DOCSLIB.ORG

Raineya Orbicola Gen. Nov., Sp. Nov. a Slightly Thermophilic Bacterium of the Phylum Bacteroidetes and the Description of Raineyaceae Fam

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Raineya Orbicola Gen. Nov., Sp. Nov. a Slightly Thermophilic Bacterium of the Phylum Bacteroidetes and the Description of Raineyaceae Fam TAXONOMIC DESCRIPTION Albuquerque et al., Int J Syst Evol Microbiol 2018;68:982–989 DOI 10.1099/ijsem.0.002556 Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. Luciana Albuquerque,1 Ana Rita M. Polónia,1 Cristina Barroso,1,2 Hugo J. C. Froufe,2 Olga Lage,3,4 Alexandre Lobo-da-Cunha,4,5 Conceiçao~ Egas1,2 and Milton S. da Costa1,* Abstract An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50 C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso- C15:0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen. nov., sp. nov. We also describe the family Raineyaceae to accommodate this new genus and species. The vast majority of the species of the phylum Bacteroidetes optimum growth temperatures of over 65 C and maximum have optimum growth temperatures that range from about growth temperatures below 80 C, were included in the phy- 25 C and 45 C, while slightly thermophilic or thermophilic lum Bacteroidetes but are now classified in the novel phy- species are very rare. Some organisms, such as Pseudozobel- lum named ‘Rhodothermaeota’ [10]. lia thermophila [1] and Lutaonella thermophila [2], have We recently isolated one strain of a slightly thermophilic slightly elevated optimum growth temperatures of around organism with an optimum growth temperature of around 40–45 C, while other species, such as Anaerophaga thermohalophila, are slightly thermophilic [3], with an opti- 50 C and a maximum growth temperature of 60 C. Phylo- mum growth temperature of around 50 C. Two other spe- genetic analysis of the 16S rRNA gene sequence showed cies classified in the phylum Bacteroidetes are thermophilic, that this organism represents a distinct lineage within the namely Thermonema lapsum [4] and Thermonema rossia- phylum Bacteroidetes. Based on phylogenetic, physiological num [5] with optimum growth temperatures of about 60 C and biochemical parameters, we are of the opinion that and a maximum growth temperature of around 65 C. Until strain SPSPC-11T represents a novel genus and species, for recently, the two species of the genus Rhodothermus, Rhodo- which we propose the name Raineya orbicola gen. nov., sp. thermus marinus and Rhodothermus profundi [6–9], with nov. We also propose that this organism represents a new Author affiliations: 1Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; 2Next Generation Sequencing Unit, Biocant, BiocantPark, Núcleo 04, Lote 8, 3060-197 Cantanhede, Portugal; 3Departamento de Biologia, Faculdade de Ciencias,^ Universidade do Porto, Rua do Campo Alegre s/n 4169-007 Porto, Portugal; 4CIMAR/CIIMAR – Centro Interdisciplinar de Investigaçao~ Marinha e Ambiental – Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto, Portugal; 5Laboratório de Biologia Celular, Instituto de Ciencias^ Biomedicas Abel Salazar, ICBAS, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal. *Correspondence: Milton S. da Costa, [email protected] Keywords: new taxa; Bacteroidetes; Raineyaceae fam. nov.; Raineya gen. nov.; Raineya orbicola sp. nov. Abbreviations: CAPSO, 3-(Cyclohexylamino)-2-hydroxy-1-propanesulfonic acid; CECT, Colección Española de Cultivos Tipo; COG, clusters of ortholo- gous groups; CRISPR, clustered regularly interspaced short palindromic repeats; G+C, guanine plus cytosine; HEPES, 4-(2-hydroxyethyl)-1-piperazi- nethanesulfonic acid; LMG, Laboratorium voor Microbiologie Universiteit Gent; MIGS, minimum information genome sequence; SEM, scanning electron microscopy; TAPS, N-[Tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid; TEM, transmission electron microscopy. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strain SPSPC-11T are KY990922, MF125287 and MF125288, respectively. The draft genome accession number of strain SPSPC-11T is NKXO00000000. One supplementary figure and three supplementary tables are available with the online version of this article. 002556 ã 2018 IUMS Downloaded from www.microbiologyresearch.org by This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited. IP: 193.137.36.94 982 On: Tue, 28 May 2019 17:47:20 Albuquerque et al., Int J Syst Evol Microbiol 2018;68:982–989 family for which we propose the name Raineyaceae fam. medium composed of Thermus basal salts containing filter- À nov. sterilized single carbon sources (2.0 g l 1), ammonium sul- À1 T fate (0.5 g l ) and a vitamin and nucleotide solution at a Strain SPSPC-11 was isolated from a reddish biofilm at the À1 final concentration of 40 µg l [15] consisting of thiamine, hot spring at S~ao Pedro do Sul in Central Portugal (40 46¢ riboflavin, pyridoxine, biotin, folic acid, inositol, nicotinic N, 8 4¢ W). The sample was maintained without tempera- acid, pantothenic acid, p-aminobenzoic acid, cyanocobala- ture control for 1 day, and then 0.001 to 0.1 ml in 10 ml min, adenine, thymine, cytosine, guanine, cytidine, uracil water were filtered through membrane filters (Gelman type À and inosine (10 ml l 1). Growth of the strain on single GN-6; pore size 0.45 µm; diameter 47 mm). The filters were carbon sources was examined by measuring the turbidity placed on the surface of solidified Thermus medium [11], of cultures in 20 ml screw capped tubes containing 10 ml the plates were wrapped in plastic to prevent evaporation medium for up to 7 days. and incubated at 45 C for up to 5 days. Cultures were puri- fied by sub-culturing and the isolates stored at –70 C in The polar lipids were extracted from freeze-dried cells and Thermus medium with 15 % (w/v) glycerol. the individual polar lipids were separated by two-dimen- sional thin-layer chromatography. To visualize phospholi- Unless otherwise stated, all biochemical and tolerance tests pids, aminolipids, glycolipids and total lipids, the following were performed, as described previously [12, 13], in liquid reagents were used, respectively, molybdenum blue, ninhy- Thermus medium or on Thermus agar plates [11] at 45 C drin, a-naphthol-sulfuric acid and molybdophosphoric acid for up to 7 days, rather than at the optimum growth temper- [16]. Lipoquinones were extracted from freeze-dried cells ature of about 50 C, because the cultures remained viable and purified by thin-layer chromatography. The purified for longer periods of time. Cell morphology and motility lipoquinones were separated by high-performance liquid were examined by phase contrast microscopy during the chromatography (HPLC) as described previously [17]. Cul- exponential growth phase. For transmission electron tures for fatty acid analysis were grown in Thermus liquid microscopy (TEM), bacteria were fixed for 2 h with 2.5 % medium at 45 C for 5, 8 and 24 h. Fatty acid methyl esters glutaraldehyde in 0.1 M cacodylate buffer (pH 7.2), washed were obtained from fresh wet biomass, separated, identified in buffer, postfixed for 4 h with buffered 2 % OsO , washed 4 and quantified with the standard MIS Library Generation in buffer, followed by 1 h in 1 % uranyl acetate, dehydrated Software, version 6.0, aerobe TSBA method (Microbial ID in ethanol and embedded in Epon. Ultrathin sections were Inc., MIDI) as described previously [18]. stained with uranyl acetate and lead citrate. For scanning electron microscopy (SEM), bacteria were initially processed Total genomic DNA was extracted following the method of as for TEM, but after postfixation a drop of bacteria sus- Nielsen et al. [19], and used for the different analyses per- pended in buffer was laid on each coverslip coated with formed. The G+C content of DNA was determined by poly-lysine. After resting for 15 min with the buffer, the bac- HPLC as described by Mesbah et al. [20] and by genome teria on the coverslips were dehydrated in ethanol and criti- sequencing (see below). PCR-amplification of 16S rRNA cal-point dried. Samples were coated with Au before being genes was carried out as described by Rainey et al. [21]. The observed. 16S rRNA gene sequence was determined by Sanger sequencing (Macrogen). The presence of flexirubin-type pigments was determined by flooding bacterial cells with 20 % KOH [14]. The absorp- The genomic DNA was prepared with the Nextera XT DNA tion spectra of pigments extracted using acetone/methanol Library Preparation Kit and sequenced using paired-end 7 : 2 (v/v) were determined at 200–900 nm with a UV–visi- 2Â300 bp on the MiSeq system (Illumina). Sequenced reads ble spectrophotometer (ThermoScientific). The growth were quality filtered with Trimmomatic [22] and assembled temperature range of the strain was examined at 5 C incre- with SPAdes (version 3.7.1; [23]) and the resulting contigs ments between 30 and 65 C by measuring the turbidity annotated with prokaryotic genome prediction [24].
Load more

Recommended publications
  • Isolation and Characterization of Culturable Thermophilic Bacteria from Hot Springs in Benguet, Philippines Socorro Martha Meg-Ay V
    International Journal of Philippine Science and Technology, Vol. 08, No. 2, 2015 14 ARTICLE Isolation and characterization of culturable thermophilic bacteria from hot springs in Benguet, Philippines Socorro Martha Meg-ay V. Daupan1 and Windell L. Rivera*1,2 1Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines 2Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines Abstract—Despite the numerous geothermal environments in the Philippines, there is limited information on the composition of thermophilic bacteria within the country. This study is the first to carry out both culture and molecular-based methods to characterize thermophilic bacteria from hot springs in the province of Benguet in the Philippines. The xylan-degrading ability of each isolate was also investigated using the Congo red method. A total of 14 phenotypically-different isolates (7 from Badekbek mud spring and 7 from Dalupirip hot spring) were characterized. Phylogenetic analysis based on the nearly complete 16S rDNA sequences revealed that all the isolates obtained from Badekbek were affiliated with Geobacillus, whereas the isolates from Dalupirip clustered into 3 major linkages of bacterial phyla, Firmicutes (72%) consisting of the genera Geobacillus and Anoxybacillus; Deinococcus-Thermus (14%) consisting of the genus Meiothermus; and Bacteroidetes consisting of the genus Thermonema (14%). In addition, xylan-degrading ability was observed in all isolates from Badekbek and in 2 isolates from Dalupirip which showed high sequence similarity with Geobacillus spp. The results are also essential in understanding the roles of the physico-chemical properties of hot spring water as a driver of thermophilic bacterial compositions.
    [Show full text]
  • The Subway Microbiome: Seasonal Dynamics and Direct Comparison Of
    Gohli et al. Microbiome (2019) 7:160 https://doi.org/10.1186/s40168-019-0772-9 RESEARCH Open Access The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities Jostein Gohli1* , Kari Oline Bøifot1,2, Line Victoria Moen1, Paulina Pastuszek3, Gunnar Skogan1, Klas I. Udekwu4 and Marius Dybwad1,2 Abstract Background: Mass transit environments, such as subways, are uniquely important for transmission of microbes among humans and built environments, and for their ability to spread pathogens and impact large numbers of people. In order to gain a deeper understanding of microbiome dynamics in subways, we must identify variables that affect microbial composition and those microorganisms that are unique to specific habitats. Methods: We performed high-throughput 16S rRNA gene sequencing of air and surface samples from 16 subway stations in Oslo, Norway, across all four seasons. Distinguishing features across seasons and between air and surface were identified using random forest classification analyses, followed by in-depth diversity analyses. Results: There were significant differences between the air and surface bacterial communities, and across seasons. Highly abundant groups were generally ubiquitous; however, a large number of taxa with low prevalence and abundance were exclusively present in only one sample matrix or one season. Among the highly abundant families and genera, we found that some were uniquely so in air samples. In surface samples, all highly abundant groups were also well represented in air samples. This is congruent with a pattern observed for the entire dataset, namely that air samples had significantly higher within-sample diversity. We also observed a seasonal pattern: diversity was higher during spring and summer.
    [Show full text]
  • Changes in Multi-Level Biodiversity and Soil Features in a Burned Beech Forest in the Southern Italian Coastal Mountain
    Article Changes in Multi-Level Biodiversity and Soil Features in a Burned Beech Forest in the Southern Italian Coastal Mountain Adriano Stinca 1,* , Maria Ravo 2, Rossana Marzaioli 1,*, Giovanna Marchese 2, Angela Cordella 2, Flora A. Rutigliano 1 and Assunta Esposito 1 1 Department of Environmental Biological and Pharmaceutical Sciences and Technologies, University of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy; fl[email protected] (F.A.R.); [email protected] (A.E.) 2 Genomix4Life S.r.l., Via Allende, 84081 Baronissi (Salerno), Italy; [email protected] (M.R.); [email protected] (G.M.); [email protected] (A.C.) * Correspondence: [email protected] (A.S.); [email protected] (R.M.) Received: 1 August 2020; Accepted: 8 September 2020; Published: 11 September 2020 Abstract: In the context of global warming and increasing wildfire occurrence, this study aims to examine, for the first time, the changes in multi-level biodiversity and key soil features related to soil functioning in a burned Mediterranean beech forest. Two years after the 2017 wildfire, changes between burned and unburned plots of beech forest were analyzed for plant communities (vascular plant and cover, bryophytes diversity, structural, chorological, and ecological variables) and soil features (main chemical properties, microbial biomass and activity, bacterial community composition, and diversity), through a synchronic study. Fire-induced changes in the micro-environmental conditions triggered a secondary succession process with colonization by many native pioneer plant species. Indeed, higher frequency (e.g., Scrophularia vernalis L., Rubus hirtus Waldst. and Kit. group, and Funaria hygrometrica Hedw.) or coverage (e.g., Verbascum thapsus L.
    [Show full text]
  • Table S4. Phylogenetic Distribution of Bacterial and Archaea Genomes in Groups A, B, C, D, and X
    Table S4. Phylogenetic distribution of bacterial and archaea genomes in groups A, B, C, D, and X. Group A a: Total number of genomes in the taxon b: Number of group A genomes in the taxon c: Percentage of group A genomes in the taxon a b c cellular organisms 5007 2974 59.4 |__ Bacteria 4769 2935 61.5 | |__ Proteobacteria 1854 1570 84.7 | | |__ Gammaproteobacteria 711 631 88.7 | | | |__ Enterobacterales 112 97 86.6 | | | | |__ Enterobacteriaceae 41 32 78.0 | | | | | |__ unclassified Enterobacteriaceae 13 7 53.8 | | | | |__ Erwiniaceae 30 28 93.3 | | | | | |__ Erwinia 10 10 100.0 | | | | | |__ Buchnera 8 8 100.0 | | | | | | |__ Buchnera aphidicola 8 8 100.0 | | | | | |__ Pantoea 8 8 100.0 | | | | |__ Yersiniaceae 14 14 100.0 | | | | | |__ Serratia 8 8 100.0 | | | | |__ Morganellaceae 13 10 76.9 | | | | |__ Pectobacteriaceae 8 8 100.0 | | | |__ Alteromonadales 94 94 100.0 | | | | |__ Alteromonadaceae 34 34 100.0 | | | | | |__ Marinobacter 12 12 100.0 | | | | |__ Shewanellaceae 17 17 100.0 | | | | | |__ Shewanella 17 17 100.0 | | | | |__ Pseudoalteromonadaceae 16 16 100.0 | | | | | |__ Pseudoalteromonas 15 15 100.0 | | | | |__ Idiomarinaceae 9 9 100.0 | | | | | |__ Idiomarina 9 9 100.0 | | | | |__ Colwelliaceae 6 6 100.0 | | | |__ Pseudomonadales 81 81 100.0 | | | | |__ Moraxellaceae 41 41 100.0 | | | | | |__ Acinetobacter 25 25 100.0 | | | | | |__ Psychrobacter 8 8 100.0 | | | | | |__ Moraxella 6 6 100.0 | | | | |__ Pseudomonadaceae 40 40 100.0 | | | | | |__ Pseudomonas 38 38 100.0 | | | |__ Oceanospirillales 73 72 98.6 | | | | |__ Oceanospirillaceae
    [Show full text]
  • 16S Rrna Metagenomic Analysis of the Bacterial Community Associated with Turf Grass Seeds from Low Moisture and High Moisture Climates
    16S rRNA metagenomic analysis of the bacterial community associated with turf grass seeds from low moisture and high moisture climates Qiang Chen, William A. Meyer, Qiuwei Zhang and James F. White Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA ABSTRACT Turfgrass investigators have observed that plantings of grass seeds produced in moist climates produce seedling stands that show greater stand evenness with reduced disease compared to those grown from seeds produced in dry climates. Grass seeds carry microbes on their surfaces that become endophytic in seedlings and promote seedling growth. We hypothesize that incomplete development of the microbiome associated with the surface of seeds produced in dry climates reduces the performance of seeds. Little is known about the influence of moisture on the structure of this microbial community. We conducted metagenomic analysis of the bacterial communities associated with seeds of three turf species (Festuca rubra, Lolium arundinacea, and Lolium perenne) from low moisture (LM) and high moisture (HM) climates. The bacterial communities were characterized by Illumina high-throughput sequencing of 16S rRNA V3–V4 regions. We performed seed germination tests and analyzed the correlations between the abundance of different bacterial groups and seed germination at different taxonomy ranks. Climate appeared to structure the bacterial communities associated with seeds. LM seeds vectored mainly Proteobacteria (89%). HM seeds vectored a denser and more diverse bacterial community that included Proteobacteria (50%) and Bacteroides (39%). Submitted 29 August 2019 At the genus level, Pedobacter (20%), Sphingomonas (13%), Massilia (12%), Pantoea Accepted 16 December 2019 (12%) and Pseudomonas (11%) were the major genera in the bacterial communities Published 10 January 2020 regardless of climate conditions.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergol
    applied sciences Article Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland Magdalena Dyda 1,2,* , Agnieszka Laudy 3, Przemyslaw Decewicz 4 , Krzysztof Romaniuk 4, Martyna Ciezkowska 4, Anna Szajewska 5 , Danuta Solecka 6, Lukasz Dziewit 4 , Lukasz Drewniak 4 and Aleksandra Skłodowska 1 1 Department of Geomicrobiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] 2 Research and Development for Life Sciences Ltd. (RDLS Ltd.), Miecznikowa 1/5a, 02-096 Warsaw, Poland 3 Laboratory of Environmental Analysis, Museum of King John III’s Palace at Wilanow, Stanislawa Kostki Potockiego 10/16, 02-958 Warsaw, Poland; [email protected] 4 Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] (P.D.); [email protected] (K.R.); [email protected] (M.C.); [email protected] (L.D.); [email protected] (L.D.) 5 The Main School of Fire Service, Slowackiego 52/54, 01-629 Warsaw, Poland; [email protected] 6 Department of Plant Molecular Ecophysiology, Institute of Experimental Plant Biology and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +48-786-28-44-96 Citation: Dyda, M.; Laudy, A.; Abstract: The aim of the presented investigation was to describe seasonal changes of microbial com- Decewicz, P.; Romaniuk, K.; munity composition in situ in different biocenoses on historical sandstone of the Northern Pergola in Ciezkowska, M.; Szajewska, A.; the Museum of King John III’s Palace at Wilanow (Poland).
    [Show full text]
  • Table S1. Sequence Counts of the Rhizosphere and Bulk Soil Metagenomes
    Table S1. Sequence counts of the rhizosphere and bulk soil metagenomes. The total number of sequences before and after quality filtering, and coverage data of contigs ≥500 bp. Original sequence files After quality filtering Coverage (Contigs ≥ 500bp long) Sample Habitat No. of sequences No. of bases Average length No. of sequences No. of bases Average length No. of mapped reads 1C4 Bulk 20109591 2975984909 147.99 19346238 2849067044 147.265 10693941 2C3 Bulk 16412612 2437520419 148.515 15668391 2292314037 146.305 8488893 4C3 Bulk 17085364 2539362024 148.63 16262162 2381077816 146.415 6679680 8C4 Bulk 19685011 2914204472 148.04 18779173 2764065885 147.185 12713236 Total 73292578 10867071823 70055964 10286524781 38575750 21R Rhizosphere 14059802 2056595556 146.275 13308646 1926423705 144.75 11606054 34R Rhizosphere 12776790 1887171712 147.7 11983209 1747001863 145.785 5664206 43R Rhizosphere 12448635 1841092827 147.895 11570365 1687972045 145.89 6966831 51R Rhizosphere 18734804 2763025902 147.48 17964991 2613876715 145.89 10727283 Total 58020031 8547885997 54827211 7975274328 34964374 Table S2. Relative frequencies of open-reading frame (ORF) hit counts for microorganisms (phylum level) in each metagenome. Number Pylum Microorganism Sample Habitat Relative_frequency 1 Unknown_archaea Archaea 1C4 Bulk_soil 0.000258256 2 Crenarchaeota Archaea 1C4 Bulk_soil 0 3 Euryarchaeota Archaea 1C4 Bulk_soil 0.001549537 4 Thaumarchaeota Archaea 1C4 Bulk_soil 0.000193692 5 Acidobacteria Bacteria 1C4 Bulk_soil 0.009716887 6 Actinobacteria Bacteria 1C4 Bulk_soil
    [Show full text]
  • Exploring the Lipidomes of Shallow-Water and Deep-Sea Hydrothermal Systems
    Exploring the lipidomes of shallow-water and deep-sea hydrothermal systems Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - Am Fachbereich Geowissenschaften der Universität Bremen vorgelegt von Miriam Sollich Bremen Mai 2018 1. Gutachter: Dr. Solveig I. Bühring 2. Gutachter: Associate Prof. Dr. Eoghan P. Reeves Tag des Promotionskolloquiums:16. Februar 2018 Den Wissenschaftlern geht es wie den Chaoten. Es ist alles da, man muss es nur suchen. - Franz Kern - CONTENTS Abstract Zusammenfassung Acknowledgements List of Abbreviations Chapter I 1 Introduction and Methods Chapter II 37 Scope and Outline Chapter III 43 Heat stress dictates the microbial lipid composition along a thermal gradient in marine sediments Chapter IV 91 Shallow-water hydrothermal systems offer ideal conditions to study archaeal lipid membrane adaptations to environmental extremes Chapter V 113 Transfer of chemosynthetic fixed carbon and its ecological significance revealed by lipid analysis of fluids at diffuse flow deep-sea vents (East Pacific Rise 9°50’N) Chapter VI 143 Concluding Remarks and Future Perspectives ABSTRACT Shallow-water and deep-sea hydrothermal systems are environments where seawater percolates downward through fractures in the oceanic crust, and becomes progressively heated and chemically altered. Finally, the entrained water is expelled into the overlying water column as a hydrothermal fluid. Hydrothermal circulation occurs at all active plate boundaries like mid-ocean ridges, submarine volcanic arcs and backarc basins. They represent one of the most extreme and dynamic ecosystems on the planet with steep physico-chemical gradients. Nevertheless, these environments are characterized by exceptional high biomass representing hotspots of life in the mostly hostile and desolated deep sea.
    [Show full text]
  • Succession and Cazyme Expression of Marine Bacterial
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; this version posted December 8, 2020. 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. Sweet and magnetic: Succession and CAZyme expression of marine bacterial communities encountering a mix of alginate and pectin particles Carina Bunse1,2,*, Hanna Koch3,4,*, Sven Breider3, Meinhard Simon1,3 and Matthias Wietz2,3# 1Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Germany 2Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Germany 3Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany 4Department of Microbiology, Radboud University Nijmegen, The Netherlands *These authors contributed equally to this work. #Corresponding author HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Am Handelshafen 12 27570 Bremerhaven Germany Email: [email protected] Telephone +49-471-48311454 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; this version posted December 8, 2020. 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. ABSTRACT Polysaccharide particles are an important nutrient source and microhabitat for marine bacteria. However, substrate-specific bacterial dynamics in a mixture of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed.
    [Show full text]
  • Seasonal Dynamics and Phylogenetic Diversity of Free-Living and Particle-Associated Bacterial Communities in Four Lakes in Northeastern Germany
    AQUATIC MICROBIAL ECOLOGY Vol. 45: 115–128, 2006 Published November 24 Aquat Microb Ecol Seasonal dynamics and phylogenetic diversity of free-living and particle-associated bacterial communities in four lakes in northeastern Germany Martin Allgaier, Hans-Peter Grossart* Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Limnology of Stratified Lakes, Alte Fischerhütte 2, 16775 Stechlin-Neuglobsow, Germany ABSTRACT: The phylogenetic diversity and seasonal dynamics of free-living and particle-associated bacterial communities were investigated in the epilimnion of 4 lakes of the Mecklenburg Lake Dis- trict, northeastern Germany. All lakes differed in their limnological features, ranging from olig- otrophic to eutrophic and dystrophic. Bacterial community structure and seasonal dynamics were analyzed by denaturing gradient gel electrophoresis (DGGE) and clone libraries of 16S rRNA gene fragments. Communities of free-living and particle-associated bacteria greatly differed among the lakes. In addition, significant differences occurred between both bacterial fractions within each lake. Seasonal changes were more pronounced in free-living than in particle-associated bacterial commu- nities. Non-metric multidimensional scaling (NMDS) analyses revealed several strong correlations between bacterial communities (both free-living and particle-associated) and environmental vari- ables such as pH, dissolved organic carbon (DOC), phytoplankton biomasses, and primary produc- tion. Phylogenetically, all cloned and sequenced 16S rRNA gene fragments belonged to already known freshwater clusters. Clone libraries of free-living bacteria were dominated by sequences of Actinobacteria, Bacteroidetes, and Betaproteobacteria, whereas those of particle-associated bacteria predominantly consisted of Cyanobacteria and Bacteroidetes sequences. Other freshwater phyla such as Alpha- and Gammaproteobacteria, Verrucomicrobia, Planctomycetes, and members of Can- didate Division OP10 were found in low proportions.
    [Show full text]
  • Raineya Orbicola Gen. Nov., Sp. Nov. a Slightly Thermophilic Bacterium of the Phylum Bacteroidetes and the Description of Raineyaceae Fam
    TAXONOMIC DESCRIPTION Albuquerque et al., Int J Syst Evol Microbiol 2018;68:982–989 DOI 10.1099/ijsem.0.002556 Raineya orbicola gen. nov., sp. nov. a slightly thermophilic bacterium of the phylum Bacteroidetes and the description of Raineyaceae fam. nov. Luciana Albuquerque,1 Ana Rita M. Polónia,1 Cristina Barroso,1,2 Hugo J. C. Froufe,2 Olga Lage,3,4 Alexandre Lobo-da-Cunha,4,5 Conceiçao~ Egas1,2 and Milton S. da Costa1,* Abstract An isolate, designated SPSPC-11T, with an optimum growth temperature of about 50 C and an optimum pH for growth between 7.5 and 8.0, was recovered from a hot spring in central Portugal. Based on phylogenetic analysis of its 16S rRNA sequence, the new organism is most closely related to the species of the genus Thermonema but with a pairwise sequence similarity of <85 %. The isolate was orange-pigmented, formed non-motile long filaments and rod-shaped cells that stain Gram-negative. The organism was strictly aerobic, oxidase-positive and catalase-positive. The major fatty acids were iso- C15:0, iso-C15 : 0 2-OH and iso-C17 : 0 3-OH. The major polar lipids were one aminophospholipid, two aminolipids and three unidentified lipids. Menaquinone 7 was the major respiratory quinone. The DNA G+C content of strain SPSPC-11T was 37.6 mol% (draft genome sequence). The high quality draft genome sequence corroborated many of the phenotypic characteristics of strain SPSPC-11T. Based on genotypic, phylogenetic, physiological and biochemical characterization we describe a new species of a novel genus represented by strain SPSPC-11T (=CECT 9012T=LMG 29233T) for which we propose the name Raineya orbicola gen.
    [Show full text]