DOCSLIB.ORG

The Influences of Microbial Diversity on Carbonate Geochemistry Across a Transition from Fresh to Saline Water in the Edwards Aquifer, Texas

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Influences of Microbial Diversity on Carbonate Geochemistry Across a Transition from Fresh to Saline Water in the Edwards Aquifer, Texas Louisiana State University LSU Digital Commons LSU Master's Theses Graduate School 2010 The nflueI nces of Microbial Diversity on Carbonate Geochemistry Across a Transition from Fresh to Saline Water in the Edwards Aquifer, Texas Cassie Jo Gray Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_theses Part of the Earth Sciences Commons Recommended Citation Gray, Cassie Jo, "The nflueI nces of Microbial Diversity on Carbonate Geochemistry Across a Transition from Fresh to Saline Water in the Edwards Aquifer, Texas" (2010). LSU Master's Theses. 4268. https://digitalcommons.lsu.edu/gradschool_theses/4268 This Thesis is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Master's Theses by an authorized graduate school editor of LSU Digital Commons. For more information, please contact [email protected]. THE INFLUENCES OF MICROBIAL DIVERSITY ON CARBONATE GEOCHEMISTRY ACROSS A TRANSITION FROM FRESH TO SALINE WATER IN THE EDWARDS AQUIFER, TEXAS A Thesis Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Master of Science in The Department of Geology and Geophysics by Cassie Jo Gray B.S., Indiana State University, 2008 May 2010 ACKNOWLEDGEMENTS First and foremost I would like to extend my utmost gratitude to my advisor, Dr. Annette Engel, for sharing her passion and knowledge of geomicrobiology, and for her patience and tough love throughout this learning and growing experience. Thanks also to my other committee members, Dr. Carol Wicks and Dr. Huiming Bao, for their insightful input into my research. Thanks to Gary Schindel and the Edwards Aquifer Authority for their permission to access the study wells. I would like to acknowledge Brendan Headd and Scott Engel for their tremendous assistance in the field, especially for help stringing the microcosms and tying knots. Thanks also to the laboratory assistants, Brendan Donnelly and Skylar White, for all their time spent on specs, gels, and mini-preps. Personal thanks are due to Issaku Kohl for his time spent helping with the IC, and to Dr. Xiaogang Xie for his assistance with the SEM. Many thanks to those family members and friends who have supported me throughout the years and encouraged me to pursue my education, even if hundreds of miles away. Thanks to the geologists at Indiana State University for providing all the opportunities that allowed me to get to where I am, and those at Louisiana State University for this wonderful two-year experience. Finally, I am forever indebted to Tara Ewer, a true friend whom encouraged me to be something in life and reach for something better before I realized I needed it. Don’t let your…sparkle fade away. Funding for this research was provided by the Louisiana Board of Regents, American Association of Petroleum Geologists (AAPG) Edward B. Picou Grant, Karst Waters Institute (KWI) William L. Wilson Scholarship, and the LSU Department of Geology and Geophysics. ii TABLE OF CONTENTS ACKNOWLEDGEMENTS…………………………………………………………….……...ii LIST OF TABLES……………………………………………………………………….….…v LIST OF FIGURES…………………………………………………………………………...vi ABSTRACT…………………………………………………………………………………viii CHAPTER 1 INTRODUCTION……………………………………………….………….…….1 The Edwards Aquifer………………………………………….………….……1 Karstification Processes…………………….………………………………….6 Subsurface Microorganisms………………….…………………………….…..9 Research Objectives…………………………….…………………………….11 Study Area………………………………………….…………………………12 Significance of Research……………………………….……………………..12 Thesis Organization……………………………………….,…………………14 2 MICROBIOLOGY ACROSS THE TRANSITION FROM FRESH TO SALINE WATER IN THE EDWARDS AQUIFER………………….…….16 Introduction…………………………………………………………….……..16 Materials and Methods………………………………………………….…….16 Results………………………………………………………………………...18 Discussion…………………………………………………………………….25 3 GEOCHEMISTRY ACROSS THE TRANSITION FROM FRESH TO SALINE WATER IN THE EDWARDS AQUIFER………………………...37 Introduction…………………………………………………………………...37 Materials and Methods………………………………………………………..37 Results………………………………………………………………………...39 Discussion……………………………………………………………........….43 4 GEOCHEMICAL AND MICROBIAL INFLUENCES ON EDWARDS AQUIFER CARBONATES………………………………………..50 Introduction…………………………………………………………………...50 Materials and Methods………………………………………………………..50 Results………………………………………………………………………...53 Discussion…………………………………………………………………….59 5 SUMMARY AND FUTURE DIRECTIONS……………………………………69 REFERENCES……………………………………………………………………………….74 iii APPENDIX A OPERATIONAL TAXONOMIC UNITS (OTUs)……………………………...85 B SEM IMAGES………………………………………………………………….92 VITA………………………………………………………………………………………...118 iv LIST OF TABLES 2.1 Distribution of major class or phylum-level taxonomy of 16S rRNA gene bacterial sequences from clones retrieved from transect wells in New Braunfels, Texas ………………………………………………………………19 3.1 Geochemical results from the first sampling of Comal Springs and transect study wells, New Braunfels, Texas...................................................................40 3.2 Geochemical results from the second sampling of Comal Springs and transect study wells, New Braunfels, Texas…………………………….......................41 4.1 Well depths, diameters, screened intervals, and microcosm suspension depths….……51 4.2 Average mass loss from calcite and dolomite microcosms and associated significance ……………………………………………………………54 v LIST OF FIGURES 1.1 The Edwards Aquifer in central Texas………………………………………………..…2 1.2 Generalized stratigraphic column of the Edwards Aquifer and associated units in the San Marcos Platform………………………………………………….…….3 1.3 (A) Map of the New Braunfels transect study wells and (B) the corresponding geologic cross section…..……………………………………………………………...13 2.1 Distribution of major classes and phyla in transect wells, in order of increasing salinity (from left to right)………………………………………………….20 2.2 Rarefaction curves for all 16S rRNA gene sequences retrieved from Edwards Aquifer study wells…………………………………………………………..21 2.3 Trees relating environmental microbial samples using hierarchical clustering analysis in UniFrac………………………………………………………….24 2.4 Principal Coordinate Analysis (PCA) obtained from UniFrac………………………...26 3.1 Piper diagrams showing the hydrochemical facies of transect study wells from (A) the first sampling and (B) second sampling…………………………………42 3.2 Chemical parameters…………………………………………………………………...44 - 3.3 Concentrations of HCO3 versus (A) [Ca], (B) [Ca+Mg], and (C) [Ca+Mg]-[SO4]…………………………………………………………………….45 3.4 Saturation indices (log IAP/Ksp) of (A) calcite, (B) dolomite, and (C) gypsum versus sulfate concentrations……………………………………………..46 3.5 Speciation of (A) [Ca] and (B) [Mg] in transect wells based on complexes modeled in PHREEQC…………………………………………………….47 4.1 Mass lost for reactive and sterile (A) calcite microcosms and (B) dolomite microcosms……...….……………………………………………….55 4.2 Average mass loss (mg) versus calcite saturation index values for each well…………56 4.3 Surficial features of mineral control chips……………………………………………..56 4.4 Cellular morphology and behavior…………………………………………………….58 4.5 Cell-surface associations………………………………………………………………58 vi 4.6 Dissolution features…………………………………………………………………….60 4.7 Secondary precipitates on experimental mineral surfaces……………………………..61 4.8 EDAX spectra for (A) iron sulfide mineral and (B) silica-bearing mineral…………...62 4.9 Number of putative cells observed on reactive calcite and dolomite chips per examined chip area (0.0625 mm2)…………………………………62 4.10 Average amount of mass loss (mg) versus the total average number of cells per microcosm………………………………………………………...63 vii ABSTRACT Microbially-mediated karstification through the production of metabolic byproducts has been well-documented in cave environments, but less is known about deep karstic settings. This research aimed to distinguish between microbial and geochemical influences on carbonate dissolution in the Edwards Aquifer, a prolific karst aquifer in central Texas, specifically from a transect of six wells across a transition from fresh to saline water in New Braunfels. For the first time, a portion of the aquifer’s bacterial diversity was examined from molecular 16S rRNA gene sequence analyses, which revealed that Alphaproteobacteria, Gammaproteobacteria, and Betaproteobacteria dominated the aquifer, with rare Bacteroidetes, Nitrospirae, and Firmicutes taxonomic groups. Local geochemical conditions for each well (H2S levels, TDS, and depth) accounted for ~83% of the genetic variability among wells. In general, putative chemoorganotrophic microorganisms were prevalent in all wells, but chemolithoautotrophs associated with sulfur oxidation were prevalent only in sulfidic wells. Sterile and reactive in situ microcosms containing experimental calcite and dolomite fragments were deployed in the transect wells for ~1 month. Most of the mineral fragments in the microcosms (~64%) had statistically significant mass loss, although fluids were saturated with respect to calcite (SI= +0.6 to +0.14) and dolomite (SI= +0.18 to +0.43). There was greater mass loss in reactive microcosms having higher surface cell densities on colonized mineral surfaces. These results suggest that microbial colonization establishes geochemical disequilibrium between mineral surfaces and bulk aquifer fluids, regardless of the metabolic potential of the microorganisms. Microbially-mediated carbonate dissolution is possible in both fresh and
Load more

Recommended publications
  • Microbial Diversity and Impact on Carbonate Geochemistry Across a Changing Geochemical Gradient in a Karst Aquifer
    The ISME Journal (2013) 7, 325–337 & 2013 International Society for Microbial Ecology All rights reserved 1751-7362/13 www.nature.com/ismej ORIGINAL ARTICLE Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer Cassie J Gray1,2 and Annette S Engel1,3 1Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA, USA; 2CH2M Hill, Baton Rouge, LA, USA and 3Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased.
    [Show full text]
  • Synthesis of Patterned Media by Self-Assembly of Magnetic
    Applied Sciences http://wjst.wu.ac.th https://doi.org/10.48048/wjst.2021.7306 Reductive Dechlorination of 1,2-dichloroethane to Ethylene by Anaerobic Enrichment Culture Containing Vulcanibacillus spp. Utumporn NGIVPROM1, Nipa MILINTAWISAMAI1,* and 2 Alissara REUNGSANG 1Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand 2Department of Biotechnology, Faculty of Technology, Khon Kaen University, Khon Kaen 40002, Thailand (*Corresponding author’s e-mail: [email protected]) Received: 10 August 2019, Revised: 26 March 2020, Accepted: 27 April 2020 Abstract Bioremediation has been widely used for clean-up of 1,2-dichloroethane (DCA) at contaminated sites. Only a small number of specific anaerobes, halorespiring bacteria (HRB), have been reported to degrade DCA. The goals of this research were the screening and isolation of HRB with capable dechlorination of DCA. HRB were screened and isolated from 7 enrichment cultures (ES1-ES7), from DCA-contaminated soils, on bicarbonate-buffered basal salts medium containing 10 mM acetate and 250 µM DCA under anaerobic conditions and analyzed by gas chromatography. The results showed that the mixed cultures of ES3 and ES5 could reductively dechlorinate DCA to ethylene via a direct reductive dihaloelimination pathway. In particular, ES5 showed rapid transformation of 250 µM DCA to ethylene within 6 days at 30 °C. Specific microbial populations of Vulcanibacillus spp., elucidated by polymerase chain reaction-denaturing gradient gel electrophoresis, were found only in ES3 and ES5, which was related to reductive dihaloelimination activities on DCA. A 16S rRNA gene analysis of isolate es5d8 from mixed culture ES5 revealed 2 strains of Vulcanibacillus spp.
    [Show full text]
  • Thermolongibacillus Cihan Et Al
    Genus Firmicutes/Bacilli/Bacillales/Bacillaceae/ Thermolongibacillus Cihan et al. (2014)VP .......................................................................................................................................................................................... Arzu Coleri Cihan, Department of Biology, Faculty of Science, Ankara University, Ankara, Turkey Kivanc Bilecen and Cumhur Cokmus, Department of Molecular Biology & Genetics, Faculty of Agriculture & Natural Sciences, Konya Food & Agriculture University, Konya, Turkey Ther.mo.lon.gi.ba.cil’lus. Gr. adj. thermos hot; L. adj. Type species: Thermolongibacillus altinsuensis E265T, longus long; L. dim. n. bacillus small rod; N.L. masc. n. DSM 24979T, NCIMB 14850T Cihan et al. (2014)VP. .................................................................................. Thermolongibacillus long thermophilic rod. Thermolongibacillus is a genus in the phylum Fir- Gram-positive, motile rods, occurring singly, in pairs, or micutes,classBacilli, order Bacillales, and the family in long straight or slightly curved chains. Moderate alka- Bacillaceae. There are two species in the genus Thermo- lophile, growing in a pH range of 5.0–11.0; thermophile, longibacillus, T. altinsuensis and T. kozakliensis, isolated growing in a temperature range of 40–70∘C; halophile, from sediment and soil samples in different ther- tolerating up to 5.0% (w/v) NaCl. Catalase-weakly positive, mal hot springs, respectively. Members of this genus chemoorganotroph, grow aerobically, but not under anaer- are thermophilic (40–70∘C), halophilic (0–5.0% obic conditions. Young cells are 0.6–1.1 μm in width and NaCl), alkalophilic (pH 5.0–11.0), endospore form- 3.0–8.0 μm in length; cells in stationary and death phases ing, Gram-positive, aerobic, motile, straight rods. are 0.6–1.2 μm in width and 9.0–35.0 μm in length.
    [Show full text]
  • Reorganising the Order Bacillales Through Phylogenomics
    Systematic and Applied Microbiology 42 (2019) 178–189 Contents lists available at ScienceDirect Systematic and Applied Microbiology jou rnal homepage: http://www.elsevier.com/locate/syapm Reorganising the order Bacillales through phylogenomics a,∗ b c Pieter De Maayer , Habibu Aliyu , Don A. Cowan a School of Molecular & Cell Biology, Faculty of Science, University of the Witwatersrand, South Africa b Technical Biology, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Germany c Centre for Microbial Ecology and Genomics, University of Pretoria, South Africa a r t i c l e i n f o a b s t r a c t Article history: Bacterial classification at higher taxonomic ranks such as the order and family levels is currently reliant Received 7 August 2018 on phylogenetic analysis of 16S rRNA and the presence of shared phenotypic characteristics. However, Received in revised form these may not be reflective of the true genotypic and phenotypic relationships of taxa. This is evident in 21 September 2018 the order Bacillales, members of which are defined as aerobic, spore-forming and rod-shaped bacteria. Accepted 18 October 2018 However, some taxa are anaerobic, asporogenic and coccoid. 16S rRNA gene phylogeny is also unable to elucidate the taxonomic positions of several families incertae sedis within this order. Whole genome- Keywords: based phylogenetic approaches may provide a more accurate means to resolve higher taxonomic levels. A Bacillales Lactobacillales suite of phylogenomic approaches were applied to re-evaluate the taxonomy of 80 representative taxa of Bacillaceae eight families (and six family incertae sedis taxa) within the order Bacillales.
    [Show full text]
  • (ST). the Table
    1 SUPPLEMENTAL MATERIALS Growth Media Modern Condition Seawater Freshwater Light T°C Atmosphere AMCONA medium BG11 medium – Synechococcus – – Synechocystis – [C] in PAL [C] in the [C] in the Gas Nutrients Modern Nutrients (ppm) Medium Medium Ocean NaNO3 CO2 ~407.8 Na2SO4 25.0mM 29mM Nitrogen 50 Standard (17.65mM) μmol (ST) NaNO NaNO 20°C O ~209’460 Nitrogen 3 3 MgSO 0.304mM photon 2 (549µM) (13.7µM) 4 /m2s FeCl3 6.56µM 2nM Ammonium 0.6g/L ZnSO 254nM 0.5nM ferric stock N ~780’790 4 2 citrate (10ml NaMoO 105nM 105nM 4 green stock/1L) 2 Table S 1 Description of the experimental condition defined as Standard Condition (ST). The table 3 shows the concentrations of fundamental elements, such as C, N, S, and Fe used for the AMCONA 4 seawater medium (Fanesi et al., 2014) and BG11 freshwater medium (Stanier et al., 1971) flushing air 5 with using air pump (KEDSUM-310 8W pump; Xiolan, China) Growth Media Possible Proterozoic T° Condition Modified Seawater Modified Freshwater Light Atmosphere AMCONA medium BG11 medium C – Synechococcus – – Synechocystis – [C] in [C] in PPr Nutrients PPr Nutrients Medium Gas ppm Medium NH Cl Na SO 3mM Nitrogen 4 3 2 4 (0.0035mM) CO 2 10’000ppm (20%) NH Cl Possible (~ 2’450% Nitrogen 4 3 MgSO 0.035mM 50 with 20ml/ (100µM) 4 Proterozoic PAL) μmol 20° min (PPr) photon C O2 20’000ppm /m2s (in Air) (~ 10% FeCl 200nM with 5ml/ 3 PAL) Ammonium 0.6g/L stock min ferric 10ml N ZnSO 0.0nM 2 4 citrate green stock/1L (100%) Base gas with NaMoO4 10.5nM 200ml/min 6 Table S 2 Description of the experimental condition defined as Possible Proterozoic Condition (PPr).
    [Show full text]
  • Bacterial Diversity and Production of Sulfide in Microcosms Containing
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Stellenbosch University SUNScholar Repository Received: 11 April 2018 Bacterial diversity and Revised: 22 June 2018 Accepted: production of sulfide in 1 August 2018 Cite as: microcosms containing Alexander A. Grigoryan, Daphne R. Jalique, Prabhakara Medihala, uncompacted bentonites Simcha Stroes-Gascoyne, Gideon M. Wolfaardt, Jennifer McKelvie, Darren R. Korber. Bacterial diversity and production of Alexander A. Grigoryan a, Daphne R. Jalique a, Prabhakara Medihala a, sulfide in microcosms containing uncompacted Simcha Stroes-Gascoyne a, Gideon M. Wolfaardt b,c, Jennifer McKelvie d, bentonites. a,∗ Heliyon 4 (2018) e00722. Darren R. Korber doi: 10.1016/j.heliyon.2018. a Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada e00722 b Department of Chemistry and Biology, Ryerson University, Toronto, Ontario, Canada c Department of Microbiology, University of Stellenbosch, Cape Town, South Africa d Nuclear Waste Management Organization, Toronto, Canada ∗ Corresponding author. E-mail address: [email protected] (D.R. Korber). Abstract Aims: This study examined the diversity and sulfide-producing activity of microorganisms in microcosms containing commercial clay products (e.g.,MX- 80, Canaprill and National Standard) similar to materials which are currently considered for use in the design specifications for deep geologic repositories (DGR) for spent nuclear fuel. Methods and results: In anoxic microcosms incubated for minimum of 60 days with 10 g l-1 NaCl, sulfide production varied with temperature, electron donor and À À bentonite type. Maximum specific sulfide production rates of 0.189 d 1, 0.549 d 1 and 0.157 dÀ1 occurred in lactate-fed MX-80, Canaprill and National Standard microcosms, respectively.
    [Show full text]
  • Thermally Enhanced Bioremediation of Petroleum Hydrocarbons
    THESIS THERMALLY ENHANCED BIOREMEDIATION OF LNAPL Submitted by Natalie Rae Zeman Department of Civil and Environmental Engineering In partial fulfillment of the requirements For the Degree of Master of Science Colorado State University Fort Collins, Colorado Spring 2013 Master’s Committee: Advisor: Susan K. De Long Co-Advisor: Thomas Sale Mary Stromberger ABSTRACT THERMALLY ENHANCED BIODEGRADATION OF LNAPL Inadvertent releases of petroleum liquids into the environment have led to widespread soil and groundwater contamination. Petroleum liquids, referred to as Light Non-Aqueous Phase Liquid (LNAPL), pose a threat to the environment and human health. The purpose of the research described herein was to evaluate thermally enhanced bioremediation as a sustainable remediation technology for rapid cleanup of LNAPL zones. Thermally enhanced LNAPL attenuation was investigated via a thermal microcosm study that considered six different temperatures: 4°C, 9°C, 22°C, 30°C, 35°C, and 40°C. Microcosms were run for a period of 188 days using soil, water and LNAPL from a decommissioned refinery in Evansville, WY. The soil microcosms simulated anaerobic subsurface conditions where sulfate reduction and methanogenesis were the pathways for biodegradation. To determine the optimal temperature range for thermal stimulation and provide guidance for design of field-scale application, both contaminant degradation and soil microbiology were monitored. CH4 and CO2 generation occurred in microcosms at 22°C, 30°C, 35°C and 40°C but was not observed at 4°C and 9°C. The total volume of biogas generated after 188 days of incubation was 19 times higher in microcosms at 22°C and 30°C compared to the microcosms at 35°C.
    [Show full text]
  • Ecology of Bacillaceae
    Ecology of Bacillaceae INES MANDIC-MULEC,1 POLONCA STEFANIC,1 and JAN DIRK VAN ELSAS2 1University of Ljubljana, Biotechnical Faculty, Department of Food Science and Technology, Vecna pot 111, 1000 Ljubljana, Slovenia; 2Department of Microbial Ecology, Centre for Ecological and Evolutionary Studies, University of Groningen, Linneausborg, Nijenborgh 7, 9747AG Groningen, Netherlands ABSTRACT Members of the family Bacillaceae are among the been found in soil, sediment, and air, as well as in un- most robust bacteria on Earth, which is mainly due to their ability conventional environments such as clean rooms in the to form resistant endospores. This trait is believed to be the Kennedy Space Center, a vaccine-producing company, key factor determining the ecology of these bacteria. and even human blood (1–3). Moreover, members of However, they also perform fundamental roles in soil ecology (i.e., the cycling of organic matter) and in plant health and the Bacillaceae have been detected in freshwater and growth stimulation (e.g., via suppression of plant pathogens and marine ecosystems, in activated sludge, in human and phosphate solubilization). In this review, we describe the high animal systems, and in various foods (including fer- functional and genetic diversity that is found within the mented foods), but recently also in extreme environ- Bacillaceae (a family of low-G+C% Gram-positive spore-forming ments such as hot solid and liquid systems (compost bacteria), their roles in ecology and in applied sciences related and hot springs, respectively), salt lakes, and salterns (4– to agriculture. We then pose questions with respect to their 6). Thus, thermophilic genera of the family Bacillaceae ecological behavior, zooming in on the intricate social behavior that is becoming increasingly well characterized for some dominate the high-temperature stages of composting members of Bacillaceae.
    [Show full text]
  • Microbial Ecology of the Dark Ocean Above, At, and Below the Seafloor
    MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, June 2011, p. 361–422 Vol. 75, No. 2 1092-2172/11/$12.00 doi:10.1128/MMBR.00039-10 Copyright © 2011, American Society for Microbiology. All Rights Reserved. Microbial Ecology of the Dark Ocean above, at, and below the Seafloor† Beth N. Orcutt,1,2 Jason B. Sylvan,2 Nina J. Knab,2 and Katrina J. Edwards2,3* Center for Geomicrobiology, Aarhus University, 8000 Aarhus, Denmark1; Marine Environmental Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 900892; and Department of Earth Sciences, University of Southern California, Los Angeles, California 900893 INTRODUCTION .......................................................................................................................................................362 DARK OCEAN HABITATS—AN OVERVIEW ......................................................................................................362 METABOLIC REACTIONS IN THE DARK OCEAN ..........................................................................................367 Electron Sources .....................................................................................................................................................369 Organic matter....................................................................................................................................................369 Hydrogen..............................................................................................................................................................369
    [Show full text]
  • Diversity and Evolutionary Dynamics of Spore Coat Proteins on Spore-Forming Species of Bacillales
    UNIVERSIDAD DE INVESTIGACIÓN DE TECNOLOGÍA EXPERIMENTAL YACHAY Escuela de Ciencias Biológicas e Ingeniería TÍTULO: Diversity and Evolutionary Dynamics of Spore Coat Proteins on Spore-forming Species of Bacillales Trabajo de integración curricular presentado como requisito para la obtención del título de Biólogo Autor: Henrry Patricio Secaira Morocho Tutor: Ph.D. José Antonio Castillo Urcuquí, marzo 2020 Agradecimiento Me gustaría agradecer a mi mentor de tesis, el Dr. José Antionio Castillo, por su inestimable apoyo y orientación durante esta investigación y redacción de tesis. Además, me gustaría agradecer a mis profesores en Yachay Tech por todas las clases, lecciones y consejos durante mi carrera. Estoy profundamente agradecido con mis amigos, compañeros de clase y familia, especialmente con mi madre y su apoyo constante durante estos años. Henrry Patricio Secaira Morocho Resumen Entre los miembros del orden de Bacillales, hay varias especies capaces de formar una estructura llamada endospora. Las endosporas permiten que las bacterias sobrevivan bajo condiciones de crecimiento desfavorables. Además, las endosporas promueven la germinación cuando las condiciones ambientales son favorables. Varias proteínas necesarias para el ensamblaje de la capa, la síntesis de la corteza y la germinación se conocen colectivamente como proteínas de la capa de esporas. Este proyecto tiene como objetivo determinar la diversidad y los procesos evolutivos de los genes de la capa de esporas en varias especies de Bacillales formadoras de esporas. Los métodos de BLASTp, Clustering y KEGG Orthology se han utilizado para determinar la existencia y diversidad de genes de la capa en ciento 141 genomas de especies formadoras de esporas. Además, las fuerzas de selección que actúan sobre los genes de la capa de esporas se han estimado utilizando los métodos Tajima’s D, dN / dS, MEME y BUSTED.
    [Show full text]
  • Literature Review
    NOVEL ANAEROBIC THERMOPHILIC BACTERIA; INTRASPECIES HETEROGENEITY AND BIOGEOGRAPHY OF THERMOANAEROBACTER ISOLATES FROM THE KAMCHATKA PENINSULA, RUSSIAN FAR EAST by ISAAC DAVID WAGNER (Under the Direction of Juergen Wiegel) ABSTRACT Thermophilic anaerobic prokaryotes are of interest from basic and applied scientific perspectives. Novel anaerobic thermophilic taxa are herein described are Caldanaerovirga acetigignens gen. nov., sp. nov.; and Thermoanaerobacter uzonensis sp. nov. Novel taxa descriptions co-authored were: Thermosediminibacter oceani gen. nov., sp. nov and Thermosediminibacter litoriperuensis sp. nov; Caldicoprobacter oshimai gen. nov., sp. nov. More than 220 anaerobic thermophilic isolates were obtained from samples collected from 11 geothermal springs within the Uzon Caldera, Geyser Valley, and Mutnovsky Volcano regions of the Kamchatka Peninsula, Russian Far East. Most strains were phylogenetically related to Thermoanaerobacter uzonensis JW/IW010T, while some were phylogenetically related to Thermoanaerobacter siderophilus SR4T. Eight protein coding genes, gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB, were amplified and sequenced from these isolates to describe and elucidate the intraspecies heterogeneity, α- and β-diversity patterns, and the spatial and physicochemical correlations to the observed genetic variation. All protein coding genes within the T. uzonensis isolates were found to be polymorphic, although the type (i.e., synonymous/ nonsynonymous substitutions) and quantity of the variation differed between gene sequence sets. The most applicable species concept for T. uzonensis must consider metapopulation/ subpopulation dynamics and acknowledge that physiological characteristics (e.g., sporulation) likely influences the flux of genetic information between subpopulations. Spatial variation in the distribution of T. uzonensis isolates was observed. Evaluation of T. uzonensis α-diversity revealed a range of genetic variation within a single geothermal spring.
    [Show full text]
  • Phylogenetic Relationships Between Bacillus Species and Related Genera Inferred from 16S Rdna Sequences
    Brazilian Journal of Microbiology (2009) 40: 505-521 ISSN 1517-8382 PHYLOGENETIC RELATIONSHIPS BETWEEN BACILLUS SPECIES AND RELATED GENERA INFERRED FROM 16S RDNA SEQUENCES Wei Wang; Mi Sun * Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China Submitted: July 14, 2008; Returned to authors for corrections: October 06, 2008; Approved: May 04, 2009. ABSTRACT Neighbor-joining, maximum-parsimony, minimum-evolution, maximum-likelihood and Bayesian trees constructed based on 16S rDNA sequences of 181 type strains of Bacillus species and related taxa manifested nine phylogenetic groups. The phylogenetic analysis showed that Bacillus was not a monophyletic group. B. subtilis was in Group 1. Group 4, 6 and 8 respectively consisted of thermophiles, halophilic or halotolerant bacilli and alkaliphilic bacilli. Group 2, 4 and 8 consisting of Bacillus species and related genera demonstrated that the current taxonomic system did not agree well with the 16S rDNA evolutionary tree s. The position of Caryophanaceae and Planococcaceae in Group 2 suggested that they might be transferred into Bacillaceae, and the heterogeneity of Group 2 implied that some Bacillus species in it might belong to several new genera. Group 9 was mainly comprised of the genera (excluding Bacillus ) of Bacillaceae, so some Bacillus species in Group 9: B. salarius , B. qingdaonensis and B. thermcloacae might not belong to Bacillus . Four Bacillus species, B. schlegelii , B. tusciae , B. edaphicus and B. mucilaginosus were clearly placed outside the nine groups. Keywords: Bacillus phylogeny; Bayesian inference; Evolutionary trees; 16S rDNA INTRODUCTION established before 2000. Bacillus has long been regarded as a In recent years, numerous new species of genus Bacillus phylogenetic heterogeneous group (1).
    [Show full text]