DOCSLIB.ORG

Σ Factors from Planctomycetes and Actinobacteria

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Σ Factors from Planctomycetes and Actinobacteria Classification and Functional Characterization of Extracytoplasmic Function (ECF) σ Factors from Planctomycetes and Actinobacteria Xiaoluo Huang Classification and Functional Characterization of Extracytoplasmic Function (ECF) σ Factors from Planctomycetes and Actinobacteria Dissertation zur Erlangung des Doktorgrades der Fakultät für Biologie der Ludwig-Maximilian-Universität München vorgelegt von Xiaoluo Huang aus Hubei, China München, 2015 Erstgutachter: Prof. Dr. Thorsten Mascher Zweitgutachter: PD Dr. Ralf Heermann Tag der Abgabe: 15.07.2015 Tag der mündlichen Prüfung: 08.09.2015 Eidesstattliche Versicherung und Erklärung Hiermit versichere ich an Eides statt, dass die vorliegende Dissertation von mir selbständig und ohne unerlaubte Hilfe angefertigt wurde. Zudem wurden keine anderen als die angegebenen Quellen verwendet. Außerdem versichere ich, dass die Dissertation keiner anderen Prüfungskommission vorgelegt wurde und ich mich nicht anderweitig einer Doktorprüfung ohne Erfolg unterzogen habe. München Xiaoluo Huang Contents Contents Abbreviations .................................................................................................................................... III List of publications presented in the thesis .................................................................................... IV Contributions to the publications .................................................................................................... V Summary .......................................................................................................................................... VII Zusammenfassung ......................................................................................................................... VIII Chapter 1 ............................................................................................................................................. 1 1 Introduction ..................................................................................................................................... 2 1.1 Overview of bacterial signal transduction systems .................................................................... 2 1.1.1 One-component systems...................................................................................................... 2 1.1.2 Two-component systems ..................................................................................................... 3 1.1.3 ECF σ factors....................................................................................................................... 6 1.2 ECF classification ...................................................................................................................... 7 1.3 Signaling mechanisms of ECF σ factors .................................................................................. 10 1.3.1 Regulated proteolysis of the anti-σ factor ......................................................................... 10 1.3.2 Conformational change of the anti-σ factor ...................................................................... 11 1.3.3 Activation of ECF σ factors by protein-protein interaction .............................................. 11 1.3.4 Activation of ECF σ factors through a partner switch mechanism ................................... 14 1.3.5 Regulation of the activity of ECF σ factors by their C-terminal extension ....................... 14 1.3.6 Transcriptional activation of ECF σ factors ...................................................................... 15 1.3.7 Activation of ECF σ factors by Ser/Thr Kinases ............................................................... 16 1.4 General features of Planctomycetes and Actinobacteria phyla ................................................ 17 1.4.1 Planctomycetes .................................................................................................................. 17 1.4.2 Actinobacteria ................................................................................................................... 18 1.4.2.1 The genus Streptomyces ............................................................................................. 19 1.5 Aims of this study .................................................................................................................... 22 Chapter 2 ........................................................................................................................................... 24 Identification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics ....................................................... 24 Supplementary files for Chapter 2...................................................................................................... 37 Chapter 3 ........................................................................................................................................... 38 Environmental sensing in Actinobateria: A comprehensive survey on the signaling capacity of this phylum. .............................................................................................................................. 38 Supplementary files for Chapter 3...................................................................................................... 58 Chapter 4 ........................................................................................................................................... 59 I Contents Defining the regulon of genes controlled by σE, a key regulator of cell envelope stress in Streptomyces coelicolor ................................................................................................................. 59 Supplementary files for Chapter 4.................................................................................................... 103 Chapter 5 ......................................................................................................................................... 105 5 Discussion ..................................................................................................................................... 106 5.1 Comparative genomics of ECF σ factors in Planctomycetes and Actinobacteria .................. 106 5.1.1 Comparative genomics, a powerful tool to identify novel ECF groups .......................... 106 5.1.2 The ECF-dependent regulation in the distinct bacterial phylum, Planctomycetes .......... 107 5.1.3 The ECF-dependent regulation in Actinobacteria ........................................................... 109 5.2 Defining the regulon of genes controlled by σE in Streptomyces ........................................... 111 5.2.1 How many genes are controlled by σE in S. coelicolor? ................................................. 111 5.2.2 Genes that are differentially transcribed in the S. coelicolor ΔsigE mutant .................... 112 5.3 Outlook ................................................................................................................................... 115 5.3.1 Assigning the remaining unclassified ECF σ factors into novel ECF groups ................. 115 5.3.2 Validation of the hypothesis obtained from comparative genomics of ECF σ factors .... 116 5.3.3 Further elucidation of the regulatory network governed by σE in Streptomyces ............. 116 Supplementary material for Chapter 5 ............................................................................................. 118 References for Chapter 1 and Chapter 5 ..................................................................................... 120 Acknowledgements ......................................................................................................................... 135 Curriculum Vitae -Xiaoluo Huang ............................................................................................... 137 II Abbreviations Abbreviations 1CS one-component system 2CS two-component system ECF extracytoplasmic function DHp dimerization and histidine phosphotransferase CA catalytic and ATPase RD receiver domain PAS Per, Arnt, Sim HAMP histidine kinases, adenyl cyclases, methyl-accepting proteins and phosphatases GAF cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA Hpt histidine phosphotransfer OMP outer membrane protein ASD anti-σ domain CLD C-terminal cupin-like domain SL σ factor like ICM intra-cytoplasmic membrane ChIP-seq chromatin immunoprecipitation-sequencing III List of publications List of publications presented in the thesis 1. Jogler C, Waldmann J, Huang X, Jogler M, Glöckner FO, Mascher T, Kolter R (2012) J Bacteriol 194: 6419-6430. 2. Huang X#, Pinto D#, Fritz G, Mascher T (2015) J Bacteriol 197: 2517-2535. (#Co-first author.) 3. Tran NT#, Huang XL#, Bush MJ, Chandra G, Pinto D, Hong HJ, Hutchings MI, Mascher T and Buttner MJ. (#co-first author, in preparation) IV Declaration Contributions to the publications Chapter 2 Jogler C, Waldmann J, Huang X, Jogler M, Glöckner FO, Mascher T, Kolter R (2012) J Bacteriol 194: 6419-6430 Christian Jogler designed the study and supervised Jost Waldmann and Mareike Jogler. He performed protein functional domain analysis and manually cured the final candidate gene set. Christian Jogler wrote major parts of the manuscript and serves as corresponding author. Jost Waldmann developed the software pipeline for comparative genomics and performed the experiment and wrote the corresponding parts of the manuscript. Xiaoluo Huang retrieved the sequences of ECF
Load more

Recommended publications
  • Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China
    Article Leaf-Associated Shifts in Bacterial and Fungal Communities in Response to Chicken Rearing Under Moso Bamboo Forests in Subtropical China Xiaoping Zhang 1, Zheke Zhong 1,*, Xu Gai 1, Jiafu Ying 2, Weifen Li 2, Xuhua Du 1, Fangyuan Bian 1 and Chuanbao Yang 1 1 China National Bamboo Research Center, Key Laboratory of Resources and Utilization of Bamboo of State Forestry Administration, Hangzhou 310012, China; [email protected] (X.Z.); [email protected] (X.G.); [email protected] (X.D.); [email protected] (F.B.); [email protected] (C.Y.) 2 College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] (J.Y.); wfl[email protected] (W.L.) * Correspondence: [email protected]; Tel.: +86-0571-88860734 Received: 25 January 2019; Accepted: 25 February 2019; Published: 1 March 2019 Abstract: Integrated bamboo-chicken farming (BCF) systems are a traditional agroforestry pattern with large economic benefits in subtropical China. However, little is known regarding the effect of this integration on the bamboo leaf-associated microbiome, which can be very important for disease control and nutrient turnover. In the present study, we compared the leaf-associated bacterial and fungal communities of moso bamboo (Phyllostachys edulis) in a BCF system and an adjacent moso bamboo forest (MBF). The results showed that Cyanobacteria and Ascomycota were the predominant microbial phyla associated with bamboo leaves. Chicken farming under the bamboo forest significantly increased the bacterial and fungal alpha diversity (observed operational taxonomic units (OTUs) and Simpson’s index) associated with bamboo leaves. Principal components analysis (PCoA) further confirmed the shifts in the bacterial and fungal communities caused by chicken farming.
    [Show full text]
  • Global Metagenomic Survey Reveals a New Bacterial Candidate Phylum in Geothermal Springs
    ARTICLE Received 13 Aug 2015 | Accepted 7 Dec 2015 | Published 27 Jan 2016 DOI: 10.1038/ncomms10476 OPEN Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs Emiley A. Eloe-Fadrosh1, David Paez-Espino1, Jessica Jarett1, Peter F. Dunfield2, Brian P. Hedlund3, Anne E. Dekas4, Stephen E. Grasby5, Allyson L. Brady6, Hailiang Dong7, Brandon R. Briggs8, Wen-Jun Li9, Danielle Goudeau1, Rex Malmstrom1, Amrita Pati1, Jennifer Pett-Ridge4, Edward M. Rubin1,10, Tanja Woyke1, Nikos C. Kyrpides1 & Natalia N. Ivanova1 Analysis of the increasing wealth of metagenomic data collected from diverse environments can lead to the discovery of novel branches on the tree of life. Here we analyse 5.2 Tb of metagenomic data collected globally to discover a novel bacterial phylum (‘Candidatus Kryptonia’) found exclusively in high-temperature pH-neutral geothermal springs. This lineage had remained hidden as a taxonomic ‘blind spot’ because of mismatches in the primers commonly used for ribosomal gene surveys. Genome reconstruction from metagenomic data combined with single-cell genomics results in several high-quality genomes representing four genera from the new phylum. Metabolic reconstruction indicates a heterotrophic lifestyle with conspicuous nutritional deficiencies, suggesting the need for metabolic complementarity with other microbes. Co-occurrence patterns identifies a number of putative partners, including an uncultured Armatimonadetes lineage. The discovery of Kryptonia within previously studied geothermal springs underscores the importance of globally sampled metagenomic data in detection of microbial novelty, and highlights the extraordinary diversity of microbial life still awaiting discovery. 1 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA. 2 Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.
    [Show full text]
  • Bacterial Community Structure in High-Arctic Snow and Freshwater As Revealed by Pyrosequencing of 16S Rrna Genes and Cultivation Annette K
    RESEARCH/REVIEW ARTICLE Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation Annette K. Møller,1 Ditte A. Søborg,1 Waleed Abu Al-Soud,2 Søren J. Sørensen2 & Niels Kroer1 1 Department of Environmental Science, Aarhus University, Frederiksborgvej 399, DK-4000 Roskilde, Denmark 2 Department of Biology, University of Copenhagen, Sølvgade 83H, DK-1307 K Copenhagen, Denmark Keywords Abstract Taxonomic diversity; microbial assemblages; bacterial density; DOC. The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA Correspondence genes and 16S rRNA gene sequencing of cultivated isolates. Both the Niels Kroer, pyrosequence and cultivation data indicated that the phylogenetic composition Department of Environmental Science, of the microbial assemblages was different within the snow layers and between Aarhus University, snow and freshwater. The highest diversity was seen in snow. In the middle Frederiksborgvej 399, and top snow layers, , and dominated, DK-4000 Roskilde, Denmark. Proteobacteria Bacteroidetes Cyanobacteria E-mail: [email protected] although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacter- oidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria.
    [Show full text]
  • Within-Arctic Horizontal Gene Transfer As a Driver of Convergent Evolution in Distantly Related 2 Microalgae
    bioRxiv preprint doi: https://doi.org/10.1101/2021.07.31.454568; this version posted August 2, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Within-Arctic horizontal gene transfer as a driver of convergent evolution in distantly related 2 microalgae 3 Richard G. Dorrell*+1,2, Alan Kuo3*, Zoltan Füssy4, Elisabeth Richardson5,6, Asaf Salamov3, Nikola 4 Zarevski,1,2,7 Nastasia J. Freyria8, Federico M. Ibarbalz1,2,9, Jerry Jenkins3,10, Juan Jose Pierella 5 Karlusich1,2, Andrei Stecca Steindorff3, Robyn E. Edgar8, Lori Handley10, Kathleen Lail3, Anna Lipzen3, 6 Vincent Lombard11, John McFarlane5, Charlotte Nef1,2, Anna M.G. Novák Vanclová1,2, Yi Peng3, Chris 7 Plott10, Marianne Potvin8, Fabio Rocha Jimenez Vieira1,2, Kerrie Barry3, Joel B. Dacks5, Colomban de 8 Vargas2,12, Bernard Henrissat11,13, Eric Pelletier2,14, Jeremy Schmutz3,10, Patrick Wincker2,14, Chris 9 Bowler1,2, Igor V. Grigoriev3,15, and Connie Lovejoy+8 10 11 1 Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, 12 INSERM, Université PSL, 75005 Paris, France 13 2CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, 14 FR2022/Tara Oceans GOSEE, 3 rue Michel-Ange, 75016 Paris, France 15 3 US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 16 Cyclotron Road, Berkeley,
    [Show full text]
  • 1 Strong Purifying Selection Is Associated with Genome
    1 Strong Purifying Selection is Associated with Genome Streamlining in Epipelagic Marinimicrobia Carolina Alejandra Martinez-Gutierrez and Frank O. Aylward Department of Biological Sciences, Virginia Tech, Blacksburg, VA Email for correspondence: [email protected] Abstract Marine microorganisms inhabiting nutrient-depleted waters play critical roles in global biogeochemical cycles due to their abundance and broad distribution. Many of these microbes share similar genomic features including small genome size, low % G+C content, short intergenic regions, and low nitrogen content in encoded amino acid residue side chains (N-ARSC), but the evolutionary drivers of these characteristics are unclear. Here we compared the strength of purifying selection across the Marinimicrobia, a candidate phylum which encompasses a broad range of phylogenetic groups with disparate genomic features, by estimating the ratio of non-synonymous and synonymous substitutions (dN/dS) in conserved marker genes. Our analysis reveals that epipelagic Marinimicrobia that exhibit features consistent with genome streamlining have significantly lower dN/dS values when compared to the mesopelagic counterparts. We also found a significant positive correlation between median dN/dS values and % G+C content, N-ARSC, and intergenic region length. We did not identify a significant correlation between dN/dS ratios and estimated genome size, suggesting the strength of selection is not a primary factor shaping genome size in this group. Our findings are generally consistent with genome streamlining theory, which postulates that many genomic features of abundant epipelagic bacteria are the result of adaptation to oligotrophic nutrient conditions. Our results are also in agreement with previous findings that genome streamlining is common in epipelagic waters, suggesting that genomes inhabiting this region of the ocean have been shaped by strong selection together with prevalent nutritional constraints characteristic of this environment.
    [Show full text]
  • Structural Features of the Vesicle of Frankia Sp. Cpi1 in Culture
    Structural features of the vesicle of Frankia sp. CpIl in culture JOHNG. TORREYAND DALECALLAHAM Cabot Foundation, Harvard University, Petersham, MA, U.S.A.01366 and Department of Botany, University of Massachusetts, Amherst, MA, U.S.A.01003 Accepted March 16, 1982 TORREY,J. G., and D. CALLAHAM.1982. Structural features of the vesicle of Frankia sp. CpII inculture. Can. J. Microbiol. 28: 749-757. The filamentous bacterium Frankia sp. CpIl of the Actinomycetales, responsible for symbiotic nitrogen fixation in the nodules of certain woody dicots, also fixes dinitrogen when grown independently of the host in a nitrogen-free synthetic nutrient medium under aerobic conditions. In structural studies of Frankla grown in culture it has been shown that the bacterial filaments form vesicles, enlarged terminal endings in which the enzyme nitrogenase is formed. Microscopic examination of cultures shows that the vesicles possess a specialized envelope consisting of a number of thin layers or laminae which In polarized light show birefringence and in freeze-etch electron microscopy are resolved as multiple (12-15) laminae approximately 35-40 A (1 A = 0.1 nm) in thickness. Comparisons are made between the structure of the veslcle envelope in cultured Frankia and the ; strikingly similar innermost laminated layer in the dinitrogen-fixing heterocysts of the cyanobacterium Anabaena. Comparable protective functions in limiting oxygen to the dinitrogen-fixing sites are suggested for these similar structures in two quite unrelated microorganisms. 1 TORREY,J. G., et D. CALLAHAM.1982. Structural features of the vesicle of Frankia sp. CpIl in culture. Can. J. Microbiol. 28: 749-757. I La bactkrie filamenteuse Frankia sp.
    [Show full text]
  • The Two-Domain Tree of Life Is Linked to a New Root for the Archaea
    The two-domain tree of life is linked to a new root for the Archaea Kasie Raymanna, Céline Brochier-Armanetb, and Simonetta Gribaldoa,1 aInstitut Pasteur, Department of Microbiology, Unit Biologie Moléculaire du Gène chez les Extrêmophiles, 75015 Paris, France; and bUniversité de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, 69622 Villeurbanne, France Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved April 17, 2015 (received for review November 02, 2014) One of the most fundamental questions in evolutionary biology is restricted taxonomic sampling, notably for the outgroup, may also the origin of the lineage leading to eukaryotes. Recent phyloge- generate or mask potential tree reconstruction artifacts (16). All nomic analyses have indicated an emergence of eukaryotes from these considerations emphasize that we have not yet found a way within the radiation of modern Archaea and specifically from a group out of the phylogenomic impasse caused by the use of universal comprising Thaumarchaeota/“Aigarchaeota” (candidate phylum)/ trees to investigate the relationships among Archaea and eu- Crenarchaeota/Korarchaeota (TACK). Despite their major im- karyotes (12). plications, these studies were all based on the reconstruction of Here, we have applied an original two-step strategy that we universal trees and left the exact placement of eukaryotes with re- proposed a few years ago which involves separately analyzing the spect to the TACK lineage unclear. Here we have applied an original markers shared between Archaea and eukaryotes and between two-step approach that involves the separate analysis of markers Archaea and Bacteria (12). This strategy allowed us to use a larger shared between Archaea and eukaryotes and between Archaea and taxonomic sampling, more markers and thus more positions, have Bacteria.
    [Show full text]
  • Phylogeny and Assemblage Composition of Frankia in Alnus Tenuifolia Nodules Across a Primary Successional Sere in Interior Alaska
    Molecular Ecology (2013) 22, 3864–3877 doi: 10.1111/mec.12339 Phylogeny and assemblage composition of Frankia in Alnus tenuifolia nodules across a primary successional sere in interior Alaska M. D. ANDERSON,*† D. L. TAYLOR† and R. W. RUESS† *Department of Biology, Macalester College, 1600 Grand Ave, Saint Paul, MN 55105, USA, †Institute of Arctic Biology, University of Alaska, Fairbanks, AK 99775, USA Abstract In nitrogen (N) fixing symbioses, host-symbiont specificity, genetic variation in bacte- rial symbionts and environmental variation represent fundamental constraints on the ecology, evolution and practical uses of these interactions, but detailed information is lacking for many naturally occurring N-fixers. This study examined phylogenetic host specificity of Frankia in field-collected nodules of two Alnus species (A. tenuifolia and A. viridis) in interior Alaska and, for A. tenuifolia, distribution, diversity, spatial auto- correlation and correlation with specific soil factors of Frankia genotypes in nodules collected from replicated habitats representing endpoints of a primary sere. Frankia genotypes most commonly associated with each host belonged to different clades within the Alnus-infective Frankia clade, and for A. tenuifolia, were divergent from previously described Frankia. A. tenuifolia nodules from early and late succession hab- itats harboured distinct Frankia assemblages. In early succession, a single genotype inhabited 71% of nodules with no discernable autocorrelation at any scale, while late succession Frankia were more diverse, differed widely among plants within a site and were significantly autocorrelated within and among plants. Early succession Frankia genotype occurrence was strongly correlated with carbon/nitrogen ratio in the mineral soil fraction, while in late succession, the most common genotypes were correlated with different soil variables.
    [Show full text]
  • Diversity and Community Structure of Marine Microbes Around the Benham Rise Underwater Plateau, Northeastern Philippines
    Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines Andrian P. Gajigan1,2, Aletta T. Yñiguez1, Cesar L. Villanoy1, Maria Lourdes San Diego-McGlone1, Gil S. Jacinto1 and Cecilia Conaco1 1 Marine Science Institute, University of the Philippines Diliman, Quezon City, Philippines 2 Current affiliation: Department of Oceanography, University of Hawaii at Manoa, USA ABSTRACT Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Corre- spondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide Submitted 8 January 2018 foundational information on the diversity of marine microbes in Philippine waters.
    [Show full text]
  • Vertically Distinct Microbial Communities in the Mariana and Kermadec Trenches
    RESEARCH ARTICLE Vertically distinct microbial communities in the Mariana and Kermadec trenches Logan M. Peoples1, Sierra Donaldson1, Oladayo Osuntokun1, Qing Xia1,2, Alex Nelson3, Jessica Blanton1, Eric E. Allen1, Matthew J. Church3,4, Douglas H. Bartlett1* 1 Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, United States of America, 2 Department of Soil Science, North Carolina State University, Raleigh, NC, United States of America, 3 Center for Microbial Oceanography: Research and Education, C- MORE Hale, University of Hawai`i at Mānoa, Honolulu, HI, United States of America, 4 Flathead Lake Biological Station, University of Montana, Polson, MT, United States of America a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 a1111111111 Abstract Hadal trenches, oceanic locations deeper than 6,000 m, are thought to have distinct micro- bial communities compared to those at shallower depths due to high hydrostatic pressures, OPEN ACCESS topographical funneling of organic matter, and biogeographical isolation. Here we evaluate the hypothesis that hadal trenches contain unique microbial biodiversity through analyses of Citation: Peoples LM, Donaldson S, Osuntokun O, Xia Q, Nelson A, Blanton J, et al. (2018) Vertically the communities present in the bottom waters of the Kermadec and Mariana trenches. Esti- distinct microbial communities in the Mariana and mates of microbial protein production indicate active populations under in situ hydrostatic Kermadec trenches. PLoS ONE 13(4): e0195102. pressures and increasing adaptation to pressure with depth. Depth, trench of collection, and https://doi.org/10.1371/journal.pone.0195102 size fraction are important drivers of microbial community structure. Many putative hadal Editor: Hauke Smidt, Wageningen University, bathytypes, such as members related to the Marinimicrobia, Rhodobacteraceae, Rhodos- NETHERLANDS pirilliceae, and Aquibacter, are similar to members identified in other trenches.
    [Show full text]
  • The Editing of Eddic Poetry Judy Quinn
    A HANDBOOK TO EDDIC POETRY This is the first comprehensive and accessible survey in English of Old Norse eddic poetry: a remarkable body of literature rooted in the Viking Age, which is a critical source for the study of early Scandinavian myths, poetics, culture, and society. Dramatically recreating the voices of the legendary past, eddic poems distil moments of high emotion as human heroes and supernatural beings alike grapple with betrayal, loyalty, mortality, and love. These poems relate the most famous deeds of gods such as Óðinn and Þórr with their adversaries the giants; they bring to life the often fraught interactions between kings, queens, and heroes as well as their encounters with valkyries, elves, dragons, and dwarfs. Written by leading international scholars, the chapters in this volume showcase the poetic riches of the eddic corpus and reveal its relevance to the history of poetics, gender studies, pre-Christian religions, art history, and archaeology. carolyne larrington is Official Fellow and Tutor at St John’s College, University of Oxford. judy quinn is Reader in Old Norse Literature in the Department of Anglo-Saxon, Norse and Celtic at the University of Cambridge. brittany schorn is a Research Associate in the Department of Anglo-Saxon, Norse and Celtic at the University of Cambridge. A HANDBOOK TO EDDIC POETRY Myths and Legends of Early Scandinavia CAROLYNE LARRINGTON University of Oxford JUDY QUINN University of Cambridge BRITTANY SCHORN University of Cambridge University Printing House, Cambridge cb2 8bs, United Kingdom Cambridge University Press is part of the University of Cambridge. It furthers the University’s mission by disseminating knowledge in the pursuit of education, learning, and research at the highest international levels of excellence.
    [Show full text]
  • Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights Into the Origin and Distribution of Nitrogen Fixation Across Bacteria and Archaea
    microorganisms Article Phylogeny of Nitrogenase Structural and Assembly Components Reveals New Insights into the Origin and Distribution of Nitrogen Fixation across Bacteria and Archaea Amrit Koirala 1 and Volker S. Brözel 1,2,* 1 Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57006, USA; [email protected] 2 Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0004, South Africa * Correspondence: [email protected]; Tel.: +1-605-688-6144 Abstract: The phylogeny of nitrogenase has only been analyzed using the structural proteins NifHDK. As nifHDKENB has been established as the minimum number of genes necessary for in silico predic- tion of diazotrophy, we present an updated phylogeny of diazotrophs using both structural (NifHDK) and cofactor assembly proteins (NifENB). Annotated Nif sequences were obtained from InterPro from 963 culture-derived genomes. Nif sequences were aligned individually and concatenated to form one NifHDKENB sequence. Phylogenies obtained using PhyML, FastTree, RapidNJ, and ASTRAL from individuals and concatenated protein sequences were compared and analyzed. All six genes were found across the Actinobacteria, Aquificae, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Deferribacteres, Firmicutes, Fusobacteria, Nitrospira, Proteobacteria, PVC group, and Spirochaetes, as well as the Euryarchaeota. The phylogenies of individual Nif proteins were very similar to the overall NifHDKENB phylogeny, indicating the assembly proteins have evolved together. Our higher resolution database upheld the three cluster phylogeny, but revealed undocu- Citation: Koirala, A.; Brözel, V.S. mented horizontal gene transfers across phyla. Only 48% of the 325 genera containing all six nif genes Phylogeny of Nitrogenase Structural and Assembly Components Reveals are currently supported by biochemical evidence of diazotrophy.
    [Show full text]