51
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Elbehery AHA, Leak DJ, Siam R. Novel thermostable antibiotic resistance enzymes from the Atlantis II Deep Red Sea brine pool. Microb Biotechnol 2016; 10:189-202. [PMID: 28004885 PMCID: PMC5270753 DOI: 10.1111/1751-7915.12468] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/29/2016] [Accepted: 11/03/2016] [Indexed: 11/29/2022] Open
Abstract
The advent of metagenomics has greatly facilitated the discovery of enzymes with useful biochemical characteristics for industrial and biomedical applications, from environmental niches. In this study, we used sequence-based metagenomics to identify two antibiotic resistance enzymes from the secluded, lower convective layer of Atlantis II Deep Red Sea brine pool (68°C, ~2200 m depth and 250‰ salinity). We assembled > 4 000 000 metagenomic reads, producing 43 555 contigs. Open reading frames (ORFs) called from these contigs were aligned to polypeptides from the Comprehensive Antibiotic Resistance Database using BLASTX. Two ORFs were selected for further analysis. The ORFs putatively coded for 3'-aminoglycoside phosphotransferase [APH(3')] and a class A beta-lactamase (ABL). Both genes were cloned, expressed and characterized for activity and thermal stability. Both enzymes were active in vitro, while only APH(3') was active in vivo. Interestingly, APH(3') proved to be thermostable (Tm = 61.7°C and ~40% residual activity after 30 min of incubation at 65°C). On the other hand, ABL was not as thermostable, with a Tm = 43.3°C. In conclusion, we have discovered two novel AR enzymes with potential application as thermophilic selection markers.
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Affiliation(s)
- Ali H A Elbehery
- Graduate Program of Biotechnology, The American University in Cairo, Cairo, Egypt.,Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Rania Siam
- Graduate Program of Biotechnology, The American University in Cairo, Cairo, Egypt.,Biology Department and YJ-Science and Technology Research Center, The American University in Cairo, Cairo, Egypt
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52
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Elbehery AHA, Aziz RK, Siam R. Insertion sequences enrichment in extreme Red sea brine pool vent. Extremophiles 2016; 21:271-282. [PMID: 27915389 DOI: 10.1007/s00792-016-0900-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 11/27/2016] [Indexed: 01/24/2023]
Abstract
Mobile genetic elements are major agents of genome diversification and evolution. Limited studies addressed their characteristics, including abundance, and role in extreme habitats. One of the rare natural habitats exposed to multiple-extreme conditions, including high temperature, salinity and concentration of heavy metals, are the Red Sea brine pools. We assessed the abundance and distribution of different mobile genetic elements in four Red Sea brine pools including the world's largest known multiple-extreme deep-sea environment, the Red Sea Atlantis II Deep. We report a gradient in the abundance of mobile genetic elements, dramatically increasing in the harshest environment of the pool. Additionally, we identified a strong association between the abundance of insertion sequences and extreme conditions, being highest in the harshest and deepest layer of the Red Sea Atlantis II Deep. Our comparative analyses of mobile genetic elements in secluded, extreme and relatively non-extreme environments, suggest that insertion sequences predominantly contribute to polyextremophiles genome plasticity.
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Affiliation(s)
- Ali H A Elbehery
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, 11835, Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Rania Siam
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, 11835, Cairo, Egypt.
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, SSE (Parcel 7), Second Floor, Office: Room 2194, AUC Avenue, New Cairo, 11835, Cairo, Egypt.
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53
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Zhang W, Ding W, Yang B, Tian R, Gu S, Luo H, Qian PY. Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool. Front Microbiol 2016; 7:1825. [PMID: 27895636 PMCID: PMC5108811 DOI: 10.3389/fmicb.2016.01825] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 10/31/2016] [Indexed: 12/20/2022] Open
Abstract
The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.
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Affiliation(s)
- Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Wei Ding
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Bo Yang
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Shuo Gu
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
| | - Haiwei Luo
- Simon F. S. Li Marine Science Laboratory, School of Life Sciences, Chinese University of Hong Kong Shatin, Hong Kong
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology Hong Kong, Hong Kong
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54
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Hou S, Pfreundt U, Miller D, Berman-Frank I, Hess WR. mdRNA-Seq analysis of marine microbial communities from the northern Red Sea. Sci Rep 2016; 6:35470. [PMID: 27759035 PMCID: PMC5069720 DOI: 10.1038/srep35470] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/28/2016] [Indexed: 01/17/2023] Open
Abstract
Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs.
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Affiliation(s)
- Shengwei Hou
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Ulrike Pfreundt
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
| | - Dan Miller
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Ilana Berman-Frank
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany
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55
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Adel M, Elbehery AHA, Aziz SK, Aziz RK, Grossart HP, Siam R. Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments. Sci Rep 2016; 6:32704. [PMID: 27596223 PMCID: PMC5011723 DOI: 10.1038/srep32704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/25/2016] [Indexed: 11/24/2022] Open
Abstract
The central rift of the Red Sea has 25 brine pools with different physical and geochemical characteristics. Atlantis II (ATIID), Discovery Deeps (DD) and Chain Deep (CD) are characterized by high salinity, temperature and metal content. Several studies reported microbial communities in these brine pools, but few studies addressed the brine pool sediments. Therefore, sediment cores were collected from ATIID, DD, CD brine pools and an adjacent brine-influenced site. Sixteen different lithologic sediment sections were subjected to shotgun DNA pyrosequencing to generate 1.47 billion base pairs (1.47 × 109 bp). We generated sediment-specific reads and attempted to annotate all reads. We report the phylogenetic and biochemical uniqueness of the deepest ATIID sulfur-rich brine pool sediments. In contrary to all other sediment sections, bacteria dominate the deepest ATIID sulfur-rich brine pool sediments. This decrease in virus-to-bacteria ratio in selected sections and depth coincided with an overrepresentation of mobile genetic elements. Skewing in the composition of viruses-to-mobile genetic elements may uniquely contribute to the distinct microbial consortium in sediments in proximity to hydrothermally active vents of the Red Sea and possibly in their surroundings, through differential horizontal gene transfer.
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Affiliation(s)
- Mustafa Adel
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
| | - Ali H A Elbehery
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
| | - Sherry K Aziz
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Egypt
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Am Neuen Palais 10, 14469 Potsdam, Germany
| | - Rania Siam
- Biology Department, Biotechnology Graduate Program and YJ-Science and Technology Research Center, American University in Cairo, Egypt
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56
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Crespo-Medina M, Bowles MW, Samarkin VA, Hunter KS, Joye SB. Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico). GEOBIOLOGY 2016; 14:483-498. [PMID: 27444236 DOI: 10.1111/gbi.12185] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/07/2016] [Indexed: 06/06/2023]
Abstract
The microbial communities thriving in deep-sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat-linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and NH4+ inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H2 S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.
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Affiliation(s)
- M Crespo-Medina
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - M W Bowles
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - V A Samarkin
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - K S Hunter
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - S B Joye
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
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57
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Nigro LM, Hyde AS, MacGregor BJ, Teske A. Phylogeography, Salinity Adaptations and Metabolic Potential of the Candidate Division KB1 Bacteria Based on a Partial Single Cell Genome. Front Microbiol 2016; 7:1266. [PMID: 27597842 PMCID: PMC4993014 DOI: 10.3389/fmicb.2016.01266] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/02/2016] [Indexed: 01/15/2023] Open
Abstract
Deep-sea hypersaline anoxic basins and other hypersaline environments contain abundant and diverse microbial life that has adapted to these extreme conditions. The bacterial Candidate Division KB1 represents one of several uncultured groups that have been consistently observed in hypersaline microbial diversity studies. Here we report the phylogeography of KB1, its phylogenetic relationships to Candidate Division OP1 Bacteria, and its potential metabolic and osmotic stress adaptations based on a partial single cell amplified genome of KB1 from Orca Basin, the largest hypersaline seafloor brine basin in the Gulf of Mexico. Our results are consistent with the hypothesis – previously developed based on 14C incorporation experiments with mixed-species enrichments from Mediterranean seafloor brines – that KB1 has adapted its proteins to elevated intracellular salinity, but at the same time KB1 apparently imports glycine betaine; this compatible solute is potentially not limited to osmoregulation but could also serve as a carbon and energy source.
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Affiliation(s)
- Lisa M Nigro
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Andrew S Hyde
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Barbara J MacGregor
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
| | - Andreas Teske
- Department of Marine Sciences, University of North Carolina at Chapel Hill Chapel Hill, NC, USA
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58
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Moissl-Eichinger C, Cockell C, Rettberg P. Venturing into new realms? Microorganisms in space. FEMS Microbiol Rev 2016; 40:722-37. [PMID: 27354346 DOI: 10.1093/femsre/fuw015] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2016] [Indexed: 12/15/2022] Open
Abstract
One of the biggest challenges of science is the determination of whether extraterrestrial life exists. Although potential habitable areas might be available for complex life, it is more likely that microbial life could exist in space. Many extremotolerant and extremophilic microbes have been found to be able to withstand numerous, combined environmental factors, such as high or low temperatures and pressures, high-salt conditions, high doses of radiation, desiccation or nutrient limitations. They may even survive the transit from one planet to another. Terrestrial Mars-analogue sites are one focus of researchers, in order to understand the microbial diversity in preparation for upcoming space missions aimed at the detection of life. However, such missions could also pose a risk with respect to contamination of the extraterrestrial environment by accidentally transferred terrestrial microorganisms. Closer to the Earth, the International Space Station is the most enclosed habitat, where humans work and live-and with them numerous microorganisms. It is still unknown how microbes adapt to this environment, possibly even creating a risk for the crew. Information on the microbiology of the ISS will have an impact on the planning and implementation of long-term human spaceflights in order to ensure a safe, stable and balanced microbiome on board.
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Affiliation(s)
- Christine Moissl-Eichinger
- Department for Internal Medicine, Medical University of Graz, 8036 Graz, Austria BioTechMed Graz, 8010 Graz, Austria
| | - Charles Cockell
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH10 4EP, UK
| | - Petra Rettberg
- Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), 51147 Cologne, Germany
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59
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Sonbol SA, Ferreira AJS, Siam R. Red Sea Atlantis II brine pool nitrilase with unique thermostability profile and heavy metal tolerance. BMC Biotechnol 2016; 16:14. [PMID: 26868129 PMCID: PMC4751646 DOI: 10.1186/s12896-016-0244-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 02/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Nitrilases, which hydrolyze nitriles in a one-step reaction into carboxylic acids and ammonia, gained increasing attention because of the abundance of nitrile compounds in nature and their use in fine chemicals and pharmaceutics. Extreme environments are potential habitats for the isolation and characterization of extremozymes including nitrilases with unique resistant properties. The Red Sea brine pools are characterized by multitude of extreme conditions. The Lower Convective Layer (LCL) of the Atlantis II Deep Brine Pool in the Red Sea is characterized by elevated temperature (68 °C), high salt concentrations (250 ‰), anoxic conditions and high heavy metal concentrations. RESULTS We identified and isolated a nitrilase from the Atlantis II Deep Brine Pool in the Red Sea LCL. The isolated 338 amino-acid nitrilase (NitraS-ATII) is part of a highly conserved operon in different bacterial phyla with indiscernible function. The enzyme was cloned, expressed and purified. Characterization of the purified NitraS-ATII revealed its selectivity towards dinitriles, which suggests a possible industrial application in the synthesis of cyanocarboxylic acids. Moreover, NitraS-ATII showed higher thermal stability compared to a closely related nitrilase, in addition to its observed tolerance towards high concentrations of selected heavy metals. CONCLUSION This enzyme sheds light on evolution of microbes in the Atlantis II Deep LCL to adapt to the diverse extreme environment and can prove to be valuable in bioremediation processes.
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Affiliation(s)
- Sarah A Sonbol
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835, Egypt.
| | - Ari J S Ferreira
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835, Egypt.
| | - Rania Siam
- Biology Department and YJ-Science and Technology Research Center, American University in Cairo, New Cairo, 11835, Egypt.
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60
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Mwirichia R, Alam I, Rashid M, Vinu M, Ba-Alawi W, Anthony Kamau A, Kamanda Ngugi D, Göker M, Klenk HP, Bajic V, Stingl U. Metabolic traits of an uncultured archaeal lineage--MSBL1--from brine pools of the Red Sea. Sci Rep 2016; 6:19181. [PMID: 26758088 PMCID: PMC4725937 DOI: 10.1038/srep19181] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 12/04/2015] [Indexed: 11/24/2022] Open
Abstract
The candidate Division MSBL1 (Mediterranean Sea Brine Lakes 1) comprises a monophyletic group of uncultured archaea found in different hypersaline environments. Previous studies propose methanogenesis as the main metabolism. Here, we describe a metabolic reconstruction of MSBL1 based on 32 single-cell amplified genomes from Brine Pools of the Red Sea (Atlantis II, Discovery, Nereus, Erba and Kebrit). Phylogeny based on rRNA genes as well as conserved single copy genes delineates the group as a putative novel lineage of archaea. Our analysis shows that MSBL1 may ferment glucose via the Embden-Meyerhof-Parnas pathway. However, in the absence of organic carbon, carbon dioxide may be fixed via the ribulose bisphosphate carboxylase, Wood-Ljungdahl pathway or reductive TCA cycle. Therefore, based on the occurrence of genes for glycolysis, absence of the core genes found in genomes of all sequenced methanogens and the phylogenetic position, we hypothesize that the MSBL1 are not methanogens, but probably sugar-fermenting organisms capable of autotrophic growth. Such a mixotrophic lifestyle would confer survival advantage (or possibly provide a unique narrow niche) when glucose and other fermentable sugars are not available.
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Affiliation(s)
- Romano Mwirichia
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Mamoon Rashid
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Manikandan Vinu
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Wail Ba-Alawi
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Allan Anthony Kamau
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - David Kamanda Ngugi
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
| | - Markus Göker
- German Collection for Microorganisms and Cell Cultures GmbH
(DSMZ), Inhoffenstraße 7b, 38124
Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Biology, Newcastle University, Newcastle
upon Tyne, United Kingdom
| | - Vladimir Bajic
- Computational Bioscience Research Center, King Abdullah
University of Science and Technology (KAUST), Thuwal,
Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and
Technology (KAUST), Thuwal, Saudi Arabia
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61
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Oren A. Life in Hypersaline Environments. THEIR WORLD: A DIVERSITY OF MICROBIAL ENVIRONMENTS 2016. [DOI: 10.1007/978-3-319-28071-4_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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62
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Antunes A, Stackebrandt E, Lima N. Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training. Trends Microbiol 2015; 24:77-79. [PMID: 26727416 DOI: 10.1016/j.tim.2015.11.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 11/19/2015] [Accepted: 11/30/2015] [Indexed: 01/12/2023]
Abstract
A survey of European Microbial Biological Resource Centers and their users provided an overview on microbiology education and training. The results identified future increases in demand despite several shortcomings and gaps in the current offer. Urgent adjustments are needed to match users' needs, integrate innovative programs, and adopt new technologies.
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Affiliation(s)
- André Antunes
- CEB - Centre of Biological Engineering, Micoteca da Universidade do Minho, University of Minho, Braga, Portugal; King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Building 3, office 4216-WS01, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia; Current address: Department of Biology, Edge Hill University, St Helens Road, Ormskirk, Lancashire L39 4QP, UK.
| | - Erko Stackebrandt
- Leibniz Institute - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Nelson Lima
- CEB - Centre of Biological Engineering, Micoteca da Universidade do Minho, University of Minho, Braga, Portugal
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63
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Ngugi DK, Blom J, Stepanauskas R, Stingl U. Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines. ISME JOURNAL 2015; 10:1383-99. [PMID: 26657763 PMCID: PMC5029188 DOI: 10.1038/ismej.2015.214] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 10/05/2015] [Accepted: 10/25/2015] [Indexed: 11/22/2022]
Abstract
Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine–seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.
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Affiliation(s)
- David Kamanda Ngugi
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Germany
| | | | - Ulrich Stingl
- Red Sea Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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64
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Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
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65
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Zhao F, Bajic VB. The Value and Significance of Metagenomics of Marine Environments. Preface. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:271-4. [PMID: 26607677 PMCID: PMC4678774 DOI: 10.1016/j.gpb.2015.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 10/31/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Fangqing Zhao
- Computational Genomics Lab, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), 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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Bargiela R, Gertler C, Magagnini M, Mapelli F, Chen J, Daffonchio D, Golyshin PN, Ferrer M. Degradation Network Reconstruction in Uric Acid and Ammonium Amendments in Oil-Degrading Marine Microcosms Guided by Metagenomic Data. Front Microbiol 2015; 6:1270. [PMID: 26635742 PMCID: PMC4656828 DOI: 10.3389/fmicb.2015.01270] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/30/2015] [Indexed: 11/13/2022] Open
Abstract
Biostimulation with different nitrogen sources is often regarded as a strategy of choice in combating oil spills in marine environments. Such environments are typically depleted in nitrogen, therefore limiting the balanced microbial utilization of carbon-rich petroleum constituents. It is fundamental, yet only scarcely accounted for, to analyze the catabolic consequences of application of biostimulants. Here, we examined such alterations in enrichment microcosms using sediments from chronically crude oil-contaminated marine sediment at Ancona harbor (Italy) amended with natural fertilizer, uric acid (UA), or ammonium (AMM). We applied the web-based AromaDeg resource using as query Illumina HiSeq meta-sequences (UA: 27,893 open reading frames; AMM: 32,180) to identify potential catabolic differences. A total of 45 (for UA) and 65 (AMM) gene sequences encoding key catabolic enzymes matched AromaDeg, and their participation in aromatic degradation reactions could be unambiguously suggested. Genomic signatures for the degradation of aromatics such as 2-chlorobenzoate, indole-3-acetate, biphenyl, gentisate, quinoline and phenanthrene were common for both microcosms. However, those for the degradation of orcinol, ibuprofen, phenylpropionate, homoprotocatechuate and benzene (in UA) and 4-aminobenzene-sulfonate, p-cumate, dibenzofuran and phthalate (in AMM), were selectively enriched. Experimental validation was conducted and good agreement with predictions was observed. This suggests certain discrepancies in action of these biostimulants on the genomic content of the initial microbial community for the catabolism of petroleum constituents or aromatics pollutants. In both cases, the emerging microbial communities were phylogenetically highly similar and were composed by very same proteobacterial families. However, examination of taxonomic assignments further revealed different catabolic pathway organization at the organismal level, which should be considered for designing oil spill mitigation strategies in the sea.
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Affiliation(s)
- Rafael Bargiela
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | | | | | - Francesca Mapelli
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy
| | | | - Daniele Daffonchio
- Department of Food, Environmental and Nutritional Sciences, University of Milan Milan, Italy ; Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | | | - Manuel Ferrer
- Systems Biotechnology, Department of Biocatalysis, Institute of Catalysis, Consejo Superior de Investigaciones Científicas Madrid, Spain
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Antunes A, Alam I, Simões MF, Daniels C, Ferreira AJS, Siam R, El-Dorry H, Bajic VB. First Insights into the Viral Communities of the Deep-sea Anoxic Brines of the Red Sea. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:304-9. [PMID: 26529193 PMCID: PMC4678784 DOI: 10.1016/j.gpb.2015.06.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 06/09/2015] [Accepted: 06/29/2015] [Indexed: 12/11/2022]
Abstract
The deep-sea brines of the Red Sea include some of the most extreme and unique environments on Earth. They combine high salinities with increases in temperature, heavy metals, hydrostatic pressure, and anoxic conditions, creating unique settings for thriving populations of novel extremophiles. Despite a recent increase of studies focusing on these unusual biotopes, their viral communities remain unexplored. The current survey explores four metagenomic datasets obtained from different brine–seawater interface samples, focusing specifically on the diversity of their viral communities. Data analysis confirmed that the particle-attached viral communities present in the brine–seawater interfaces were diverse and generally dominated by Caudovirales, yet appearing distinct from sample to sample. With a level of caution, we report the unexpected finding of Phycodnaviridae, which infects algae and plants, and trace amounts of insect-infecting Iridoviridae. Results from Kebrit Deep revealed stratification in the viral communities present in the interface: the upper-interface was enriched with viruses associated with typical marine bacteria, while the lower-interface was enriched with haloviruses and halophages. These results provide first insights into the unexplored viral communities present in deep-sea brines of the Red Sea, representing one of the first steps for ongoing and future sampling efforts and studies.
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Affiliation(s)
- André Antunes
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Intikhab Alam
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Marta Filipa Simões
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Camille Daniels
- Red Sea Research Center (RSRC), Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Ari J S Ferreira
- Biology Department, American University in Cairo, New Cairo 11835, Egypt
| | - Rania Siam
- Biology Department, American University in Cairo, New Cairo 11835, Egypt
| | - Hamza El-Dorry
- Biology Department, American University in Cairo, New Cairo 11835, Egypt
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), 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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68
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Abstract
Metagenomics has significantly advanced the field of marine microbial ecology, revealing the vast diversity of previously unknown microbial life forms in different marine niches. The tremendous amount of data generated has enabled identification of a large number of microbial genes (metagenomes), their community interactions, adaptation mechanisms, and their potential applications in pharmaceutical and biotechnology-based industries. Comparative metagenomics reveals that microbial diversity is a function of the local environment, meaning that unique or unusual environments typically harbor novel microbial species with unique genes and metabolic pathways. The Red Sea has an abundance of unique characteristics; however, its microbiota is one of the least studied among marine environments. The Red Sea harbors approximately 25 hot anoxic brine pools, plus a vibrant coral reef ecosystem. Physiochemical studies describe the Red Sea as an oligotrophic environment that contains one of the warmest and saltiest waters in the world with year-round high UV radiations. These characteristics are believed to have shaped the evolution of microbial communities in the Red Sea. Over-representation of genes involved in DNA repair, high-intensity light responses, and osmoregulation were found in the Red Sea metagenomic databases suggesting acquisition of specific environmental adaptation by the Red Sea microbiota. The Red Sea brine pools harbor a diverse range of halophilic and thermophilic bacterial and archaeal communities, which are potential sources of enzymes for pharmaceutical and biotechnology-based application. Understanding the mechanisms of these adaptations and their function within the larger ecosystem could also prove useful in light of predicted global warming scenarios where global ocean temperatures are expected to rise by 1-3°C in the next few decades. In this review, we provide an overview of the published metagenomic studies that were conducted in the Red Sea, and the bio-prospecting potential of the Red Sea microbiota. Furthermore, we discuss the limitations of the previous studies and the need for generating a large and representative metagenomic database of the Red Sea to help establish a dynamic model of the Red Sea microbiota.
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Affiliation(s)
- Hayedeh Behzad
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Martin Augusto Ibarra
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology, Computer, Electrical, and Mathematical Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Thuwal 23955-6900, Saudi Arabia; King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering Division, Thuwal 23955-6900, Saudi Arabia.
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69
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Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor. Appl Microbiol Biotechnol 2015; 100:1183-1195. [PMID: 26428236 DOI: 10.1007/s00253-015-7007-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/02/2015] [Accepted: 09/12/2015] [Indexed: 10/23/2022]
Abstract
The success of biotechnological processes is based on the availability of efficient and highly specific biocatalysts, which can satisfy industrial demands. Extreme and remote environments like the deep brine pools of the Red Sea represent highly interesting habitats for the discovery of novel halophilic and thermophilic enzymes. Haloferax volcanii constitutes a suitable expression system for halophilic enzymes obtained from such brine pools. We developed a batch process for the cultivation of H. volcanii H1895 in controlled stirred-tank bioreactors utilising knockouts of components of the flagella assembly system. The standard medium Hv-YPC was supplemented to reach a higher cell density. Without protein expression, cell dry weight reaches 10 g L(-1). Two halophilic alcohol dehydrogenases were expressed under the control of the tryptophanase promoter p.tna with 16.8 and 3.2 mg gCDW (-1), respectively, at a maximum cell dry weight of 6.5 g L(-1). Protein expression was induced by the addition of L-tryptophan. Investigation of various expression strategies leads to an optimised two-step induction protocol introducing 6 mM L-tryptophan at an OD650 of 0.4 followed by incubation for 16 h and a second induction step with 3 mM L-tryptophan followed by a final incubation time of 4 h. Compared with the uncontrolled shaker-flask cultivations used until date, dry cell mass concentrations were improved by a factor of more than 5 and cell-specific enzyme activities showed an up to 28-fold increased yield of the heterologous proteins.
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70
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Guan Y, Hikmawan T, Antunes A, Ngugi D, Stingl U. Diversity of methanogens and sulfate-reducing bacteria in the interfaces of five deep-sea anoxic brines of the Red Sea. Res Microbiol 2015; 166:688-99. [PMID: 26192212 DOI: 10.1016/j.resmic.2015.07.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/02/2015] [Accepted: 07/02/2015] [Indexed: 11/24/2022]
Abstract
Oceanic deep hypersaline anoxic basins (DHABs) are characterized by drastic changes in physico-chemical conditions in the transition from overlaying seawater to brine body. Brine-seawater interfaces (BSIs) of several DHABs across the Mediterranean Sea have been shown to possess methanogenic and sulfate-reducing activities, yet no systematic studies have been conducted to address the potential functional diversity of methanogenic and sulfate-reducing communities in the Red Sea DHABs. Here, we evaluated the relative abundance of Bacteria and Archaea using quantitative PCR and conducted phylogenetic analyses of nearly full-length 16S rRNA genes as well as functional marker genes encoding the alpha subunits of methyl-coenzyme M reductase (mcrA) and dissimilatory sulfite reductase (dsrA). Bacteria predominated over Archaea in most locations, the majority of which were affiliated with Deltaproteobacteria, while Thaumarchaeota were the most prevalent Archaea in all sampled locations. The upper convective layers of Atlantis II Deep, which bear increasingly harsh environmental conditions, were dominated by members of the class Thermoplasmata (Marine Benthic Group E and Mediterranean Sea Brine Lakes Group 1). Our study revealed unique microbial compositions, the presence of niche-specific groups, and collectively, a higher diversity of sulfate-reducing communities compared to methanogenic communities in all five studied locations.
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Affiliation(s)
- Yue Guan
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Tyas Hikmawan
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - André Antunes
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia
| | - David Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology, 23955-6900, Thuwal, Saudi Arabia.
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71
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Marine extremophiles: a source of hydrolases for biotechnological applications. Mar Drugs 2015; 13:1925-65. [PMID: 25854643 PMCID: PMC4413194 DOI: 10.3390/md13041925] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/22/2015] [Accepted: 03/25/2015] [Indexed: 12/26/2022] Open
Abstract
The marine environment covers almost three quarters of the planet and is where evolution took its first steps. Extremophile microorganisms are found in several extreme marine environments, such as hydrothermal vents, hot springs, salty lakes and deep-sea floors. The ability of these microorganisms to support extremes of temperature, salinity and pressure demonstrates their great potential for biotechnological processes. Hydrolases including amylases, cellulases, peptidases and lipases from hyperthermophiles, psychrophiles, halophiles and piezophiles have been investigated for these reasons. Extremozymes are adapted to work in harsh physical-chemical conditions and their use in various industrial applications such as the biofuel, pharmaceutical, fine chemicals and food industries has increased. The understanding of the specific factors that confer the ability to withstand extreme habitats on such enzymes has become a priority for their biotechnological use. The most studied marine extremophiles are prokaryotes and in this review, we present the most studied archaea and bacteria extremophiles and their hydrolases, and discuss their use for industrial applications.
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72
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Oren A. Halophilic microbial communities and their environments. Curr Opin Biotechnol 2015; 33:119-24. [PMID: 25727188 DOI: 10.1016/j.copbio.2015.02.005] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 01/04/2015] [Accepted: 02/13/2015] [Indexed: 10/23/2022]
Abstract
Use of culture-independent studies have greatly increased our understanding of the microbiology of hypersaline lakes (the Dead Sea, Great Salt Lake) and saltern ponds in recent years. Exciting new information has become available on the microbial processes in Antarctic lakes and in deep-sea brines. These studies led to the recognition of many new lineages of microorganisms not yet available for study in culture, and their cultivation in the laboratory is now a major challenge. Studies of the metabolic potentials of different halophilic microorganisms, Archaea as well as Bacteria, shed light on the possibilities and the limitations of life at high salt concentrations, and also show their potential for applications in bioremediation.
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Affiliation(s)
- Aharon Oren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel.
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73
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Sorokin DY, Abbas B, Geleijnse M, Pimenov NV, Sukhacheva MV, van Loosdrecht MCM. Methanogenesis at extremely haloalkaline conditions in the soda lakes of Kulunda Steppe (Altai, Russia). FEMS Microbiol Ecol 2015; 91:fiv016. [PMID: 25764464 DOI: 10.1093/femsec/fiv016] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2015] [Indexed: 11/13/2022] Open
Abstract
Microbial methanogenesis at extreme conditions of saline alkaline soda lakes has, so far, been poorly investigated. Despite the obvious domination of sulfidogenesis as the therminal anaerobic process in the hypersaline soda lakes of Kulunda Steppe (Altai, southwestern Siberia), high concentrations of methane were detected in the anaerobic sediments. Potential activity measurements with different substrates gave results significantly deviating from what is commonly found in hypersaline habitats with neutral pH. In particular, not only a non-competitive methylotrophic pathway was active, but also lithotrophic and, in some cases, even acetate-dependent methanogenesis was found to be present in hypersaline soda lake sediments. All three pathways were functioning exclusively within the alkaline pH range between 8 and 10.5, while the salt concentration was the key factor influencing the activity. Methylotrophic and, to a lesser extent, lithotrophic methanogenesis were active up to soda-saturating conditions (4 M total Na(+)). Acetate-dependent methanogenesis was observed at salinities below 3 M total Na(+). Detection of methanogens in sediments using the mcrA gene as a functional marker demonstrated domination of methylotrophic genera Methanolobus and Methanosalsum and lithotrophic Methanocalculus. In a few cases, acetoclastic Methanosaeta was detected, as well as two deep lineage methanogens. Cultivation results corresponded well to the mcrA-based observations. Enrichments for natronophilic methylotrophic methanogens resulted in isolation of Methanolobus strains at moderate salinity, while at salt concentrations above 2 M Na(+) a novel member of the genus Methanosalsum was dominating. Enrichments with H2 or formate invariably resulted in domination of close relatives of Methanocalculus natronophilus. Enrichments with acetate at low salt concentration yielded two acetoclastic alkaliphilic Methanosaeta cultures, while at salinity above 1 M Na(+) syntrophic associations were apparently responsible for the observed acetate conversion to methane. Overall, the results indicated the presence of functionally structured and active methanogenic populations in Siberian hypersaline soda lakes.
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Affiliation(s)
- Dimitry Y Sorokin
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Ben Abbas
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Mitchell Geleijnse
- Department of Biotechnology, Delft University of Technology, 2628 BC Delft, the Netherlands
| | - Nikolai V Pimenov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/2, 117811 Moscow, Russia
| | - Marina V Sukhacheva
- Centre Bioengineering, Russian Academy of Sciences, Prospect 60-let Octyabrya 7/1, 117312 Moscow, Russia
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74
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Kamanda Ngugi D, Blom J, Alam I, Rashid M, Ba-Alawi W, Zhang G, Hikmawan T, Guan Y, Antunes A, Siam R, El Dorry H, Bajic V, Stingl U. Comparative genomics reveals adaptations of a halotolerant thaumarchaeon in the interfaces of brine pools in the Red Sea. THE ISME JOURNAL 2015; 9:396-411. [PMID: 25105904 PMCID: PMC4303633 DOI: 10.1038/ismej.2014.137] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 05/29/2014] [Accepted: 06/21/2014] [Indexed: 02/05/2023]
Abstract
The bottom of the Red Sea harbors over 25 deep hypersaline anoxic basins that are geochemically distinct and characterized by vertical gradients of extreme physicochemical conditions. Because of strong changes in density, particulate and microbial debris get entrapped in the brine-seawater interface (BSI), resulting in increased dissolved organic carbon, reduced dissolved oxygen toward the brines and enhanced microbial activities in the BSI. These features coupled with the deep-sea prevalence of ammonia-oxidizing archaea (AOA) in the global ocean make the BSI a suitable environment for studying the osmotic adaptations and ecology of these important players in the marine nitrogen cycle. Using phylogenomic-based approaches, we show that the local archaeal community of five different BSI habitats (with up to 18.2% salinity) is composed mostly of a single, highly abundant Nitrosopumilus-like phylotype that is phylogenetically distinct from the bathypelagic thaumarchaea; ammonia-oxidizing bacteria were absent. The composite genome of this novel Nitrosopumilus-like subpopulation (RSA3) co-assembled from multiple single-cell amplified genomes (SAGs) from one such BSI habitat further revealed that it shares ∼54% of its predicted genomic inventory with sequenced Nitrosopumilus species. RSA3 also carries several, albeit variable gene sets that further illuminate the phylogenetic diversity and metabolic plasticity of this genus. Specifically, it encodes for a putative proline-glutamate 'switch' with a potential role in osmotolerance and indirect impact on carbon and energy flows. Metagenomic fragment recruitment analyses against the composite RSA3 genome, Nitrosopumilus maritimus, and SAGs of mesopelagic thaumarchaea also reiterate the divergence of the BSI genotypes from other AOA.
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Affiliation(s)
- David Kamanda Ngugi
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Intikhab Alam
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mamoon Rashid
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Wail Ba-Alawi
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Guishan Zhang
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Tyas Hikmawan
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yue Guan
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andre Antunes
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Rania Siam
- Department of Biology, American University in Cairo, Cairo, Egypt
| | - Hamza El Dorry
- Department of Biology, American University in Cairo, Cairo, Egypt
| | - Vladimir Bajic
- Computational Bioscience Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Ulrich Stingl
- Red Sea Research Centre, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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75
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A halophilic bacterium inhabiting the warm, CaCl2-rich brine of the perennially ice-covered Lake Vanda, McMurdo Dry Valleys, Antarctica. Appl Environ Microbiol 2015; 81:1988-95. [PMID: 25576606 DOI: 10.1128/aem.03968-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Lake Vanda is a perennially ice-covered and stratified lake in the McMurdo Dry Valleys, Antarctica. The lake develops a distinct chemocline at about a 50-m depth, where the waters transition from cool, oxic, and fresh to warm, sulfidic, and hypersaline. The bottom water brine is unique, as the highly chaotropic salts CaCl2 and MgCl2 predominate, and CaCl2 levels are the highest of those in any known microbial habitat. Enrichment techniques were used to isolate 15 strains of heterotrophic bacteria from the Lake Vanda brine. Despite direct supplementation of the brine samples with different organic substrates in primary enrichments, the same organism, a relative of the halophilic bacterium Halomonas (Gammaproteobacteria), was isolated from all depths sampled. The Lake Vanda (VAN) strains were obligate aerobes and showed broad pH, salinity, and temperature ranges for growth, consistent with the physicochemical properties of the brine. VAN strains were halophilic and quite CaCl2 tolerant but did not require CaCl2 for growth. The fact that only VAN strain-like organisms appeared in our enrichments hints that the highly chaotropic nature of the Lake Vanda brine may place unusual physiological constraints on the bacterial community that inhabits it.
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76
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77
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Taxonomic, Ecological and Historical Considerations on the Deep-Water Benthic Mollusc Fauna of the Red Sea. THE RED SEA 2015. [DOI: 10.1007/978-3-662-45201-1_29] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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78
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Abdallah RZ, Adel M, Ouf A, Sayed A, Ghazy MA, Alam I, Essack M, Lafi FF, Bajic VB, El-Dorry H, Siam R. Aerobic methanotrophic communities at the Red Sea brine-seawater interface. Front Microbiol 2014; 5:487. [PMID: 25295031 PMCID: PMC4172156 DOI: 10.3389/fmicb.2014.00487] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 08/28/2014] [Indexed: 01/16/2023] Open
Abstract
The central rift of the Red Sea contains 25 brine pools with different physicochemical conditions, dictating the diversity and abundance of the microbial community. Three of these pools, the Atlantis II, Kebrit and Discovery Deeps, are uniquely characterized by a high concentration of hydrocarbons. The brine-seawater interface, described as an anoxic-oxic (brine-seawater) boundary, is characterized by a high methane concentration, thus favoring aerobic methane oxidation. The current study analyzed the aerobic free–living methane-oxidizing bacterial communities that potentially contribute to methane oxidation at the brine-seawater interfaces of the three aforementioned brine pools, using metagenomic pyrosequencing, 16S rRNA pyrotags and pmoA library constructs. The sequencing of 16S rRNA pyrotags revealed that these interfaces are characterized by high microbial community diversity. Signatures of aerobic methane-oxidizing bacteria were detected in the Atlantis II Interface (ATII-I) and the Kebrit Deep Upper (KB-U) and Lower (KB-L) brine-seawater interfaces. Through phylogenetic analysis of pmoA, we further demonstrated that the ATII-I aerobic methanotroph community is highly diverse. We propose four ATII-I pmoA clusters. Most importantly, cluster 2 groups with marine methane seep methanotrophs, and cluster 4 represent a unique lineage of an uncultured bacterium with divergent alkane monooxygenases. Moreover, non-metric multidimensional scaling (NMDS) based on the ordination of putative enzymes involved in methane metabolism showed that the Kebrit interface layers were distinct from the ATII-I and DD-I brine-seawater interfaces.
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Affiliation(s)
- Rehab Z Abdallah
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt
| | - Mustafa Adel
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Amged Ouf
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Ahmed Sayed
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Mohamed A Ghazy
- Department of Biology, American University in Cairo Cairo, Egypt
| | - Intikhab Alam
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Feras F Lafi
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Vladimir B Bajic
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Saudi Arabia
| | - Hamza El-Dorry
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt
| | - Rania Siam
- Biotechnology Graduate Program, American University in Cairo Cairo, Egypt ; Department of Biology, American University in Cairo Cairo, Egypt ; YJ-Science and Technology Research Center, American University in Cairo Cairo, Egypt
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79
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Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/532687] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The advent of molecular tools in microbial ecology paved the way to exploit the diversity of microbes in extreme environments. Here, we review these tools as applied in one of the most polyextreme habitats known on our planet, namely, deep hypersaline anoxic basins (DHABs), located at ca. 3000–3500 m depth in the Eastern Mediterranean Sea. Molecular gene signatures amplified from environmental DHAB samples identified a high degree of genetic novelty, as well as distinct communities in the DHABs. Canonical correspondence analyses provided strong evidence that salinity, ion composition, and anoxia were the strongest selection factors shaping protistan community structures, largely preventing cross-colonization among the individual basins. Thus, each investigated basin represents a unique habitat (“isolated islands of evolution”), making DHABs ideal model sites to test evolutionary hypotheses. Fluorescence in situ hybridization assays using specifically designed probes revealed that the obtained genetic signatures indeed originated from indigenous polyextremophiles. Electron microscopy imaging revealed unknown ciliates densely covered with prokaryote ectosymbionts, which may enable adaptations of eukaryotes to DHAB conditions. The research reviewed here significantly advanced our knowledge on polyextremophile eukaryotes, which are excellent models for a number of biological research areas, including ecology, diversity, biotechnology, evolutionary research, physiology, and astrobiology.
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Grötzinger SW, Alam I, Ba Alawi W, Bajic VB, Stingl U, Eppinger J. Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). Front Microbiol 2014; 5:134. [PMID: 24778629 PMCID: PMC3985023 DOI: 10.3389/fmicb.2014.00134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/16/2014] [Indexed: 11/13/2022] Open
Abstract
Reliable functional annotation of genomic data is the key-step in the discovery of novel enzymes. Intrinsic sequencing data quality problems of single amplified genomes (SAGs) and poor homology of novel extremophile's genomes pose significant challenges for the attribution of functions to the coding sequences identified. The anoxic deep-sea brine pools of the Red Sea are a promising source of novel enzymes with unique evolutionary adaptation. Sequencing data from Red Sea brine pool cultures and SAGs are annotated and stored in the Integrated Data Warehouse of Microbial Genomes (INDIGO) data warehouse. Low sequence homology of annotated genes (no similarity for 35% of these genes) may translate into false positives when searching for specific functions. The Profile and Pattern Matching (PPM) strategy described here was developed to eliminate false positive annotations of enzyme function before progressing to labor-intensive hyper-saline gene expression and characterization. It utilizes InterPro-derived Gene Ontology (GO)-terms (which represent enzyme function profiles) and annotated relevant PROSITE IDs (which are linked to an amino acid consensus pattern). The PPM algorithm was tested on 15 protein families, which were selected based on scientific and commercial potential. An initial list of 2577 enzyme commission (E.C.) numbers was translated into 171 GO-terms and 49 consensus patterns. A subset of INDIGO-sequences consisting of 58 SAGs from six different taxons of bacteria and archaea were selected from six different brine pool environments. Those SAGs code for 74,516 genes, which were independently scanned for the GO-terms (profile filter) and PROSITE IDs (pattern filter). Following stringent reliability filtering, the non-redundant hits (106 profile hits and 147 pattern hits) are classified as reliable, if at least two relevant descriptors (GO-terms and/or consensus patterns) are present. Scripts for annotation, as well as for the PPM algorithm, are available through the INDIGO website.
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Affiliation(s)
- Stefan W Grötzinger
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
| | - Intikhab Alam
- Division of Biological Sciences and Engineering, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
| | - Wail Ba Alawi
- Division of Biological Sciences and Engineering, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
| | - Vladimir B Bajic
- Division of Biological Sciences and Engineering, Computational Bioscience Research Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
| | - Ulrich Stingl
- Division of Biological Sciences and Engineering, Red Sea Research Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
| | - Jörg Eppinger
- Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia
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81
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Werner J, Ferrer M, Michel G, Mann AJ, Huang S, Juarez S, Ciordia S, Albar JP, Alcaide M, La Cono V, Yakimov MM, Antunes A, Taborda M, da Costa MS, Hai T, Glöckner FO, Golyshina OV, Golyshin PN, Teeling H. Halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader. Environ Microbiol 2014; 16:2525-37. [PMID: 24428220 PMCID: PMC4257568 DOI: 10.1111/1462-2920.12393] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 01/05/2014] [Indexed: 11/28/2022]
Abstract
Euryarchaea from the genus Halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: Halorhabdus utahensis AX-2(T) from the shallow Great Salt Lake of Utah, and Halorhabdus tiamatea SARL4B(T) from the Shaban deep-sea hypersaline anoxic lake (DHAL) in the Red Sea. We sequenced the H. tiamatea genome to elucidate its niche adaptations. Among sequenced archaea, H. tiamatea features the highest number of glycoside hydrolases, the majority of which were expressed in proteome experiments. Annotations and glycosidase activity measurements suggested an adaptation towards recalcitrant algal and plant-derived hemicelluloses. Glycosidase activities were higher at 2% than at 0% or 5% oxygen, supporting a preference for low-oxygen conditions. Likewise, proteomics indicated quinone-mediated electron transport at 2% oxygen, but a notable stress response at 5% oxygen. Halorhabdus tiamatea furthermore encodes proteins characteristic for thermophiles and light-dependent enzymes (e.g. bacteriorhodopsin), suggesting that H. tiamatea evolution was mostly not governed by a cold, dark, anoxic deep-sea habitat. Using enrichment and metagenomics, we could demonstrate presence of similar glycoside hydrolase-rich Halorhabdus members in the Mediterranean DHAL Medee, which supports that Halorhabdus species can occupy a distinct niche as polysaccharide degraders in hypersaline environments.
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Affiliation(s)
- Johannes Werner
- Max Planck Institute for Marine Microbiology, Bremen, Germany; Jacobs University Bremen gGmbH, Bremen, Germany
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82
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Abd El Razak A, Ward AC, Glassey J. Screening of marine bacterial producers of polyunsaturated fatty acids and optimisation of production. MICROBIAL ECOLOGY 2014; 67:454-464. [PMID: 24292901 DOI: 10.1007/s00248-013-0332-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 11/12/2013] [Indexed: 06/02/2023]
Abstract
Water samples from three different environments including Mid Atlantic Ridge, Red Sea and Mediterranean Sea were screened in order to isolate new polyunsaturated fatty acids (PUFAs) bacterial producers especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Two hundred and fifty-one isolates were screened for PUFA production and among them the highest number of producers was isolated from the Mid-Atlantic Ridge followed by the Red Sea while no producers were found in the Mediterranean Sea samples. The screening strategy included a simple colourimetric method followed by a confirmation via GC/MS. Among the tested producers, an isolate named 66 was found to be a potentially high PUFA producer producing relatively high levels of EPA in particular. A Plackett-Burman statistical design of experiments was applied to screen a wide number of media components identifying glycerol and whey as components of a production medium. The potential low-cost production medium was optimised by applying a response surface methodology to obtain the highest productivity converting industrial by-products into value-added products. The maximum achieved productivity of EPA was 20 mg/g, 45 mg/l, representing 11% of the total fatty acids, which is approximately five times more than the amount produced prior to optimisation. The production medium composition was 10.79 g/l whey and 6.87 g/l glycerol. To our knowledge, this is the first investigation of potential bacteria PUFA producers from Mediterranean and Red Seas providing an evaluation of a colourimetric screening method as means of rapid screening of a large number of isolates.
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Affiliation(s)
- Ahmed Abd El Razak
- School of Chemical Engineering and Advanced Materials, CEAM, Merz Court, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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83
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Alam I, Antunes A, Kamau AA, Ba Alawi W, Kalkatawi M, Stingl U, Bajic VB. INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PLoS One 2013; 8:e82210. [PMID: 24324765 PMCID: PMC3855842 DOI: 10.1371/journal.pone.0082210] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/22/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The next generation sequencing technologies substantially increased the throughput of microbial genome sequencing. To functionally annotate newly sequenced microbial genomes, a variety of experimental and computational methods are used. Integration of information from different sources is a powerful approach to enhance such annotation. Functional analysis of microbial genomes, necessary for downstream experiments, crucially depends on this annotation but it is hampered by the current lack of suitable information integration and exploration systems for microbial genomes. RESULTS We developed a data warehouse system (INDIGO) that enables the integration of annotations for exploration and analysis of newly sequenced microbial genomes. INDIGO offers an opportunity to construct complex queries and combine annotations from multiple sources starting from genomic sequence to protein domain, gene ontology and pathway levels. This data warehouse is aimed at being populated with information from genomes of pure cultures and uncultured single cells of Red Sea bacteria and Archaea. Currently, INDIGO contains information from Salinisphaera shabanensis, Haloplasma contractile, and Halorhabdus tiamatea - extremophiles isolated from deep-sea anoxic brine lakes of the Red Sea. We provide examples of utilizing the system to gain new insights into specific aspects on the unique lifestyle and adaptations of these organisms to extreme environments. CONCLUSIONS We developed a data warehouse system, INDIGO, which enables comprehensive integration of information from various resources to be used for annotation, exploration and analysis of microbial genomes. It will be regularly updated and extended with new genomes. It is aimed to serve as a resource dedicated to the Red Sea microbes. In addition, through INDIGO, we provide our Automatic Annotation of Microbial Genomes (AAMG) pipeline. The INDIGO web server is freely available at http://www.cbrc.kaust.edu.sa/indigo.
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Affiliation(s)
- Intikhab Alam
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
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84
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Sagar S, Esau L, Holtermann K, Hikmawan T, Zhang G, Stingl U, Bajic VB, Kaur M. Induction of apoptosis in cancer cell lines by the Red Sea brine pool bacterial extracts. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 13:344. [PMID: 24305113 PMCID: PMC4235048 DOI: 10.1186/1472-6882-13-344] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/28/2013] [Indexed: 01/17/2023]
Abstract
BACKGROUND Marine microorganisms are considered to be an important source of bioactive molecules against various diseases and have great potential to increase the number of lead molecules in clinical trials. Progress in novel microbial culturing techniques as well as greater accessibility to unique oceanic habitats has placed the marine environment as a new frontier in the field of natural product drug discovery. METHODS A total of 24 microbial extracts from deep-sea brine pools in the Red Sea have been evaluated for their anticancer potential against three human cancer cell lines. Downstream analysis of these six most potent extracts was done using various biological assays, such as Caspase-3/7 activity, mitochondrial membrane potential (MMP), PARP-1 cleavage and expression of γH2Ax, Caspase-8 and -9 using western blotting. RESULTS In general, most of the microbial extracts were found to be cytotoxic against one or more cancer cell lines with cell line specific activities. Out of the 13 most active microbial extracts, six extracts were able to induce significantly higher apoptosis (>70%) in cancer cells. Mechanism level studies revealed that extracts from Chromohalobacter salexigens (P3-86A and P3-86B(2)) followed the sequence of events of apoptotic pathway involving MMP disruption, caspase-3/7 activity, caspase-8 cleavage, PARP-1 cleavage and Phosphatidylserine (PS) exposure, whereas another Chromohalobacter salexigens extract (K30) induced caspase-9 mediated apoptosis. The extracts from Halomonas meridiana (P3-37B), Chromohalobacter israelensis (K18) and Idiomarina loihiensis (P3-37C) were unable to induce any change in MMP in HeLa cancer cells, and thus suggested mitochondria-independent apoptosis induction. However, further detection of a PARP-1 cleavage product, and the observed changes in caspase-8 and -9 suggested the involvement of caspase-mediated apoptotic pathways. CONCLUSION Altogether, the study offers novel findings regarding the anticancer potential of several halophilic bacterial species inhabiting the Red Sea (at the depth of 1500-2500 m), which constitute valuable candidates for further isolation and characterization of bioactive molecules.
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85
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Mohamed YM, Ghazy MA, Sayed A, Ouf A, El-Dorry H, Siam R. Isolation and characterization of a heavy metal-resistant, thermophilic esterase from a Red Sea brine pool. Sci Rep 2013; 3:3358. [PMID: 24285146 PMCID: PMC6506439 DOI: 10.1038/srep03358] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/07/2013] [Indexed: 11/09/2022] Open
Abstract
The Red Sea Atlantis II brine pool is an extreme environment that displays multiple harsh conditions such as high temperature, high salinity and high concentrations of multiple, toxic heavy metals. The survival of microbes in such an environment by utilizing resistant enzymes makes them an excellent source of extremophilic enzymes. We constructed a fosmid metagenomic library using DNA isolated from the deepest and most secluded layer of this pool. We report the isolation and biochemical characterization of an unusual esterase: EstATII. EstATII is thermophilic (optimum temperature, 65°C), halotolerant (maintains its activity in up to 4.5 M NaCl) and maintains at least 60% of its activity in the presence of a wide spectrum of heavy metals. The combination of biochemical characteristics of the Red Sea Atlantis II brine pool esterase, i.e., halotolerance, thermophilicity and resistance to heavy metals, makes it a potentially useful biocatalyst.
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Affiliation(s)
- Yasmine M Mohamed
- 1] Biology Department, American University in Cairo, Cairo, Egypt [2] YJ-The Science and Technology Research Center, American University in Cairo, Cairo, Egypt
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86
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Sayed A, Ghazy MA, Ferreira AJS, Setubal JC, Chambergo FS, Ouf A, Adel M, Dawe AS, Archer JAC, Bajic VB, Siam R, El-Dorry H. A novel mercuric reductase from the unique deep brine environment of Atlantis II in the Red Sea. J Biol Chem 2013; 289:1675-87. [PMID: 24280218 DOI: 10.1074/jbc.m113.493429] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A unique combination of physicochemical conditions prevails in the lower convective layer (LCL) of the brine pool at Atlantis II (ATII) Deep in the Red Sea. With a maximum depth of over 2000 m, the pool is characterized by acidic pH (5.3), high temperature (68 °C), salinity (26%), low light levels, anoxia, and high concentrations of heavy metals. We have established a metagenomic dataset derived from the microbial community in the LCL, and here we describe a gene for a novel mercuric reductase, a key component of the bacterial detoxification system for mercuric and organomercurial species. The metagenome-derived gene and an ortholog from an uncultured soil bacterium were synthesized and expressed in Escherichia coli. The properties of their products show that, in contrast to the soil enzyme, the ATII-LCL mercuric reductase is functional in high salt, stable at high temperatures, resistant to high concentrations of Hg(2+), and efficiently detoxifies Hg(2+) in vivo. Interestingly, despite the marked functional differences between the orthologs, their amino acid sequences differ by less than 10%. Site-directed mutagenesis and kinetic analysis of the mutant enzymes, in conjunction with three-dimensional modeling, have identified distinct structural features that contribute to extreme halophilicity, thermostability, and high detoxification capacity, suggesting that these were acquired independently during the evolution of this enzyme. Thus, our work provides fundamental structural insights into a novel protein that has undergone multiple biochemical and biophysical adaptations to promote the survival of microorganisms that reside in the extremely demanding environment of the ATII-LCL.
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Affiliation(s)
- Ahmed Sayed
- From the Department of Biology and the Science and Technology Research Center, School of Sciences and Engineering, The American University in Cairo, AUC Avenue, P. O. Box 74, New Cairo 11835, Egypt
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87
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The limits for life under multiple extremes. Trends Microbiol 2013; 21:204-12. [DOI: 10.1016/j.tim.2013.01.006] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 01/28/2013] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
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88
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Sagar S, Esau L, Hikmawan T, Antunes A, Holtermann K, Stingl U, Bajic VB, Kaur M. Cytotoxic and apoptotic evaluations of marine bacteria isolated from brine-seawater interface of the Red Sea. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2013; 13:29. [PMID: 23388148 PMCID: PMC3598566 DOI: 10.1186/1472-6882-13-29] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 02/01/2013] [Indexed: 11/10/2022]
Abstract
Background High salinity and temperature combined with presence of heavy metals and low oxygen renders deep-sea anoxic brines of the Red Sea as one of the most extreme environments on Earth. The ability to adapt and survive in these extreme environments makes inhabiting bacteria interesting candidates for the search of novel bioactive molecules. Methods Total 20 i.e. lipophilic (chloroform) and hydrophilic (70% ethanol) extracts of marine bacteria isolated from brine-seawater interface of the Red Sea were tested for cytotoxic and apoptotic activity against three human cancer cell lines, i.e. HeLa (cervical carcinoma), MCF-7 (Breast Adenocarcinoma) and DU145 (Prostate carcinoma). Results Among these, twelve extracts were found to be very active after 24 hours of treatment, which were further evaluated for their cytotoxic and apoptotic effects at 48 hr. The extracts from the isolates P1-37B and P3-37A (Halomonas) and P1-17B (Sulfitobacter) have been found to be the most potent against tested cancer cell lines. Conclusion Overall, bacterial isolates from the Red Sea displayed promising results and can be explored further to find novel drug-like molecules. The cell line specific activity of the extracts may be attributed to the presence of different polarity compounds or the cancer type i.e. biological differences in cell lines and different mechanisms of action of programmed cell death prevalent in different cancer cell lines.
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89
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Oren A. Life in Magnesium- and Calcium-Rich Hypersaline Environments: Salt Stress by Chaotropic Ions. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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90
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Life at High Salt and Low Oxygen: How Do the Halobacteriaceae Cope with Low Oxygen Concentrations in Their Environment? CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2013. [DOI: 10.1007/978-94-007-6488-0_24] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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91
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Unique prokaryotic consortia in geochemically distinct sediments from Red Sea Atlantis II and discovery deep brine pools. PLoS One 2012; 7:e42872. [PMID: 22916172 PMCID: PMC3423430 DOI: 10.1371/journal.pone.0042872] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 07/12/2012] [Indexed: 12/02/2022] Open
Abstract
The seafloor is a unique environment, which allows insights into how geochemical processes affect the diversity of biological life. Among its diverse ecosystems are deep-sea brine pools - water bodies characterized by a unique combination of extreme conditions. The ‘polyextremophiles’ that constitute the microbial assemblage of these deep hot brines have not been comprehensively studied. We report a comparative taxonomic analysis of the prokaryotic communities of the sediments directly below the Red Sea brine pools, namely, Atlantis II, Discovery, Chain Deep, and an adjacent brine-influenced site. Analyses of sediment samples and high-throughput pyrosequencing of PCR-amplified environmental 16S ribosomal RNA genes (16S rDNA) revealed that one sulfur (S)-rich Atlantis II and one nitrogen (N)-rich Discovery Deep section contained distinct microbial populations that differed from those found in the other sediment samples examined. Proteobacteria, Actinobacteria, Cyanobacteria, Deferribacteres, and Euryarchaeota were the most abundant bacterial and archaeal phyla in both the S- and N-rich sections. Relative abundance-based hierarchical clustering of the 16S rDNA pyrotags assigned to major taxonomic groups allowed us to categorize the archaeal and bacterial communities into three major and distinct groups; group I was unique to the S-rich Atlantis II section (ATII-1), group II was characteristic for the N-rich Discovery sample (DD-1), and group III reflected the composition of the remaining sediments. Many of the groups detected in the S-rich Atlantis II section are likely to play a dominant role in the cycling of methane and sulfur due to their phylogenetic affiliations with bacteria and archaea involved in anaerobic methane oxidation and sulfate reduction.
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93
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Klevjer TA, Torres DJ, Kaartvedt S. Distribution and diel vertical movements of mesopelagic scattering layers in the Red Sea. MARINE BIOLOGY 2012; 159:1833-1841. [PMID: 24391275 PMCID: PMC3873044 DOI: 10.1007/s00227-012-1973-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 05/21/2012] [Indexed: 05/27/2023]
Abstract
The mesopelagic zone of the Red Sea represents an extreme environment due to low food concentrations, high temperatures and low oxygen waters. Nevertheless, a 38 kHz echosounder identified at least four distinct scattering layers during the daytime, of which the 2 deepest layers resided entirely within the mesopelagic zone. Two of the acoustic layers were found above a mesopelagic oxygen minimum zone (OMZ), one layer overlapped with the OMZ, and one layer was found below the OMZ. Almost all organisms in the deep layers migrated to the near-surface waters during the night. Backscatter from a 300 kHz lowered Acoustic Doppler Current Profiler indicated a layer of zooplankton within the OMZ. They carried out DVM, yet a portion remained at mesopelagic depths during the night. Our acoustic measurements showed that the bulk of the acoustic backscatter was restricted to waters shallower than 800 m, suggesting that most of the biomass in the Red Sea resides above this depth.
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Affiliation(s)
- Thor A. Klevjer
- King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Daniel J. Torres
- Woods Hole Oceanographic Institution, MS #30, Woods Hole, MA 02543 USA
| | - Stein Kaartvedt
- King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
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Genome sequence of Salinisphaera shabanensis, a gammaproteobacterium from the harsh, variable environment of the brine-seawater interface of the Shaban Deep in the Red Sea. J Bacteriol 2011; 193:4555-6. [PMID: 21705588 DOI: 10.1128/jb.05459-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the genome of Salinisphaera shabanensis, isolated from a brine-seawater interface and representing a new order within the Gammaproteobacteria. Its adaptations to physicochemical and nutrient availability fluctuations include six genes encoding heavy metal-translocating P-type ATPases and multiple genes involved in iron uptake, siderophore production, and poly-β-hydroxybutyrate synthesis.
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95
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Genome sequence of Halorhabdus tiamatea, the first archaeon isolated from a deep-sea anoxic brine lake. J Bacteriol 2011; 193:4553-4. [PMID: 21705593 DOI: 10.1128/jb.05462-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the draft genome of Halorhabdus tiamatea, the first member of the Archaea ever isolated from a deep-sea anoxic brine. Genome comparison with Halorhabdus utahensis revealed some striking differences, including a marked increase in genes associated with transmembrane transport and putative genes for a trehalose synthase and a lactate dehydrogenase.
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96
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Genome sequence of Haloplasma contractile, an unusual contractile bacterium from a deep-sea anoxic brine lake. J Bacteriol 2011; 193:4551-2. [PMID: 21705599 DOI: 10.1128/jb.05461-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the draft genome of Haloplasma contractile, isolated from a deep-sea brine and representing a new order between Firmicutes and Mollicutes. Its complex morphology with contractile protrusions might be strongly influenced by the presence of seven MreB/Mbl homologs, which appears to be the highest copy number ever reported.
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