Phylogeny of the Family Halomonadaceae Based on 23S and 16S Rdna Sequence Analyses
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The Hydrocarbon Biodegradation Potential of Faroe-Shetland Channel Bacterioplankton
THE HYDROCARBON BIODEGRADATION POTENTIAL OF FAROE-SHETLAND CHANNEL BACTERIOPLANKTON Angelina G. Angelova Submitted for the degree of Doctor of Philosophy Heriot Watt University School of Engineering and Physical Sciences July 2017 The copyright in this thesis is owned by the author. Any quotation from the thesis or use of any of the information contained in it must acknowledge this thesis as the source of the quotation or information. ABSTRACT The Faroe-Shetland Channel (FSC) is an important gateway for dynamic water exchange between the North Atlantic Ocean and the Nordic Seas. In recent years it has also become a frontier for deep-water oil exploration and petroleum production, which has raised the risk of oil pollution to local ecosystems and adjacent waterways. In order to better understand the factors that influence the biodegradation of spilled petroleum, a prerequisite has been recognized to elucidate the complex dynamics of microbial communities and their relationships to their ecosystem. This research project was a pioneering attempt to investigate the FSC’s microbial community composition, its response and potential to degrade crude oil hydrocarbons under the prevailing regional temperature conditions. Three strategies were used to investigate this. Firstly, high throughput sequencing and 16S rRNA gene-based community profiling techniques were utilized to explore the spatiotemporal patterns of the FSC bacterioplankton. Monitoring proceeded over a period of 2 years and interrogated the multiple water masses flowing through the region producing 2 contrasting water cores: Atlantic (surface) and Nordic (subsurface). Results revealed microbial profiles more distinguishable based on water cores (rather than individual water masses) and seasonal variability patterns within each core. -
Genomic Insight Into the Host–Endosymbiont Relationship of Endozoicomonas Montiporae CL-33T with Its Coral Host
ORIGINAL RESEARCH published: 08 March 2016 doi: 10.3389/fmicb.2016.00251 Genomic Insight into the Host–Endosymbiont Relationship of Endozoicomonas montiporae CL-33T with its Coral Host Jiun-Yan Ding 1, Jia-Ho Shiu 1, Wen-Ming Chen 2, Yin-Ru Chiang 1 and Sen-Lin Tang 1* 1 Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, 2 Department of Seafood Science, Laboratory of Microbiology, National Kaohsiung Marine University, Kaohsiung, Taiwan The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33T. Its genome had potential sign of ongoing genome erosion and gene exchange with its Edited by: Rekha Seshadri, host. Testosterone degradation and type III secretion system are commonly present in Department of Energy Joint Genome Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Institute, USA Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, Reviewed by: this bacterium could move into coral cells via endocytosis after binding to coral’s Eph Kathleen M. Morrow, University of New Hampshire, USA receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase Jean-Baptiste Raina, are possible type III secretion effectors that might help coral to prevent mitochondrial University of Technology Sydney, Australia dysfunction and promote gluconeogenesis, especially under stress conditions. -
Metagenomic Insights Into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines
Lawrence Berkeley National Laboratory Recent Work Title Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines. Permalink https://escholarship.org/uc/item/9xc5s0v5 Journal Frontiers in microbiology, 7(FEB) ISSN 1664-302X Authors Vavourakis, Charlotte D Ghai, Rohit Rodriguez-Valera, Francisco et al. Publication Date 2016 DOI 10.3389/fmicb.2016.00211 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 25 February 2016 doi: 10.3389/fmicb.2016.00211 Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines Charlotte D. Vavourakis 1, Rohit Ghai 2, 3, Francisco Rodriguez-Valera 2, Dimitry Y. Sorokin 4, 5, Susannah G. Tringe 6, Philip Hugenholtz 7 and Gerard Muyzer 1* 1 Microbial Systems Ecology, Department of Aquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands, 2 Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain, 3 Department of Aquatic Microbial Ecology, Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Ceskéˇ Budejovice,ˇ Czech Republic, 4 Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia, 5 Department of Biotechnology, Delft University of Technology, Delft, Netherlands, 6 The Department of Energy Joint Genome Institute, Walnut Creek, CA, USA, 7 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration Edited by: of sodium carbonates in the absence of major divalent cations. -
Prokaryotic Biodiversity of Halophilic Microorganisms Isolated from Sehline Sebkha Salt Lake (Tunisia)
Vol. 8(4), pp. 355-367, 22 January, 2014 DOI: 10.5897/AJMR12.1087 ISSN 1996-0808 ©2014 Academic Journals African Journal of Microbiology Research http://www.academicjournals.org/AJMR Full Length Research Paper Prokaryotic biodiversity of halophilic microorganisms isolated from Sehline Sebkha Salt Lake (Tunisia) Abdeljabbar HEDI1,2*, Badiaa ESSGHAIER1, Jean-Luc CAYOL2, Marie-Laure FARDEAU2 and Najla SADFI1 1Laboratoire Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Université de Tunis El Manar 2092, Tunisie. 2Laboratoire de Microbiologie et de Biotechnologie des Environnements Chauds UMR180, IRD, Université de Provence et de la Méditerranée, ESIL case 925, 13288 Marseille cedex 9, France. Accepted 7 February, 2013 North of Tunisia consists of numerous ecosystems including extreme hypersaline environments in which the microbial diversity has been poorly studied. The Sehline Sebkha is an important source of salt for food. Due to its economical importance with regards to its salt value, a microbial survey has been conducted. The purpose of this research was to examine the phenotypic features as well as the physiological and biochemical characteristics of the microbial diversity of this extreme ecosystem, with the aim of screening for metabolites of industrial interest. Four samples were obtained from 4 saline sites for physico-chemical and microbiological analyses. All samples studied were hypersaline (NaCl concentration ranging from 150 to 260 g/L). A specific halophilic microbial community was recovered from each site and initial characterization of isolated microorganisms was performed by using both phenotypic and phylogenetic approaches. The 16S rRNA genes from 77 bacterial strains and two archaeal strains were isolated and phylogenetically analyzed and belonged to two phyla Firmicutes and gamma-proteobacteria of the domain Bacteria. -
Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341 -
Halomonas Almeriensis Sp. Nov., a Moderately Halophilic, 1 Exopolysaccharide-Producing Bacterium from Cabo De Gata
1 Halomonas almeriensis sp. nov., a moderately halophilic, 2 exopolysaccharide-producing bacterium from Cabo de Gata (Almería, 3 south-east Spain). 4 5 Fernando Martínez-Checa, Victoria Béjar, M. José Martínez-Cánovas, 6 Inmaculada Llamas and Emilia Quesada. 7 8 Microbial Exopolysaccharide Research Group, Department of Microbiology, 9 Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja 10 s/n, 18071 Granada, Spain. 11 12 Running title: Halomonas almeriensis sp. nov. 13 14 Keywords: Halomonas; exopolysaccharides; halophilic bacteria; hypersaline 15 habitats. 16 17 Subject category: taxonomic note; new taxa; γ-Proteobacteria 18 19 Author for correspondence: 20 E. Quesada: 21 Tel: +34 958 243871 22 Fax: +34 958 246235 23 E-mail: [email protected] 24 25 26 The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene 27 sequence of strain M8T is AY858696. 28 29 30 31 32 33 34 1 Summary 2 3 Halomonas almeriensis sp. nov. is a Gram-negative non-motile rod isolated 4 from a saltern in the Cabo de Gata-Níjar wild-life reserve in Almería, south-east 5 Spain. It is moderately halophilic, capable of growing at concentrations of 5% to 6 25% w/v of sea-salt mixture, the optimum being 7.5% w/v. It is chemo- 7 organotrophic and strictly aerobic, produces catalase but not oxidase, does not 8 produce acid from any sugar and does not synthesize hydrolytic enzymes. The 9 most notable difference between this microorganism and other Halomonas 10 species is that it is very fastidious in its use of carbon source. It forms mucoid 11 colonies due to the production of an exopolysaccharide (EPS). -
Downloaded Halomonas Elongata: High-Afnity Betaine Transport System and Choline- from NCBI Database
Rekadwad et al. BMC Res Notes (2021) 14:296 https://doi.org/10.1186/s13104-021-05689-3 BMC Research Notes RESEARCH NOTE Open Access The diversity of unique 1,4,5,6-Tetrahydro- 2-methyl-4-pyrimidinecarboxylic acid coding common genes and Universal stress protein in Ectoine TRAP cluster (UspA) in 32 Halomonas species Bhagwan Narayan Rekadwad1* , Wen‑Jun Li2 and P. D. Rekha1 Abstract Objectives: To decipher the diversity of unique ectoine‑coding housekeeping genes in the genus Halomonas. Results: In Halomonas, 1,4,5,6‑Tetrahydro‑2‑methyl‑4‑pyrimidinecarboxylic acid has a crucial role as a stress‑tolerant chaperone, a compatible solute, a cell membrane stabilizer, and a reduction in cell damage under stressful conditions. Apart from the current 16S rRNA biomarker, it serves as a blueprint for identifying Halomonas species. Halomonas elongata 1H9 was found to have 11 ectoine‑coding genes. The presence of a superfamily of conserved ectoine‑ coding among members of the genus Halomonas was discovered after genome annotations of 93 Halomonas spp. As a result of the inclusion of 11 single copy ectoine coding genes in 32 Halomonas spp., genome‑wide evaluations of ectoine coding genes indicate that 32 Halomonas spp. have a very strong association with H. elongata 1H9, which has been proven evidence‑based approach to elucidate phylogenetic relatedness of ectoine‑coding child taxa in the genus Halomonas. Total 32 Halomonas species have a single copy number of 11 distinct ectoine‑coding genes that help Halomonas spp., produce ectoine under stressful conditions. Furthermore, the existence of the Universal stress protein (UspA) gene suggests that Halomonas species developed directly from primitive bacteria, highlighting its role during the progression of microbial evolution. -
Levan Production Potentials from Different Hypersaline Environments in Turkey
LEVAN PRODUCTION POTENTIALS FROM DIFFERENT HYPERSALINE ENVIRONMENTS IN TURKEY Hakan Çakmak1, Pınar Aytar Çelik*2,3, Seval Çınar4, Emir Zafer Hoşgün5, M. Burçin Mutlu4 , Ahmet Çabuk6 Address(es): 1Department of Biotechnology and Biosafety, Eskişehir Osmangazi University, Eskişehir, Turkey. 2Department of Biomedical Engineering, Eskişehir Osmangazi University, Eskişehir, Turkey. 3Horse Breeding Vocational School, Eskişehir Osmangazi University, Eskişehir, Turkey. 4Department of Biology, Eskişehir Technical University, Eskişehir, Turkey. 5Department of Chemical Department, Eskişehir Technical University, Eskişehir, Turkey. 6Department of Biology, Eskişehir Osmangazi University, Eskişehir, Turkey. *Corresponding author: [email protected] doi: 10.15414/jmbfs.2020.10.1.61-64 ARTICLE INFO ABSTRACT Received 9. 12. 2019 12 halophilic strains from different hypersaline environments such as solar salterns in Tuzlagözü (Sivas), Fadlum (Sivas), Kemah Revised 12. 3. 2020 (Erzincan), a hypersaline spring water in Pülümür (Tunceli) and a saline lake in Delice (Kırıkkale) belonging to Turkey, were Accepted 12. 3. 2020 investigated in terms of levan production. After incubation and ethyl alcohol treatment, dialysis process was operated for partial Published 1. 8. 2020 purification. Levan amounts in our samples after hydrolysis were calculated based on the amount of sugar obtained by acid hydrolysis of standard levan. Sugar amount of samples were determined using by high performance liquid chromatography system (HPLC). 1H- Nuclear Magnetic Resonance (1H-NMR) spectra of the levan sample and standard were recorded. The results obtained by HPLC Regular article analysis showed that Chromohalobacter canadensis strain 85B had highest production potential as 234.67 mg levan/g biomass. The chemical shifts of 1H-NMR spectrum of the extracted levan also showed high similarity to those of pure levan isolated from Erwinia herbicola. -
Chromohalobacter Salexigens Type Strain (1H11T) Alex Copeland1, Kathleen O’Connor2, Susan Lucas1, Alla Lapidus1, Kerrie W
Standards in Genomic Sciences (2011) 5:379-388 DOI:10.4056/sigs.2285059 Complete genome sequence of the halophilic and highly halotolerant Chromohalobacter salexigens type strain (1H11T) Alex Copeland1, Kathleen O’Connor2, Susan Lucas1, Alla Lapidus1, Kerrie W. Berry1, John C. Detter1,3, Tijana Glavina Del Rio1, Nancy Hammon1, Eileen Dalin1, Hope Tice1, Sam Pit- luck1, David Bruce1,3, Lynne Goodwin1,3, Cliff Han1,3, Roxanne Tapia1,3, Elizabeth Saund- ers1,3, Jeremy Schmutz3, Thomas Brettin1,4 Frank Larimer1,4, Miriam Land1,4, Loren Hauser1,4, Carmen Vargas5, Joaquin J. Nieto5, Nikos C. Kyrpides1, Natalia Ivanova1, Markus Göker6, Hans-Peter Klenk6*, Laszlo N. Csonka2*, and Tanja Woyke1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 5 Department of Microbiology and Parasitology, University of Seville, Spain 6 Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany *Corresponding authors: [email protected], [email protected] Keywords: aerobic, chemoorganotrophic, Gram-negative, motile, moderately halophilic, halo tolerant, ectoine synthesis, Halomonadaceae, Gammaproteobacteria, DOEM 2004 Chromohalobacter salexigens is one of nine currently known species of the genus Chromoha- lobacter in the family Halomonadaceae. It is the most halotolerant of the so-called ‘mod- erately halophilic bacteria’ currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11T and Halomonas elongata are the first and the second members of the family Halomonada- ceae with a completely sequenced genome. -
Halomonas Maura Sp. Nov., a Novel Moderately Halophilic, Exopolysaccharide-Producing Bacterium
International Journal of Systematic and Evolutionary Microbiology (2001), 51, 1625–1632 Printed in Great Britain Halomonas maura sp. nov., a novel moderately halophilic, exopolysaccharide-producing bacterium Microbial Samir Bouchotroch, Emilia Quesada, Ana del Moral, Inmaculada Llamas Exopolysaccharides Research Group, Department of and Victoria Be! jar Microbiology, Faculty of Pharmacy, Campus Universitario de Cartuja, Author for correspondence: Emilia Quesada. Tel: j34 958 243871. Fax: j34 958 246235. University of Granada, e-mail: equesada!platon.ugr.es 18071 Granada, Spain Four moderately halophilic, exopolysaccharide-producing bacterial strains isolated from soil samples collected from a saltern at Asilah (Morocco) are reported. These four strains were initially considered to belong to the genus Halomonas. Their DNA GMC contents varied between 622 and 641 mol%. DNA–DNA hybridization revealed a considerable degree of DNA–DNA similarity amongst all four strains (755–808%). Nevertheless, similarity with the reference strains of phylogenetically close relatives was lower than 40%. 16S rRNA gene sequences were compared with those of other species of Halomonas and other Gram-negative bacteria and they were sufficiently distinct phylogenetically from other recognized Halomonas species to warrant their designation as a novel species. The name Halomonas maura sp. nov. is therefore proposed, with strain S-31T (l CECT 5298T l DSM 13445T) as the type strain. The fatty acid composition of strain S-31T revealed the presence of 18:1ω7c,16:1ω7c/2-OH i15:0 and 16:0 as the major components. Growth rate analysis showed that strain S-31T had specific cationic requirements for NaM and Mg2M. Keywords: exopolysaccharides, moderately halophilic bacteria, Halomonas INTRODUCTION In the course of our studies into hypersaline environ- ments, a group of Halomonas eurihalina strains were The family Halomonadaceae includes the genera isolated that synthesized large quantities of exopoly- Halomonas, Chromohalobacter and Zymobacter. -
An Astrobiological Study of an Alkaline-Saline Hydrothermal Environment, Relevant to Understanding the Habitability of Mars
An astrobiological study of an alkaline-saline hydrothermal environment, relevant to understanding the habitability of Mars A thesis submitted for the Degree of Doctor of Philosophy By Lottie Elizabeth Davis Department of Earth Sciences University College London March 2012 1 I, Lottie Elizabeth Davis confirm that the work presented in this thesis is my own. Where information has been derived from other sources, I confirm that this has been indicated in the thesis. 2 Declaration Abstract The on going exploration of planets such as Mars is producing a wealth of data which is being used to shape a better understanding of potentially habitable environments beyond the Earth. On Mars, the relatively recent identification of minerals which indicate the presence of neutral/alkaline aqueous activity has increased the number of potentially habitable environments which require characterisation and exploration. The study of terrestrial analogue environments enables us to develop a better understanding of where life can exist, what types of organisms can exist and what evidence of that life may be preserved. The study of analogue environments is necessary not only in relation to the possibility of identifying extinct/extant indigenous life on Mars, but also for understanding the potential for contamination. As well as gaining an insight into the habitability of an environment, it is also essential to understand how to identify such environments using the instruments available to missions to Mars. It is important to be aware of instrument limitations to ensure that evidence of a particular environment is not overlooked. This work focuses upon studying the bacterial and archaeal diversity of Lake Magadi, a hypersaline and alkaline soda lake, and its associated hydrothermal springs. -
Microbial Diversity of Soda Lake Habitats
Microbial Diversity of Soda Lake Habitats Von der Gemeinsamen Naturwissenschaftlichen Fakultät der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Susanne Baumgarte aus Fritzlar 1. Referent: Prof. Dr. K. N. Timmis 2. Referent: Prof. Dr. E. Stackebrandt eingereicht am: 26.08.2002 mündliche Prüfung (Disputation) am: 10.01.2003 2003 Vorveröffentlichungen der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Gemeinsamen Naturwissenschaftlichen Fakultät, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht: Publikationen Baumgarte, S., Moore, E. R. & Tindall, B. J. (2001). Re-examining the 16S rDNA sequence of Halomonas salina. International Journal of Systematic and Evolutionary Microbiology 51: 51-53. Tagungsbeiträge Baumgarte, S., Mau, M., Bennasar, A., Moore, E. R., Tindall, B. J. & Timmis, K. N. (1999). Archaeal diversity in soda lake habitats. (Vortrag). Jahrestagung der VAAM, Göttingen. Baumgarte, S., Tindall, B. J., Mau, M., Bennasar, A., Timmis, K. N. & Moore, E. R. (1998). Bacterial and archaeal diversity in an African soda lake. (Poster). Körber Symposium on Molecular and Microsensor Studies of Microbial Communities, Bremen. II Contents 1. Introduction............................................................................................................... 1 1.1. The soda lake environment .................................................................................