and Proteobacteria with a strikingly high abundance of Archaea (18% brine and 13% salt). Alpha diversity has higher values in salt than in the brine. The study of the halophiles in the Karak salt mine provides clues for species contributing to the maintenance of biogeochemical cycles of the ecosystem. This is the first report of a metagenomic study of any hypersaline region of Pakistan.
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Affiliation(s)
- Leena Mavis Cycil
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.,Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Wolf Pecher
- Institute of Marine and Environmental Technology, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States.,Yale Gordon College of Arts and Sciences, University of Baltimore, Baltimore, MD, United States
| | - Ryan McDonald
- Institute of Marine and Environmental Technology, Department of Marine Biotechnology, University of Maryland, Baltimore County, Baltimore, MD, United States
| | - Maria AbdulSalam
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fariha Hasan
- Applied Environmental and Geomicrobiology Laboratory, Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
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13
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AbdelWahed MG, Badiea EA, Ouf A, Sayed AA. Molecular and functional characterization of unique thermo-halophilic thioredoxin from the metagenome of an exotic environment. Int J Biol Macromol 2020; 153:767-778. [PMID: 32142845 DOI: 10.1016/j.ijbiomac.2020.03.011] [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: 10/10/2019] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 11/30/2022]
Abstract
The lower convective layer (LCL) at Atlantis II brine pool of the Red sea represents one of the exceptional, unique ecosystems. Thioredoxin is a multi-functional antioxidant redox protein that has a crucial role in various vital cellular processes. In the current study, a functional metagenomics approach was used to isolate and characterize thioredoxin from the LCL of Atlantis II Deep brine pool (Trx-ATII). From the metagenomic DNA of the LCL, the thioredoxin gene was directly retrieved and sequenced. Sequence analysis showed that the gene belonged to thioredoxin-like superfamily with classical Trx motif (-CXXC-). Phylogenetic analysis revealed that Trx-ATII was closely related to Trx of Prochlorococcus marinus with a maximum identity of 86%. Successfully, Trx-ATII was cloned and expressed in E. coli, where the purified protein had M.wt of 16 kDa. Characterization studies revealed that Trx-ATII protein is halophilic; can tolerate up to 2.5 M NaCl and thermostable, where 90% of its activity was retained at 60 °C. Trx-ATII can reduce both DTNB and insulin disulfide- containing substrates. In conclusion, a unique thioredoxin protein was isolated from a harsh environment that can maintain its activity under extreme conditions of salinity and temperature as a promising redox protein for biotechnological applications.
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Affiliation(s)
| | - Elham A Badiea
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Amged Ouf
- Biology Department, American University in Cairo, Egypt
| | - Ahmed A Sayed
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt; Children Cancer Hospital, 57357 Cairo, Egypt.
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14
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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15
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Alqahtani MF, Bajracharya S, Katuri KP, Ali M, Ragab A, Michoud G, Daffonchio D, Saikaly PE. Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool. Front Microbiol 2019; 10:2563. [PMID: 31787955 PMCID: PMC6855130 DOI: 10.3389/fmicb.2019.02563] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/23/2019] [Indexed: 11/13/2022] Open
Abstract
Homoacetogens are efficient CO2 fixing bacteria using H2 as electron donor to produce acetate. These organisms can be enriched at the biocathode of microbial electrosynthesis (MES) for electricity-driven CO2 reduction to acetate. Studies exploring homoacetogens in MES are mainly conducted using pure or mix-culture anaerobic inocula from samples with standard environmental conditions. Extreme marine environments host unique microbial communities including homoacetogens that may have unique capabilities due to their adaptation to harsh environmental conditions. Anaerobic deep-sea brine pools are hypersaline and metalliferous environments and homoacetogens can be expected to live in these environments due to their remarkable metabolic flexibility and energy-efficient biosynthesis. However, brine pools have never been explored as inocula for the enrichment of homacetogens in MES. Here we used the saline water from a Red Sea brine pool as inoculum for the enrichment of halophilic homoacetogens at the biocathode (-1 V vs. Ag/AgCl) of MES. Volatile fatty acids, especially acetate, along with hydrogen gas were produced in MES systems operated at 25 and 10% salinity. Acetate concentration increased when MES was operated at a lower salinity ∼3.5%, representing typical seawater salinity. Amplicon sequencing and genome-centric metagenomics of matured cathodic biofilm showed dominance of the genus Marinobacter and phylum Firmicutes at all tested salinities. Seventeen high-quality draft metagenome-assembled genomes (MAGs) were extracted from the biocathode samples. The recovered MAGs accounted for 87 ± 4% of the quality filtered sequence reads. Genome analysis of the MAGs suggested CO2 fixation via Wood-Ljundahl pathway by members of the phylum Firmicutes and the fixed CO2 was possibly utilized by Marinobacter sp. for growth by consuming O2 escaping from the anode to the cathode for respiration. The enrichment of Marinobacter sp. with homoacetogens was only possible because of the specific cathodic environment in MES. These findings suggest that in organic carbon-limited saline environments, Marinobacter spp. can live in consortia with CO2 fixing bacteria such as homoacetogens, which can provide them with fixed carbon as a source of carbon and energy.
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Affiliation(s)
- Manal F Alqahtani
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Suman Bajracharya
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Krishna P Katuri
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Muhammad Ali
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Ala'a Ragab
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology, Red Sea Research Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology, Red Sea Research Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
| | - Pascal E Saikaly
- King Abdullah University of Science and Technology, Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division, Thuwal, Saudi Arabia
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16
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Ullah R, Yasir M, Bibi F, Abujamel TS, Hashem AM, Sohrab SS, Al-Ansari A, Al-Sofyani AA, Al-Ghamdi AK, Al-Sieni A, Azhar EI. Taxonomic diversity of antimicrobial-resistant bacteria and genes in the Red Sea coast. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 677:474-483. [PMID: 31063890 DOI: 10.1016/j.scitotenv.2019.04.283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/26/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
Despite development of a record number of recreational sites and industrial zones on the Red Sea coast in the last decade, antibiotic-resistant bacteria in this environment remain largely unexplored. In this study, 16S rDNA sequencing was used to identify bacteria isolated from 12 sediment samples collected from the Red Sea coastal, offshore, and mangroves sites. Quantitative PCR was used to estimate the quantity of antimicrobial resistance genes (ARGs) in genomic DNA in the samples. A total of 470 bacteria were isolated and classified into 137 distinct species, including 10 candidate novel species. Site-specific bacterial communities inhabiting the Red Sea were apparent. Relatively, more resistant isolates were recovered from the coast, and samples from offshore locations contained the most multidrug-resistant bacteria. Eighteen ARGs were detected in this study encoding resistance to aminoglycoside, beta-lactam, sulfonamide, macrolide, quinolone, and tetracycline antibiotics. The qnrS, aacC2, ermC, and blaTEM-1 genes were commonly found in coastal and offshore sites. Relatively higher abundance of ARGs, including aacC2 and aacC3, were found in the apparently anthropogenically contaminated (beach) samples from coast compared to other collected samples. In conclusion, a relative increase in antimicrobial-resistant isolates was found in sediment samples from the Red Sea, compared to other studies. Anthropogenic activities likely contribute to this increase in bacterial diversity and ARGs.
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Affiliation(s)
- Riaz Ullah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Turki S Abujamel
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Anwar M Hashem
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Al-Ansari
- Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmohsin A Al-Sofyani
- Marine Biology Department, Faculty of Marine Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed K Al-Ghamdi
- Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulbasit Al-Sieni
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia; Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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Masoud MS, Abdel-Halim AM, El Ashmawy AA. Seasonal variation of nutrient salts and heavy metals in mangrove (Avicennia marina) environment, Red Sea, Egypt. ENVIRONMENTAL MONITORING AND ASSESSMENT 2019; 191:425. [PMID: 31183611 DOI: 10.1007/s10661-019-7543-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
In the Egyptian Red Sea coast, nutrient salts, major ions, and heavy metals ion concentrations were examined in mangroves and the results were compared to respective concentrations in a reference area. Water samples were collected during the four seasons of 2012 from three different mangrove regions, Safaga, Abo Gheson, and El Quseer, besides, a mangrove free region, Marsa Alam. A temporal variation in the chemical composition of seawater of the mangrove and reference regions was recorded. Phosphorous and nitrogen forms were measured and calculated. Fe, Mn, Cu, Zn, Ni, Cr, Cd, and Pb ions were measured in water samples. Redfield nitrogen to phosphorous ratio explained the oligotrophic nature of the Red Sea. Ca and Mg ions besides total alkalinity showed negligible variations. The relatively greater concentration values of ammonium, 242.11 μg/l, dissolved inorganic nitrogen, 315.55 μg/l, and oxidizable organic matter, 0.4 mg-O2/l, may be caused by the impact of mangroves. Seawater contamination by heavy metals was assessed, using the metal index, in the mangrove regions which, compared to the reference region, were highly contaminated. Analysis of variance showed no significant variation among mangrove stations. Principal component analysis suggested that El Quseer and Safaga, mangrove regions, were contaminated by metal ions. Safaga possessed the highest concentration of Cd and Zn ions, while the highest concentrations of Mn, Cu, Ni, and Pb ions were observed at El Quseer. This may be attributed to industrial and shipping activities. It is concluded that the mangrove ecosystem along the Red Sea highly affects marine environment.
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Affiliation(s)
- Mamdouh S Masoud
- Chemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Ahmed M Abdel-Halim
- Marine Chemistry Lab, National Institute of Oceanography and Fisheries, Kayetbai Street, Alexandria, Egypt
| | - Ahmed A El Ashmawy
- Marine Chemistry Lab, National Institute of Oceanography and Fisheries, Kayetbai Street, Alexandria, Egypt.
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18
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Badiea EA, Sayed AA, Maged M, Fouad WM, Said MM, Esmat AY. A novel thermostable and halophilic thioredoxin reductase from the Red Sea Atlantis II hot brine pool. PLoS One 2019; 14:e0217565. [PMID: 31150456 PMCID: PMC6544261 DOI: 10.1371/journal.pone.0217565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/14/2019] [Indexed: 11/19/2022] Open
Abstract
The highly extreme conditions of the lower convective layer in the Atlantis II (ATII) Deep brine pool of the Red Sea make it an ideal environment for the search for novel enzymes that can function under extreme conditions. In the current study, we isolated a novel sequence of a thioredoxin reductase (TrxR) enzyme from the metagenomic dataset established from the microbial community that resides in the lower convective layer of Atlantis II. The gene was cloned, expressed and characterized for redox activity, halophilicity, and thermal stability. The isolated thioredoxin reductase (ATII-TrxR) was found to belong to the high-molecular-weight class of thioredoxin reductases. A search for conserved domains revealed the presence of an extra domain (Crp) in the enzyme sequence. Characterization studies of ATII-TrxR revealed that the enzyme was halophilic (maintained activity at 4 M NaCl), thermophilic (optimum temperature was 65°C) and thermostable (60% of its activity was retained at 70°C). Additionally, the enzyme utilized NADH in addition to NADPH as an electron donor. In conclusion, a novel thermostable and halophilic thioredoxin reductase has been isolated with a unique sequence that adapts to the harsh conditions of the brine pools making this protein a good candidate for biological research and industrial applications.
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Affiliation(s)
- Elham A. Badiea
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo, Egypt
| | - Ahmed A. Sayed
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
- Children Cancer Hospital, Cairo, Egypt
| | - Mohamad Maged
- Faculty of Biotechnology, October University for Modern Sciences and Arts, 6th October City, Cairo, Egypt
| | - Walid M. Fouad
- Department of Biology, School of Sciences and Engineering, American University in Cairo, New Cairo, Egypt
| | - Mahmoud M. Said
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Amr Y. Esmat
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
- * E-mail:
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19
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Qiao Y, Jia B, Hu Z, Sun C, Xiang Y, Wei C. MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms. Biol Direct 2018; 13:15. [PMID: 30134953 PMCID: PMC6104016 DOI: 10.1186/s13062-018-0220-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 08/08/2018] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Many methods have been developed for metagenomic sequence classification, and most of them depend heavily on genome sequences of the known organisms. A large portion of sequencing sequences may be classified as unknown, which greatly impairs our understanding of the whole sample. RESULT Here we present MetaBinG2, a fast method for metagenomic sequence classification, especially for samples with a large number of unknown organisms. MetaBinG2 is based on sequence composition, and uses GPUs to accelerate its speed. A million 100 bp Illumina sequences can be classified in about 1 min on a computer with one GPU card. We evaluated MetaBinG2 by comparing it to multiple popular existing methods. We then applied MetaBinG2 to the dataset of MetaSUB Inter-City Challenge provided by CAMDA data analysis contest and compared community composition structures for environmental samples from different public places across cities. CONCLUSION Compared to existing methods, MetaBinG2 is fast and accurate, especially for those samples with significant proportions of unknown organisms. REVIEWERS This article was reviewed by Drs. Eran Elhaik, Nicolas Rascovan, and Serghei Mangul.
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Affiliation(s)
- Yuyang Qiao
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ben Jia
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Shanghai Center for Bioinformation Technology, Shanghai, 201203 China
| | - Zhiqiang Hu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chen Sun
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Shanghai Center for Bioinformation Technology, Shanghai, 201203 China
| | - Yijin Xiang
- School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025 China
| | - Chaochun Wei
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- Shanghai Center for Bioinformation Technology, Shanghai, 201203 China
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240 China
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20
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Shreadah MA, El Moneam NMA, Al-Assar SA, Nabil-Adam A. Phytochemical and pharmacological screening of Sargassium vulgare from Suez Canal, Egypt. Food Sci Biotechnol 2018; 27:963-979. [PMID: 30263825 DOI: 10.1007/s10068-018-0323-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/03/2018] [Accepted: 01/18/2018] [Indexed: 12/16/2022] Open
Abstract
The current study investigates the phytochemical and pharmaceutical activities of Sargassium vulgare (SVE) collected from the Suez Canal. The prescreening using cytotoxicity was tested against hepatocellular carcinoma cell lines. Furthermore the SVE inhibit cell growth effectively with IC50 = 20.8 µg/ml. The pharmacological studies revealed high antioxidant capacity at all examined concentrations. On the meantime, anticancer assay carried out using tyrosine kinase (PTK) and sphingosine kinase 1 inhibitor screening assays revealed inhibition with 75.73 and 80.01%; respectively. Furthermore, the anti-inflammatory profiling revealed that the activities against COX1, COX2, IL6 and TNF were 77.39, 88.35, 75.38 and 71.24%; respectively. Additionally, the anti-Alzheimer results showed high activity at 1 mg with 76.33%. Finally the antiviral activities using reverse transcriptase inhibition assay give 92.24%. Consequently, it can be easily conclude that the SVE collected from the Suez Canal are excellent source of natural products for nutritional and pharmaceutical applications.
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Affiliation(s)
- Mohamed A Shreadah
- 1Marine Biotechnology and Natural Products Lab (MBNP), National Institute of Oceanography and Fisheries (NIOF), Alexandria, Egypt
| | - Nehad M Abd El Moneam
- 2Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samy A Al-Assar
- 3Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Asmaa Nabil-Adam
- 1Marine Biotechnology and Natural Products Lab (MBNP), National Institute of Oceanography and Fisheries (NIOF), Alexandria, Egypt
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21
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Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Appl Microbiol Biotechnol 2017; 101:4837-4851. [PMID: 28528426 PMCID: PMC5486811 DOI: 10.1007/s00253-017-8310-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/03/2023]
Abstract
The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.
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Haferburg G, Gröning JAD, Schmidt N, Kummer NA, Erquicia JC, Schlömann M. Microbial diversity of the hypersaline and lithium-rich Salar de Uyuni, Bolivia. Microbiol Res 2017; 199:19-28. [PMID: 28454706 DOI: 10.1016/j.micres.2017.02.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 02/25/2017] [Indexed: 10/20/2022]
Abstract
Salar de Uyuni, situated in the Southwest of the Bolivian Altiplano, is the largest salt flat on Earth. Brines of this athalassohaline hypersaline environment are rich in lithium and boron. Due to the ever- increasing commodity demand, the industrial exploitation of brines for metal recovery from the world's biggest lithium reservoir is likely to increase substantially in the near future. Studies on the composition of halophilic microbial communities in brines of the salar have not been published yet. Here we report for the first time on the prokaryotic diversity of four brine habitats across the salar. The brine is characterized by salinity values between 132 and 177 PSU, slightly acidic to near-neutral pH and lithium and boron concentrations of up to 2.0 and 1.4g/L, respectively. Community analysis was performed after sequencing the V3-V4 region of the 16S rRNA genes employing the Illumina MiSeq technology. The mothur software package was used for sequence processing and data analysis. Metagenomic analysis revealed the occurrence of an exclusively archaeal community comprising 26 halobacterial genera including only recently identified genera like Halapricum, Halorubellus and Salinarchaeum. Despite the high diversity of the halobacteria-dominated community in sample P3 (Shannon-Weaver index H'=3.12 at 3% OTU cutoff) almost 40% of the Halobacteriaceae-assigned sequences could not be classified on the genus level under stringent filtering conditions. Even if the limited taxonomic resolution of the V3-V4 region for halobacteria is considered, it seems likely to discover new, hitherto undescribed genera of the family halobacteriaceae in this particular habitat of Salar de Uyuni in future.
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Affiliation(s)
- Götz Haferburg
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany.
| | | | - Nadja Schmidt
- Institute of Hydrogeology and Environmental Geology, TU Bergakademie Freiberg, Gustav-Zeuner-Straße 12, 09599 Freiberg, Germany
| | - Nicolai-Alexeji Kummer
- Institute of Hydrogeology and Environmental Geology, TU Bergakademie Freiberg, Gustav-Zeuner-Straße 12, 09599 Freiberg, Germany
| | | | - Michael Schlömann
- Interdisciplinary Ecological Center, Environmental Microbiology Group, TU Bergakademie Freiberg, Leipziger Strasse 29, 09599 Freiberg, Germany
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23
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Isolation and characterization of marine-derived actinomycetes with cytotoxic activity from the Red Sea coast. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2016.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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24
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Parages ML, Gutiérrez-Barranquero JA, Reen FJ, Dobson ADW, O'Gara F. Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts. Mar Drugs 2016; 14:E62. [PMID: 27007381 PMCID: PMC4810074 DOI: 10.3390/md14030062] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 02/18/2016] [Accepted: 03/11/2016] [Indexed: 12/21/2022] Open
Abstract
In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts.
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Affiliation(s)
- María L Parages
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| | - José A Gutiérrez-Barranquero
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth WA 6845, Australia.
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