DOCSLIB.ORG

P^I"~ SUBMITTED to the DEPARTMENT of L \IL.~D EARTH, ATMOSPHERIC and PLANETARY SCIENCES in PARTIAL FULFILLMENT of the REQUIREMENTS for the DEGREE OF

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
P^I Molecular studies of the sources and significance of archaeal lipids in the oceans by Sara Ann Lincoln MIA IsJ:S' iNSTITUTE B.S. Geosciences B.S. Geological Oceanography L T University of Rhode Island (2006) P^I"~ SUBMITTED TO THE DEPARTMENT OF L \IL.~d EARTH, ATMOSPHERIC AND PLANETARY SCIENCES IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN GEOCHEMISTRY SEPTEMBER 2013 © Massachusetts Institute of Technology All rights reserved. Author:................. Department of Earth, Atmospheric and Planetary Sciences Certified by:........................... Roger E. Summons Professor of Geobiology Department of Earth, Atmospheric and Planetary Sciences Thesis supervisor ..................#......r....... ........................................................ Edward F. DeLong Morton and Claire Goulder amily P fessor in Environmental Systems Depar e Civil and Environmental Engineering 7) Thesis supervisor Accepted by: ...................................... Robert van der Hilst Schlumberger Professor of Earth Sciences Head, Department of Earth, Atmospheric and Planetary Sciences THIS PAGE INTENTIONALLY LEFT BLANK Molecular studies of the sources and significance of archaeal lipids in the oceans by Sara Ann Lincoln Submitted to the Department of Earth, Atmospheric and Planetary Sciences on July 29, 2013 in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Geochemistry ABSTRACT Marine archaea are ubiquitous and abundant in the modem oceans and have a geologic record extending >100 million years. However, factors influencing the populations of the major clades - chemolithoautotrophic Marine Group I Thaumarchaeota (MG-I) and heterotrophic Marine Group II Euryarchaeota (MG-II) - and their membrane lipid signatures are not well understood. Here, I paired techniques of organic geochemistry and molecular biology to explore the sources and significance of archaeal tetraether lipids in the marine water column. Using metagenomics, 16S rDNA pyrosequencing, QPCR and mass spectrometric analyses, I found that uncultivated MG-IL Euryarchaeota synthesize glycerol dialkyl glycerol tetraether (GDGT) lipids - including crenarchaeol, previously thought limited to autotrophic Thaumarchaeota. This finding has important implications for paleoenvironmental proxies reliant upon GDGTs. To investigate the effects of organic matter and bicarbonate + ammonia amendments on archaeal tetraether lipids and microbial community composition, I conducted large scale microcosm experiments. Experimental conditions did not promote the overall growth of archaea, but several changes in tetraether lipid abundance and relative ring distribution suggest that future incubation labeling studies using whole seawater may be valuable in probing the metabolism of individual archaeal clades in mixed populations. A rapid decrease in GDGT concentrations was observed within the first 44 h of the experiment, suggesting that the residence time of these compounds in the open ocean may be short. Changes in functional gene representation and microbial community composition over the course of the experiment provide potential insight into mechanisms of copiotrophy and the identity of bacteria that may degrade GDGTs. Finally, I present the results of a study of the sources and patterns of bacterial and archaeal GDGTs detected in the Lost City Hydrothermal Vent Field. Branched GDGTs, generally considered markers of terrestrial input to marine sediments, were detected in carbonate chimneys of this alkaline site near the mid-Atlantic Ridge. A relatively 3 uncommon H-shaped GDGT was also present, and appears to be a marker of hydrothermal archaeal input rather than a mesophilic euryarchaeotal signal. Taken together, the work presented in this thesis emphasizes the necessity of understanding the biological underpinnings of archaeal lipids in the environment, increasingly used as biomarkers in microbial ecology and paleoenvironmental reconstruction. Thesis Supervisors: Roger E. Summons Professor of Geobiology Department of Earth, Atmospheric and Planetary Sciences Edward F. DeLong Morton and Claire Goulder Family Professor in Environmental Systems Department of Civil and Environmental Engineering 4 Acknowledgments I have immense gratitude for the many people who have supported the work represented in this thesis. Most of all, I am indebted to my advisors, Roger Summons and Ed DeLong, for their generosity, patience and good humor throughout this journey. I also appreciate the enthusiastic support and insight that my committee members Mick Follows and Edward Boyle have shown for my thesis research. When I first started talking to Roger about potential graduate studies he had the wonderful idea of introducing me to Ed. Though I had little background in organic geochemistry, they seemed inexplicably excited to take me on as a student and to let me work in a second area - marine microbiology - in which I had even less experience. Their leap of faith has proved very rewarding for me, and I'll be forever grateful that they took it. It would be an honor to work with one scientist of their caliber, but it has been my good fortune to work with two. I am deeply inspired by their passionate dedication to answering fundamental questions about how microbial life drives and shapes our planet. Trying to bridge disciplines can be, at turns, exhilarating, frustrating, and terrifying - like most experiences that help people grow. Roger and Ed have patiently helped me through a few iterations of each of those stages while guiding my thesis research and fostering my development as a scientist. I have also benefitted from time spent with the outstanding groups of researchers that both Ed and Roger have drawn together in their labs. Learning the once foreign languages of mass spectrometry and metagenomics would have been impossible - and far less fun - without them. In the DeLong lab I was especially lucky to work with John Eppley, Tracy Mincer, Jay McCarren, Frank Stewart, Jess Bryant, Julie Maresca and Chon Martinez, all of whom graciously answered the sometimes stupid questions of a newcomer to the field without disdain, and were always generous with their time. Similarly, Alex Bradley, Gordon Love, Amy Kelly, Lindsay Hays and Laura Sherman quickly and cheerfully eased the steepness of the organic geochemistry learning curve for me in my early days in the Summons lab. Florence Schubotz has been an invaluable source of LCMS wisdom in the last few years. At MIT I have been given the opportunity and freedom to explore the exciting interface between geochemistry and environmental microbiology. When at a loss to explain what I do in just one word, as hyphens and prefixes (bio-geo-eco-oceano- meta-chem-microbio ... ologist?) run through my head, I recall what Maria Zuber told my entering class during orientation: "Nature doesn't care what you call yourself; just follow the interesting questions." That spirit infuses groundbreaking 5 interdisciplinary research across EAPS and, especially, in the E25 geobiology community. It was wonderful to witness it grow and flourish, especially with the arrival of Tanja Bosak and Shuhei Ono. I have appreciated both the discussions I have had with them and their lab members and the ready access they granted me to their labs. Many times their centrifuge/plate reader/flowhood/balance/lysozyme etc. saved the day! Rick Kayser in the Boyle lab has also been a great resource. EAPS also has great administrative staff, without whom I would have been lost. Many thanks to Vicki McKenna, Carol Sprague, Jacqui Taylor and Allison Provaire in the Green Building. In E25 Alla Skorokhod, Mary Eliff and Lesly Adkins- Shellie guided me through paperwork and shipping emergencies, and offered me candy, sympathy and advice on many occasions. I spent a lot of time in my first few years in Woods Hole and am grateful to have had the opportunity to work closely with Joan Bernhard, Dan McCorkle and Helena Filipsson there. Helen Fredricks, Melissa Soule and Sean Sylva were cheerful and invaluable fonts of technical wisdom in Fye. I miss the meals, beers and rants shared with WHOI friends, especially James Saenz, Laura Hmelo, Dave Griffith, Maya Bhatia, Eoghan Reeves, and Fern Gibbons. Thanks especially to Fern and Maya for letting me stay with you so often! Oceanography is inherently collaborative. I participated in six research cruises during my Ph.D. and none of the work presented here would have been possible without the expertise, support and friendship of the many people with whom I have gone to sea. I was lucky to work with DeLong labmates Jess Bryant, Liz Ottesen, Frank Stewart, Jay McCarren, and Adrian Sharma in the field, but am also indebted to a large cast of collaborators, support scientists and crew, especially: Stefan Sievert, Osvaldo Ulloa, Gadiel Alarcon, Alejandra Prieto-Davo, Sam Wilson, Julie Robidart, Tara Clemente, Blake Watkins, and Cesar Hormazabal Fritz. My time at C-MORE Hale in Manoa was productive, and I appreciate the access that David Karl and the other scientists gave me to their labs and resources. More generally, I have benefitted greatly from participation in the Center for Microbial Oceanography: Research and Education (C-MORE), and it has been great to see how science operates at that scale. I am thankful to both C-MORE and the Agouron Institute for funding my thesis research through grants to Ed and Roger. Other funding that made this work possible came from the Linden Earth System Fellowship, the Martin Family
Load more

Recommended publications
  • The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
    SUPPLEMENTARY INFORMATIONARTICLES https://doi.org/10.1038/s41559-020-1221-7 In the format provided by the authors and unedited. The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Linzhou Li1,2,13, Sibo Wang1,3,13, Hongli Wang1,4, Sunil Kumar Sahu 1, Birger Marin 5, Haoyuan Li1, Yan Xu1,4, Hongping Liang1,4, Zhen Li 6, Shifeng Cheng1, Tanja Reder5, Zehra Çebi5, Sebastian Wittek5, Morten Petersen3, Barbara Melkonian5,7, Hongli Du8, Huanming Yang1, Jian Wang1, Gane Ka-Shu Wong 1,9, Xun Xu 1,10, Xin Liu 1, Yves Van de Peer 6,11,12 ✉ , Michael Melkonian5,7 ✉ and Huan Liu 1,3 ✉ 1State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China. 2Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. 3Department of Biology, University of Copenhagen, Copenhagen, Denmark. 4BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China. 5Institute for Plant Sciences, Department of Biological Sciences, University of Cologne, Cologne, Germany. 6Department of Plant Biotechnology and Bioinformatics (Ghent University) and Center for Plant Systems Biology, Ghent, Belgium. 7Central Collection of Algal Cultures, Faculty of Biology, University of Duisburg-Essen, Essen, Germany. 8School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China. 9Department of Biological Sciences and Department of Medicine, University of Alberta, Edmonton, Alberta, Canada. 10Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, China. 11College of Horticulture, Nanjing Agricultural University, Nanjing, China. 12Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
    [Show full text]
  • Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics
    Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics Jonathan L. Klassen* Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada Abstract Background: Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Methodology/Principal Findings: Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family
    [Show full text]
  • Biogeography and Habitat Modelling of High-Alpine Bacteria
    ARTICLE Received 7 Apr 2010 | Accepted 15 Jul 2010 | Published 10 Aug 2010 DOI: 10.1038/ncomms1055 Biogeography and habitat modelling of high-alpine bacteria Andrew J. King1 , Kristen R. Freeman1 , Katherine F. McCormick1 , Ryan C. Lynch1 , Catherine Lozupone2 , 3 , Rob Knight 2 & Steven K. Schmidt1 Soil microorganisms dominate terrestrial biogeochemical cycles; however, we know very little about their spatial distribution and how changes in the distributions of specifi c groups of microbes translate into landscape and global patterns of biogeochemical processes. In this paper, we use a nested sampling scheme at scales ranging from 2 to 2,000 m to show that bacteria have signifi cant spatial autocorrelation in community composition up to a distance of 240 m, and that this pattern is driven by changes in the relative abundance of specifi c bacterial clades across the landscape. Analysis of clade habitat distribution models and spatial co-correlation maps identifi ed soil pH, plant abundance and snow depth as major variables structuring bacterial communities across this landscape, and revealed an unexpected and important oligotrophic niche for the Rhodospirillales in soil. Furthermore, our global analysis of high-elevation soils from the Andes, Rockies, Himalayas and Alaskan range shows that habitat distribution models for bacteria have a strong predictive power across the entire globe. 1 Department of Ecology and Evolutionary Biology, University of Colorado , Boulder , Colorado 80309 , USA . 2 Department of Chemistry and Biochemistry, University of Colorado , Boulder , Colorado 80309 , USA . 3 Washington University School of Medicine , St Louis , Missouri 63108 , USA . Correspondence and requests for materials should be addressed to S.K.S.
    [Show full text]
  • View and Research Objectives
    University of Alberta Carotenoid diversity in novel Hymenobacter strains isolated from Victoria Upper Glacier, Antarctica, and implications for the evolution of microbial carotenoid biosynthesis by Jonathan Lee Klassen A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Microbiology and Cell Biotechnology Department of Biological Sciences ©Jonathan Lee Klassen Fall 2009 Edmonton, Alberta Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission. Examining Committee Dr. Julia Foght, Department of Biological Science Dr. Phillip Fedorak, Department of Biological Sciences Dr. Brenda Leskiw, Department of Biological Sciences Dr. David Bressler, Department of Agriculture, Food and Nutritional Science Dr. Jeffrey Lawrence, Department of Biological Sciences, University of Pittsburgh Abstract Many diverse microbes have been detected in or isolated from glaciers, including novel taxa exhibiting previously unrecognized physiological properties with significant biotechnological potential. Of 29 unique phylotypes isolated from Victoria Upper Glacier, Antarctica (VUG), 12 were related to the poorly studied bacterial genus Hymenobacter including several only distantly related to previously described taxa.
    [Show full text]
  • 1 Anoxygenic Phototrophic Chloroflexota Member Uses a Type
    Anoxygenic phototrophic Chloroflexota member uses a Type I reaction center Supplementary Materials J. M. Tsuji, N. A. Shaw, S. Nagashima, J. J. Venkiteswaran, S. L. Schiff, S. Hanada, M. Tank, J. D. Neufeld Correspondence to: [email protected]; [email protected]; [email protected] This PDF file includes: Materials and Methods Supplementary Text, Sections S1 to S4 Figs. S1 to S9 Tables S1 to S3 1 Materials and Methods Enrichment cultivation of ‘Ca. Chx. allophototropha’ To culture novel anoxygenic phototrophs, we sampled Lake 227, a seasonally anoxic and ferruginous Boreal Shield lake at the International Institute for Sustainable Development Experimental Lakes Area (IISD-ELA; near Kenora, Canada). Lake 227 develops up to ~100 μM concentrations of dissolved ferrous iron in its anoxic water column (31), and anoxia is more pronounced than expected naturally due to the long-term experimental eutrophication of the lake (32). The lake’s physico-chemistry has been described in detail previously (31). We collected water from the illuminated portion of the upper anoxic zone of Lake 227 in September 2017, at 3.875 and 5 m depth, and transported this water anoxically and chilled in 120 mL glass serum bottles, sealed with black rubber stoppers (Geo-Microbial Technology Company; Ochelata, Oklahoma, USA), to the laboratory. Water was supplemented with 2% v/v of a freshwater medium containing 8 mM ferrous chloride (33) and was distributed anoxically into 120 mL glass serum bottles, also sealed with black rubber stoppers (Geo-Microbial Technology Company), that had a headspace of dinitrogen gas at 1.5 atm final pressure.
    [Show full text]
  • Microbial Diversity of Thermophiles with Biomass Deconstruction Potential in a Foliage-­Rich Hot Spring
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Universiti Teknologi Malaysia Institutional Repository Received: 9 December 2017 | Revised: 29 January 2018 | Accepted: 12 February 2018 DOI: 10.1002/mbo3.615 ORIGINAL RESEARCH Microbial diversity of thermophiles with biomass deconstruction potential in a foliage- rich hot spring Li Sin Lee1 | Kian Mau Goh2 | Chia Sing Chan2 | Geok Yuan Annie Tan1 | Wai-Fong Yin1 | Chun Shiong Chong2 | Kok-Gan Chan1,3 1ISB (Genetics), Faculty of Science, University of Malaysia, Kuala Abstract Lumpur, Malaysia The ability of thermophilic microorganisms and their enzymes to decompose biomass 2 Faculty of Biosciences and Medical have attracted attention due to their quick reaction time, thermostability, and de- Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia creased risk of contamination. Exploitation of efficient thermostable glycoside hy- 3Jiangsu University, Zhenjiang, China drolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for Correspondence Kok-Gan Chan, International Genome biomass degradation at high temperatures have not yet been thoroughly studied. We Centre, Jiangsu University, Zhenjiang, China. examined a Malaysian Y- shaped Sungai Klah hot spring located within a wooded area. Email: [email protected] The fallen foliage that formed a thick layer of biomass bed under the heated water of Funding information the Y- shaped Sungai Klah hot spring was an ideal environment for the discovery and Postgraduate Research Fund grant, Grant/ Award Number: PG124-2016A; University analysis of microbial biomass decay communities. We sequenced the hypervariable of Malaya, Grant/Award Number: GA001- regions of bacterial and archaeal 16S rRNA genes using total community DNA ex- 2016 and GA002-2016; Universiti Teknologi Malaysia GUP, Grant/Award Number: tracted from the hot spring.
    [Show full text]
  • Izumi Et Al. Thermotomaculum Hydrothermale Gen. Nov., Sp. Nov., A
    Izumi et al. 1 Thermotomaculum hydrothermale gen. nov., sp. nov., a novel heterotrophic 2 thermophile within the phylum Acidobacteria from a deep-sea hydrothermal vent 3 chimney in the Southern Okinawa Trough 4 5 Hiroshi Izumi1, Takuro Nunoura2, Masayuki Miyazaki2, Sayaka Mino1, Tomohiro Toki3, 6 Ken Takai2, Yoshihiko Sako4, Tomoo Sawabe1 and Satoshi Nakagawa1,2* 7 8 1Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 9 Minato-cho, Hakodate 041-8611, Japan. 10 2Subsurface Geobiology Advanced Research (SUGAR) Project, Institute of 11 Biogeosciences, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 12 2-15 Natsushima-cho, Yokosuka 237-0061, Japan. 13 3Faculty of Science, University of the Ryukyus, 1 Senbaru, Nishihara 903-0213, Japan. 14 4Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate 15 School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Sakyo-ku, 16 Kyoto 606–8502, Japan. 17 18 Submitted to Extremophiles 19 20 21 Correspondence: 22 Satoshi Nakagawa 23 Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 24 Minato-cho, Hakodate 041-8611, Japan. 25 Phone: +81-138-40-5570; Fax: +81-138-40-5570; 26 Email: [email protected] 27 Izumi et al. 27 Abstract 28 A novel heterotrophic, thermophilic bacterium, designated strain AC55T, was isolated 29 from a deep-sea hydrothermal vent chimney at the Hatoma Knoll in the Okinawa 30 Trough, Japan. Cells of strain AC55T were non-motile, long rods (2.0-6.8 !m long and 31 0.3-0.6 !m wide). The strain was an obligatory anaerobic heterotroph capable of 32 fermentative growth on complex proteinaceous substances.
    [Show full text]
  • Classification: Biological Sciences-Microbiology N-Methyl-Bacillithiol, a New Metabolite Discovered in the Chlorobiaceae, Indica
    bioRxiv preprint doi: https://doi.org/10.1101/173617; this version posted August 8, 2017. 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 Classification: Biological Sciences-Microbiology 2 N-methyl-bacillithiol, a new metabolite discovered in the Chlorobiaceae, indicates that 3 bacillithiol and derivatives are widely phylogenetically distributed. 4 Jennifer Hirasa,1, Sunil V. Sharmab, Vidhyavathi Ramana,2, Ryan A. J. Tinsonb , Miriam Arbachb, 5 Dominic F. Rodriguesb, Javiera Norambuenac, Chris J. Hamiltonb, and Thomas E. Hansona,d,3 6 7 a-School of Marine Science and Policy and Delaware Biotechnology Institute, University of 8 Delaware, Newark, DE 19711, USA 9 b-School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, 10 UK 11 c-Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 12 08901, USA 13 d-Department of Biological Sciences, University of Delaware, Newark, DE 19711, USA 14 15 1-Current Address: Corning Incorporated, Corning, NY 14830, USA; E-mail: 16 [email protected] 17 2-Current Address: Noble Research Institute, 2510 Sam Noble Parkway 18 Ardmore, OK 73401, USA; E-mail: [email protected] 19 3-Corresponding Author: 282 DBI, 15 Innovation Way, Newark, DE 19711 U. S. A.; Telephone: 20 1-302-831-3404; E-mail: [email protected] 21 22 Keywords: low molecular weight thiol, sulfur oxidation, Chlorobiaceae, Chlorobaculum tepidum 23 bioRxiv preprint doi: https://doi.org/10.1101/173617; this version posted August 8, 2017.
    [Show full text]
  • The Influence of Temperature and Ph on Bacterial Community Composition of Microbial Mats in Hot Springs from Costa Rica
    Received: 28 March 2019 | Revised: 1 May 2019 | Accepted: 20 May 2019 DOI: 10.1002/mbo3.893 ORIGINAL ARTICLE The influence of temperature and pH on bacterial community composition of microbial mats in hot springs from Costa Rica Lorena Uribe‐Lorío1 | Laura Brenes‐Guillén1 | Walter Hernández‐Ascencio1 | Raúl Mora‐Amador2 | Gino González2 | Carlos J. Ramírez‐Umaña2 | Beatriz Díez3 | Carlos Pedrós‐Alió4 1Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Abstract Rica, Ciudad Universitaria Rodrigo Facio, San We used the 16S rRNA gene pyrosequencing approach to investigate the microbial José, Costa Rica diversity and community composition in several Costa Rican hot springs alongside the 2Escuela Centroamericana de Geología, Universidad de Costa Rica, San José, Costa latitudinal axis of the country, with a range of temperatures (37–63°C), pH (6–7.5) and Rica other geochemical conditions. A principal component analyses of the physicochemi- 3Departamento de Microbiología y Genética, Pontificia Universidad Católica de cal parameters showed the samples were separated into three geochemically dis- Chile, Santiago, Chile tinct habitats associated with the location (North, Central, and South). Cyanobacteria 4 Departamento de Biología de Sistemas, and Chloroflexi comprised 93% of the classified community, the former being the Centro Nacional de Biotecnología, CSIC, Madrid, Spain most abundant phylum in all samples except for Rocas Calientes 1, (63°C, pH 6), where Chloroflexi and Deinococcus‐Thermus represented 84% of the OTUs. Chloroflexi Correspondence Lorena Uribe-Lorío, CIBCM, University of were more abundant as temperature increased. Proteobacteria, Bacteriodetes and Costa Rica, Ciudad Universitaria Rodrigo Deinococcus‐Thermus comprised 5% of the OTUs represented.
    [Show full text]
  • GSP PI Meeting 2012 Abstracts
    DOE/SC-0142 2012 Genomic Science Awardee Meeting X Bethesda, Maryland February 26-29, 2012 [Revised: March 1, 2012] Prepared for the Prepared by U.S. Department of Energy Biological and Environmental Research Information System Office of Science Oak Ridge National Laboratory Office of Biological and Environmental Research Oak Ridge, TN 37830 Germantown, MD 20874-1290 Managed by UT-Battelle, LLC For the U.S. Department of Energy http://genomicscience.energy.gov Under contract DE-AC05-00OR22725 Systems Biology Strategies and Technologies for Understanding Microbes, Plants, and Communities particle associated bacteria have smaller genomes that are enriched for transporters, depleted in regulatory components and encode a proteome with relatively less nitrogen content. Influence141 of Habitat on Diversity and Overall patterns of diversity and richness are significantly Evolution of Surface Ocean Microbes higher for bacterial communities collected on larger pore- size filters. Intra- and inter-relationships between sites based Andrew E. Allen1* ([email protected]), Lisa Z. Allen,1,2 on diversity measures suggest that larger size class or parti- Jonathan H. Badger,1 Christopher L. Dupont,1 John P. cle-associated bacterial communities and those that inhabit McCrow,1 Ian T. Paulsen,4 Mathangi Thiagarajan,5 Doug more productive waters are significantly more variable. 5 6 1 B. Rusch, Jed Fuhrman, Kenneth H. Nealson, Shibu This work was funded by the Office of Biological and Environmental Yooseph, and J. Craig Venter1 Research in the DOE Office of Science (DE-FC02-02ER63453) 1Microbial and Environmental Genomics, J. Craig Venter Institute, San Diego, Calif.; 2Scripps Institution of Oceanography, University of California-San Diego, La Jolla; 3Division of Biological Sciences, University of California-San Diego, La Jolla; 4Macquarie University, Influence142 of Nutrients and Currents on the Sydney, NSW, Australia; 5Informatics, J.
    [Show full text]
  • The Origin of Phototrophy Reveals the Importance of Pri
    Preprints (www.preprints.org) | NOT PEER-REVIEWED | Posted: 1 December 2020 1 The Origin of Phototrophy Reveals the Importance of Pri- 2 ority Effects for Evolutionary Innovation 1 1 3 Anthony Burnetti ,William C. Ratcliff 1 4 Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, USA. 5 The history of life on Earth has been shaped by a series of major evolutionary innovations. 6 While some of these innovations occur repeatedly, some of the most important evolutionary 7 innovations (e.g., the origin of life itself, eukaryotes, or the genetic code) are evolutionary 8 singularities, arising just once in the history of life. This historical fact has often been in- 9 terpreted to mean that singularities are particularly difficult, low-probability evolutionary 10 events, thus making the long-term course of life on Earth highly contingent on their chance 11 appearances. Alternatively, singularities may arise from evolutionary priority effects, where 12 first-movers suppress subsequent independent origins. Here, we disentangle these hypothe- 13 ses by examining a distinctive innovation: phototrophy. The ability to use light to generate 14 metabolic energy evolved twice, preserving information about the origins of rare, transfor- 15 mative innovations that is lost when examining singular innovations. We show that the two 16 forms of phototrophy occupy opposite ends of several key trade-offs: efficiency of light cap- 17 ture vs. return on investment in protein infrastructure, dependence on limiting nutrients vs. 18 metabolic versatility, and complexity vs. simplicity. Our results suggest that the ‘dual singu- 19 larity’ of phototrophy exists due to evolutionary interactions between nascent phototrophs, 20 with phototrophic niche space too large for a first mover to fill all niches and fully suppress fu- 1 © 2020 by the author(s).
    [Show full text]
  • Supplemental Online Information
    Supplementary Online Information 1. Photographs of Octopus and Mushroom Spring. See Supplementary Figure 1. 2. Reference genomes used in this study. See Supplementary Table 1. 3. Detailed Materials and Methods. DNA extraction. The uppermost 1 mm-thick green layer from each microbial mat core was physically removed using a razor blade and DNA was extracted using either enzymatic or mechanical bead- beating lysis protocols. The two methods resulted in different abundances of community members (see below) (Bhaya et al., 2007; Klatt et al. 2007). For enzymatic lysis and DNA extraction, frozen mat samples were thawed, resuspended in 100 μl Medium DH (Castenholz's Medium D with 5 mM HEPES, pH = 8.2; Castenholz, 1988), and homogenized with a sterile mini-pestle in 2 ml screw cap tubes. Medium DH (900 μl) was added to the homogenized sample, then lysozyme (ICN Biomedicals, Irvine, CA) was added to ~200 μg ml-1, and the mixture was incubated for 45 min at 37 °C. Sodium docecyl sulfate (110 μl of 10% (w/v) solution) and Proteinase K (Qiagen, Valencia, CA) (to 200 μg ml- 1) were added, and the mixture was incubated on a shaker for 50 min at 50 °C. Microscopic analysis suggested efficient lysis of Synechococcus spp. cells, but a possible bias against some filamentous community members (Supplementary Figure 2). Phase contrast micrographs were obtained with a Zeiss Axioskop 2 Plus (Carl Zeiss Inc., Thornwood NY, USA) using a Plan NeoFluar magnification objective, and autofluorescence was detected using a HBO 100 mercury arc lamp as excitation source and a standard epifluorescence filter set (Leistungselektronik Jena GmbH, Jena, Germany).
    [Show full text]