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Duchâtellier G, Oehlert AM, Shernisky H, Pollier CGL, Swart PK, Howes B, Purkis SJ. Sedimentary porewaters record regional tectonic and climate events that perturbed a deep-sea brine pool in the Gulf of Aqaba, Red Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168804. [PMID: 38036117 DOI: 10.1016/j.scitotenv.2023.168804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
Brine pools in deep-sea environments provide unique perspectives into planetary and geological processes, extremophile microbial communities, and sedimentary records. The NEOM Brine Pool Complex was the first deep-sea brine pool system found in the Gulf of Aqaba, representing a significant extension of the geographical range and depositional setting of Red Sea brine pools. Here, we use a combination of brine pool samples collected via cast using a conductivity, temperature, depth instrument (CTD), as well as interstitial porewaters extracted from a sediment core collected in the NEOM Brine Pool to characterize the chemical composition and subsurface evolution of the brine. New results indicate that the NEOM brines and the subsurface porewaters may originate from different sources. Elemental concentrations suggest the brines in the NEOM pool are likely derived from dissolution of sub-seabed evaporites. In contrast, the sedimentary porewaters appear to have been influenced by periodic turbidite flows, generated either by earthquakes, submarine landslides, or flash floods, in which normal marine waters from the overlying Red Sea became entrained, periodically disturbing the chemistry of the brine pool. Thus, sediment porewaters beneath brine pools may record transient and dynamic changes in these deep marine depositional environments, reflecting the interplay between climate, tectonics, and sedimentation patterns along a rapidly urbanizing coastline. In concert, new results from NEOM extend the range and chemical constraints on Red Sea Brine Pools and highlight the dynamic interplay between Red Sea Deep water, dissolving evaporites, turbidites, and subsurface fluids that produce these unique depositional environments which host microbial life at the edge of habitability. In concert with sedimentological indicators, the chemistry of porewaters beneath deep-sea brine pools may present detailed records of natural hazards arising from interactions between the atmosphere, lithosphere, hydrosphere, and anthroposphere.
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Affiliation(s)
- Gaëlle Duchâtellier
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Amanda M Oehlert
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA.
| | - Hannah Shernisky
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Clément G L Pollier
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Peter K Swart
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Bolton Howes
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
| | - Sam J Purkis
- Department of Marine Geosciences, Rosenstiel School of Marine, Atmospheric and Earth Science, University of Miami, Miami, FL 33149, USA
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2
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Chen C, Yi R, Igisu M, Sakaguchi C, Afrin R, Potiszil C, Kunihiro T, Kobayashi K, Nakamura E, Ueno Y, Antunes A, Wang A, Chandru K, Hao J, Jia TZ. Spectroscopic and Biophysical Methods to Determine Differential Salt-Uptake by Primitive Membraneless Polyester Microdroplets. SMALL METHODS 2023; 7:e2300119. [PMID: 37203261 DOI: 10.1002/smtd.202300119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/23/2023] [Indexed: 05/20/2023]
Abstract
α-Hydroxy acids are prebiotic monomers that undergo dehydration synthesis to form polyester gels, which assemble into membraneless microdroplets upon aqueous rehydration. These microdroplets are proposed as protocells that can segregate and compartmentalize primitive molecules/reactions. Different primitive aqueous environments with a variety of salts could have hosted chemistries that formed polyester microdroplets. These salts could be essential cofactors of compartmentalized prebiotic reactions or even directly affect protocell structure. However, fully understanding polyester-salt interactions remains elusive, partially due to technical challenges of quantitative measurements in condensed phases. Here, spectroscopic and biophysical methods are applied to analyze salt uptake by polyester microdroplets. Inductively coupled plasma mass spectrometry is applied to measure the cation concentration within polyester microdroplets after addition of chloride salts. Combined with methods to determine the effects of salt uptake on droplet turbidity, size, surface potential and internal water distribution, it was observed that polyester microdroplets can selectively partition salt cations, leading to differential microdroplet coalescence due to ionic screening effects reducing electrostatic repulsion forces between microdroplets. Through applying existing techniques to novel analyses related to primitive compartment chemistry and biophysics, this study suggests that even minor differences in analyte uptake can lead to significant protocellular structural change.
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Affiliation(s)
- Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Motoko Igisu
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Chie Sakaguchi
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Rehana Afrin
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Christian Potiszil
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Tak Kunihiro
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Katsura Kobayashi
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Eizo Nakamura
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8551, Japan
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau, SAR, China
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW, 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW, 2052, Australia
- RNA Institute, UNSW Sydney, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Synthetic Biology, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia, Selangor, 43650, Malaysia
| | - Jihua Hao
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
- Deep Space Exploration Laboratory/CAS Laboratory of Crust-Mantle Materials and Environments, University of Science and Technology of China, Hefei, 230026, China
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
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3
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Briscoe L, Halperin E, Garud NR. SNV-FEAST: microbial source tracking with single nucleotide variants. Genome Biol 2023; 24:101. [PMID: 37121994 PMCID: PMC10150486 DOI: 10.1186/s13059-023-02927-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/06/2023] [Indexed: 05/02/2023] Open
Abstract
Elucidating the sources of a microbiome can provide insight into the ecological dynamics responsible for the formation of these communities. Source tracking approaches to date leverage species abundance information; however, single nucleotide variants (SNVs) may be more informative because of their high specificity to certain sources. To overcome the computational burden of utilizing all SNVs for a given sample, we introduce a novel method to identify signature SNVs for source tracking. Signature SNVs used as input into a previously designed source tracking algorithm, FEAST, can more accurately estimate contributions than species and provide novel insights, demonstrated in three case studies.
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Affiliation(s)
- Leah Briscoe
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Nandita R Garud
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA, USA.
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4
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Elbehery AHA, Beason E, Siam R. Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools. Arch Microbiol 2023; 205:195. [PMID: 37061654 DOI: 10.1007/s00203-023-03531-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/19/2023] [Accepted: 03/31/2023] [Indexed: 04/17/2023]
Abstract
Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.
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Affiliation(s)
- Ali H A Elbehery
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt.
| | - Elisabeth Beason
- University of Medicine and Health Sciences, Basseterre, West Indies, Saint Kitts and Nevis
| | - Rania Siam
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, Cairo, Egypt.
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5
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Lazar CS, Schmidt F, Elvert M, Heuer VB, Hinrichs KU, Teske AP. Microbial diversity gradients in the geothermal mud volcano underlying the hypersaline Urania Basin. Front Microbiol 2022; 13:1043414. [PMID: 36620052 PMCID: PMC9812581 DOI: 10.3389/fmicb.2022.1043414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Mud volcanoes transport deep fluidized sediment and their microbial communities and thus provide a window into the deep biosphere. However, mud volcanoes are commonly sampled at the surface and not probed at greater depths, with the consequence that their internal geochemistry and microbiology remain hidden from view. Urania Basin, a hypersaline seafloor basin in the Mediterranean, harbors a mud volcano that erupts fluidized mud into the brine. The vertical mud pipe was amenable to shipboard Niskin bottle and multicorer sampling and provided an opportunity to investigate the downward sequence of bacterial and archaeal communities of the Urania Basin brine, fluid mud layers and consolidated subsurface sediments using 16S rRNA gene sequencing. These microbial communities show characteristic, habitat-related trends as they change throughout the sample series, from extremely halophilic bacteria (KB1) and archaea (Halodesulfoarchaeum spp.) in the brine, toward moderately halophilic and thermophilic endospore-forming bacteria and uncultured archaeal lineages in the mud fluid, and finally ending in aromatics-oxidizing bacteria, uncultured spore formers, and heterotrophic subsurface archaea (Thermoplasmatales, Bathyarchaeota, and Lokiarcheota) in the deep subsurface sediment at the bottom of the mud volcano. Since these bacterial and archaeal lineages are mostly anaerobic heterotrophic fermenters, the microbial ecosystem in the brine and fluidized mud functions as a layered fermenter for the degradation of sedimentary biomass and hydrocarbons. By spreading spore-forming, thermophilic Firmicutes during eruptions, the Urania Basin mud volcano likely functions as a source of endospores that occur widely in cold seafloor sediments.
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Affiliation(s)
- Cassandre Sara Lazar
- Department of Biological Sciences, Université du Québec à Montréal, Montréal, QC, Canada
| | - Frauke Schmidt
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Verena B. Heuer
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- Organic Geochemistry Group, Department of Geosciences, MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Andreas P. Teske
- Department of Earth, Marine and Environmental Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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6
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Ziko L, AbdelRaheem O, Nabil M, Aziz RK, Siam R. Bioprospecting the microbiome of Red Sea Atlantis II brine pool for peptidases and biosynthetic genes with promising antibacterial activity. Microb Cell Fact 2022; 21:109. [PMID: 35655185 PMCID: PMC9161539 DOI: 10.1186/s12934-022-01835-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/05/2022] [Indexed: 11/23/2022] Open
Abstract
Background The search for novel antimicrobial agents is crucial as antibiotic-resistant pathogens continue to emerge, rendering the available antibiotics no longer effective. Likewise, new anti-cancer drugs are needed to combat the emergence of multi-drug resistant tumors. Marine environments are wealthy sources for natural products. Additionally, extreme marine environments are interesting niches to search for bioactive natural compounds. In the current study, a fosmid library of metagenomic DNA isolated from Atlantis II Deep Lower Convective Layer (ATII LCL), was functionally screened for antibacterial activity as well as anticancer effects. Results Two clones exhibited antibacterial effects against the marine Bacillus Cc6 strain, namely clones 102-5A and 88-1G and they were further tested against eleven other challenging strains, including six safe relatives of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), a safe relative to Mycobacterium tuberculosis and four resistant clinical isolates. Clone 88-1G resulted in clear zones of inhibition against eight bacterial strains, while clone 102-5A resulted in zones of inhibition against five bacterial strains. The whole cell lysates of clone 88-1G showed 15% inhibition of Mtb ClpP protease -Mycobacterium tuberculosis drug target-, while whole cell lysates of clone 102-5A showed 19% inhibition of Mtb ClpP protease. Whole cell lysates from the selected clones exhibited anticancer effects against MCF-7 breast cancer cells (cell viability at 50% v/v was 46.2% ± 9.9 for 88-1G clone and 38% ± 7 for 102-5A clone), U2OS osteosarcoma cells (cell viability at 50% v/v was 64.6% ± 12.3 for 88-1G clone and 28.3% ± 1.7 for 102-5A clone) and 1BR hTERT human fibroblast cells (cell viability at 50% v/v was 74.4% ± 5.6 for 88-1G clone and 57.6% ± 8.9 for 102-5A clone). Sequencing of 102-5A and 88-1G clones, and further annotation detected putative proteases and putative biosynthetic genes in clones 102-5A and 88-1G, respectively. Conclusions The ATII LCL metagenome hosts putative peptidases and biosynthetic genes that confer antibiotic and anti-cancer effects. The tested clones exhibited promising antibacterial activities against safe relative strains to ESKAPE pathogens and Mycobacterium tuberculosis. Thus, searching the microbial dark matter of extreme environments is a promising approach to identify new molecules with pharmaceutical potential use. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01835-z.
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Affiliation(s)
- Laila Ziko
- School of Life and Medical Sciences, University of Hertfordshire, Hosted by Global Academic Foundation, 11865, New Administrative Capital, Egypt.,Department of Biology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt
| | - Omnia AbdelRaheem
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt
| | - Marina Nabil
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562, Cairo, Egypt.,Microbiology and Immunology Research Program, Children's Cancer Hospital Egypt 57357, 11617, Cairo, Egypt
| | - Rania Siam
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, 11835, New Cairo, Egypt. .,University of Medicine and Health Sciences, Basseterre, West Indies, Saint Kitts and Nevis.
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7
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Ahmed SF, Abdallah RZ, Siam R. Evaluation of a Thermophilic, Psychrostable, and Heavy Metal-Resistant Red Sea Brine Pool Esterase. Mar Drugs 2022; 20:md20050274. [PMID: 35621925 PMCID: PMC9144027 DOI: 10.3390/md20050274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Lipolytic enzymes catalyze the hydrolysis and synthesis of ester compounds. They are valuable in the pulp, food, and textile industries. This study aims to comprehensively evaluate the extreme properties of a hormone-sensitive lipase (EstATII-TM) isolated from the Red Sea Atlantis II brine pool. EstATII-TM was cloned, expressed, and its biochemical activities were assessed under different conditions. EstATII-TM catalytic properties and resistance to different metal ions were compared to commercial thermophilic esterases under different temperatures. Phylogenetically, EstATII-TM was assigned to the GDSAG motif subfamily of hormone-sensitive lipase. The optimal enzyme activity was evident at a temperature of 30 °C and pH 7–8. The enzyme retained 84.9% of its activity at 0.5 M NaCl. EstATII-TM maintained 93% to 97% activity at −40 and −20 °C, respectively. EstATII-TM activity was significantly enhanced, up to 10-fold, at temperatures ranging from 45 to 65 °C in the presence of 1 mM Cu2+, Cd2+, Ba2+, Mn2+, and Zn2+. EstATII-TM showed superior catalytic activity and resistance-to/enhancement-by metal ions compared to two commercial thermophilic esterases. The Red Sea Atlantis II brine EstATII-TM is characterized by tolerance to high temperatures, stability to hot and cold conditions, as well as toxic heavy metal contamination, making it an ideal candidate for industrial processes.
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Affiliation(s)
- Shimaa F. Ahmed
- Biology Department, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (S.F.A.); (R.Z.A.)
| | - Rehab Z. Abdallah
- Biology Department, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (S.F.A.); (R.Z.A.)
- Max Planck institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Rania Siam
- Biology Department, School of Sciences and Engineering, The American University in Cairo, New Cairo 11835, Egypt; (S.F.A.); (R.Z.A.)
- University of Medicine and Health Sciences, Basseterre, Saint Kitts and Nevis
- Correspondence:
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8
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Solchaga JI, Busalmen JP, Nercessian D. Unraveling Anaerobic Metabolisms in a Hypersaline Sediment. Front Microbiol 2022; 13:811432. [PMID: 35369499 PMCID: PMC8966722 DOI: 10.3389/fmicb.2022.811432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The knowledge on the microbial diversity inhabiting hypersaline sediments is still limited. In particular, existing data about anaerobic hypersaline archaea and bacteria are scarce and refer to a limited number of genera. The approach to obtain existing information has been almost exclusively attempting to grow every organism in axenic culture on the selected electron acceptor with a variety of electron donors. Here, a different approach has been used to interrogate the microbial community of submerged hypersaline sediment of Salitral Negro, Argentina, aiming at enriching consortia performing anaerobic respiration of different electron acceptor compounds, in which ecological associations can maximize the possibilities of successful growth. Growth of consortia was demonstrated on all offered electron acceptors, including fumarate, nitrate, sulfate, thiosulfate, dimethyl sulfoxide, and a polarized electrode. Halorubrum and Haloarcula representatives are here shown for the first time growing on lactate, using fumarate or a polarized electrode as the electron acceptor; in addition, they are shown also growing in sulfate-reducing consortia. Halorubrum representatives are for the first time shown to be growing in nitrate-reducing consortia, probably thanks to reduction of N2O produced by other consortium members. Fumarate respiration is indeed shown for the first time supporting growth of Halanaeroarchaeum and Halorhabdus belonging to the archaea, as well as growth of Halanaerobium, Halanaerobaculum, Sporohalobacter, and Acetohalobium belonging to the bacteria. Finally, evidence is presented suggesting growth of nanohaloarchaea in anaerobic conditions.
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Affiliation(s)
- Juan Ignacio Solchaga
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
| | - Juan Pablo Busalmen
- Laboratorio de Bioelectroquímica, INTEMA - CONICET, Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Débora Nercessian
- Instituto de Investigaciones Biológicas, Universidad Nacional de Mar del Plata - CONICET, Mar del Plata, Argentina
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9
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Renn D, Shepard L, Vancea A, Karan R, Arold ST, Rueping M. Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. Front Microbiol 2021; 12:732856. [PMID: 34777282 PMCID: PMC8578733 DOI: 10.3389/fmicb.2021.732856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 10/05/2021] [Indexed: 11/23/2022] Open
Abstract
The Red Sea is a marine environment with unique chemical characteristics and physical topographies. Among the various habitats offered by the Red Sea, the deep-sea brine pools are the most extreme in terms of salinity, temperature and metal contents. Nonetheless, the brine pools host rich polyextremophilic bacterial and archaeal communities. These microbial communities are promising sources for various classes of enzymes adapted to harsh environments - extremozymes. Extremozymes are emerging as novel biocatalysts for biotechnological applications due to their ability to perform catalytic reactions under harsh biophysical conditions, such as those used in many industrial processes. In this review, we provide an overview of the extremozymes from different Red Sea brine pools and discuss the overall biotechnological potential of the Red Sea proteome.
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Affiliation(s)
- Dominik Renn
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Organic Chemistry, RWTH Aachen, Aachen, Germany
| | - Lera Shepard
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Ram Karan
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Centre de Biologie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging (ExMI), University Clinic, RWTH Aachen, Aachen, Germany
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10
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Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. THE ISME JOURNAL 2021; 15:2351-2365. [PMID: 33649556 PMCID: PMC8319295 DOI: 10.1038/s41396-021-00931-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 02/08/2021] [Indexed: 02/03/2023]
Abstract
Deep-sea hypersaline anoxic basins are polyextreme environments in the ocean's interior characterized by the high density of brines that prevents mixing with the overlaying seawater, generating sharp chemoclines and redoxclines up to tens of meters thick that host a high concentration of microbial communities. Yet, a fundamental understanding of how such pycnoclines shape microbial life and the associated biogeochemical processes at a fine scale, remains elusive. Here, we applied high-precision sampling of the brine-seawater transition interface in the Suakin Deep, located at 2770 m in the central Red Sea, to reveal previously undocumented fine-scale community structuring and succession of metabolic groups along a salinity gradient only 1 m thick. Metagenomic profiling at a 10-cm-scale resolution highlighted spatial organization of key metabolic pathways and corresponding microbial functional units, emphasizing the prominent role and significance of salinity and oxygen in shaping their ecology. Nitrogen cycling processes are especially affected by the redoxcline with ammonia oxidation processes being taxa and layers specific, highlighting also the presence of novel microorganisms, such as novel Thaumarchaeota and anammox, adapted to the changing conditions of the chemocline. The findings render the transition zone as a critical niche for nitrogen cycling, with complementary metabolic networks, in turn underscoring the biogeochemical complexity of deep-sea brines.
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11
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Font-Verdera F, Liébana R, Aldeguer-Riquelme B, Gangloff V, Santos F, Viver T, Rosselló-Móra R. Inverted microbial community stratification and spatial-temporal stability in hypersaline anaerobic sediments from the S'Avall solar salterns. Syst Appl Microbiol 2021; 44:126231. [PMID: 34332366 DOI: 10.1016/j.syapm.2021.126231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/01/2021] [Accepted: 07/06/2021] [Indexed: 11/25/2022]
Abstract
The anaerobic hypersaline sediments of an ephemeral pond from the S'Avall solar salterns constituted an excellent study system because of their easy accessibility, as well as the analogy of their microbial assemblages with some known deep-sea hypersaline anaerobic brines. By means of shotgun metagenomics and 16S rRNA gene amplicon sequencing, the microbial composition of the sediment was shown to be stable in time and space. The communities were formed by prokaryote representatives with a clear inferred anaerobic metabolism, mainly related to the methane, sulfur and nitrate cycles. The most conspicuous finding was the inverted nature of the vertical stratification. Contrarily to what could be expected, a methanogenic archaeal metabolism was found to dominate in the upper layers, whereas Bacteria with fermentative and anaerobic respiration metabolisms increased with depth. We could demonstrate the methanogenic nature of the members of candidate lineages DHVE2 and MSBL1, which were present in high abundance in this system, and described, for the first time, viruses infecting these lineages. Members of the putatively active aerobic genera Salinibacter and Halorubrum were detected especially in the deepest layers for which we hypothesize that either oxygen could be sporadically available, or they could perform anaerobic metabolisms. We also report a novel repertoire of virus species thriving in these sediments, which had special relevance because of their lysogenic lifestyles.
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Affiliation(s)
- Francisca Font-Verdera
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain.
| | - Raquel Liébana
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Borja Aldeguer-Riquelme
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Valentin Gangloff
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, Universidad de Alicante, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Esporles, Spain
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12
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Ghori NUH, Wise MJ, Whiteley AS. Temporal Microbial Community Dynamics Within a Unique Acid Saline Lake. Front Microbiol 2021; 12:649594. [PMID: 34248867 PMCID: PMC8264302 DOI: 10.3389/fmicb.2021.649594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 06/04/2021] [Indexed: 11/13/2022] Open
Abstract
Lake Magic is an extremely acidic, hypersaline lake found in Western Australia, with the highest concentrations of aluminum and silica in the world. Previous studies of Lake Magic diversity have revealed that the lake hosts acid- and halotolerant bacterial and fungal species. However, they have not canvassed microbial population dynamics across flooding, evapo-concentration and desiccation stages. In this study, we used amplicon sequencing and potential function prediction on sediment and salt mat samples. We observed that the bacterial and fungal diversity in Lake Magic is strongly driven by carbon, temperature, pH and salt concentrations at the different stages of the lake. We also saw that the fungal diversity decreased as the environmental conditions became more extreme. However, prokaryotic diversity was very dynamic and bacteria dominated archaeal species, both in abundance and diversity, perhaps because bacteria better tolerate the extreme variation in conditions. Bacterial species diversity was the highest during early flooding stage and decreased during more stressful conditions. We observed an increase in acid tolerant and halotolerant species in the sediment, involved in functions such as sulfur and iron metabolism, i.e., species involved in buffering the external environment. Thus, due to activity within the microbial community, the environmental conditions in the sediment do not change to the same degree as conditions in the salt mat, resulting in the sediment becoming a safe haven for microbes, which are able to thrive during the extreme conditions of the evapo-concentration and desiccation stages.
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Affiliation(s)
- Noor-Ul-Huda Ghori
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.,The Marshall Centre of Infectious Diseases, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia
| | - Michael J Wise
- The Marshall Centre of Infectious Diseases, School of Biological Sciences, The University of Western Australia, Perth, WA, Australia.,Department of Computer Science and Engineering, The University of Western Australia, Perth, WA, Australia
| | - Andrew S Whiteley
- School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.,Centre for Environment and Life Sciences, CSIRO Land Water, Perth, WA, Australia
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13
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Abou Khalil C, Prince VL, Prince RC, Greer CW, Lee K, Zhang B, Boufadel MC. Occurrence and biodegradation of hydrocarbons at high salinities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 762:143165. [PMID: 33131842 DOI: 10.1016/j.scitotenv.2020.143165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Hypersaline environments are found around the world, above and below ground, and many are exposed to hydrocarbons on a continuous or a frequent basis. Some surface hypersaline environments are exposed to hydrocarbons because they have active petroleum seeps while others are exposed because of oil exploration and production, or nearby human activities. Many oil reservoirs overlie highly saline connate water, and some national oil reserves are stored in salt caverns. Surface hypersaline ecosystems contain consortia of halophilic and halotolerant microorganisms that decompose organic compounds including hydrocarbons, and subterranean ones are likely to contain the same. However, the rates and extents of hydrocarbon biodegradation are poorly understood in such ecosystems. Here we describe hypersaline environments potentially or likely to become contaminated with hydrocarbons, including perennial and transient environments above and below ground, and discuss what is known about the microbes degrading hydrocarbons and the extent of their activities. We also discuss what limits the microbial hydrocarbon degradation in hypersaline environments and whether there are opportunities for inhibiting (oil storage) or stimulating (oil spills) such biodegradation as the situation requires.
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Affiliation(s)
- Charbel Abou Khalil
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | | | | | - Charles W Greer
- National Research Council Canada, Energy, Mining and Environment Research Centre, Montreal, QC H4P 2R2, Canada
| | - Kenneth Lee
- Fisheries and Oceans Canada, Ecosystem Science, Ottawa, ON K1A 0E6, Canada
| | - Baiyu Zhang
- Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University of Newfoundland, St. John's, NL A1B 3X5, Canada
| | - Michel C Boufadel
- Center for Natural Resources, Department of Civil and Environmental Engineering, New Jersey Institute of Technology, Newark, NJ 07102, USA.
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14
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Sysoev M, Grötzinger SW, Renn D, Eppinger J, Rueping M, Karan R. Bioprospecting of Novel Extremozymes From Prokaryotes-The Advent of Culture-Independent Methods. Front Microbiol 2021; 12:630013. [PMID: 33643258 PMCID: PMC7902512 DOI: 10.3389/fmicb.2021.630013] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Extremophiles are remarkable organisms that thrive in the harshest environments on Earth, such as hydrothermal vents, hypersaline lakes and pools, alkaline soda lakes, deserts, cold oceans, and volcanic areas. These organisms have developed several strategies to overcome environmental stress and nutrient limitations. Thus, they are among the best model organisms to study adaptive mechanisms that lead to stress tolerance. Genetic and structural information derived from extremophiles and extremozymes can be used for bioengineering other nontolerant enzymes. Furthermore, extremophiles can be a valuable resource for novel biotechnological and biomedical products due to their biosynthetic properties. However, understanding life under extreme conditions is challenging due to the difficulties of in vitro cultivation and observation since > 99% of organisms cannot be cultivated. Consequently, only a minor percentage of the potential extremophiles on Earth have been discovered and characterized. Herein, we present a review of culture-independent methods, sequence-based metagenomics (SBM), and single amplified genomes (SAGs) for studying enzymes from extremophiles, with a focus on prokaryotic (archaea and bacteria) microorganisms. Additionally, we provide a comprehensive list of extremozymes discovered via metagenomics and SAGs.
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Affiliation(s)
- Maksim Sysoev
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Stefan W. Grötzinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Magnus Rueping
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Institute for Experimental Molecular Imaging, University Clinic, RWTH Aachen University, Aachen, Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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15
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Al-Dhabaan FA. Mycoremediation of crude oil contaminated soil by specific fungi isolated from Dhahran in Saudi Arabia. Saudi J Biol Sci 2021; 28:73-77. [PMID: 33424285 PMCID: PMC7783675 DOI: 10.1016/j.sjbs.2020.08.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 11/08/2022] Open
Abstract
Crude oil biodegrading microorganism considers the key role for environmental preserving. In this investigation, crude oil biodegrading fungal strains have been isolated in polluted soil of crude-oil at khurais oil ground in Kingdom of Saudi Arabia. Among of 22 fungal isolates, only three isolates reflected potential capability for oil degradation. These isolates were identified and submitted to GenBank as (A1) Aspergillus polyporicola (MT448790), (A2) Aspergillus spelaeus (MT448791) and (A3) Aspergillus niger (MT459302) through internal-transcribed spacer-regions (ITS1&ITS2) for sequencing in molecular marker. Comparing with controls, strain (A1) Aspergillus niger was superior for biodegradation ability (58%) comparing with Aspergillus polyporicola and Aspergillus spelaeus degrading were showed 47 and 51% respectively. Employed CO2 evolution as indicator for petroleum oil biodegradation by the fungal isolates reflected that, Aspergillus niger emission highest CO2 (28.6%) comparing with Aspergillus spelaeus and Aspergillus polyporicola which showed 13% and 12.4% respectively. capability of Aspergillus sp. to tolerate and adapted oil pollutants with successful growth rate on them, indicated that it can be employed as mycoremediation agent for recovering restoring ecosystem when contaminated by crude oil.
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Affiliation(s)
- Fahad A Al-Dhabaan
- Dept. of Biology, Science and Humanities College, Shaqra University, Alquwayiyah, Saudi Arabia
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16
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Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution. CRYSTALS 2020. [DOI: 10.3390/cryst10110964] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.
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17
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AbdelWahed MG, Badiea EA, Ouf A, Sayed AA. Molecular and functional characterization of unique thermo-halophilic thioredoxin from the metagenome of an exotic environment. Int J Biol Macromol 2020; 153:767-778. [PMID: 32142845 DOI: 10.1016/j.ijbiomac.2020.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/02/2020] [Accepted: 03/02/2020] [Indexed: 11/30/2022]
Abstract
The lower convective layer (LCL) at Atlantis II brine pool of the Red sea represents one of the exceptional, unique ecosystems. Thioredoxin is a multi-functional antioxidant redox protein that has a crucial role in various vital cellular processes. In the current study, a functional metagenomics approach was used to isolate and characterize thioredoxin from the LCL of Atlantis II Deep brine pool (Trx-ATII). From the metagenomic DNA of the LCL, the thioredoxin gene was directly retrieved and sequenced. Sequence analysis showed that the gene belonged to thioredoxin-like superfamily with classical Trx motif (-CXXC-). Phylogenetic analysis revealed that Trx-ATII was closely related to Trx of Prochlorococcus marinus with a maximum identity of 86%. Successfully, Trx-ATII was cloned and expressed in E. coli, where the purified protein had M.wt of 16 kDa. Characterization studies revealed that Trx-ATII protein is halophilic; can tolerate up to 2.5 M NaCl and thermostable, where 90% of its activity was retained at 60 °C. Trx-ATII can reduce both DTNB and insulin disulfide- containing substrates. In conclusion, a unique thioredoxin protein was isolated from a harsh environment that can maintain its activity under extreme conditions of salinity and temperature as a promising redox protein for biotechnological applications.
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Affiliation(s)
| | - Elham A Badiea
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Amged Ouf
- Biology Department, American University in Cairo, Egypt
| | - Ahmed A Sayed
- Biochemistry Department, Faculty of Science, Ain Shams University, Cairo, Egypt; Children Cancer Hospital, 57357 Cairo, Egypt.
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18
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Vogler M, Karan R, Renn D, Vancea A, Vielberg MT, Grötzinger SW, DasSarma P, DasSarma S, Eppinger J, Groll M, Rueping M. Crystal Structure and Active Site Engineering of a Halophilic γ-Carbonic Anhydrase. Front Microbiol 2020; 11:742. [PMID: 32411108 PMCID: PMC7199487 DOI: 10.3389/fmicb.2020.00742] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 03/30/2020] [Indexed: 11/27/2022] Open
Abstract
Environments previously thought to be uninhabitable offer a tremendous wealth of unexplored microorganisms and enzymes. In this paper, we present the discovery and characterization of a novel γ-carbonic anhydrase (γ-CA) from the polyextreme Red Sea brine pool Discovery Deep (2141 m depth, 44.8°C, 26.2% salt) by single-cell genome sequencing. The extensive analysis of the selected gene helps demonstrate the potential of this culture-independent method. The enzyme was expressed in the bioengineered haloarchaeon Halobacterium sp. NRC-1 and characterized by X-ray crystallography and mutagenesis. The 2.6 Å crystal structure of the protein shows a trimeric arrangement. Within the γ-CA, several possible structural determinants responsible for the enzyme's salt stability could be highlighted. Moreover, the amino acid composition on the protein surface and the intra- and intermolecular interactions within the protein differ significantly from those of its close homologs. To gain further insights into the catalytic residues of the γ-CA enzyme, we created a library of variants around the active site residues and successfully improved the enzyme activity by 17-fold. As several γ-CAs have been reported without measurable activity, this provides further clues as to critical residues. Our study reveals insights into the halophilic γ-CA activity and its unique adaptations. The study of the polyextremophilic carbonic anhydrase provides a basis for outlining insights into strategies for salt adaptation, yielding enzymes with industrially valuable properties, and the underlying mechanisms of protein evolution.
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Affiliation(s)
- Malvina Vogler
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Ram Karan
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Dominik Renn
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandra Vancea
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Marie-Theres Vielberg
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Stefan W. Grötzinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Priya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Shiladitya DasSarma
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Jörg Eppinger
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Michael Groll
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Garching, Germany
| | - Magnus Rueping
- KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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19
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Animal bioturbation preserved in Pleistocene magadiite at Lake Magadi, Kenya Rift Valley, and its implications for the depositional environment of bedded magadiite. Sci Rep 2020; 10:6794. [PMID: 32321943 PMCID: PMC7176717 DOI: 10.1038/s41598-020-63505-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/18/2020] [Indexed: 11/22/2022] Open
Abstract
Magadiite, a rare hydrous sodium-silicate mineral [NaSi7O13(OH)3·4(H2O)], was discovered about 50 years ago in sediments around Lake Magadi, a hypersaline alkaline lake fed by hot springs in the semi-arid southern Kenya Rift Valley. Today this harsh lacustrine environment excludes most organisms except microbial extremophiles, a few invertebrates (mostly insects), highly adapted fish (Alcolapia sp.), and birds including flamingos. Burrows discovered in outcrops of the High Magadi Beds (~25–9 ka) that predate the modern saline (trona) pan show that beetles and other invertebrates inhabit this extreme environment when conditions become more favourable. Burrows (cm-scale) preserved in magadiite in the High Magadi Beds are filled with mud, silt and sand from overlying sediments. Their stratigraphic context reveals upward-shallowing cycles from mud to interlaminated mud-magadiite to magadiite in dm-scale units. The burrows were formed when the lake floor became fresher and oxygenated, after a period when magadiite precipitated in shallow saline waters. The burrows, probably produced by beetles, show that trace fossils can provide evidence for short-term (possibly years to decades) changes in the contemporary environment that might not otherwise be recognised or preserved physically or chemically in the sediment record.
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20
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Microbial ecology and biogeochemistry of hypersaline sediments in Orca Basin. PLoS One 2020; 15:e0231676. [PMID: 32315331 PMCID: PMC7173876 DOI: 10.1371/journal.pone.0231676] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/28/2020] [Indexed: 11/21/2022] Open
Abstract
In deep ocean hypersaline basins, the combination of high salinity, unusual ionic composition and anoxic conditions represents significant challenges for microbial life. We used geochemical porewater characterization and DNA sequencing based taxonomic surveys to enable environmental and microbial characterization of anoxic hypersaline sediments and brines in the Orca Basin, the largest brine basin in the Gulf of Mexico. Full-length bacterial 16S rRNA gene clone libraries from hypersaline sediments and the overlying brine were dominated by the uncultured halophilic KB1 lineage, Deltaproteobacteria related to cultured sulfate-reducing halophilic genera, and specific lineages of heterotrophic Bacteroidetes. Archaeal clones were dominated by members of the halophilic methanogen genus Methanohalophilus, and the ammonia-oxidizing Marine Group I (MG-I) within the Thaumarchaeota. Illumina sequencing revealed higher phylum- and subphylum-level complexity, especially in lower-salinity sediments from the Orca Basin slope. Illumina and clone library surveys consistently detected MG-I Thaumarchaeota and halotolerant Deltaproteobacteria in the hypersaline anoxic sediments, but relative abundances of the KB1 lineage differed between the two sequencing methods. The stable isotopic composition of dissolved inorganic carbon and methane in porewater, and sulfate concentrations decreasing downcore indicated methanogenesis and sulfate reduction in the anoxic sediments. While anaerobic microbial processes likely occur at low rates near their maximal salinity thresholds in Orca Basin, long-term accumulation of reaction products leads to high methane concentrations and reducing conditions within the Orca Basin brine and sediments.
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21
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Bourtsoukidis E, Pozzer A, Sattler T, Matthaios VN, Ernle L, Edtbauer A, Fischer H, Könemann T, Osipov S, Paris JD, Pfannerstill EY, Stönner C, Tadic I, Walter D, Wang N, Lelieveld J, Williams J. The Red Sea Deep Water is a potent source of atmospheric ethane and propane. Nat Commun 2020; 11:447. [PMID: 31992702 PMCID: PMC6987153 DOI: 10.1038/s41467-020-14375-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/02/2020] [Indexed: 11/21/2022] Open
Abstract
Non-methane hydrocarbons (NMHCs) such as ethane and propane are significant atmospheric pollutants and precursors of tropospheric ozone, while the Middle East is a global emission hotspot due to extensive oil and gas production. Here we compare in situ hydrocarbon measurements, performed around the Arabian Peninsula, with global model simulations that include current emission inventories (EDGAR) and state-of-the-art atmospheric circulation and chemistry mechanisms (EMAC model). While measurements of high mixing ratios over the Arabian Gulf are adequately simulated, strong underprediction by the model was found over the northern Red Sea. By examining the individual sources in the model and by utilizing air mass back-trajectory investigations and Positive Matrix Factorization (PMF) analysis, we deduce that Red Sea Deep Water (RSDW) is an unexpected, potent source of atmospheric NMHCs. This overlooked underwater source is comparable with total anthropogenic emissions from entire Middle Eastern countries, and significantly impacts the regional atmospheric chemistry.
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Affiliation(s)
- E Bourtsoukidis
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany.
| | - A Pozzer
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - T Sattler
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - V N Matthaios
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - L Ernle
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - A Edtbauer
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - H Fischer
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - T Könemann
- Department of Multiphase Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - S Osipov
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - J-D Paris
- Laboratoire des Sciences du Climat et de l'Environnement, CEA-CNRS-UVSQ, UMR8212, IPSL, Gif-Sur-Yvette, France
| | - E Y Pfannerstill
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - C Stönner
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - I Tadic
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - D Walter
- Department of Multiphase Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
- Max Planck Institute for Biogeochemistry, Hans-Knöll-Straße 10, 07745, Jena, Germany
| | - N Wang
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
| | - J Lelieveld
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
- Energy, Environment and Water Research Center, The Cyprus Institute, Nicosia, Cyprus
| | - J Williams
- Department of Atmospheric Chemistry, Max Planck Institute for Chemistry, Mainz, 55128, Germany
- Energy, Environment and Water Research Center, The Cyprus Institute, Nicosia, Cyprus
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22
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Duarte CM, Røstad A, Michoud G, Barozzi A, Merlino G, Delgado-Huertas A, Hession BC, Mallon FL, Afifi AM, Daffonchio D. Discovery of Afifi, the shallowest and southernmost brine pool reported in the Red Sea. Sci Rep 2020; 10:910. [PMID: 31969577 PMCID: PMC6976674 DOI: 10.1038/s41598-020-57416-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/31/2019] [Indexed: 12/14/2022] Open
Abstract
The previously uncharted Afifi brine pool was discovered in the eastern shelf of the southern Red Sea. It is the shallowest brine basin yet reported in the Red Sea (depth range: 353.0 to 400.5 m). It presents a highly saline (228 g/L), thalassohaline, cold (23.3 °C), anoxic brine, inhabited by the bacterial classes KB1, Bacteroidia and Clostridia and the archaeal classes Methanobacteria and Deep Sea Euryarcheota Group. Functional assignments deduced from the taxonomy indicate methanogenesis and sulfur respiration to be important metabolic processes in this environment. The Afifi brine was remarkably enriched in dissolved inorganic carbon due to microbial respiration and in dissolved nitrogen, derived from anammox processes and denitrification, according to high δ15N values (+6.88‰, AIR). The Afifi brine show a linear increase in δ18O and δD relative to seawater that differs from the others Red Sea brine pools, indicating a non-hydrothermal origin, compatible with enrichment in evaporitic environments. Afifi brine was probably formed by venting of fossil connate waters from the evaporitic sediments beneath the seafloor, with a possible contribution from the dehydration of gypsum to anhydrite. Such origin is unique among the known Red Sea brine pools.
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Affiliation(s)
- Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Anders Røstad
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Alan Barozzi
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Giuseppe Merlino
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Antonio Delgado-Huertas
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.,Instituto Andaluz de Ciencias de la Tierra, CSIC-UGR, Avda. de las Palmeras 4, 18100, Armilla, Spain
| | - Brian C Hession
- Coastal and Marine Resources Core Lab (CMOR), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Francis L Mallon
- Coastal and Marine Resources Core Lab (CMOR), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Abdulakader M Afifi
- Ali I. Al-Naimi Petroleum Engineering Research Center (ANPERC), Physical Science and Engineering Division (PSE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC) and Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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Jin M, Gai Y, Guo X, Hou Y, Zeng R. Properties and Applications of Extremozymes from Deep-Sea Extremophilic Microorganisms: A Mini Review. Mar Drugs 2019; 17:md17120656. [PMID: 31766541 PMCID: PMC6950199 DOI: 10.3390/md17120656] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/09/2023] Open
Abstract
The deep sea, which is defined as sea water below a depth of 1000 m, is one of the largest biomes on the Earth, and is recognised as an extreme environment due to its range of challenging physical parameters, such as pressure, salinity, temperature, chemicals and metals (such as hydrogen sulphide, copper and arsenic). For surviving in such extreme conditions, deep-sea extremophilic microorganisms employ a variety of adaptive strategies, such as the production of extremozymes, which exhibit outstanding thermal or cold adaptability, salt tolerance and/or pressure tolerance. Owing to their great stability, deep-sea extremozymes have numerous potential applications in a wide range of industries, such as the agricultural, food, chemical, pharmaceutical and biotechnological sectors. This enormous economic potential combined with recent advances in sampling and molecular and omics technologies has led to the emergence of research regarding deep-sea extremozymes and their primary applications in recent decades. In the present review, we introduced recent advances in research regarding deep-sea extremophiles and the enzymes they produce and discussed their potential industrial applications, with special emphasis on thermophilic, psychrophilic, halophilic and piezophilic enzymes.
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Affiliation(s)
- Min Jin
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
| | - Yingbao Gai
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Xun Guo
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Yanping Hou
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
| | - Runying Zeng
- State Key Laboratory Breeding Base of Marine Genetic Resource, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (M.J.); (Y.G.); (X.G.); (Y.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, China
- Correspondence: ; Tel.: +86-592-2195323
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Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses. Genes (Basel) 2019; 10:genes10110891. [PMID: 31694288 PMCID: PMC6895999 DOI: 10.3390/genes10110891] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/15/2019] [Accepted: 10/26/2019] [Indexed: 12/13/2022] Open
Abstract
Intermediate-salinity environments are distributed around the world. Here, we present a snapshot characterization of two Peruvian thalassohaline environments at high altitude, Maras and Acos, which provide an excellent opportunity to increase our understanding of these ecosystems. The main goal of this study was to assess the structure and functional diversity of the communities of microorganisms in an intermediate-salinity environment, and we used a metagenomic shotgun approach for this analysis. These Andean hypersaline systems exhibited high bacterial diversity and abundance of the phyla Proteobacteria, Bacteroidetes, Balneolaeota, and Actinobacteria; in contrast, Archaea from the phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota were identified in low abundance. Acos harbored a more diverse prokaryotic community and a higher number of unique species compared with Maras. In addition, we obtained the draft genomes of two bacteria, Halomonas elongata and Idiomarina loihiensis, as well as the viral genomes of Enterobacteria lambda-like phage and Halomonas elongata-like phage and 27 partial novel viral halophilic genomes. The functional metagenome annotation showed a high abundance of sequences associated with detoxification, DNA repair, cell wall and capsule formation, and nucleotide metabolism; sequences for these functions were overexpressed mainly in bacteria and also in some archaea and viruses. Thus, their metabolic profiles afford a decrease in oxidative stress as well as the assimilation of nitrogen, a critical energy source for survival. Our work represents the first microbial characterization of a community structure in samples collected from Peruvian hypersaline systems.
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Rettberg P, Antunes A, Brucato J, Cabezas P, Collins G, Haddaji A, Kminek G, Leuko S, McKenna-Lawlor S, Moissl-Eichinger C, Fellous JL, Olsson-Francis K, Pearce D, Rabbow E, Royle S, Saunders M, Sephton M, Spry A, Walter N, Wimmer Schweingruber R, Treuet JC. Biological Contamination Prevention for Outer Solar System Moons of Astrobiological Interest: What Do We Need to Know? ASTROBIOLOGY 2019; 19:951-974. [PMID: 30762429 PMCID: PMC6767865 DOI: 10.1089/ast.2018.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
To ensure that scientific investments in space exploration are not compromised by terrestrial contamination of celestial bodies, special care needs to be taken to preserve planetary conditions for future astrobiological exploration. Significant effort has been made and is being taken to address planetary protection in the context of inner Solar System exploration. In particular for missions to Mars, detailed internationally accepted guidelines have been established. For missions to the icy moons in the outer Solar System, Europa and Enceladus, the planetary protection requirements are so far based on a probabilistic approach and a conservative estimate of poorly known parameters. One objective of the European Commission-funded project, Planetary Protection of Outer Solar System, was to assess the existing planetary protection approach, to identify inherent knowledge gaps, and to recommend scientific investigations necessary to update the requirements for missions to the icy moons.
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Affiliation(s)
- Petra Rettberg
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
- Address correspondence to: Petra Rettberg, German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Research Group Astrobiology, Linder Höhe, 51147 Köln, Germany
| | - André Antunes
- GEMM—Group for Extreme and Marine Microbiology, Department of Biology, Edge Hill University, Ormskirk, United Kingdom
| | - John Brucato
- Department of Physics and Astronomy, Astrophysical Observatory of Arcetri, National Institute for Astrophysics (INAF), Florence, Italy
| | - Patricia Cabezas
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Geoffrey Collins
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Alissa Haddaji
- Committee on Space Research (COSPAR), Montpellier, France
| | - Gerhard Kminek
- Committee on Space Research (COSPAR), Montpellier, France
| | - Stefan Leuko
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | | | | | - Jean-Louis Fellous
- Department of Physics and Astronomy, Wheaton College, Massachusetts, Norton, Massachusetts
| | - Karen Olsson-Francis
- Faculty of Science, Technology, Engineering & Mathematics, School of Environment, Earth & Ecosystem Sciences, The Open University, Milton Keynes, United Kingdom
| | - David Pearce
- Department of Applied Sciences, Northumbria University, Newcastle, United Kingdom
| | - Elke Rabbow
- Research Group Astrobiology, Radiation Biology Department, German Aerospace Center (DLR), Institute of Aerospace Medicine, Köln, Germany
| | - Samuel Royle
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Mark Saunders
- Independent Consultant for the US National Academies of Sciences (NAS), Washington, District of Columbia
| | - Mark Sephton
- Faculty of Engineering, Department of Earth Science & Engineering, Imperial College, London, United Kingdom
| | - Andy Spry
- Carl Sagan Center, SETI, Mountain View, California
| | - Nicolas Walter
- Science Connect–European Science Foundation (ESF), Strasbourg, France
| | - Robert Wimmer Schweingruber
- Institut für Experimentelle und Angewandte Physik, Abteilung Extraterrestrische Physik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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Marine Fungi: Biotechnological Perspectives from Deep-Hypersaline Anoxic Basins. DIVERSITY 2019. [DOI: 10.3390/d11070113] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Deep-sea hypersaline anoxic basins (DHABs) are one of the most hostile environments on Earth. Even though DHABs have hypersaline conditions, anoxia and high hydrostatic pressure, they host incredible microbial biodiversity. Among eukaryotes inhabiting these systems, recent studies demonstrated that fungi are a quantitatively relevant component. Here, fungi can benefit from the accumulation of large amounts of organic material. Marine fungi are also known to produce bioactive molecules. In particular, halophilic and halotolerant fungi are a reservoir of enzymes and secondary metabolites with valuable applications in industrial, pharmaceutical, and environmental biotechnology. Here we report that among the fungal taxa identified from the Mediterranean and Red Sea DHABs, halotolerant halophilic species belonging to the genera Aspergillus and Penicillium can be used or screened for enzymes and bioactive molecules. Fungi living in DHABs can extend our knowledge about the limits of life, and the discovery of new species and molecules from these environments can have high biotechnological potential.
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Esau L, Zhang G, Sagar S, Stingl U, Bajic VB, Kaur M. Mining the deep Red-Sea brine pool microbial community for anticancer therapeutics. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2019; 19:142. [PMID: 31221160 PMCID: PMC6587256 DOI: 10.1186/s12906-019-2554-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/09/2019] [Indexed: 12/31/2022]
Abstract
BACKGROUND Microbial species in the brine pools of the Red Sea and the brine pool-seawater interfaces are exposed to high temperature, high salinity, low oxygen levels and high concentrations of heavy metals. As adaptations to these harsh conditions require a large suite of secondary metabolites, these microbes have a huge potential as a source of novel anticancer molecules. METHODS A total of 60 ethyl-acetate extracts of newly isolated strains from extreme environments of the Red-Sea were isolated and tested against several human cancer cell lines for potential cytotoxic and apoptotic activities. RESULTS Isolates from the Erba brine-pool accounted for 50% of active bacterial extracts capable of inducing 30% or greater inhibition of cell growth. Among the 60 extracts screened, seven showed selectivity towards triple negative BT20 cells compared to normal fibroblasts. CONCLUSION In this study, we identified several extracts able to induce caspase-dependent apoptosis in various cancer cell lines. Further investigations and isolation of the active compounds of these Red Sea brine pool microbes may offer a chemotherapeutic potential for cancers with limited treatment options.
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Ziko L, Adel M, Malash MN, Siam R. Insights into Red Sea Brine Pool Specialized Metabolism Gene Clusters Encoding Potential Metabolites for Biotechnological Applications and Extremophile Survival. Mar Drugs 2019; 17:md17050273. [PMID: 31071993 PMCID: PMC6562949 DOI: 10.3390/md17050273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/12/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
The recent rise in antibiotic and chemotherapeutic resistance necessitates the search for novel drugs. Potential therapeutics can be produced by specialized metabolism gene clusters (SMGCs). We mined for SMGCs in metagenomic samples from Atlantis II Deep, Discovery Deep and Kebrit Deep Red Sea brine pools. Shotgun sequence assembly and secondary metabolite analysis shell (antiSMASH) screening unraveled 2751 Red Sea brine SMGCs, pertaining to 28 classes. Predicted categorization of the SMGC products included those (1) commonly abundant in microbes (saccharides, fatty acids, aryl polyenes, acyl-homoserine lactones), (2) with antibacterial and/or anticancer effects (terpenes, ribosomal peptides, non-ribosomal peptides, polyketides, phosphonates) and (3) with miscellaneous roles conferring adaptation to the environment/special structure/unknown function (polyunsaturated fatty acids, ectoine, ladderane, others). Saccharide (80.49%) and putative (7.46%) SMGCs were the most abundant. Selected Red Sea brine pool sites had distinct SMGC profiles, e.g., for bacteriocins and ectoine. Top promising candidates, SMs with pharmaceutical applications, were addressed. Prolific SM-producing phyla (Proteobacteria, Actinobacteria, Cyanobacteria), were ubiquitously detected. Sites harboring the largest numbers of bacterial and archaeal phyla, had the most SMGCs. Our results suggest that the Red Sea brine niche constitutes a rich biological mine, with the predicted SMs aiding extremophile survival and adaptation.
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Affiliation(s)
- Laila Ziko
- Graduate Program of Biotechnology, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
| | - Mustafa Adel
- Graduate Program of Biotechnology, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
| | - Mohamed N Malash
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
- Microbiology and Immunology Department, Faculty of Pharmacy, Ahram Canadian University, Giza 12581, Egypt.
| | - Rania Siam
- Biology Department, School of Sciences and Engineering, American University in Cairo, New Cairo, Cairo 11835, Egypt.
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Guan Y, Ngugi DK, Vinu M, Blom J, Alam I, Guillot S, Ferry JG, Stingl U. Comparative Genomics of the Genus Methanohalophilus, Including a Newly Isolated Strain From Kebrit Deep in the Red Sea. Front Microbiol 2019; 10:839. [PMID: 31068917 PMCID: PMC6491703 DOI: 10.3389/fmicb.2019.00839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/02/2019] [Indexed: 01/25/2023] Open
Abstract
Halophilic methanogens play an important role in the carbon cycle in hypersaline environments, but are under-represented in culture collections. In this study, we describe a novel Methanohalophilus strain that was isolated from the sulfide-rich brine-seawater interface of Kebrit Deep in the Red Sea. Based on physiological and phylogenomic features, strain RSK, which is the first methanogenic archaeon to be isolated from a deep hypersaline anoxic brine lake of the Red Sea, represents a novel species of this genus. In order to compare the genetic traits underpinning the adaptations of this genus in diverse hypersaline environments, we sequenced the genome of strain RSK and compared it with genomes of previously isolated and well characterized species in this genus (Methanohalophilus mahii, Methanohalophilus halophilus, Methanohalophilus portucalensis, and Methanohalophilus euhalobius). These analyses revealed a highly conserved genomic core of greater than 93% of annotated genes (1490 genes) containing pathways for methylotrophic methanogenesis, osmoprotection through salt-out strategy, and oxidative stress response, among others. Despite the high degree of genomic conservation, species-specific differences in sulfur and glycogen metabolisms, viral resistance, amino acid, and peptide uptake machineries were also evident. Thus, while Methanohalophilus species are found in diverse extreme environments, each genotype also possesses adaptive traits that are likely relevant in their respective hypersaline habitats.
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Affiliation(s)
- Yue Guan
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - David K. Ngugi
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Manikandan Vinu
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Jochen Blom
- Bioinformatik und Systembiologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sylvain Guillot
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - James G. Ferry
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, United States
| | - Ulrich Stingl
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Department of Microbiology and Cell Science, UF/IFAS Fort Lauderdale Research and Education Center, University of Florida, Davie, FL, United States
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Ziko L, Saqr AHA, Ouf A, Gimpel M, Aziz RK, Neubauer P, Siam R. Antibacterial and anticancer activities of orphan biosynthetic gene clusters from Atlantis II Red Sea brine pool. Microb Cell Fact 2019; 18:56. [PMID: 30885206 PMCID: PMC6423787 DOI: 10.1186/s12934-019-1103-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/06/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cancer and infectious diseases are problematic because of continuous emergence of drug resistance. One way to address this enormous global health threat is bioprospecting the unlikeliest environments, such as extreme marine niches, which have tremendous biodiversity that is barely explored. One such environment is the Red Sea brine pool, Atlantis II Deep (ATII). Here, we functionally screened a fosmid library of metagenomic DNA isolated from the ATII lower convective layer (LCL) for antibacterial and anticancer activities. RESULTS Selected clones, 14-7E and 10-2G, displayed antibacterial effects on the marine strain Bacillus sp. Cc6. Moreover, whole cell lysates from 14-7E and 10-2G exhibited decreased cell viability against MCF-7 (39.1% ± 6.6, 42% ± 8.1 at 50% v/v) and U2OS cells (35.7% ± 1.9, 79.9% ± 5.9 at 50% v/v), respectively. By sequencing the insert DNA from 14-7E and 10-2G, we identified two putative orphan biosynthetic gene clusters. Both clusters harbored putative ATP-binding cassette (ABC) transporter permeases and S-adenosylmethionine-related genes. Interestingly, the biosynthetic gene cluster identified on 14-7E is of archaeal origin and harbors a putative transcription factor. Several identified genes may be responsible for the observed antibacterial and anticancer activities. The 14-7E biosynthetic gene cluster may be encoding enzymes producing a specialized metabolite (effect of detected genes involved in C-C bond formation and glycosylation). The bioactivity may also be due to predicted subtilases encoded by this cluster. The 10-2G cluster harbored putative glycosyltransferase and non-ribosomal peptide synthase genes; thus the observed activity of this clone could be caused by a bioactive peptide. CONCLUSIONS The ATII LCL prokaryotic metagenome hosts putative orphan biosynthetic gene clusters that confer antibiotic and anticancer effects. Further biochemical studies should characterize the detected bioactive components, and the potential use of 14-7E metabolite for antibiosis and 10-2G metabolite as a selective anti-breast cancer drug.
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Affiliation(s)
- Laila Ziko
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, Egypt
| | - Al-Hussein A Saqr
- 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, Cairo, 11835, Egypt
| | - Amged Ouf
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, 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, Cairo, 11835, Egypt
| | - Matthias Gimpel
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK24, 13355, Berlin, Germany
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Department of Biotechnology, Technische Universität Berlin, Ackerstrasse 76, ACK24, 13355, Berlin, Germany
| | - Rania Siam
- Graduate Program of Biotechnology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Cairo, 11835, 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, Cairo, 11835, Egypt.
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Jaspers C, Fraune S, Arnold AE, Miller DJ, Bosch TCG, Voolstra CR. Resolving structure and function of metaorganisms through a holistic framework combining reductionist and integrative approaches. ZOOLOGY 2019; 133:81-87. [PMID: 30979392 DOI: 10.1016/j.zool.2019.02.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/20/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023]
Abstract
Current research highlights the importance of associated microbes in contributing to the functioning, health, and even adaptation of their animal, plant, and fungal hosts. As such, we are witnessing a shift in research that moves away from focusing on the eukaryotic host sensu stricto to research into the complex conglomerate of the host and its associated microorganisms (i.e., microbial eukaryotes, archaea, bacteria, and viruses), the so-called metaorganism, as the biological entity. While recent research supports and encourages the adoption of such an integrative view, it must be understood that microorganisms are not involved in all host processes and not all associated microorganisms are functionally important. As such, our intention here is to provide a critical review and evaluation of perspectives and limitations relevant to studying organisms in a metaorganism framework and the functional toolbox available to do so. We note that marker gene-guided approaches that primarily characterize microbial diversity are a first step in delineating associated microbes but are not sufficient to establish proof of their functional relevance. More sophisticated tools and experiments are necessary to reveal the specific functions of associated microbes. This can be accomplished through the study of metaorganisms in less complex environments, the targeted manipulation of microbial associates, or work at the mechanistic level with the toolbox available in model systems. We conclude that the metaorganism framework is a powerful new concept to help provide answers to longstanding biological questions such as the evolution and ecology of organismal complexity and the importance of organismal symbioses to ecosystem functioning. The intricacy of the metaorganism requires a holistic framework combining reductionist and integrative approaches to resolve the structure and function of its member species and to disclose the various roles that microorganisms play in the biology of their hosts.
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Affiliation(s)
- Cornelia Jaspers
- GEOMAR - Helmholtz Centre for Ocean Research Kiel, Evolutionary Ecology of Marine Fishes, Düsternbrooker Weg 20, 24105 Kiel, Germany; National Institute of Aquatic Resources, Technical University of Denmark, DTU Aqua, Kemitorvet, Building 202, 2800 Kgs. Lyngby, Denmark
| | - Sebastian Fraune
- Zoological Institute, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - A Elizabeth Arnold
- School of Plant Sciences and the Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85719, USA
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies and Department of Molecular and Cell Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Thomas C G Bosch
- Zoological Institute, Kiel University, Am Botanischen Garten 9, 24118 Kiel, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Ramadan E, Maged M, El Hosseiny A, Chambergo FS, Setubal JC, El Dorry H. Molecular Adaptations of Bacterial Mercuric Reductase to the Hypersaline Kebrit Deep in the Red Sea. Appl Environ Microbiol 2019; 85:e01431-18. [PMID: 30504211 PMCID: PMC6365835 DOI: 10.1128/aem.01431-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/20/2018] [Indexed: 11/20/2022] Open
Abstract
The hypersaline Kebrit Deep brine pool in the Red Sea is characterized by high levels of toxic heavy metals. Here, we describe two structurally related mercuric reductases (MerAs) from this site which were expressed in Escherichia coli Sequence similarities suggest that both genes are derived from proteobacteria, most likely the Betaproteobacteria or Gammaproteobacteria We show that one of the enzymes (K35NH) is strongly inhibited by NaCl, while the other (K09H) is activated in a NaCl-dependent manner. We infer from this difference that the two forms might support the detoxification of mercury in bacterial microorganisms that employ the compatible solutes and salt-in strategies, respectively. Three-dimensional structure modeling shows that all amino acid substitutions unique to each type are located outside the domain responsible for formation of the active MerA homodimer, and the vast majority of these are found on the surface of the molecule. Moreover, K09H exhibits the predominance of acidic over hydrophobic side chains that is typical of halophilic salt-dependent proteins. These findings enhance our understanding of how selection pressures imposed by two environmental stressors have endowed MerA enzymes with catalytic properties that can potentially function in microorganisms that utilize distinct mechanisms for osmotic balance in hypersaline environments.IMPORTANCE Analysis of two structurally homologous but catalytically distinct mercuric reductases from the Kebrit Deep brine in the Red Sea sheds light on the adaptations that enable microorganisms to cope simultaneously with extreme salinity and toxic mercury compounds. One is strongly inhibited by high NaCl concentrations, while the other exhibits NaCl-dependent activation. Their different activity profiles imply that they may derive from bacterial microorganisms that utilize compatible solutes and salt-in strategies, respectively, to maintain osmotic balance. Three-dimensional modeling reveals that regions not involved in formation of the active homodimer are conserved between the two. However, in the NaCl-dependent form, distinct amino acid substitutions are found in areas that are critical for stability in high salt. The work provides insights into how two environmental stressors have shaped the structure of orthologous enzymes through selection and adaptation, enabling them to retain their catalytic function in what may be very different cellular contexts.
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Affiliation(s)
- Eman Ramadan
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Mohamad Maged
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Ahmed El Hosseiny
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
| | - Felipe S Chambergo
- Escola de Artes Ciências e Humanidades, Universidade de São Paulo, São Paulo, Brazil
| | - João C Setubal
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Hamza El Dorry
- Department of Biology, School of Sciences and Engineering, The American University in Cairo, New Cairo, Egypt
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Labrado AL, Brunner B, Bernasconi SM, Peckmann J. Formation of Large Native Sulfur Deposits Does Not Require Molecular Oxygen. Front Microbiol 2019; 10:24. [PMID: 30740094 PMCID: PMC6355691 DOI: 10.3389/fmicb.2019.00024] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/09/2019] [Indexed: 01/05/2023] Open
Abstract
Large native (i.e., elemental) sulfur deposits can be part of caprock assemblages found on top of or in lateral position to salt diapirs and as stratabound mineralization in gypsum and anhydrite lithologies. Native sulfur is formed when hydrocarbons come in contact with sulfate minerals in presence of liquid water. The prevailing model for native sulfur formation in such settings is that sulfide produced by sulfate-reducing bacteria is oxidized to zero-valent sulfur in presence of molecular oxygen (O2). Although possible, such a scenario is problematic because: (1) exposure to oxygen would drastically decrease growth of microbial sulfate-reducing organisms, thereby slowing down sulfide production; (2) on geologic timescales, excess supply with oxygen would convert sulfide into sulfate rather than native sulfur; and (3) to produce large native sulfur deposits, enormous amounts of oxygenated water would need to be brought in close proximity to environments in which ample hydrocarbon supply sustains sulfate reduction. However, sulfur stable isotope data from native sulfur deposits emplaced at a stage after the formation of the host rocks indicate that the sulfur was formed in a setting with little solute exchange with the ambient environment and little supply of dissolved oxygen. We deduce that there must be a process for the formation of native sulfur in absence of an external oxidant for sulfide. We hypothesize that in systems with little solute exchange, sulfate-reducing organisms, possibly in cooperation with other anaerobic microbial partners, drive the formation of native sulfur deposits. In order to cope with sulfide stress, microbes may shift from harmful sulfide production to non-hazardous native sulfur production. We propose four possible mechanisms as a means to form native sulfur: (1) a modified sulfate reduction process that produces sulfur compounds with an intermediate oxidation state, (2) coupling of sulfide oxidation to methanogenesis that utilizes methylated compounds, acetate or carbon dioxide, (3) ammonium oxidation coupled to sulfate reduction, and (4) sulfur comproportionation of sulfate and sulfide. We show these reactions are thermodynamically favorable and especially useful in environments with multiple stressors, such as salt and dissolved sulfide, and provide evidence that microbial species functioning in such environments produce native sulfur. Integrating these insights, we argue that microbes may form large native sulfur deposits in absence of light and external oxidants such as O2, nitrate, and metal oxides. The existence of such a process would not only explain enigmatic occurrences of native sulfur in the geologic record, but also provide an explanation for cryptic sulfur and carbon cycling beneath the seabed.
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Affiliation(s)
- Amanda L. Labrado
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | - Benjamin Brunner
- Department of Geological Sciences, The University of Texas at El Paso, El Paso, TX, United States
| | | | - Jörn Peckmann
- Centrum für Erdsystemforschung und Nachhaltigkeit, Universität Hamburg, Hamburg, Germany
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Thermal Stability of a Mercuric Reductase from the Red Sea Atlantis II Hot Brine Environment as Analyzed by Site-Directed Mutagenesis. Appl Environ Microbiol 2019; 85:AEM.02387-18. [PMID: 30446558 DOI: 10.1128/aem.02387-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 11/11/2018] [Indexed: 01/28/2023] Open
Abstract
The lower convective layer (LCL) of the Atlantis II brine pool of the Red Sea is a unique environment in terms of high salinity, temperature, and high concentrations of heavy metals. Mercuric reductase enzymes functional in such extreme conditions could be considered a potential tool in the environmental detoxification of mercurial poisoning and might alleviate ecological hazards in the mining industry. Here, we constructed a mercuric reductase library from Atlantis II, from which we identified genes encoding two thermostable mercuric reductase (MerA) isoforms: one is halophilic (designated ATII-LCL) while the other is not (designated ATII-LCL-NH). The ATII-LCL MerA has a short motif composed of four aspartic acids (4D414-417) and two characteristic signature boxes that played a crucial role in its thermal stability. To further understand the mechanism behind the thermostability of the two studied enzymes, we mutated the isoform ATII-LCL-NH and found that the substitution of 2 aspartic acids (2D) at positions 415 and 416 enhanced the thermal stability, while other mutations had the opposite effect. The 2D mutant showed superior thermal tolerance, as it retained 81% of its activity after 10 min of incubation at 70°C. A three-dimensional structure prediction revealed newly formed salt bridges and H bonds in the 2D mutant compared to the parent molecule. To the best of our knowledge, this study is the first to rationally design a mercuric reductase with enhanced thermal stability, which we propose to have a strong potential in the bioremediation of mercurial poisoning.IMPORTANCE The Red Sea is an attractive environment for bioprospecting. There are 25 brine-filled deeps in the Red Sea. The Atlantis II brine pool is the biggest and hottest of such hydrothermal ecosystems. We generated an environmental mercuric reductase library from the lowermost layer of the Atlantis II brine pool, in which we identified two variants of the mercuric reductase enzyme (MerA). One is the previously described halophilic and thermostable ATII-LCL MerA and the other is a nonhalophilic relatively less thermostable enzyme, designated ATII-LCL-NH MerA. We used the ATII-LCL-NH enzyme as a parent molecule to locate the amino acid residues involved in the noticeably higher thermotolerance of the homolog ATII-LCL MerA. Moreover, we designed a novel enzyme with superior thermal stability. This enzyme might have strong potential in the bioremediation of mercuric toxicity.
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Submarine Landslides Induce Massive Waves in Subsea Brine Pools. Sci Rep 2019; 9:128. [PMID: 30644410 PMCID: PMC6333809 DOI: 10.1038/s41598-018-36781-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/23/2018] [Indexed: 11/25/2022] Open
Abstract
Subsea hypersaline anoxic brine pools are among the most extreme habitable environments on Earth that offer clues to life on other planets. Brine is toxic to macrofauna as remotely operated vehicles commonly observe dead and preserved remains in brine pools. While brine pools are often assumed to be stable stratified systems, we show that underwater landslides can cause significant disturbances. Moreover, landslides create large-amplitude waves upon impact with the brine pool, similar to tsunami waves. We focus on the Orca Basin brine pool in the deepwater Gulf of Mexico, which contains numerous landslide deposits and blocks that originated from scarps several hundred meters above the brine pool. The impact of massive fast-moving landslides generated waves with amplitude on the order of 100 s of meters, which rival the largest known ocean waves. Brine waves can negatively affect biological communities and potentially overspill to spread hypersaline brine into surrounding basins.
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Akal AL, Karan R, Hohl A, Alam I, Vogler M, Grötzinger SW, Eppinger J, Rueping M. A polyextremophilic alcohol dehydrogenase from the Atlantis II Deep Red Sea brine pool. FEBS Open Bio 2018; 9:194-205. [PMID: 30761247 PMCID: PMC6356862 DOI: 10.1002/2211-5463.12557] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/06/2018] [Accepted: 10/15/2018] [Indexed: 12/15/2022] Open
Abstract
Enzymes originating from hostile environments offer exceptional stability under industrial conditions and are therefore highly in demand. Using single-cell genome data, we identified the alcohol dehydrogenase (ADH) gene, adh/a1a, from the Atlantis II Deep Red Sea brine pool. ADH/A1a is highly active at elevated temperatures and high salt concentrations (optima at 70 °C and 4 m KCl) and withstands organic solvents. The polyextremophilic ADH/A1a exhibits a broad substrate scope including aliphatic and aromatic alcohols and is able to reduce cinnamyl-methyl-ketone and raspberry ketone in the reverse reaction, making it a possible candidate for the production of chiral compounds. Here, we report the affiliation of ADH/A1a to a rare enzyme family of microbial cinnamyl alcohol dehydrogenases and explain unique structural features for halo- and thermoadaptation.
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Affiliation(s)
- Anastassja L Akal
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Ram Karan
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Adrian Hohl
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Intikhab Alam
- Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Malvina Vogler
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Center for Integrated Protein Science Munich at the Department of Chemistry Technical University of Munich (TUM) Garching Germany
| | - Stefan W Grötzinger
- Computational Bioscience Research Center (CBRC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Institute of Biochemical Engineering Technical University of Munich (TUM) Garching Germany
| | - Jörg Eppinger
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Magnus Rueping
- KAUST Catalysis Center (KCC) King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia.,Institute of Organic Chemistry RWTH Aachen Aachen Germany
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38
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Vander Roost J, Daae FL, Steen IH, Thorseth IH, Dahle H. Distribution Patterns of Iron-Oxidizing Zeta- and Beta-Proteobacteria From Different Environmental Settings at the Jan Mayen Vent Fields. Front Microbiol 2018; 9:3008. [PMID: 30574135 PMCID: PMC6292416 DOI: 10.3389/fmicb.2018.03008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/20/2018] [Indexed: 12/26/2022] Open
Abstract
Iron oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.
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Affiliation(s)
- Jan Vander Roost
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Frida Lise Daae
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Ida Helene Steen
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
| | - Ingunn Hindeness Thorseth
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen, Bergen, Norway.,Department of Biology, University of Bergen, Bergen, Norway
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39
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Jones RM, Goordial JM, Orcutt BN. Low Energy Subsurface Environments as Extraterrestrial Analogs. Front Microbiol 2018; 9:1605. [PMID: 30072971 PMCID: PMC6058055 DOI: 10.3389/fmicb.2018.01605] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 06/27/2018] [Indexed: 11/13/2022] Open
Abstract
Earth's subsurface is often isolated from phototrophic energy sources and characterized by chemotrophic modes of life. These environments are often oligotrophic and limited in electron donors or electron acceptors, and include continental crust, subseafloor oceanic crust, and marine sediment as well as subglacial lakes and the subsurface of polar desert soils. These low energy subsurface environments are therefore uniquely positioned for examining minimum energetic requirements and adaptations for chemotrophic life. Current targets for astrobiology investigations of extant life are planetary bodies with largely inhospitable surfaces, such as Mars, Europa, and Enceladus. Subsurface environments on Earth thus serve as analogs to explore possibilities of subsurface life on extraterrestrial bodies. The purpose of this review is to provide an overview of subsurface environments as potential analogs, and the features of microbial communities existing in these low energy environments, with particular emphasis on how they inform the study of energetic limits required for life. The thermodynamic energetic calculations presented here suggest that free energy yields of reactions and energy density of some metabolic redox reactions on Mars, Europa, Enceladus, and Titan could be comparable to analog environments in Earth's low energy subsurface habitats.
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Affiliation(s)
| | | | - Beth N. Orcutt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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40
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Merlino G, Barozzi A, Michoud G, Ngugi DK, Daffonchio D. Microbial ecology of deep-sea hypersaline anoxic basins. FEMS Microbiol Ecol 2018; 94:4995905. [DOI: 10.1093/femsec/fiy085] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/09/2018] [Indexed: 01/12/2023] Open
Affiliation(s)
- Giuseppe Merlino
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Alan Barozzi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Grégoire Michoud
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - David Kamanda Ngugi
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
| | - Daniele Daffonchio
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center (RSRC), Thuwal 23955-6900, Saudi Arabia
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41
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High-Quality Draft Single-Cell Genome Sequence Belonging to the Archaeal Candidate Division SA1, Isolated from Nereus Deep in the Red Sea. GENOME ANNOUNCEMENTS 2018; 6:6/19/e00383-18. [PMID: 29748404 PMCID: PMC5946040 DOI: 10.1128/genomea.00383-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Candidate division SA1 encompasses a phylogenetically coherent archaeal group ubiquitous in deep hypersaline anoxic brines around the globe. Recently, the genome sequences of two cultivated representatives from hypersaline soda lake sediments were published. Here, we present a single-cell genome sequence from Nereus Deep in the Red Sea that represents a putatively novel family within SA1.
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42
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Takahashi M, Takahashi E, Joudeh LI, Marini M, Das G, Elshenawy MM, Akal A, Sakashita K, Alam I, Tehseen M, Sobhy MA, Stingl U, Merzaban JS, Di Fabrizio E, Hamdan SM. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea. FASEB J 2018; 32:3346-3360. [PMID: 29401622 PMCID: PMC6051491 DOI: 10.1096/fj.201700862rr] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The deep-sea brines of the Red Sea are remote and unexplored environments characterized by high temperatures, anoxic water, and elevated concentrations of salt and heavy metals. This environment provides a rare system to study the interplay between halophilic and thermophilic adaptation in biologic macromolecules. The present article reports the first DNA polymerase with halophilic and thermophilic features. Biochemical and structural analysis by Raman and circular dichroism spectroscopy showed that the charge distribution on the protein’s surface mediates the structural balance between stability for thermal adaptation and flexibility for counteracting the salt-induced rigid and nonfunctional hydrophobic packing. Salt bridge interactions via increased negative and positive charges contribute to structural stability. Salt tolerance, conversely, is mediated by a dynamic structure that becomes more fixed and functional with increasing salt concentration. We propose that repulsive forces among excess negative charges, in addition to a high percentage of negatively charged random coils, mediate this structural dynamism. This knowledge enabled us to engineer a halophilic version of Thermococcus kodakarensis DNA polymerase.—Takahashi, M., Takahashi, E., Joudeh, L. I., Marini, M., Das, G., Elshenawy, M. M., Akal, A., Sakashita, K., Alam, I., Tehseen, M., Sobhy, M. A., Stingl, U., Merzaban, J. S., Di Fabrizio, E., Hamdan, S. M. Dynamic structure mediates halophilic adaptation of a DNA polymerase from the deep-sea brines of the Red Sea.
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Affiliation(s)
- Masateru Takahashi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Etsuko Takahashi
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Luay I Joudeh
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Monica Marini
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Gobind Das
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Mohamed M Elshenawy
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Anastassja Akal
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia.,KAUST Catalysis Center, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Kosuke Sakashita
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Intikhab Alam
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia; and
| | - Muhammad Tehseen
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Mohamed A Sobhy
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Ulrich Stingl
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia.,Fort Lauderdale Research and Education Center, University of Florida, Davie, Florida, USA
| | - Jasmeen S Merzaban
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Enzo Di Fabrizio
- Physical Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
| | - Samir M Hamdan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Jeddah, Saudi Arabia
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43
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Mora-Ruiz MDR, Cifuentes A, Font-Verdera F, Pérez-Fernández C, Farias ME, González B, Orfila A, Rosselló-Móra R. Biogeographical patterns of bacterial and archaeal communities from distant hypersaline environments. Syst Appl Microbiol 2017; 41:139-150. [PMID: 29352612 DOI: 10.1016/j.syapm.2017.10.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 10/22/2017] [Accepted: 10/23/2017] [Indexed: 01/21/2023]
Abstract
Microorganisms are globally distributed but new evidence shows that the microbial structure of their communities can vary due to geographical location and environmental parameters. In this study, 50 samples including brines and sediments from Europe, Spanish-Atlantic and South America were analysed by applying the operational phylogenetic unit (OPU) approach in order to understand whether microbial community structures in hypersaline environments exhibited biogeographical patterns. The fine-tuned identification of approximately 1000 OPUs (almost equivalent to "species") using multivariate analysis revealed regionally distinct taxa compositions. This segregation was more diffuse at the genus level and pointed to a phylogenetic and metabolic redundancy at the higher taxa level, where their different species acquired distinct advantages related to the regional physicochemical idiosyncrasies. The presence of previously undescribed groups was also shown in these environments, such as Parcubacteria, or members of Nanohaloarchaeota in anaerobic hypersaline sediments. Finally, an important OPU overlap was observed between anoxic sediments and their overlaying brines, indicating versatile metabolism for the pelagic organisms.
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Affiliation(s)
- M Del R Mora-Ruiz
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain.
| | - A Cifuentes
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
| | - F Font-Verdera
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
| | - C Pérez-Fernández
- Environmental Microbiology Laboratory, Puerto Rico University, Rio Piedras campus, Puerto Rico
| | - M E Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales Microbiológicos (PROIMI), CCT, CONICET, San Miguel de Tucumán, Tucumán, Argentina
| | - B González
- Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez - Center of Applied Ecology and Sustainability, Santiago, Chile
| | - A Orfila
- Marine Technology and Operational Oceanography Department, IMEDEA (CSIC-UIB), Esporles, Spain
| | - R Rosselló-Móra
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Spain
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44
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Selbmann L, Pacelli C, Zucconi L, Dadachova E, Moeller R, de Vera JP, Onofri S. Resistance of an Antarctic cryptoendolithic black fungus to radiation gives new insights of astrobiological relevance. Fungal Biol 2017; 122:546-554. [PMID: 29801799 DOI: 10.1016/j.funbio.2017.10.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/25/2017] [Accepted: 10/26/2017] [Indexed: 11/18/2022]
Abstract
The Antarctic black meristematic fungus Cryomyces antarcticus CCFEE 515 occurs endolithically in the McMurdo Dry Valleys of Antarctica, one of the best analogue for Mars environment on Earth. To date, this fungus is considered one of the best eukaryotic models for astrobiological studies and has been repeatedly selected for space experiments in the last decade. The obtained results are reviewed here, with special focus on responses to space relevant irradiation, UV radiation, and both sparsely and densely ionizing radiation, which represent the major injuries for a putative space-traveller. The remarkable resistance of this model organism to space stress, its radioresistance in particular, and mechanisms involved, significantly contributed to expanding our concept of limits for life and provided new insights on the origin and evolution of life in planetary systems, habitability, and biosignatures for life detection as well as on human protection during space missions.
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Affiliation(s)
- Laura Selbmann
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
| | - Claudia Pacelli
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
| | - Laura Zucconi
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
| | - Ekaterina Dadachova
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Canada.
| | - Ralf Moeller
- German Aerospace Center (DLR), Institute of Aerospace Medicine, Radiation Biology Department, Space Microbiology Research Group, Cologne (Köln), Germany.
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Institute of Planetary Research, Management and Infrastructure, Astrobiological Laboratories, Rutherfordstr. 2, 12489 Berlin, Germany.
| | - Silvano Onofri
- Department of Ecological and Biological Sciences (DEB), University of Tuscia, Largo dell'Università snc, 01100 Viterbo, Italy.
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45
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Zhang G, Haroon MF, Zhang R, Dong X, Liu D, Xiong Q, Xun W, Dong X, Stingl U. Ponticoccus marisrubri sp. nov., a moderately halophilic marine bacterium of the family Rhodobacteraceae. Int J Syst Evol Microbiol 2017; 67:4358-4364. [PMID: 28984559 DOI: 10.1099/ijsem.0.002280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain SJ5A-1T, a Gram-stain-negative, coccus-shaped, non-motile, aerobic bacterium, was isolated from the brine-seawater interface of the Erba Deep in the Red Sea, Saudi Arabia. The colonies of strain SJ5A-1T have a beige to pale-brown pigmentation, are approximately 0.5-0.7 µm in diameter, and are catalase and oxidase positive. Growth occurred optimally at 30-33 °C, pH 7.0-7.5, and in the presence of 9.0-12.0 % NaCl (w/v). Phylogenetic analysis of the 16S rRNA gene indicates that strain SJ5A-1T is a member of the genus Ponticoccus within the family Rhodobacteraceae. Ponticoccus litoralis DSM 18986T is the most closely related described species based on 16S rRNA gene sequence identity (96.7 %). The DNA-DNA hybridization value between strain SJ5A-1T and P. litoralis DSM 18986T was 36.7 %. The major respiratory quinone of strain SJ5A-1T is Q-10; it predominantly uses the fatty acids C18 : 1 (54.2 %), C18 : 0 (11.2 %), C16 : 0 (8.6 %), 11-methyl C18 : 1ω7c (7.7 %), C19 : 0cyclo ω8c (3.3 %), and C12 : 1 3-OH (3.5 %), and its major polar lipids are phosphatidylethanolamine, phosphatidylglycerol, phosphocholine, an unknown aminolipid, an unknown phospholipid and two unknown lipids. The genome draft of strain SJ5A-1T as presented here is 4 562 830 bp in size and the DNA G+C content is 68.0 mol%. Based on phenotypic, phylogenetic and genotypic data, strain SJ5A-1T represents a novel species in the genus Ponticoccus, for which we propose the name Ponticoccus marisrubri sp. nov. The type strain of P. marisrubri is SJ5A-1T (=JCM 19520T=ACCC19863T).
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Affiliation(s)
- Guishan Zhang
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mohamed Fauzi Haroon
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
| | - Ruifu Zhang
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiaoyan Dong
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Di Liu
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Qin Xiong
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Weibing Xun
- Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Key Laboratory of Microbial Resources Collection and Preservation, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ulrich Stingl
- King Abdullah University of Science and Technology (KAUST), Red Sea Research Center, Thuwal 23955-6900, Saudi Arabia
- Department of Microbiology and Cell Science, University of Florida, Institute for Food and Agricultural Sciences (IFAS), Fort Lauderdale Research and Education Center, Fort Lauderdale (Davie), FL33314, USA
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46
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Vander Roost J, Thorseth IH, Dahle H. Microbial analysis of Zetaproteobacteria and co-colonizers of iron mats in the Troll Wall Vent Field, Arctic Mid-Ocean Ridge. PLoS One 2017; 12:e0185008. [PMID: 28931087 PMCID: PMC5607188 DOI: 10.1371/journal.pone.0185008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/05/2017] [Indexed: 11/30/2022] Open
Abstract
Over the last decade it has become increasingly clear that Zetaproteobacteria are widespread in hydrothermal systems and that they contribute to the biogeochemical cycling of iron in these environments. However, how chemical factors control the distribution of Zetaproteobacteria and their co-occurring taxa remains elusive. Here we analysed iron mats from the Troll Wall Vent Field (TWVF) located at the Arctic Mid-Ocean Ridge (AMOR) in the Norwegian-Greenland Sea. The samples were taken at increasing distances from high-temperature venting chimneys towards areas with ultraslow low-temperature venting, encompassing a large variety in geochemical settings. Electron microscopy revealed the presence of biogenic iron stalks in all samples. Using 16S rRNA gene sequence profiling we found that relative abundances of Zetaproteobacteria in the iron mats varied from 0.2 to 37.9%. Biogeographic analyses of Zetaproteobacteria, using the ZetaHunter software, revealed the presence of ZetaOtus 1, 2 and 9, supporting the view that they are cosmopolitan. Relative abundances of co-occurring taxa, including Thaumarchaeota, Euryarchaeota and Proteobacteria, also varied substantially. From our results, combined with results from previous microbiological and geochemical analyses of the TWVF, we infer that the distribution of Zetaproteobacteria is connected to fluid-flow patterns and, ultimately, variations in chemical energy landscapes. Moreover, we provide evidence for iron-oxidizing members of Gallionellaceae being widespread in TWVF iron mats, albeit at low relative abundances.
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Affiliation(s)
- Jan Vander Roost
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
| | - Ingunn Hindenes Thorseth
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Earth Science, University of Bergen, Bergen, Norway
| | - Håkon Dahle
- Centre for Geobiology, University of Bergen, Bergen, Norway
- Department of Biology, University of Bergen, Bergen, Norway
- * E-mail:
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47
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Shehab NA, Ortiz-Medina JF, Katuri KP, Hari AR, Amy G, Logan BE, Saikaly PE. Enrichment of extremophilic exoelectrogens in microbial electrolysis cells using Red Sea brine pools as inocula. BIORESOURCE TECHNOLOGY 2017; 239:82-86. [PMID: 28500892 DOI: 10.1016/j.biortech.2017.04.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/25/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Applying microbial electrochemical technologies for the treatment of highly saline or thermophilic solutions is challenging due to the lack of proper inocula to enrich for efficient exoelectrogens. Brine pools from three different locations (Valdivia, Atlantis II and Kebrit) in the Red Sea were investigated as potential inocula sources for enriching exoelectrogens in microbial electrolysis cells (MECs) under thermophilic (70°C) and hypersaline (25% salinity) conditions. Of these, only the Valdivia brine pool produced high and consistent current 6.8±2.1A/m2-anode in MECs operated at a set anode potential of +0.2V vs. Ag/AgCl (+0.405V vs. standard hydrogen electrode). These results show that exoelectrogens are present in these extreme environments and can be used to startup MEC under thermophilic and hypersaline conditions. Bacteroides was enriched on the anode of the Valdivia MEC, but it was not detected in the open circuit voltage reactor seeded with the Valdivia brine pool.
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Affiliation(s)
- Noura A Shehab
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Research Product Development Innovations, The Business Gate Qurtubah, Riyadh 13244, Saudi Arabia
| | - Juan F Ortiz-Medina
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Krishna P Katuri
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ananda Rao Hari
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Gary Amy
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Bruce E Logan
- Department of Civil and Environmental Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Pascal E Saikaly
- Biological and Environmental Sciences and Engineering Division, Water Desalination and Reuse Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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48
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Ullah R, Yasir M, Khan I, Bibi F, Sohrab SS, Al-Ansari A, Al-Abbasi F, Al-Sofyani AA, Daur I, Lee SW, Azhar EI. Comparative bacterial community analysis in relatively pristine and anthropogenically influenced mangrove ecosystems on the Red Sea. Can J Microbiol 2017; 63:649-660. [PMID: 28376307 DOI: 10.1139/cjm-2016-0587] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Mangrove habitats are ecologically important ecosystems that are under severe pressure worldwide because of environmental changes and human activities. In this study, 16S rRNA gene amplicon deep-sequencing was used to compare bacterial communities in Red Sea mangrove ecosystems at anthropogenically influenced coastal sites with those at a relatively pristine island site. In total, 32 phyla were identified from the mangrove rhizospheres, with Proteobacteria predominating at each of the studied sites; however, the relative abundance was significantly decreased at the coastal sites (Mastorah, MG-MS; Ar-Rayis, MG-AR) compared with the pristine island site near Dhahban (MG-DBI). The phyla Actinobacteria, Firmicutes, Acidobacteria, Chloroflexi, Spirochetes, and Planctomycetes were present at a relative abundance of >1% at the MG-MS and MG-AR sites, but their concentration was <1% at the MG-DBI site. A total of 1659 operational taxonomic units (OTUs) were identified at the species level, and approximately 945 OTUs were shared across the different sampling sites. Multivariate principal coordinate data analysis separated the MG-DBI site from the MG-AR and MG-MS cluster. Specific bacterial taxa were enriched at each location, and in particular, the genera Pseudoalteromonas and Cobetia were predominantly identified in the MG-DBI site compared with the anthropogenically influenced coastal sites.
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Affiliation(s)
- Riaz Ullah
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,b Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Muhammad Yasir
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Khan
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,b Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sayed Sartaj Sohrab
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Al-Ansari
- c Department of Environmental Sciences, Faculty of Meteorology, Environment and Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahad Al-Abbasi
- b Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulmohsin A Al-Sofyani
- d Marine Biology Department, Faculty of Marine Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ihsanullah Daur
- e Department of Arid Land Agriculture, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Seon-Woo Lee
- f Department of Applied Biology, Dong-A University, Busan 49315, Republic of Korea
| | - Esam I Azhar
- a Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,g Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
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49
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Zhang G, Gu J, Zhang R, Rashid M, Haroon MF, Xun W, Ruan Z, Dong X, Stingl U. Haloprofundus marisrubri gen. nov., sp. nov., an extremely halophilic archaeon isolated from a brine-seawater interface. Int J Syst Evol Microbiol 2017; 67:9-16. [PMID: 27902200 DOI: 10.1099/ijsem.0.001559] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We isolated a Gram-stain-negative, pink-pigmented, motile, pleomorphic, extremely halophilic archaeon from the brine-seawater interface of Discovery Deep in the Saudi Arabian Red Sea. This strain, designated SB9T, was capable of growth within a wide range of temperatures and salinity, but required MgCl2. Cells lysed in distilled water, but at 7.0 % (w/v) NaCl cell lysis was prevented. The major polar lipids from strain SB9T were phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, an unidentified glycolipid and two unidentified phospholipids. The major respiratory quinones of strain SB9T were menaquinones MK8 (66 %) and MK8 (VIII-H2) (34 %). Analysis of the 16S rRNA gene sequence revealed that strain SB9T was closely related to species in the genera Halogranum and Haloplanus; in particular, it shared highest sequence similarity with the type strain of Halogranum rubrum (93.4 %), making it its closest known relative. The unfinished draft genome of strain SB9Twas 3 931 127 bp in size with a total G+C content of 62.53 mol% and contained 3917 ORFs, 50 tRNAs and eight rRNAs. Based on comparisons with currently available genomes, the highest average nucleotide identity value was 83 % to Halogranum salarium B-1T (GenBank accession no. GCA_000283335.1). These data indicate that this new isolate cannot be classified into any recognized genera of the family Haloferacaceae, and therefore strain SB9T is considered to be a representative of a novel species of a new genus within this family, for which the name Haloprofundus marisrubri gen. nov., sp. nov. is proposed. The type strain of Haloprofundus marisrubri is SB9T (=JCM 19565T=CGMCC 1.14959T).
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Affiliation(s)
- Guishan Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.,Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jingang Gu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mamoon Rashid
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mohamed Fauzi Haroon
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Weibing Xun
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Zhiyong Ruan
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ulrich Stingl
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Florida Research and Education Center, Davie, Fl, USA.,Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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50
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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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