The Life of Brine: Halophiles in 2001 Comment Mike Dyall-Smith* and Michael Danson
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Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2*
J. Microbiol. Biotechnol. (2013), 23(12), 1645–1653 http://dx.doi.org/10.4014/jmb.1308.08015 Research Article Minireview jmb Diversity of Halophilic Archaea in Fermented Foods and Human Intestines and Their Application Han-Seung Lee1,2* 1Department of Bio-Food Materials, College of Medical and Life Sciences, Silla University, Busan 617-736, Republic of Korea 2Research Center for Extremophiles, Silla University, Busan 617-736, Republic of Korea Received: August 8, 2013 Revised: September 6, 2013 Archaea are prokaryotic organisms distinct from bacteria in the structural and molecular Accepted: September 9, 2013 biological sense, and these microorganisms are known to thrive mostly at extreme environments. In particular, most studies on halophilic archaea have been focused on environmental and ecological researches. However, new species of halophilic archaea are First published online being isolated and identified from high salt-fermented foods consumed by humans, and it has September 10, 2013 been found that various types of halophilic archaea exist in food products by culture- *Corresponding author independent molecular biological methods. In addition, even if the numbers are not quite Phone: +82-51-999-6308; high, DNAs of various halophilic archaea are being detected in human intestines and much Fax: +82-51-999-5458; interest is given to their possible roles. This review aims to summarize the types and E-mail: [email protected] characteristics of halophilic archaea reported to be present in foods and human intestines and pISSN 1017-7825, eISSN 1738-8872 to discuss their application as well. Copyright© 2013 by The Korean Society for Microbiology Keywords: Halophilic archaea, fermented foods, microbiome, human intestine, Halorubrum and Biotechnology Introduction Depending on the optimal salt concentration needed for the growth of strains, halophilic microorganisms can be Archaea refer to prokaryotes that used to be categorized classified as halotolerant (~0.3 M), halophilic (0.2~2.0 M), as archaeabacteria, a type of bacteria, in the past. -
Extracellular Hydrolases Producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India
Int.J.Curr.Microbiol.App.Sci (2016) 5(11): 51-64 International Journal of Current Microbiology and Applied Sciences ISSN: 2319-7706 Volume 5 Number 11 (2016) pp. 51-64 Journal homepage: http://www.ijcmas.com Original Research Article http://dx.doi.org/10.20546/ijcmas.2016.511.006 Extracellular Hydrolases producing Haloarchaea from Marine Salterns at Okhamadhi, Gujarat, India Bhavini N. Rathod1, Harshil H. Bhatt2 and Vivek N. Upasani1* 1Department of Microbiology, M.G. Science Institute, Ahmedabad- 380009, India 2Kadi Sarva Vishwavidyalay Gandhinagar-23, India *Corresponding author ABSTRACT Haloarchaea thrive in hypersaline environments such as marine salterns, saline soils, soda lakes, salted foods, etc. The lysis of marine phyto- and zoo-planktons such as algae, diatoms, shrimps, purple and green bacteria, fish, etc. releases K e yw or ds biopolymers namely cellulose, starch, chitin, proteins, lipids, etc. in the saline Extremozymes , ecosystems. The chemorganotrophic haloarchaea therefore, need to produce haloarchaea, hydrolytic enzymes to utilize these substrates. However, the raw solar salt used for hydrolases, preservation can cause spoilage of foods due to the growth of halobacteria leading Halobacterium, to economic loss. We report here the isolation and identification of extracellular Haloferax, hydrolases (substrates casein, gelatin, starch, and Tweens: 20, 60, 40, 80) Halopetinus, producing haloarchaea isolated from the salt and brine samples collected from Okhamadhi marine salterns at Okhamadhi, Gujarat, India. Morphological, -
The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts
biomolecules Review The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts Laura Matarredona ,Mónica Camacho, Basilio Zafrilla , María-José Bonete and Julia Esclapez * Agrochemistry and Biochemistry Department, Biochemistry and Molecular Biology Area, Faculty of Science, University of Alicante, Ap 99, 03080 Alicante, Spain; [email protected] (L.M.); [email protected] (M.C.); [email protected] (B.Z.); [email protected] (M.-J.B.) * Correspondence: [email protected]; Tel.: +34-965-903-880 Received: 31 July 2020; Accepted: 24 September 2020; Published: 29 September 2020 Abstract: Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. -
Determination of Hydrolytic Enzyme Capabilities of Halophilic Archaea Isolated from Hides and Skins and Their Phenotypic and Phylogenetic Identification by S
33 DETERMinATION OF HYDROLYTic ENZYME CAPABILITIES OF HALOPHILIC ARCHAEA ISOLATED FROM HIDES AND SKins AND THEIR PHENOTYpic AND PHYLOGENETic IDENTIFicATION by S. T. B LG School of Health, Canakkale Onsekiz Mart University, Terzioglu Campus Canakkale, Turkey, 17100. and B. MER ÇL YaPiCi Biology Department, Faculty of Arts and Science, Canakkale ONSEKIZ MART UNIVERSITY, TERZIOGLU CAMPUS, Canakkale, Turkey, 17100. and İsmail Karaboz Basic and Industrial Microbiology Section, Biology Department, Faculty of Science, Ege University, Bornova, İzmi r, Turkey, 35100. ABSTRACT INTRODUCTION This research aims to isolate extremely halophilic archaea The main constituent of the raw hide is protein, mainly from salted hides, to determine the capacities of their collagen (33% w/w), and remainder is moisture and fat. During hydrolytic enzymes, and to identify them by using phenotypic storage of raw hide, collagen’s excessive proteolysis by and molecular methods. Domestic and imported salted hide lysosomal autolysis or proteolytic bacterial enzymes can lead and skin samples obtained from eight different sources were to the disintegration of the structure of collagen fibers.1 used as the research material. 186 extremely halophilic Biodeterioration is among the major causes of impairment of microorganisms were isolated from salted raw hides and aesthetic, functional and other properties of leather and other skins. Some biochemical, antibiotic sensitivity, pH, NaCl, biopolymers or organic materials and the products made from temperature tolerance and quantitative and qualitative them. Due to the fact that prevention of biological degradation hydrolytic enzyme tests were performed on these isolates. In is very important in conservation and processing of leather, our study, taking into account the phenotypic findings of the great effort is being made for decontamination of these research, 34 of 186 isolates were selected. -
Diversity of Haloquadratum and Other Haloarchaea in Three, Geographically Distant, Australian Saltern Crystallizer Ponds
Extremophiles (2010) 14:161–169 DOI 10.1007/s00792-009-0295-6 ORIGINAL PAPER Diversity of Haloquadratum and other haloarchaea in three, geographically distant, Australian saltern crystallizer ponds Dickson Oh • Kate Porter • Brendan Russ • David Burns • Mike Dyall-Smith Received: 13 October 2009 / Accepted: 1 December 2009 / Published online: 20 December 2009 Ó The Author(s) 2009. This article is published with open access at Springerlink.com Abstract Haloquadratum walsbyi is frequently a domi- were present at all three sites and, overall, 98% of the nant member of the microbial communities in hypersaline Haloquadratum-related sequences displayed B2% diver- waters. 16S rRNA gene sequences indicate that divergence gence from that of the type strain. While haloarchaeal within this species is very low but relatively few sites have diversity at each site was relatively low (9–16 OTUs), been examined, particularly in the southern hemisphere. seven phylogroups (clones and/or isolates) and 4 different The diversity of Haloquadratum was examined in three clones showed B90% sequence identity to classified taxa, coastal, but geographically distant saltern crystallizer and appear to represent novel genera. Six of these branched ponds in Australia, using both culture-independent and together in phylogenetic tree reconstructions, forming a culture-dependent methods. Two 97%-OTU, comprising clade (MSP8-clade) whose members were only distantly Haloquadratum- and Halorubrum-related sequences, were related to classified taxa. Such sequences have only rarely shared by all three sites, with the former OTU representing been previously detected but were found at all three Aus- about 40% of the sequences recovered at each site. tralian crystallizers. -
Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks
Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez M¨unchen, 2009 Reconstruction, Modeling & Analysis of Haloarchaeal Metabolic Networks Orland Gonzalez Dissertation an der Fakult¨at f¨ur Mathematik, Informatik und Statistik der Ludwig-Maximilians-Universit¨at M¨unchen vorgelegt von Orland Gonzalez aus Manila M¨unchen, den 02.03.2009 Erstgutachter: Prof. Dr. Ralf Zimmer Zweitgutachter: Prof. Dr. Dieter Oesterhelt Tag der m¨undlichen Pr¨ufung: 21.01.2009 Contents Summary xiii Zusammenfassung xvi 1 Introduction 1 2 The Halophilic Archaea 9 2.1NaturalEnvironments............................. 9 2.2Taxonomy.................................... 11 2.3PhysiologyandMetabolism.......................... 14 2.3.1 Osmoadaptation............................ 14 2.3.2 NutritionandTransport........................ 16 2.3.3 Motility and Taxis ........................... 18 2.4CompletelySequencedGenomes........................ 19 2.5DynamicsofBlooms.............................. 20 2.6Motivation.................................... 21 3 The Metabolism of Halobacterium salinarum 23 3.1TheModelArchaeon.............................. 24 3.1.1 BacteriorhodopsinandOtherRetinalProteins............ 24 3.1.2 FlexibleBioenergetics......................... 26 3.1.3 Industrial Applications ......................... 27 3.2IntroductiontoMetabolicReconstructions.................. 27 3.2.1 MetabolismandMetabolicPathways................. 27 3.2.2 MetabolicReconstruction....................... 28 3.3Methods.................................... -
Microbial Diversity Associated with Halite Within The
MICROBIAL DIVERSITY ASSOCIATED WITH HALITE WITHIN THE WASTE ISOLATION PILOT PLANT Actinide Chemistry and Repository Science Program LA-UR-13-22595 Earth & Environmental Sciences Division 12 Los Alamos National Laboratory—Carlsbad Operations ABSTRACT METHODS Microbial activity is considered by many to have potentially Collection adverse effects on nuclear waste repositories. Due to Samples were retrieved from two different panels within the WIPP horizon. A long-handled pick was used to pry away the outer layer of halite, then to remove halite from the underlying stratum. Samples were handled aseptically, segregated by insufficient knowledge about the microbial communities halite appearance (clear versus argillaceous), and placed into sterile plastic bags. indigenous to the Waste Isolation Pilot Plant (WIPP) at the time of its inception, those same effects were attributed to Cultivation these organisms as well. However, significant differences Samples were not sterilized prior to processing in the lab. Approximately exist between the communities present in low- and high-ionic 50 grams of halite were dissolved in generic growth media at two salt strength matrices. concentrations. Media contained (in g/L): NaCl 100 or 175; yeast extract, 0.5; casamino acids, 0.5; soluble starch, 0.2; MgCl 2·6H2O, 20; KCl, 2.0; CaCl ·2H O, 0.2; sodium pyruvate, 0.02, ATCC trace elements, 1 ml; pH Studies have been underway to gain a better understanding of 2 2 adjusted with Tris buffer to ~7.5. Flasks were incubated at room temperature the microbial ecology in the WIPP and the potential effect of in the dark, while stirring. Periodic subcultures were made onto solid media. -
Exploring the Diversity of Extremely Halophilic Archaea in Food-Grade Salts
International Journal of Food Microbiology 191 (2014) 36–44 Contents lists available at ScienceDirect International Journal of Food Microbiology journal homepage: www.elsevier.com/locate/ijfoodmicro Exploring the diversity of extremely halophilic archaea in food-grade salts Olivier Henriet, Jeanne Fourmentin, Bruno Delincé, Jacques Mahillon ⁎ Laboratory of Food and Environmental Microbiology, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium article info abstract Article history: Salting is one of the oldest means of food preservation: adding salt decreases water activity and inhibits microbial Received 28 April 2014 development. However, salt is also a source of living bacteria and archaea. The occurrence and diversity of viable Received in revised form 7 August 2014 archaea in this extreme environment were assessed in 26 food-grade salts from worldwide origin by cultivation Accepted 13 August 2014 on four culture media. Additionally, metagenomic analysis of 16S rRNA gene was performed on nine salts. Viable Available online 20 August 2014 archaea were observed in 14 salts and colony counts reached more than 105 CFU per gram in three salts. All fi Keywords: archaeal isolates identi ed by 16S rRNA gene sequencing belonged to the Halobacteriaceae family and were Food-grade salt related to 17 distinct genera among which Haloarcula, Halobacterium and Halorubrum were the most represented. Halophilic archaea High-throughput sequencing generated extremely different profiles for each salt. Four of them contained a single High salinity media major genus (Halorubrum, Halonotius or Haloarcula) while the others had three or more genera of similar Metagenomics occurrence. The number of distinct genera per salt ranged from 21 to 27. -
Appendix: Lakes of the East African Rift System
Appendix: Lakes of the East African Rift System Alkalinity Country Lake Latitude Longitude Type Salinity [‰]pH [meq LÀ1] Djibouti Assal 11.658961 42.406998 Hypersaline 158–277a,d NA NA Ethiopia Abaja/Abaya 6.311204 37.847671 Fresh-subsaline <0.1–0.9j,t 8.65–9.01j,t 8.8–9.4j,t Ethiopia A¯ bay Ha¯yk’ 7.940916 38.357706 NA NA NA NA Ethiopia Abbe/Abhe Bad 11.187832 41.784325 Hypersaline 160a 8f NA Ethiopia Abijata/Abiyata 7.612998 38.597603 Hypo-mesosaline 4.41–43.84f,j,t 9.3–10.0f,t 102.3–33.0f,j Ethiopia Afambo 11.416091 41.682701 NA NA NA NA Ethiopia Afrera (Giulietti)/ 13.255318 40.899925 Hypersaline 169.49g 6.55g NA Afdera Ethiopia Ara Shatan 8.044060 38.351119 NA NA NA NA Ethiopia Arenguade/Arenguadi 8.695324 38.976388 Sub-hyposaline 1.58–5.81r,t 9.75–10.30r,t 34.8–46.0t Ethiopia Awassa/Awasa 7.049786 38.437614 Fresh-subsaline <0.1–0.8f,j,t 8.70–8.92f,t 3.8–8.4f,t Ethiopia Basaka/Beseka/ 8.876931 39.869957 Sub-hyposaline 0.89–5.3c,j,t 9.40–9.45j,t 27.5–46.5j,t Metahara Ethiopia Bischoftu/Bishoftu 8.741815 38.982053 Fresh-subsaline <0.1–0.6t 9.49–9.53t 14.6t Ethiopia Budamada 7.096464 38.090773 NA NA NA NA Ethiopia Caddabassa 10.208165 40.477524 NA NA NA NA Ethiopia Chamo 5.840081 37.560654 Fresh-subsaline <0.1–1.0j,t 8.90–9.20j,t 12.0–13.2j,t Ethiopia Chelekleka 8.769979 38.972268 NA NA NA NA Ethiopia Chitu/Chiltu/Chittu 7.404516 38.420191 Meso-hypersaline 19.01–64.16 10.10–10.50 22.6–715.0f,t f,j,t f,j,t Ethiopia Gemeri/Gummare/ 11.532507 41.664848 Fresh-subsaline <0.10–0.70a,f 8f NA Gamari Ethiopia Guda/Babogaya/ 8.787114 38.993297 -
Great Salt Lake Utah
Great Salt Lake Utah edited by David L. Alles Western Washington University e-mail: [email protected] Last Updated 2013-8-27 Note: In PDF format most of the images in this web paper can be enlarged for greater detail. 1 Pediastrum a flat colony of Green Algae Introduction This series of papers and essays on the importance of plankton and phytoplankton is centrally important in understanding humanities roles in the future of all of life on Earth. This essay is presented to show how complex our roles is. For it is not only marine and freshwater bodies of water that are involved. Hypersaline bodies of water found in inland closed basins also play a part in this story and provide a unique picture of the role played by halophilic bacterium and algae in life on Earth. The Great Salt Lake in the state of Utah in the United States is only one example. 2 Some facts about the Great Salt Lake 1. It is the largest U.S. lake west of the Mississippi River. 2. It is the 4th largest terminal lake (no outlet) in the world. 3. It is a remnant of Lake Bonneville, a prehistoric freshwater lake that was 10 times larger than the current Great Salt Lake. 4. It is about 75 miles long, and 28 miles wide, and covers 1,700 square miles and has a maximum depth of about 35 feet. 5. The lake is hypersaline and is typically 3-5 times saltier than the ocean. 6. It is fish free, the largest aquatic animals are brine shrimp and brine flies. -
Halobacterium Salinarum: Polyextremophile Model for Life Inside Martian Halite
Eighth International Conference on Mars (2014) 1477.pdf Halobacterium salinarum: Polyextremophile Model for Life Inside Martian Halite. A. Srivastava1, Depart- ment of Bioinformatics and Biotechnology, BioAxis DNA Research Centre Private Limited, Hyderabad (13-51, Sri Lakshmi Nagar colony, L B Nagar, Hyderabad-500068, A.P., India, [email protected]) Introduction: It is essential to define and under- eral studies have come into light that isolated and cul- stand the limits of life here on Earth before we can tivated halophilic microorganisms from ancient salt anticipate the potential for life on extraterrestrial des- deposits, provided detailed taxonomic descriptions, tinations. Indeed, when we consider the prospects of and retrieved DNA from ancient sediments [9-19], extraterrestrial life, we should not be confined to the which again strongly supported the presence of biolog- Earth-centric point of view of life, however, there are ical material in evaporites of great geological age and compelling lines of evidence at terrestrial analogues suggested important astrobiological implications [20]. for extraterrestrial environments that project them as Among halophiles, Halobacterium salinarum seems to plausible models to those extraterrestrial sites, to study be a versatile microorganism and can be attributed as life at those extreme ends. The present work briefly a poly-extremophile. reviews the recent studies on long-term survival po- Halobacterium salinarum is a model organism tential of Halobacterium salinarum in ancient terres- from the halophilic branch of Archaea [21] that has trial halite, seeks to understand its poly-extremophilic been isolated from a single fluid inclusion in a 97 000- life-style, and studies the possible survival potential of year-old halite crystal from Death Valley [13]. -
Haloarchaeal Species Genesis: Diversity, Recombination, and Evolution Nikhil Ram Mohan University of Connecticut - Storrs, R [email protected]
University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 7-26-2016 Haloarchaeal Species Genesis: Diversity, Recombination, and Evolution Nikhil Ram Mohan University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Ram Mohan, Nikhil, "Haloarchaeal Species Genesis: Diversity, Recombination, and Evolution" (2016). Doctoral Dissertations. 1207. https://opencommons.uconn.edu/dissertations/1207 Haloarchaeal Species Genesis: Diversity, Recombination, and Evolution Nikhil Ram Mohan University of Connecticut, 2016 ABSTRACT The processes key to the generation of new species in eukaryotes is well understood but the same is not true for the prokaryotic world. Allopatric speciation is widely accepted as the driving force in eukaryotic species genesis. However, little is known about prokaryotic speciation primarily due to the abundance of prokaryotes in this world. They inhabit every fathomable niche, present high cell densities, complex community structures, and are easily dispersed between large distances. For example, a gram of soil or a milliliter of seawater house millions and millions of a vast variety of microorganisms. This complexity in the prokaryotic world makes inferring an overall evolutionary processes extremely difficult. To reduce the complexity, the system studied needs to be narrowed down. This thesis focusses on one environment that is so extreme that it is conducive for the growth of only certain groups of organisms. The system is characterized by high salinity, much greater than that of seawater, which is a prerequisite for the survival of an entire class of Archaea call the Halobacteria (Haloarchaea). Studying these environments reduces the microbial complexity in comparison to some of the more easily habitable areas like soil or water.