DOCSLIB.ORG

The Influence of Invasive Jellyfish Blooms on The

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Influence of Invasive Jellyfish Blooms on The Biol Invasions DOI 10.1007/s10530-014-0810-2 MOLECULAR TOOLS The influence of invasive jellyfish blooms on the aquatic microbiome in a coastal lagoon (Varano, SE Italy) detected by an Illumina-based deep sequencing strategy Caterina Manzari • Bruno Fosso • Marinella Marzano • Anita Annese • Rosa Caprioli • Anna Maria D’Erchia • Carmela Gissi • Marianna Intranuovo • Ernesto Picardi • Monica Santamaria • Simonetta Scorrano • Giuseppe Sgaramella • Loredana Stabili • Stefano Piraino • Graziano Pesole Received: 14 November 2013 / Accepted: 31 October 2014 Ó The Author(s) 2014. This article is published with open access at Springerlink.com Abstract The rapid expansion of multicellular microbial taxonomic and functional diversity. Here native and alien species outbreaks in aquatic and we used an effective and highly sensitive experimental terrestrial ecosystems (bioinvasions) may produce strategy, bypassing the efficiency bottleneck of the significant impacts on bacterial community dynamics traditional bacterial isolation and culturing method, to and nutrient pathways with major ecological implica- identify changes of the planktonic microbial commu- tions. In aquatic ecosystems, bioinvasions may cause nity inhabiting a marine coastal lagoon (Varano, adverse effects on the water quality resulting from Adriatic Sea) under the influence of an outbreak- changes in biological, chemical and physical proper- forming alien jellyfish species. Water samples were ties linked to significant transformations of the collected from two areas that differed in their level of confinement inside in the lagoon and jellyfish densities (W, up to 12.4 medusae m-3; E, up to 0.03 medusae Caterina Manzari, Bruno Fosso and Marinella Marzano have -3 contributed equally to this work. m ) to conduct a snapshot microbiome analysis by a metagenomic approach. After extraction of the genetic Stefano Piraino and Graziano Pesole are senior authors. material in the environmental water samples, we deep- sequenced metagenomic amplicons of the V5–V6 Electronic supplementary material The online version of region of the 16S rRNA bacterial gene by an Illumina this article (doi:10.1007/s10530-014-0810-2) contains supple- MiSeq platform. Experiments were carried out in mentary material, which is available to authorized users. C. Manzari Á B. Fosso Á A. Annese Á R. Caprioli Á S. Scorrano Á S. Piraino A. M. D’Erchia Á M. Intranuovo Á E. Picardi Á G. Pesole Consorzio Nazionale Interuniversitario per le Scienze del Dipartimento di Bioscienze, Biotecnologie e Mare (Co.N.I.S.Ma.), Via Isonzo 32, 00198 Rome, Italy Biofarmaceutica, Universita` degli Studi di Bari ‘‘Aldo Moro’’, Via Orabona 4, 70126 Bari, Italy R. Caprioli Á S. Piraino Dipartimento di Scienze e Tecnologie Biologiche e M. Marzano Á A. M. D’Erchia Á E. Picardi Á Ambientali (DiSTeBA), Universita` del Salento, M. Santamaria Á G. Sgaramella Á G. Pesole (&) Via Monteroni, 73100 Lecce, Italy Istituto di Biomembrane e Bioenergetica (IBBE), CNR, Via Amendola 165/A, 70126 Bari, Italy C. Gissi e-mail: [email protected]; [email protected] Dipartimento di Bioscienze, Universita` degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy R. Caprioli Dipartimento di Biologia Animale, Universita` degli Studi di Modena e Reggio Emilia, Via G. Campi 213/d, 41100 Modena, Italy 123 C. Manzari et al. triplicates, so six libraries of dual indexed amplicons they participate in essential biogeochemical processes of 420 bp were successfully sequenced on the MiSeq such as the carbon, nitrogen and sulphur cycles in platform using a 2 9 250 bp paired-end sequencing terrestrial and aquatic ecosystems, are producers and strategy. Approximately 7.5 million paired-end reads decomposers in food webs (Dorigo et al. 2005; Kisand (i.e. 15 million total reads) were generated, with an et al. 2012; Zehr 2010), and are primarily responsible average of 2.5 million reads (1.25 M pairs) per sample for degradation of a large variety of natural organic replicate. The sequence data, analyzed through a novel compounds (Ogawa et al. 2001). bioinformatics pipeline (BioMaS), showed that the Aquatic environments harbor abundant and diverse structure of the resident bacterial community was microbial communities that ensure their functioning and significantly affected by the occurrence of jellyfish sustainability (Azam and Malfatti 2007; Zinger et al. outbreaks. Clear qualitative and quantitative differ- 2012). In recent decades, the importance of bacterio- ences were found between the western and eastern plankton has been persuasively demonstrated in nutrient areas (characterized by many or few jellyfish), with 84 cycling and food-web structure in the marine environ- families, 153 genera and 324 species in the W samples, ment (Azam 1998;Cho1990) and a multitude of marine and 104 families, 199 genera and 331 species in the E bacteria have been isolated in ocean sites and different samples. Significant differences between the two coastal areas of temperate, tropical and polar zones sampling areas were particularly detected in the (Pommier et al. 2005; Rusch et al. 2007; Stabili and occurrence of 16 families, 22 genera and 61 species Cavallo 2011). Aquatic microbes are genetically, phys- of microbial taxa. This is the first time that a NGS iologically and ecologically diverse, and exhibit many platform has been used to screen the impact of jellyfish different physiological responses, adaptation and evo- bioinvasions on the aquatic microbiome, providing a lutionary patterns (Bahgat 2011; Kemp and Aller 2004). preliminary assessment of jellyfish-driven changes of The microbiota composition varies as a function of the functional and structural microbial biodiversity. water class (e.g. oceans, lakes, rivers, springs, ponds and ground water) and it is affected by different factors such Keywords Metagenomics Á Next-generation as water salinity, organic compound concentration, sequencing platforms Á Marine microbial ecology Á turbidity, temperature, and contamination sources Jellyfish biomass (Bahgat 2011). Study of the overall biodiversity is crucial for assessing and monitoring aquatic ecosystems; however, the composition, abundance, and distribution patterns of Introduction microbial communities usually remain poorly explored (Kisand et al. 2012; Zinger et al. 2012). The recent advent of next generation sequencing Previously, difficulties in collecting representative technologies has revolutionized microbiome research, samples in particular habitats (e.g. deep sea) and allowing unprecedented depth and resolution at experimental limitations related to the characteriza- affordable costs and, thus, enabling large-scale studies tion of the uncultivable microbes have been the two of microorganisms living in taxonomically and phys- main limitations for comprehensive assessments of the ically complex habitats. Because microbes have lived microbial communities living in certain environments on Earth for more than 3 billion years, they are (Kisand et al. 2012). This view recently changed with ubiquitous and play important roles in the Earth’s the development of culture-independent approaches, ecosystems (Kowalchuk et al. 2008). In particular, such as metagenomics. As defined by Thomas et al. (2012), metagenomics represent the direct genetic S. Scorrano analysis of genomes contained in an environmental Dipartimento di Scienze Ecologiche e Biologiche (DEB), sample, without isolation or culture of individual Universita` della Tuscia, Largo dell’ Universita`, organisms. The metagenomic approach is experienc- 01100 Viterbo, Italy ing an explosive improvement since the advent of L. Stabili high-throughput Next-Generation Sequencing (NGS) Istituto per l’Ambiente Marino Costiero (IAMC), CNR, technologies, which allow an unprecedented large- Via Roma 3, 74100 Taranto, Italy scale identification of organisms and communities 123 The influence of invasive jellyfish blooms through the production of an enormous amount of also the case for the Varano lagoon, a coastal lagoonal genetic data (Bourlat et al. 2013). Either of two habitat with a strong aquaculture vocation and tradi- experimental strategies can be applied starting from tion. The Varano ecosystem was invaded by the moon the total extracted DNA: (1) the entire metagenome is jellyfish Aurelia sp. more than 10 years ago and now sequenced by a shotgun approach, or (2) gene markers has a persistent population with high densities in some specific for a given taxon are selectively sequenced parts (Belmonte et al. 2011; Manini et al. 2005; after their amplification by PCR primer pairs able to Scorrano 2014). function over a broad taxonomic range (amplicon- The invasion of Aurelia jellyfish in coastal lagoons based approach). The second approach is the most often can be related to the introduction of mussel common strategy applied in various ecological set- culture rafts bearing the polyp stages, which asexually tings and is used to investigate prokaryotic diversity release great numbers of medusae into the water through analysis of hypervariable regions of the 16S column (Lo et al. 2008; Purcell, 2012). In Varano rRNA gene (Hajibabaei et al. 2011; Klindworth et al. lagoon, eventually a year-round resident population 2013). Illumina/Solexa represents the NGS sequenc- was established with high densities of jellyfish (mean ing system most widely used for amplicon-based 4.5 ind) in spring and summer months. Molecular COI metagenomic studies (Luo et al. 2012), providing barcoding assigned the Varano jellyfish population to optimal performances in terms of time, costs
Load more

Recommended publications
  • A Polysaccharide-Degrading Marine Bacterium Flammeovirga Sp. MY04 and Its Extracellular Agarase System
    中国科技论文在线 http://www.paper.edu.cn J. Ocean Univ. China (Oceanic and Coastal Sea Research) DOI 10.1007/s11802-012-1929-3 ISSN 1672-5182, 2012 11 (3): 375-382 http://www.ouc.edu.cn/xbywb/ E-mail:[email protected] A Polysaccharide-Degrading Marine Bacterium Flammeovirga sp. MY04 and Its Extracellular Agarase System HAN Wenjun1), 2), 3), GU Jingyan1), 3), YAN Qiujie2), LI Jungang2), WU Zhihong3), *, GU Qianqun1), *, and LI Yuezhong3) 1) Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, P. R . C hi n a 2) School of Life Science and Biotechnology, Mianyang Normal University, Mianyang 621000, P. R. China 3) State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, P. R. China (Received February 2, 2012; revised April 8, 2012; accepted May 29, 2012) © Ocean University of China, Science Press and Springer-Verlag Berlin Heidelberg 2012 Abstract Bacteria of the genus Flammeovirga can digest complex polysaccharides (CPs), but no details have been reported re- garding the CP depolymerases of these bacteria. MY04, an agarolytic marine bacterium isolated from coastal sediments, has been identified as a new member of the genus Flammeovirga. The MY04 strain is able to utilize multiple CPs as a sole carbon source and -1 -1 grows well on agarose, mannan, or xylan. This strain produces high concentrations of extracellular proteins (490 mg L ± 18.2 mg L liquid culture) that exhibit efficient and extensive degradation activities on various polysaccharides, especially agarose. These pro- -1 -1 teins have an activity of 310 U mg ± 9.6 U mg proteins.
    [Show full text]
  • {Replace with the Title of Your Dissertation}
    The Mechanism of Foaming in Deep-Pit Swine Manure Storage A Dissertation SUBMITTED TO THE FACULTY OF UNIVERSITY OF MINNESOTA BY Mi Yan IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Adviser: Bo Hu October, 2016 © Mi Yan 2016 i Acknowledgements There are many people that contribute to this PhD thesis with their work, advice or encouragement. First of all, I would like to thank my advisor Dr. Bo Hu, who gave me the opportunity and long term support to write this dissertation. He gave me the freedom to work on my idea and plans, and gave great suggestions when I need support. There are many difficult time during this research, but there is always great support provided from him, from technical discussion to mental encouragement. I am also grateful to my committee members Dr. Larry Jacobson, Dr. Steve Severtson and Dr. Gerald Shurson. They took time from their tight schedule to make critical remarks and helpful suggestions, as well as their confidence on me and my work. Thanks are also dedicated to several experts, particularly to Dr. Chuck Clanton and David Schmidt for their valuable inputs and inspiring discussions. Besides valuable discussions, Dr. Brian Hetchler and Dr. Neslihan Akdeniz provide a great amount of valuable samples for experiments. I am also grateful to Dr. Michael Sadowsky that provided great help in microbial sequencing analysis, to Dr. LeeAnn Higgins and Dr. Susan Viper that provided great help in proteomic analysis. My colleagues at Bioproducts and Biosystems Engineering played an important role towards the successful completion of this dissertation.
    [Show full text]
  • The Subway Microbiome: Seasonal Dynamics and Direct Comparison Of
    Gohli et al. Microbiome (2019) 7:160 https://doi.org/10.1186/s40168-019-0772-9 RESEARCH Open Access The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities Jostein Gohli1* , Kari Oline Bøifot1,2, Line Victoria Moen1, Paulina Pastuszek3, Gunnar Skogan1, Klas I. Udekwu4 and Marius Dybwad1,2 Abstract Background: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. Methods: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. Results: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer.
    [Show full text]
  • The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
    FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities.
    [Show full text]
  • Imperialibacter Roseus Gen. Nov., Sp. Nov., a Novel Bacterium of the Family Flammeovirgaceae Isolated from Permian Groundwater
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4136–4140 DOI 10.1099/ijs.0.052662-0 Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater Hui Wang,1,2,3 Junde Li,1 Tianling Zheng,2 Russell T. Hill3 and Xiaoke Hu1 Correspondence 1Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China Xiaoke Hu 2Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, [email protected] Xiamen University, Xiamen 361005, China 3Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1v6c/C16 : 1v7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycoli- pids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T (5CICC 10659T5KCTC 32399T). Bacteria affiliated with the family Flammeovirgaceae of the staining was performed according to the method described phylum Bacteroidetes are widely distributed in various by Gerhardt et al.
    [Show full text]
  • Bacterial Community Change Through Drinking Water Treatment Processes
    Int. J. Environ. Sci. Technol. (2015) 12:1867–1874 DOI 10.1007/s13762-014-0540-0 ORIGINAL PAPER Bacterial community change through drinking water treatment processes X. Liao • C. Chen • Z. Wang • C.-H. Chang • X. Zhang • S. Xie Received: 28 August 2012 / Revised: 30 September 2013 / Accepted: 5 March 2014 / Published online: 18 March 2014 Ó Islamic Azad University (IAU) 2014 Abstract The microbiological quality of drinking water Introduction has aroused increasing attention due to potential public health risks. Knowledge of the bacterial ecology in the The microbiological quality of drinking water has aroused effluents of drinking water treatment units will be of practical increasing attention due to potential public health risks. importance. However, the bacterial community in the The conventional treatment process, composed of coagu- effluents of drinking water filters remains poorly understood. lation–flocculation, sedimentation, rapid sand filtration, The changes of the density of viable heterotrophic bacteria and disinfection, is still widely used by drinking water and bacterial populations through a pilot-scale drinking producers to remove turbidity and pathogens. The con- water treatment process were investigated using heterotro- ventional treatment process is not efficient in removal of phic plate counts and clone library analysis, respectively. biodegradable dissolved organic carbon (BDOC) that is The pilot-scale treatment process was composed of preozo- mainly responsible for the microbial regrowth in drinking nation, rapid mixing, flocculation, sedimentation, sand fil- water distribution systems (DWDS). Biological activated tration postozonation, and biological activated carbon carbon (BAC) filtration can perform well in reduction of (BAC) filtration. The results indicated that heterotrophic organic pollutants after the attachment of the indigenous plate counts decreased dramatically through the drinking microbiota attached to the porous surface of granular water treatment processes.
    [Show full text]
  • 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.
    [Show full text]
  • Antibus Revised Thesis 11-16 For
    Molecular and Cultivation-based Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica A thesis submitted to Kent State University in partial fulfillment of the requirements for the degree of Master of Science by Doug Antibus December, 2009 Thesis written by Doug Antibus B.S., Kent State University, 2007 M.S., Kent State University, 2009 Approved by Dr. Christopher B. Blackwood Advisor Dr. James L. Blank Chair, Department of Biological Sciences Dr. Timothy Moerland Dean, College of Arts and Sciences iii TABLE OF CONTENTS LIST OF TABLES………………………………………………………………………..iv LIST OF FIGURES ……………………………………………………………………...vi ACKNOWLEDGEMENTS…………………………………………………………......viii CHAPTER I: General Introduction……………………………………………………….1 CHAPTER II: Molecular Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica: A Legacy of Genetic Diversity Introduction……………………………………………………………....22 Results and Discussion……………………………………………..……27 Methods…………………………………………………………………..51 Literature Cited…………………………………………………………..59 CHAPTER III: Recovery of Viable Bacteria from Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica Introduction………………………………………………..……………..78 Methods…………………………………………………………………..80 Results……………………………………………………………...…….88 Discussion…………………………………………………………...….106 Literature Cited………………………………………………………....109 CHAPTER IV: General Discussion…………………………………………………….120 iii LIST OF TABLES Chapter II: Molecular Characterization of Ancient Algal Mats from the McMurdo Dry Valleys, Antarctica: A Legacy of Genetic Diversity
    [Show full text]
  • OMICS Driven Microbial Ecology Hunt for a Core Microbiome
    Environmental Microbiology, Volume 14, Issue 1, January 2012 VOLUME 14 NUMBER 1 JANUARY 2012 www.env-micro.com ISSN 1462-2912 Contents environmental microbiology Correspondence 140 Microbial rhodopsins on leaf surfaces of terrestrial plants N. Atamna-Ismaeel, O. M. Finkel, F. Glaser, I. Sharon, R. Schneider, 1 Omics for understanding microbial functional dynamics A. F. Post, J. L. Spudich, C. von Mering, J. A. Vorholt, D. Iluz, O. Béjà & J. K. Jansson, J. D. Neufeld, M. A. Moran & J. A. Gilbert S. Belkin 147 Photoautotrophic symbiont and geography are major factors affecting highly Minireviews structured and diverse bacterial communities in the lichen microbiome 4 Beyond the Venn diagram: the hunt for a core microbiome B. P. Hodkinson, N. R. Gottel, C. W. Schadt & F. Lutzoni A. Shade & J. Handelsman 162 Phosphate transporters in marine phytoplankton and their viruses: environmental cross-domain commonalities in viral-host gene exchanges 13 Targeted metagenomics: a high-resolution metagenomics approach for specifi c A. Monier, R. M. Welsh, C. Gentemann, G. Weinstock, E. Sodergren, gene clusters in complex microbial communities E. V. Armbrust, J. A. Eisen & A. Z. Worden H. Suenaga 177 Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria Research articles A. M. Garcia Costas, Z. Liu, L. P. Tomsho, S. C. Schuster, D. M. Ward & 23 Microbial metatranscriptomics in a permanent marine oxygen minimum zone D. A. Bryant F. J. Stewart, O. Ulloa & E. F. DeLong 191 Transcriptional responses of surface water marine microbial assemblages 41 Genome content of uncultivated marine Roseobacters in the surface ocean to deep-sea water amendment microbiology H.
    [Show full text]
  • Inter-Domain Horizontal Gene Transfer of Nickel-Binding Superoxide Dismutase 2 Kevin M
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426412; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Inter-domain Horizontal Gene Transfer of Nickel-binding Superoxide Dismutase 2 Kevin M. Sutherland1,*, Lewis M. Ward1, Chloé-Rose Colombero1, David T. Johnston1 3 4 1Department of Earth and Planetary Science, Harvard University, Cambridge, MA 02138 5 *Correspondence to KMS: [email protected] 6 7 Abstract 8 The ability of aerobic microorganisms to regulate internal and external concentrations of the 9 reactive oxygen species (ROS) superoxide directly influences the health and viability of cells. 10 Superoxide dismutases (SODs) are the primary regulatory enzymes that are used by 11 microorganisms to degrade superoxide. SOD is not one, but three separate, non-homologous 12 enzymes that perform the same function. Thus, the evolutionary history of genes encoding for 13 different SOD enzymes is one of convergent evolution, which reflects environmental selection 14 brought about by an oxygenated atmosphere, changes in metal availability, and opportunistic 15 horizontal gene transfer (HGT). In this study we examine the phylogenetic history of the protein 16 sequence encoding for the nickel-binding metalloform of the SOD enzyme (SodN). A comparison 17 of organismal and SodN protein phylogenetic trees reveals several instances of HGT, including 18 multiple inter-domain transfers of the sodN gene from the bacterial domain to the archaeal domain.
    [Show full text]
  • Phylogeny of the Family Halomonadaceae Based on 23S and 16S Rdna Sequence Analyses
    International Journal of Systematic and Evolutionary Microbiology (2002), 52, 241–249 Printed in Great Britain Phylogeny of the family Halomonadaceae based on 23S and 16S rDNA sequence analyses 1 Lehrstuhl fu$ r David R. Arahal,1,2 Wolfgang Ludwig,1 Karl H. Schleifer1 Mikrobiologie, Technische 2 Universita$ tMu$ nchen, and Antonio Ventosa 85350 Freising, Germany 2 Departamento de Author for correspondence: Antonio Ventosa. Tel: j34 954556765. Fax: j34 954628162. Microbiologı!ay e-mail: ventosa!us.es Parasitologı!a, Facultad de Farmacia, Universidad de Sevilla, 41012 Seville, Spain In this study, we have evaluated the phylogenetic status of the family Halomonadaceae, which consists of the genera Halomonas, Chromohalobacter and Zymobacter, by comparative 23S and 16S rDNA analyses. The genus Halomonas illustrates very well a situation that occurs often in bacterial taxonomy. The use of phylogenetic tools has permitted the grouping of several genera and species believed to be unrelated according to conventional taxonomic techniques. In addition, the number of species of the genus Halomonas has increased as a consequence of new descriptions, particularly during the last few years, but their features are too heterogeneous to justify their placement in the same genus and, therefore, a re-evaluation seems necessary. We have determined the complete sequences (about 2900 bases) of the 23S rDNA of 18 species of the genera Halomonas and Chromohalobacter and resequenced the complete 16S rDNA sequences of seven species of Halomonas. The results of our analysis show that two phylogenetic groups (respectively containing five and seven species) can be distinguished within the genus Halomonas. Six other species cannot be assigned to either of the above-mentioned groups.
    [Show full text]
  • Life in the Cold Biosphere: the Ecology of Psychrophile
    Life in the cold biosphere: The ecology of psychrophile communities, genomes, and genes Jeff Shovlowsky Bowman A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2014 Reading Committee: Jody W. Deming, Chair John A. Baross Virginia E. Armbrust Program Authorized to Offer Degree: School of Oceanography i © Copyright 2014 Jeff Shovlowsky Bowman ii Statement of Work This thesis includes previously published and submitted work (Chapters 2−4, Appendix 1). The concept for Chapter 3 and Appendix 1 came from a proposal by JWD to NSF PLR (0908724). The remaining chapters and appendices were conceived and designed by JSB. JSB performed the analysis and writing for all chapters with guidance and editing from JWD and co- authors as listed in the citation for each chapter (see individual chapters). iii Acknowledgements First and foremost I would like to thank Jody Deming for her patience and guidance through the many ups and downs of this dissertation, and all the opportunities for fieldwork and collaboration. The members of my committee, Drs. John Baross, Ginger Armbrust, Bob Morris, Seelye Martin, Julian Sachs, and Dale Winebrenner provided valuable additional guidance. The fieldwork described in Chapters 2, 3, and 4, and Appendices 1 and 2 would not have been possible without the help of dedicated guides and support staff. In particular I would like to thank Nok Asker and Lewis Brower for giving me a sample of their vast knowledge of sea ice and the polar environment, and the crew of the icebreaker Oden for a safe and fascinating voyage to the North Pole.
    [Show full text]