DOCSLIB.ORG

Investigation of Whole Genome Phylogeny and Genetic Analysis of Cyclic Lipopeptide Biosynthesis Genes in Antagonistic Strains of Bacillus

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Investigation of Whole Genome Phylogeny and Genetic Analysis of Cyclic Lipopeptide Biosynthesis Genes in Antagonistic Strains of Bacillus Investigation of Whole Genome Phylogeny and Genetic Analysis of Cyclic Lipopeptide Biosynthesis Genes in Antagonistic Strains of Bacillus by Emma Groulx A thesis submitted to the Faculty of Graduate and Postdoctoral Affairs in partial fulfillment of the requirements for the degree of Master of Science in Biology To Carleton University Ottawa, Ontario © 2017 Emma Groulx Acknowledgements I would first like to thank Dr. Myron Smith and Dr. Tyler J. Avis for being my co- supervisors and providing me with support and guidance throughout my graduate studies. I greatly appreciate the opportunity to continue my education and gain more research experience. Special thanks go out to Dr. Alex Wong and Dr. Nicolas Rodrigue for their guidance and assistance in data analysis and interpretation of results. I would like to thank Prabhjeet Basra for assistance with sequencing protocols and assessment of sequencing data. I would also like to thank Thomas Bujaki for technical assistance and for emotional support over the past two years. Lastly, I would like to thank all my family and friends who supported me throughout my graduate years. ii Abstract Disease suppressive composts and soil were found to contain bacteria belonging to the genus Bacillus that were antagonistic to plant pathogens. It is known that these species of bacteria produce antimicrobial compounds called cyclic lipopeptides. These bacteria produce three families of lipopeptides (surfactins, fengycins and iturins), however not all the isolates produce all of the lipopeptides. The genetics behind the production of these lipopeptides is not as well known. The objective of this study was to confirm the identity of the bacterial isolates using whole genome phylogeny and identify the Bacillus cyclic lipopeptide biosynthesis genes. Fifteen isolates of Bacillus subtilis, two isolates of B. megaterium and one isolate each of B. badius and Brevibacillus borstelensis were sequenced using an Illumina Miseq system and phylogenetic analysis was performed using protein-coding alignments. The cyclic lipopeptide genes were identified using nucleotide and protein blasts. It was shown that the identity of the bacterial isolates resembled the identity assigned using 16S rRNA sequences, with the exception of B. subtilis isolates CU12 and M9-3. It was also determined that the B. subtilis isolates and the B. borstelensis isolate possessed the gene operons for the cyclic lipopeptides whereas B. megaterium and B. badius isolates did not. Key Words: Bacillus, biocontrol, Brevibacillus, cyclic lipopeptides, phylogenetics. iii Table of contents Acknowledgements ......................................................................................................................... ii Abstract .......................................................................................................................................... iii Table of contents ............................................................................................................................ iv List of tables ................................................................................................................................... vi List of figures ............................................................................................................................... viii Chapter 1: Introduction ................................................................................................................... 1 1.1. Food security .................................................................................................................... 1 1.2. Fungicides ........................................................................................................................ 1 1.3. Biological control ............................................................................................................. 2 1.4. Composts as sources of microbial control agents ............................................................ 3 1.5. Bacillus and related bacteria ............................................................................................ 3 1.5.1. Bacillus .......................................................................................................................... 3 1.5.2. Brevibacillus .................................................................................................................. 4 1.6. Cyclic lipopeptides ........................................................................................................... 5 1.6.1. Surfactin......................................................................................................................... 6 1.6.2. Iturin .............................................................................................................................. 6 1.6.3. Fengycin ........................................................................................................................ 7 1.6.4. Nonribosomal peptide synthetases of Bacillus cyclic lipopeptides ............................... 8 1.7. Species identification ....................................................................................................... 9 1.8. Objectives and hypotheses ............................................................................................. 11 1.8.1. Objectives .................................................................................................................... 11 1.8.2. Hypotheses................................................................................................................... 11 Chapter 2: Materials and methods ................................................................................................ 12 2.1. Bacteria material ................................................................................................................ 12 2.2. Whole-genome sequencing and assembly.......................................................................... 13 2.3. Multiple sequence alignment and phylogenetic analysis ................................................... 14 2.4. Identification of CLP genes................................................................................................ 15 iv Chapter 3: Results ......................................................................................................................... 17 3.1. General assembly statistics................................................................................................. 17 3.2. Phylogenetic analysis ......................................................................................................... 18 3.2.1. Brevibacillus phylogenetic relationships ..................................................................... 18 3.2.2. Bacillus phylogenetic relationships ............................................................................. 20 3.3. BLAST analysis of cyclic lipopeptide biosynthesis genes ................................................ 23 Chapter 4: Discussion ................................................................................................................... 27 4.1. Evaluation of phylogenetic relationships of Bacillus and Brevibacillus isolates ............... 27 4.2. Evaluation of CLP biosynthesis genes ............................................................................... 31 4.3. Future work ........................................................................................................................ 40 Chapter 5: Conclusion................................................................................................................... 41 Chapter 6: References ................................................................................................................... 42 Appendixes ................................................................................................................................... 55 v List of tables Table 1: Identity and source of bacteria isolates from compost material ................................ 12 Table 2: Reference genomes in Bacillus phylogenetic tree, obtained from NCBI ................. 14 Table 3: Reference genomes in Brevibacillus phylogenetic tree, obtained from NCBI ......... 15 Table 4: Statistics for the Bacillus and Brevibacillus genome assemblies ............................. 17 Table 5: Summary of nucleotide BLAST hits of CLP genes in bacterial isolates .................. 25 Table 6: Summary of nucleotide and protein BLAST results for CLP genes in bacterial isolates ……………………………………………………………………………………... 26 Table 7: Cyclic lipopeptides produced and presence of CLP genes by bacterial isolates ...... 35 Table A1: Nucleotide and protein BLAST results of CLP genes for Bacillus subtilis isolate B9-1 …................................................................................................................................ 56 Table A2: Nucleotide and protein BLAST results of CLP genes for Bacillus subtilis isolate B9-5 .................................................................................................................................... 57 Table A3: Nucleotide and protein BLAST results of CLP genes for Bacillus subtilis isolate B9-7 .................................................................................................................................... 58 Table A4: Nucleotide and protein BLAST results of CLP genes for Bacillus subtilis isolate B9-8 ...................................................................................................................................
Load more

Recommended publications
  • Biochemical Characterization and 16S Rdna Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Available online at www.sciencedirect.com ScienceDirect IERI Procedia 5 ( 2013 ) 258 – 264 2013 International Conference on Agricultural and Natural Resources Engineering Biochemical Characterization and 16S rDNA Sequencing of Lipolytic Thermophiles from Selayang Hot Spring, Malaysia a a a a M.J., Norashirene , H., Umi Sarah , M.H, Siti Khairiyah and S., Nurdiana aFaculty of Applied Sciences, Universiti Teknologi MARA, 40450 Shah Alam, Selangor, Malaysia. Abstract Thermophiles are well known as organisms that can withstand extreme temperature. Thermoenzymes from thermophiles have numerous potential for biotechnological applications due to their integral stability to tolerate extreme pH and elevated temperature. Because of the industrial importance of lipases, there is ongoing interest in the isolation of new bacterial strain producing lipases. Six isolates of lipases producing thermophiles namely K7S1T53D5, K7S1T53D6, K7S1T53D11, K7S1T53D12, K7S2T51D14 and K7S2T51D19 were isolated from the Selayang Hot Spring, Malaysia. The sampling site is neutral in pH with a highest recorded temperature of 53°C. For the screening and isolation of lipolytic thermopiles, selective medium containing Tween 80 was used. Thermostability and the ability to degrade the substrate even at higher temperature was proved and determined by incubation of the positive isolates at temperature 53°C. Colonies with circular borders, convex in elevation with an entire margin and opaque were obtained. 16S rDNA gene amplification and sequence analysis were done for bacterial identification. The isolate of K7S1T53D6 was derived of genus Bacillus that is the spore forming type, rod shaped, aerobic, with the ability to degrade lipid.
    [Show full text]
  • Proposal for Two New Genera, Brevibacillus Gen. Nov. and Aneurinibacillus Gen
    INTERNATIONAL JOURNALOF SYSTEMATIC BACTERIOLOGY,OCt. 1996, p. 939-946 Vol. 46, No. 4 0020-7713/96/$04.00+0 Copyright 0 1996, International Union of Microbiological Societies Proposal for Two New Genera, Brevibacillus gen. nov. and Aneurinibacillus gen. nov. OSAMU SHIDA,'" HIROAKI TAKAGI,' KIYOSHI KADOWAKI,l AND KAZUO KOMAGATA' Research Laboratory, Higeta Shoyu Co., Ltd., Choshi, Chiba 288, and Department of Agricultural Chemistry, Faculty of Agriculture, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156, Japan 16s rRNA gene sequences of the type strains of 11 species belonging to the Bacillus brevis and Bacillus aneurinolyticus groups were determined. On the basis of the results of gene sequence analyses, these species were separated into two clusters. The B. brevis cluster included 10 species, namely, Bacillus brevis, Bacillus agri, Bacillus centrosporus, Bacillus choshinensis, Bacillus parabrevis, Bacillus reuszeri, Bacillus formosus, Bacillus borstelensis, Bacillus luterosporus, and Bacillus thermoruber. Bacillus aneurinolyticus and Bacillus migulunus belonged to the B. aneurinolyticus cluster. Moreover, the two clusters were phylogenetically distinct from other Bacillus, Amphibacillus, Sporoluctobacillus, Paenibacillus, and Alicyclobacillus species. On the basis of our data, we propose reclassification of the B. brevis cluster as Brevibacillus gen. nov. and reclassification of the B. aneurinolyticus cluster as Aneurinibacillus gen. nov. By using 16s rRNA gene sequence alignments, two specific PCR amplification primers were designed for differentiating the two new genera from each other and from other aerobic, endospore-formingorganisms. The aerobic, rod-shaped, endospore-forming genus Bacillus is a systematically diverse taxon (5).The members of this genus exhibit a wide range of DNA base compositions, and the major amino acid compositions of the cell walls of these organisms 8.
    [Show full text]
  • Paenibacillaceae Cover
    The Family Paenibacillaceae Strain Catalog and Reference • BGSC • Daniel R. Zeigler, Director The Family Paenibacillaceae Bacillus Genetic Stock Center Catalog of Strains Part 5 Daniel R. Zeigler, Ph.D. BGSC Director © 2013 Daniel R. Zeigler Bacillus Genetic Stock Center 484 West Twelfth Avenue Biological Sciences 556 Columbus OH 43210 USA www.bgsc.org The Bacillus Genetic Stock Center is supported in part by a grant from the National Sciences Foundation, Award Number: DBI-1349029 The author disclaims any conflict of interest. Description or mention of instrumentation, software, or other products in this book does not imply endorsement by the author or by the Ohio State University. Cover: Paenibacillus dendritiformus colony pattern formation. Color added for effect. Image courtesy of Eshel Ben Jacob. TABLE OF CONTENTS Table of Contents .......................................................................................................................................................... 1 Welcome to the Bacillus Genetic Stock Center ............................................................................................................. 2 What is the Bacillus Genetic Stock Center? ............................................................................................................... 2 What kinds of cultures are available from the BGSC? ............................................................................................... 2 What you can do to help the BGSC ...........................................................................................................................
    [Show full text]
  • Identification and Classification of Known and Putative Antimicrobial Compounds Produced by a Wide Variety of Bacillales Species Xin Zhao1,2 and Oscar P
    Zhao and Kuipers BMC Genomics (2016) 17:882 DOI 10.1186/s12864-016-3224-y RESEARCH ARTICLE Open Access Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species Xin Zhao1,2 and Oscar P. Kuipers1* Abstract Background: Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. Results: We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. Conclusions: Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified. Keywords: Antimicrobials, Bacillales, Bacillus, Genome-mining, Lanthipeptides, Sactipeptides, Thiopeptides, NRPs, PKs Background (bacteriocins) [4], as well as non-ribosomally synthesized Most of the species of the genus Bacillus and related peptides (NRPs) and polyketides (PKs) [5].
    [Show full text]
  • Product Sheet Info
    Product Information Sheet for NR-602 Brevibacillus parabrevis, Strain BG Washington, DC: U.S. Government Printing Office, 2007; see www.cdc.gov/od/ohs/biosfty/bmbl5/bmbl5toc.htm. Catalog No. NR-602 Disclaimers: (Derived from ATCC® 8185™) You are authorized to use this product for research use only. It is not intended for human use. For research only. Not for human use. Use of this product is subject to the terms and conditions of Contributor: the BEI Resources Material Transfer Agreement (MTA). The ATCC® MTA is available on our Web site at www.beiresources.org. Product Description: While BEI Resources uses reasonable efforts to include Bacteria Classification: Paenibacillaceae, Brevibacillus accurate and up-to-date information on this product sheet, ® Agent: Brevibacillus parabrevis neither ATCC nor the U.S. Government make any Strain: BG (NRS 751) warranties or representations as to its accuracy. Citations from scientific literature and patents are provided for ® Material Provided: informational purposes only. Neither ATCC nor the U.S. Each vial contains approximately 0.5 mL of bacterial culture Government warrants that such information has been in 0.5X Tryptic Soy Broth supplemented with 10% glycerol. confirmed to be accurate. Packaging/Storage: This product is sent with the condition that you are responsible for its safe storage, handling, use and disposal. NR-602 was packaged aseptically, in screw-capped plastic ® cryovials. The product is provided frozen and should be ATCC and the U.S. Government are not liable for any stored at -60°C or colder immediately upon arrival. For damages or injuries arising from receipt and/or use of this long-term storage, the vapor phase of a liquid nitrogen product.
    [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]
  • Brevibacillus Massiliensis Sp. Nov
    Standards in Genomic Sciences (2013) 8:1-14 DOI:10.4056/sigs.3466975 Non-contiguous finished genome sequence and description of Brevibacillus massiliensis sp. nov. Perrine Hugon1†, Ajay Kumar Mishra1†, Jean-Christophe Lagier1, Thi Thien Nguyen1, Carine Couderc1, Didier Raoult1 and Pierre-Edouard Fournier1* 1Aix-Marseille Université, URMITE, Faculté de médecine, France † These two authors have equal contribution * Corresponding author: Pierre-Edouard Fournier ([email protected]) Keywords: Brevibacillus massiliensis, genome, culturomics, taxono-genomics Brevibacillus massiliensis strain phRT sp. nov. is the type strain of B. massiliensis sp. nov., a new species within the genus Brevibacillus. This strain was isolated from the fecal flora of a woman suffering from morbid obesity. B. massiliensis is a Gram-positive aerobic rod-shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,051,018 bp long genome (1 chromosome but no plasmid) contains 5,051 protein-coding and 84 RNA genes, and exhibits a G+C content of 53.1%. Introduction Brevibacillus massiliensis strain phRT (= CSUR brevis and B. centrosporus were isolated from in- P177 = DSM 25447) is the type strain of B. door dust in schools, day care centers for children massiliensis sp. nov. This bacterium is a Gram- and animal sheds [26], and fecal flora of children, positive, spore-forming, indole negative, aerobic respectively [27]. However, several Brevibacillus and motile bacillus that was isolated from the species are also frequently isolated from humans, stool of a 26-year-old woman suffering from mor- notably in nosocomial infections, causing breast bid obesity.
    [Show full text]
  • Supplemental Fig Final
    Aneurinibacillus aneurinilyticus Aneurinibacillus terranovensis LMG 22483 Aneurinibacillus terranovensis DSM 18919 Bacillus thuringiensiskurstaki Bacillus thuringiensis kurstaki HD73 Bacillus thuringiensis Bacillus thuringiensis HD 789 Bacillus thuringiensis Bt407 Geobacillus stearothermophilus 3 Bacillus thuringiensis IS5056 Bacillus thuringiensis HD771 A426 Bacillus mycoides Rock3 17 Bacillus cereus A Bacillus anthracis TCC12856 T3 YIM 70157 L ysinibacillus sphaericus C3 41 YBT Y412MC61 YBT Bacillus cereus F837/76 L 1518 ysinibacillus fusiformis H1k 1520 Bacillus pumilus MTCC B6033 Bacillus pumilus S1 Bacillus pumilus SAFR 032 A Sporolactobacillus laevolacticus L Salinibacillus aidingensis NSP7.3 AnoxybacillusBacillus flavithermus ysinibacillusgelatini LMG WK1sp 21880 GY32−1 TCC 10987 Bacillus azotoformans Alkalibacillus haloalkaliphilus C5 01 Caldibacillus debilis DSM 16016 Geobacillus sp WCH70 Ames Geobacillus sp Geobacillus kaustophilus HT Geobacillusirgibacillus sp C56 sp SK37 6 BacillusBacillus macauensis halodurans ZFHKF C 1251 V Caldalkalibacillus thermarum HA6 Bacillus amyloliquefaciens M27 Marinococcus halotolerans LPs and PKs3 count Halobacillus halophilus DSM 2266 Lysinibacillus fusiformis RB−21 Halobacillus kuroshimensis IS Hb7 1 Halobacillus karajensis DSM 14948 Halobacillus trueperi HT Halobacillus sp BAB 2008 Halobacillus dabanensis HD 02 Bacillus amyloliquefaciens IT45 Bacillus licheniformis 9945A Bacillus atrophaeus 1942 Bacillus amyloliquefaciens UCMB5036 Bacillus subtilis SMY Bacillus amyloliquefaciens W2 Paenibacillus
    [Show full text]
  • Phylogenetic Determinants of Toxin Gene Distribution in Genomes of Brevibacillus Laterosporus ⁎ Travis R
    Genomics xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Genomics journal homepage: www.elsevier.com/locate/ygeno Original Article Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus ⁎ Travis R. Glarea, , Abigail Durranta, Colin Berryb, Leopoldo Palmac, M. Marsha Ormskirka, Murray P. Coxd a Bio-Protection Research Centre, PO Box 85084, Lincoln University, Lincoln, New Zealand b Cardiff School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, UK c Universidad Nacional de Villa María, Instituto A.P. de Ciencias Básicas y Aplicadas, Av. Arturo Jauretche 1555, Villa María 5900, Córdoba, Argentina d Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand ARTICLE INFO ABSTRACT Keywords: Brevibacillus laterosporus is a globally ubiquitous, spore forming bacterium, strains of which have shown toxic Genomes activity against invertebrates and microbes and several have been patented due to their commercial potential. Toxins Relatively little is known about this bacterium. Here, we examined the genomes of six published and five newly Phylogeny determined genomes of B. laterosporus, with an emphasis on the relationships between known and putative toxin Virulence encoding genes, as well as the phylogenetic relationships between strains. Phylogenetically, strain relationships Bacillales are similar using average nucleotide identity (ANI) values and multi-gene approaches, although PacBio se- quencing revealed multiple copies of the 16S rDNA gene which lessened utility at the strain level. Based on ANI values, the New Zealand isolates were distant from other isolates and may represent a new species. While all of the genomes examined shared some putative toxicity or virulence related proteins, many specific genes were only present in a subset of strains.
    [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]
  • Supporting Information for Latent Functional Diversity May Accelerate Microbial Community Responses to Environmental Fluctuation
    1 Supporting Information for 2 Latent functional diversity may accelerate microbial 3 community responses to environmental fluctuations 4 Thomas P. Smith, Shorok Mombrikotb, Emma Ransome, Dimitrios-Georgios Kontopoulos, Samraat Pawar, Thomas Bell 5 Contents 6 1 Details of isolated strains 1 7 2 Phylum differences seen in alternative datasets 3 8 3 Alternative model of trait evolution 3 9 1 Details of isolated strains 10 Full details of all the isolates and their taxonomy as determined through 16S sequencing is shown in 11 Table S1. Whilst there is taxonomic diversity in the isolates, there were also genetically similar isolates 12 (tentatively the same \species" or \ecotypes") which were obtained more than once. In particular, isolates 13 from the Bacillus cereus group, which consists of several genetically similar species - B. anthracis, B. 14 cereus, B. mycoides, B. thuringiensis and B. weihenstephanensis [Logan and Vos, 2015], were commonly 15 found across many temperature treatments. Their close genetic relatedness prevents 16S rDNA sequences 16 from being a good tool for accurate species delimitation [Ash et al., 1991], so taxonomy was assigned 17 based on phenotypic characteristics. B. mycoides were differentiated from other Bacillus cereus groups 18 strains by rhizoid colony architecture [Logan and Vos, 2015]. Strains displaying cold tolerance (growth at ◦ 19 5 C) were designated as B. weihenstephanensis [Lechner et al., 1998, Logan and Vos, 2015]. Finally, two 20 strains with highest BLAST matches to B. cereus, B. mycoides and B. weihenstephanensis but displaying 21 neither cold tolerance, nor rhizoid colonies, were designated B. cereus. Due to the high similarity of 16S 22 sequences across this group, these strains do not cluster into monophyletic species groups.
    [Show full text]