Between Saltworks Biology and Solar Salt Quality
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Identification of Early Salinity Stress-Responsive Proteins In
International Journal of Molecular Sciences Article Identification of Early Salinity Stress-Responsive Proteins in Dunaliella salina by isobaric tags for relative and absolute quantitation (iTRAQ)-Based Quantitative Proteomic Analysis Yuan Wang 1,2,†, Yuting Cong 2,†, Yonghua Wang 3, Zihu Guo 4, Jinrong Yue 2, Zhenyu Xing 2, Xiangnan Gao 2 and Xiaojie Chai 2,* 1 Key Laboratory of Hydrobiology in Liaoning Province’s Universities, Dalian Ocean University, Dalian 116021, China; [email protected] 2 College of fisheries and life science, Dalian Ocean University, Dalian 116021, China; [email protected] (Y.C.); [email protected] (J.Y.); [email protected] (Z.X.); [email protected] (X.G.) 3 Bioinformatics Center, College of Life Sciences, Northwest A&F University, Yangling 712100, China; [email protected] 4 College of Life Sciences, Northwest University, Xi’an, Shaanxi 710069, China; [email protected] * Correspondence: [email protected] † These authors contribute equally to the work. Received: 22 November 2018; Accepted: 16 January 2019; Published: 30 January 2019 Abstract: Salt stress is one of the most serious abiotic factors that inhibit plant growth. Dunaliella salina has been recognized as a model organism for stress response research due to its high capacity to tolerate extreme salt stress. A proteomic approach based on isobaric tags for relative and absolute quantitation (iTRAQ) was used to analyze the proteome of D. salina during early response to salt stress and identify the differentially abundant proteins (DAPs). A total of 141 DAPs were identified in salt-treated samples, including 75 upregulated and 66 downregulated DAPs after 3 and 24 h of salt stress. -
Marine-Freshwater Prokaryotic Transitions Require Extensive Changes in the Predicted Proteome Pedro J
Cabello-Yeves and Rodriguez-Valera Microbiome (2019) 7:117 https://doi.org/10.1186/s40168-019-0731-5 RESEARCH Open Access Marine-freshwater prokaryotic transitions require extensive changes in the predicted proteome Pedro J. Cabello-Yeves1 and Francisco Rodriguez-Valera1,2* Abstract Background: The adaptation of a marine prokaryote to live in freshwater environments or vice versa is generally believed to be an unusual and evolutionary demanding process. However, the reasons are not obvious given the similarity of both kinds of habitats. Results: We have found major differences at the level of the predicted metaproteomes of marine and freshwater habitats with more acidic values of the isoelectric points (pI) in marine microbes. Furthermore, by comparing genomes of marine-freshwater phylogenetic relatives, we have found higher pI values (basic shift) in the freshwater ones. This difference was sharper in secreted > cytoplasmic > membrane proteins. The changes are concentrated on the surface of soluble proteins. It is also detectable at the level of total amino acid composition and involves similarly core and flexible genome- encoded proteins. Conclusions: The marked changes at the level of protein amino acid composition and pI provide a tool to predict the preferred habitat of a culture or a metagenome-assembled genome (MAG). The exact physiological explanation for such variations in the pIs and electrostatic surface potentials is not known yet. However, these changes might reflect differences in membrane bioenergetics derived from the absence of significant Na+ concentrations in most freshwater habitats. In any case, the changes in amino acid composition in most proteins imply that a long evolutionary time is required to adapt from one type of habitat to the other. -
A Mini Review-Effect of Dunaliella Salina on Growth and Health of Shrimps
International Journal of Fisheries and Aquatic Studies 2020; 8(5): 317-319 E-ISSN: 2347-5129 P-ISSN: 2394-0506 (ICV-Poland) Impact Value: 5.62 A mini review-effect of Dunaliella salina on growth and (GIF) Impact Factor: 0.549 IJFAS 2020; 8(5): 317-319 health of shrimps © 2020 IJFAS www.fisheriesjournal.com Received: 08-07-2020 Dian Yuni Pratiwi Accepted: 14-08-2020 Dian Yuni Pratiwi Abstract Lecturer of Faculty, Department Dunaliella salina is a unicellular green algae that can be used as a natural food for shrimp. This of Fisheries and Marine Science, microalgae provides various nutrients such as protein, carbohydrates, lipids, pigments and others. Several Universitas Padjadjaran, studies have shown that Dunaliella salina can increase the growth performance of shrimps. Not only that, Indonesia Dunaliella salina also grant various health effects. High β-carotene and phenol in Dunaliella salina can increase immune system. This review was examined the optimum growth condition for Dunaliellla salina, nutrition contained in Dunaliella salina, and effect of Dunaliella salina for growth and health of shrimps such as Fenneropenaeus indicus, Penaeus monodon, and Litopenaeus vannamei. This review recommendation for Dunaliella salina as a potential feed for other. Keywords: Dunaliella salina, Fenneropenaeus indicus, Penaeus monodon, Litopenaeus vannamei, growth, health 1. Introduction Shrimp is one of popular seafood in the world community. The United States, China, Europe, and Japan are the major consuming regions, while Indonesia, China, India, Vietnam are major producing regions. In 2019, the global shrimp market size reached a volume of 5.10 Million [1] Tons . Popular types of shrimp for consumption are Litopenaeus vannamei, Penaeus monodon [1] and Fenneropenaeus indicus [2]. -
The Changing Technology of Post Medieval Sea Salt Production in England
1 Heritage, Uses and Representations of the Sea. Centro de Investigação Transdisiplinar Cultura, Espaço e Memoría (CITCEM) Porto, Faculdade de Letras da Universidade do Porto, 20-22 October 2011. The changing technology of post medieval sea salt production in England Jeremy Greenwood Composition of seawater Sea water contains 3.5% evaporites of which salt (sodium chloride) comprises 77.8%. The remainder is known as bittern as it includes the bitter tasting, aperient and deliquescent sulphates of magnesium (Epsom salt) and sodium (Glauber’s salt) as well as about 11% magnesium chloride. 2 Successful commercial salt making depends on the fractional crystallisation of seawater producing the maximum amount of salt without contamination by bittern salts. As seawater is evaporated, very small amounts of calcium carbonate are precipitated followed by some calcium sulphate. This is followed by the crystallisation of sodium chloride but before this is complete, bitter Epsom salt appears; something that needs to be avoided.1 In Continental Europe, evaporation of sea water is achieved solely by the energy of the wind and sun but this is not possible in the English climate so other techniques were developed. 1 http://www.solarsaltharvesters.com/notes.htm SOLAR SALT ENGINEERING 3 Evaporation vessel Briquetage The earliest known English method of coastal saltmaking has been found in the late Bronze Age. This involved boiling seawater in crude clay dishes supported by clay firebars (briquetage) and was widespread in Europe. This technique continued into the Iron Age and into the Roman period with variations inevitably occurring in the industry, although the dating of saltworks is very problematical.2 Detailed interpretation continues to be a matter of dispute. -
Supporting Information
Supporting Information Lozupone et al. 10.1073/pnas.0807339105 SI Methods nococcus, and Eubacterium grouped with members of other Determining the Environmental Distribution of Sequenced Genomes. named genera with high bootstrap support (Fig. 1A). One To obtain information on the lifestyle of the isolate and its reported member of the Bacteroidetes (Bacteroides capillosus) source, we looked at descriptive information from NCBI grouped firmly within the Firmicutes. This taxonomic error was (www.ncbi.nlm.nih.gov/genomes/lproks.cgi) and other related not surprising because gut isolates have often been classified as publications. We also determined which 16S rRNA-based envi- Bacteroides based on an obligate anaerobe, Gram-negative, ronmental surveys of microbial assemblages deposited near- nonsporulating phenotype alone (6, 7). A more recent 16S identical sequences in GenBank. We first downloaded the gbenv rRNA-based analysis of the genus Clostridium defined phylo- files from the NCBI ftp site on December 31, 2007, and used genetically related clusters (4, 5), and these designations were them to create a BLAST database. These files contain GenBank supported in our phylogenetic analysis of the Clostridium species in the HGMI pipeline. We thus designated these Clostridium records for the ENV database, a component of the nonredun- species, along with the species from other named genera that dant nucleotide database (nt) where 16S rRNA environmental cluster with them in bootstrap supported nodes, as being within survey data are deposited. GenBank records for hits with Ͼ98% these clusters. sequence identity over 400 bp to the 16S rRNA sequence of each of the 67 genomes were parsed to get a list of study titles Annotation of GTs and GHs. -
The Ecology of Dunaliella in High-Salt Environments Aharon Oren
Oren Journal of Biological Research-Thessaloniki (2014) 21:23 DOI 10.1186/s40709-014-0023-y REVIEW Open Access The ecology of Dunaliella in high-salt environments Aharon Oren Abstract Halophilic representatives of the genus Dunaliella, notably D. salina and D. viridis, are found worldwide in salt lakes and saltern evaporation and crystallizer ponds at salt concentrations up to NaCl saturation. Thanks to the biotechnological exploitation of D. salina for β-carotene production we have a profound knowledge of the physiology and biochemistry of the alga. However, relatively little is known about the ecology of the members of the genus Dunaliella in hypersaline environments, in spite of the fact that Dunaliella is often the main or even the sole primary producer present, so that the entire ecosystem depends on carbon fixed by this alga. This review paper summarizes our knowledge about the occurrence and the activities of different Dunaliella species in natural salt lakes (Great Salt Lake, the Dead Sea and others), in saltern ponds and in other salty habitats where members of the genus have been found. Keywords: Dunaliella, Hypersaline, Halophilic, Great Salt Lake, Dead Sea, Salterns Introduction salt adaptation. A number of books and review papers When the Romanian botanist Emanoil C. Teodoresco have therefore been devoted to the genus [5-7]. How- (Teodorescu) (1866–1949) described the habitat of the ever, the ecological aspects of the biology of Dunaliella new genus of halophilic unicellular algae Dunaliella,it are generally neglected. A recent monograph did not was known from salterns and salt lakes around the devote a single chapter to ecological aspects, and con- Mediterranean and the Black Sea [1-3]. -
Dialogue on the Nomenclature and Classification of Prokaryotes
G Model SYAPM-25929; No. of Pages 10 ARTICLE IN PRESS Systematic and Applied Microbiology xxx (2018) xxx–xxx Contents lists available at ScienceDirect Systematic and Applied Microbiology journal homepage: www.elsevier.de/syapm Dialogue on the nomenclature and classification of prokaryotes a,∗ b Ramon Rosselló-Móra , William B. Whitman a Marine Microbiology Group, IMEDEA (CSIC-UIB), 07190 Esporles, Spain b Department of Microbiology, University of Georgia, Athens, GA 30602, USA a r t i c l e i n f o a b s t r a c t Keywords: The application of next generation sequencing and molecular ecology to the systematics and taxonomy Bacteriological code of prokaryotes offers enormous insights into prokaryotic biology. This discussion explores some major Taxonomy disagreements but also considers the opportunities associated with the nomenclature of the uncultured Nomenclature taxa, the use of genome sequences as type material, the plurality of the nomenclatural code, and the roles Candidatus of an official or computer-assisted taxonomy. Type material © 2018 Elsevier GmbH. All rights reserved. Is naming important when defined here as providing labels Prior to the 1980s, one of the major functions of Bergey’s Manual for biological entities? was to associate the multiple names in current usage with the cor- rect organism. For instance, in the 1948 edition of the Manual, 21 Whitman and 33 names were associated with the common bacterial species now named Escherichia coli and Bacillus subtilis, respectively [5]. When discussing the nomenclature of prokaryotes, we must first This experience illustrates that without a naming system gener- establish the role and importance of naming. -
Seasonal Fluctuations in Ionic Concentrations Drive Microbial Succession in a Hypersaline Lake Community
The ISME Journal (2014) 8, 979–990 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE Seasonal fluctuations in ionic concentrations drive microbial succession in a hypersaline lake community Sheila Podell1, Joanne B Emerson2,3, Claudia M Jones2, Juan A Ugalde1, Sue Welch4, Karla B Heidelberg5, Jillian F Banfield2,6 and Eric E Allen1,7 1Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA; 2Department of Earth and Planetary Sciences, University of California, Berkeley, CA, USA; 3Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA; 4School of Earth Sciences, Byrd Polar Research Center, Ohio State University, Columbus, OH, USA; 5Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA; 6Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA and 7Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA Microbial community succession was examined over a two-year period using spatially and temporally coordinated water chemistry measurements, metagenomic sequencing, phylogenetic binning and de novo metagenomic assembly in the extreme hypersaline habitat of Lake Tyrrell, Victoria, Australia. Relative abundances of Haloquadratum-related sequences were positively correlated with co-varying concentrations of potassium, magnesium and sulfate, -
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. -
Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain)
marine drugs Article Characterization of the Microbial Population Inhabiting a Solar Saltern Pond of the Odiel Marshlands (SW Spain) Patricia Gómez-Villegas, Javier Vigara and Rosa León * Laboratory of Biochemistry and Molecular Biology, Faculty of Experimental Sciences, Marine International Campus of Excellence (CEIMAR), University of Huelva, 21071 Huelva, Spain; [email protected] (P.G.-V.); [email protected] (J.V.) * Correspondence: [email protected]; Tel.: +34-959-219-951 Received: 28 June 2018; Accepted: 8 September 2018; Published: 12 September 2018 Abstract: The solar salterns located in the Odiel marshlands, in southwest Spain, are an excellent example of a hypersaline environment inhabited by microbial populations specialized in thriving under conditions of high salinity, which remains poorly explored. Traditional culture-dependent taxonomic studies have usually under-estimated the biodiversity in saline environments due to the difficulties that many of these species have to grow at laboratory conditions. Here we compare two molecular methods to profile the microbial population present in the Odiel saltern hypersaline water ponds (33% salinity). On the one hand, the construction and characterization of two clone PCR amplified-16S rRNA libraries, and on the other, a high throughput 16S rRNA sequencing approach based on the Illumina MiSeq platform. The results reveal that both methods are comparable for the estimation of major genera, although massive sequencing provides more information about the less abundant ones. The obtained data indicate that Salinibacter ruber is the most abundant genus, followed by the archaea genera, Halorubrum and Haloquadratum. However, more than 100 additional species can be detected by Next Generation Sequencing (NGS). In addition, a preliminary study to test the biotechnological applications of this microbial population, based on its ability to produce and excrete haloenzymes, is shown. -
MICROBIOLOGICAL and ECOPHYSIOLOGICAL CHARACTERIZATION of GREEN ALGAE Dunaliella Sp
MICROBIOLOGICAL AND ECOPHYSIOLOGICAL CHARACTERIZATION OF GREEN ALGAE Dunaliella sp. FOR IMPROVEMENT OF CAROTENOID PRODUCTION Muhammad Zainuri 1) Hermin Pancasakti Kusumaningrum*2 ), and Endang Kusdiyantini 2), 1) Laboratory of Biological Oceanography, Department of marine Sciences, Faculty of Fisheries and Marine Sciences, Diponegoro University 2) Microbiogenetics Laboratory, Faculty of Mathematics and Natural Sciences, Diponegoro University, Jl. Prof. Soedarto, UNDIP, Tembalang, Semarang. 50275. e-mail : [email protected] Abstract An isolate of green algae Dunaliella sp. from BBAP Jepara is usually used as a source for carotenoid supplement for marine animal cultivation in the local area. In order to improve carotenoid production especially detection of biosynthetic pathway from the organisms investigated in this study, the main purpose of this study is characterizing Dunaliella sp. based on it’s microbiological and ecophysiological characters. The research was done by characterize the growth, the cell and colonies microbiologically, total pigment production, and also characterize all of the ecophysiological factors affecting the algal growth and survival. The results of this research showed that Dunaliella sp. posseses typical characteristic of green eucaryote alga, in their growth and ecological condition. The extreme characters which was toleration ability to high salinity environment of was used to conclude Dunaliella sp. as Dunaliella salina. Key words : algae, Dunaliella sp. , microbiological, ecophysiological, characterization Introduction serve as precursors of many hormones Green algae are simple (Vershinin, 1999 in Lee and Schmidt- photosynthetic eukaryotes which are Dannert, 2002). Carotenoids are used responsible for up to 50% of the planet's commercially as food colorants, animal atmospheric carbon fixation. The recent feed supplements and, more recently, as discoveries of health related beneficial nutraceuticals for cosmetic and properties attributed to algal carotenoids pharmaceutical purposes. -
Community Respiration Studies in Saltern Crystallizer Ponds
Vol. 56: 255–261, 2009 AQUATIC MICROBIAL ECOLOGY Printed September 2009 doi: 10.3354/ame01298 Aquat Microb Ecol Published online May 19, 2009 Contribution to AME Special 2 ‘Progress and perspectives in aquatic primary productivity’ OPENPEN ACCESSCCESS Community respiration studies in saltern crystallizer ponds Mareike Warkentin1, Rhena Schumann1, Aharon Oren2,* 1Department of Biological Sciences, Applied Ecology, University of Rostock, Albert-Einstein-Strasse 3, 18059 Rostock, Germany 2The Institute of Life Sciences, and the Moshe Shilo Minerva Center for Marine Biogeochemistry, The Hebrew University of Jerusalem, Jerusalem, Israel ABSTRACT: To measure community respiration by the heterotrophic Archaea (dominated by Halo- quadratum) and Bacteria (Salinibacter) in the NaCl-saturated crystallizer brines of the solar salterns in Eilat, Israel, and to obtain information on the substrates preferred by the community as energy sources, we used 2 complementary approaches: monitoring of changes in oxygen concentration using planar optode sensors in short (up to 30 min) experiments, and long-term (up to 40–50 h) incubations using Winkler titration to assess changes in oxygen levels. Respiration rates measured were ~3 fmol cell–1 h–1. Respiration was markedly stimulated by glycerol, dihydroxyacetone and pyruvate, but not by yeast extract, succinate, and fumarate. These findings are discussed in view of genomic informa- tion on the dominant heterotrophic organisms in the community as well as the outcome of earlier studies on the behavior of halophilic prokaryotes in situ and in laboratory cultures. Despite the low in situ respiration rate, the oxygen uptake studies added information on the activities of the heterotro- phic communities in salt-saturated ecosystems and on the substrates metabolized by the microorgan- isms present.