Viral Regulation of Nutrient Assimilation by Algae and Prokaryotes
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Updating the Taxonomic Toolbox: Classification of Alteromonas Spp
1 Updating the taxonomic toolbox: classification of Alteromonas spp. 2 using Multilocus Phylogenetic Analysis and MALDI-TOF Mass 3 Spectrometry a a a 4 Hooi Jun Ng , Hayden K. Webb , Russell J. Crawford , François a b b c 5 Malherbe , Henry Butt , Rachel Knight , Valery V. Mikhailov and a, 6 Elena P. Ivanova * 7 aFaculty of Life and Social Sciences, Swinburne University of Technology, 8 PO Box 218, Hawthorn, Vic 3122, Australia 9 bBioscreen, Bio21 Institute, The University of Melbourne, Vic 3010, Australia 10 cG.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian 11 Academy of Sciences, Vladivostok 690022, Russian Federation 12 13 *Corresponding author: Tel: +61-3-9214-5137. Fax: +61-3-9214-5050. 14 E-mail: [email protected] 15 16 Abstract 17 Bacteria of the genus Alteromonas are Gram-negative, strictly aerobic, motile, 18 heterotrophic marine bacteria, known for their versatile metabolic activities. 19 Identification and classification of novel species belonging to the genus Alteromonas 20 generally involves DNA-DNA hybridization (DDH) as distinct species often fail to be 1 21 resolved at the 97% threshold value of the 16S rRNA gene sequence similarity. In this 22 study, the applicability of Multilocus Phylogenetic Analysis (MLPA) and Matrix- 23 Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF 24 MS) for the differentiation of Alteromonas species has been evaluated. Phylogenetic 25 analysis incorporating five house-keeping genes (dnaK, sucC, rpoB, gyrB, and rpoD) 26 revealed a threshold value of 98.9% that could be considered as the species cut-off 27 value for the delineation of Alteromonas spp. -
Dilution-To-Extinction Culturing of SAR11 Members and Other Marine Bacteria from the Red Sea
Dilution-to-extinction culturing of SAR11 members and other marine bacteria from the Red Sea Thesis written by Roslinda Mohamed In Partial Fulfillment of the Requirements For the Degree of Master of Science (MSc.) in Marine Science King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia December 2013 2 The thesis of Roslinda Mohamed is approved by the examination committee. Committee Chairperson: Ulrich Stingl Committee Co-Chair: NIL Committee Members: Pascal Saikaly David Ngugi King Abdullah University of Science and Technology 2013 3 Copyright © December 2013 Roslinda Mohamed All Rights Reserved 4 ABSTRACT Dilution-to-extinction culturing of SAR11 members and other marine bacteria from the Red Sea Roslinda Mohamed Life in oceans originated about 3.5 billion years ago where microbes were the only life form for two thirds of the planet’s existence. Apart from being abundant and diverse, marine microbes are involved in nearly all biogeochemical processes and are vital to sustain all life forms. With the overgrowing number of data arising from culture-independent studies, it became necessary to improve culturing techniques in order to obtain pure cultures of the environmentally significant bacteria to back up the findings and test hypotheses. Particularly in the ultra-oligotrophic Red Sea, the ubiquitous SAR11 bacteria has been reported to account for more than half of the surface bacterioplankton community. It is therefore highly likely that SAR11, and other microbial life that exists have developed special adaptations that enabled them to thrive successfully. Advances in conventional culturing have made it possible for abundant, unculturable marine bacteria to be grown in the lab. -
Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment
Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen. -
Genome of Phaeocystis Globosa Virus Pgv-16T Highlights the Common Ancestry of the Largest Known DNA Viruses Infecting Eukaryotes
Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes Sebastien Santinia, Sandra Jeudya, Julia Bartolia, Olivier Poirota, Magali Lescota, Chantal Abergela, Valérie Barbeb, K. Eric Wommackc, Anna A. M. Noordeloosd, Corina P. D. Brussaardd,e,1, and Jean-Michel Claveriea,f,1 aStructural and Genomic Information Laboratory, Unité Mixte de Recherche 7256, Centre National de la Recherche Scientifique, Aix-Marseille Université, 13288 Marseille Cedex 9, France; bCommissariat à l’Energie Atomique–Institut de Génomique, 91057 Evry Cedex, France; cDepartment of Plant and Soil Sciences, University of Delaware, Newark, DE 19711; dDepartment of Biological Oceanography, Royal Netherlands Institute for Sea Research, NL-1790 AB Den Burg (Texel), The Netherlands; eAquatic Microbiology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands; and fService de Santé Publique et d’Information Médicale, Hôpital de la Timone, Assistance Publique–Hôpitaux de Marseille, FR-13385 Marseille, France Edited by James L. Van Etten, University of Nebraska, Lincoln, NE, and approved May 1, 2013 (received for review February 22, 2013) Large dsDNA viruses are involved in the population control of many viruses: 730 kb and 1.28 Mb for CroV and Megavirus chilensis, globally distributed species of eukaryotic phytoplankton and have respectively. Other studies, targeting virus-specific genes [e.g., a prominent role in bloom termination. The genus Phaeocystis (Hap- DNA polymerase B (8) or capsid proteins (9)] have suggested tophyta, Prymnesiophyceae) includes several high-biomass-forming a close phylogenetic relationship between Mimivirus and several phytoplankton species, such as Phaeocystis globosa, the blooms of giant dsDNA viruses infecting various unicellular algae such as which occur mostly in the coastal zone of the North Atlantic and the Pyramimonas orientalis (Chlorophyta, Prasinophyceae), Phaeocys- North Sea. -
Impacts of Biogenic Polyunsaturated Aldehydes on Metabolism and Community
https://doi.org/10.5194/bg-2020-243 Preprint. Discussion started: 24 July 2020 c Author(s) 2020. CC BY 4.0 License. 1 Impacts of biogenic polyunsaturated aldehydes on metabolism and community 2 composition of particle-attached bacteria in coastal hypoxia 3 Zhengchao Wu1,2, Qian P. Li1,2,3,*, Zaiming Ge1,3, Bangqin Huang4, Chunming Dong5 4 1State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese 5 Academy of Sciences, Guangzhou, China 6 2Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China 7 3College of Marine Science, University of the Chinese Academy of Sciences, Beijing, China 8 4Fujian Provincial Key Laboratory of Coastal Ecology and Environmental Studies, State Key Laboratory of 9 Marine Environmental Science, Xiamen University, Xiamen, China 10 5Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, MNR, Xiamen, China 11 *Correspondence to: Qian Li ([email protected]) 12 13 Abstract. Eutrophication-driven coastal hypoxia is of great interest recently, though its mechanisms are not 14 fully understood. Here, we showed elevated concentrations of particulate and dissolved polyunsaturated 15 aldehydes (PUAs) associated with the hypoxic waters meanly dominated by particle-attached bacteria (PAB) 16 in the bottom water of a salt-wedge estuary. Particle-adsorbed PUAs of ~10 micromoles per liter particle in 17 the hypoxic waters were directly quantified for the first time using large-volume-filtration followed with 18 on-site derivation and extraction of the adsorbed PUAs. PUAs-amended incubation experiments for PAB 19 retrieved from the low-oxygen waters were also performed to explore the impacts of PUAs on the growth 20 and metabolism of PAB and associated oxygen utilization. -
Resilience of Microbial Communities After Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms
microorganisms Article Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms Tim Piel 1,†, Giovanni Sandrini 1,†,‡, Gerard Muyzer 1 , Corina P. D. Brussaard 1,2 , Pieter C. Slot 1, Maria J. van Herk 1, Jef Huisman 1 and Petra M. Visser 1,* 1 Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands; [email protected] (T.P.); [email protected] (G.S.); [email protected] (G.M.); [email protected] (C.P.D.B.); [email protected] (P.C.S.); [email protected] (M.J.v.H.); [email protected] (J.H.) 2 Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherland Institute for Sea Research, 1790 AB Den Burg, The Netherlands * Correspondence: [email protected]; Tel.: +31-20-5257073 † These authors have contributed equally to this work. ‡ Current address: Department of Technology & Sources, Evides Water Company, 3006 AL Rotterdam, The Netherlands. Abstract: Applying low concentrations of hydrogen peroxide (H2O2) to lakes is an emerging method to mitigate harmful cyanobacterial blooms. While cyanobacteria are very sensitive to H2O2, little Citation: Piel, T.; Sandrini, G.; is known about the impacts of these H2O2 treatments on other members of the microbial com- Muyzer, G.; Brussaard, C.P.D.; Slot, munity. In this study, we investigated changes in microbial community composition during two P.C.; van Herk, M.J.; Huisman, J.; −1 lake treatments with low H2O2 concentrations (target: 2.5 mg L ) and in two series of controlled Visser, P.M. -
Genome Sequence of Shimia Str. SK013, a Representative of the Roseobacter Group Isolated from Marine Sediment
Lawrence Berkeley National Laboratory Recent Work Title Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment. Permalink https://escholarship.org/uc/item/37s1p8pr Journal Standards in genomic sciences, 11(1) ISSN 1944-3277 Authors Kanukollu, Saranya Voget, Sonja Pohlner, Marion et al. Publication Date 2016 DOI 10.1186/s40793-016-0143-0 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Kanukollu et al. Standards in Genomic Sciences (2016) 11:25 DOI 10.1186/s40793-016-0143-0 EXTENDED GENOME REPORT Open Access Genome sequence of Shimia str. SK013, a representative of the Roseobacter group isolated from marine sediment Saranya Kanukollu1, Sonja Voget2, Marion Pohlner1, Verona Vandieken1, Jörn Petersen3, Nikos C. Kyrpides4,5, Tanja Woyke4, Nicole Shapiro4, Markus Göker3, Hans-Peter Klenk6, Heribert Cypionka1 and Bert Engelen1* Abstract Shimia strain SK013 is an aerobic, Gram-negative, rod shaped alphaproteobacterium affiliated with the Roseobacter group within the family Rhodobacteraceae. The strain was isolated from surface sediment (0–1 cm) of the Skagerrak at 114 m below sea level. The 4,049,808 bp genome of Shimia str. SK013 comprises 3,981 protein-coding genes and 47 RNA genes. It contains one chromosome and no extrachromosomal elements. The genome analysis revealed the presence of genes for a dimethylsulfoniopropionate lyase, demethylase and the trimethylamine methyltransferase (mttB) as well as genes for nitrate, nitrite and dimethyl sulfoxide reduction. This indicates that Shimia str. SK013 is able to switch from aerobic to anaerobic metabolism and thus is capable of aerobic and anaerobic sulfur cycling at the seafloor. -
Which Organisms Are Used for Anti-Biofouling Studies
Table S1. Semi-systematic review raw data answering: Which organisms are used for anti-biofouling studies? Antifoulant Method Organism(s) Model Bacteria Type of Biofilm Source (Y if mentioned) Detection Method composite membranes E. coli ATCC25922 Y LIVE/DEAD baclight [1] stain S. aureus ATCC255923 composite membranes E. coli ATCC25922 Y colony counting [2] S. aureus RSKK 1009 graphene oxide Saccharomycetes colony counting [3] methyl p-hydroxybenzoate L. monocytogenes [4] potassium sorbate P. putida Y. enterocolitica A. hydrophila composite membranes E. coli Y FESEM [5] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) K. pneumonia ATCC13883 P. aeruginosa BAA-1744 composite membranes E. coli Y SEM [6] (unspecified/unique sample type) S. aureus (unspecified/unique sample type) graphene oxide E. coli ATCC25922 Y colony counting [7] S. aureus ATCC9144 P. aeruginosa ATCCPAO1 composite membranes E. coli Y measuring flux [8] (unspecified/unique sample type) graphene oxide E. coli Y colony counting [9] (unspecified/unique SEM sample type) LIVE/DEAD baclight S. aureus stain (unspecified/unique sample type) modified membrane P. aeruginosa P60 Y DAPI [10] Bacillus sp. G-84 LIVE/DEAD baclight stain bacteriophages E. coli (K12) Y measuring flux [11] ATCC11303-B4 quorum quenching P. aeruginosa KCTC LIVE/DEAD baclight [12] 2513 stain modified membrane E. coli colony counting [13] (unspecified/unique colony counting sample type) measuring flux S. aureus (unspecified/unique sample type) modified membrane E. coli BW26437 Y measuring flux [14] graphene oxide Klebsiella colony counting [15] (unspecified/unique sample type) P. aeruginosa (unspecified/unique sample type) graphene oxide P. aeruginosa measuring flux [16] (unspecified/unique sample type) composite membranes E. -
Session #1 Abstracts
Poster Session 1 1. A Comparative Genomics Approach to Understanding the Roles of P53 Binding Sites Nicole Pelletier, Adrian Acuna Higaki and Lei Zhou, University of Florida Cancer is one of the leading causes of mortality worldwide, with over 8 million deaths per year. In more than 50% of cancers, the transcription factor P53 comes into play, serving as a tumor suppressor that exerts distinct anti-proliferative functions in response to a variety of oncogenic stressors. Through ChIP-Seq analysis, thousands of P53 binding sites in mammalian genomes have been previously identified, yet the functionality of these binding sites remains to be established. It is hypothesized that mutations or epigenetic silencing of non-coding regulatory sequences of P53 target genes play just as an important role in cancers as do the extensively studied coding regions of p53. By using Drosophila as a model organism, a comparative genomic approach to identify functional P53 binding sites and determine their roles in tumorigenesis is proposed. To do this, a library of significant P53 binding sites must first be established by looking at upregulated and downregulated genes obtained from RNA-seq and comparing them to our ChIP-Seq data. Next, CRISPR-Cas9 will be used to generate Drosophila models containing mutations in the P53 binding sites near the Drosophila pro-apoptotic genes Hid and Rpr. Selected adult flies containing the CRISPR-Cas9 induced mutations near the specific bindings sites will undergo irradiation induced DNA damage to assess their functional importance. By using this approach we will discover functional roles of non-coding regulatory regions in tumorigenesis and contribute to apoptosis inducing cancer therapies. -
Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services
Pioneering Soil Viromics to Elucidate Viral Impacts on Soil Ecosystem Services DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Gareth Trubl Graduate Program in Microbiology The Ohio State University 2018 Dissertation Committee: Virginia Rich, Advisor Matthew Sullivan, Co-Advisor Kelly Wrighton Matthew Anderson Copyrighted by Gareth Trubl 2018 Abstract Permafrost contains 30–50% of global soil carbon (C) and is rapidly thawing. While the fate of this C is unknown, it will be shaped in part by microbes and their associated viruses, which modulate microbial activities via mortality and metabolic control. To date, viral research in soils has been outpaced by that in aquatic environments due to the technical challenges of accessing soil viruses, compounded by the dramatic physicochemical heterogeneity in soils. The Stordalen Mire long-term ecological field site in Arctic Sweden encompasses a mosaic of natural permafrost thaw stages, and has been well characterized biogeochemically and microbiologically, making it an ideal site to characterize the soil virosphere and its potential impacts on the C cycle. A viral resuspension protocol was developed to generate quantitatively- amplified dsDNA viromes. The protocol yielded ~108 virus-like particles (VLPs) g−1 of soil across three thaw-stage habitats, and seven resulting viromes yielded 53 vOTUs. Viral-specific bioinformatics methods were used to recover viral populations, define their gene content, connect them to other related viruses (globally) and potential hosts (locally). Only 15% of these vOTUs had genetic similarity to publicly available viruses in the RefSeq database, and ∼30% of the genes could be annotated, supporting the concept of soils as reservoirs of substantial undescribed viral genetic diversity. -
Rapport Nederlands
Moleculaire detectie van bacteriën in dekaarde Dr. J.J.P. Baars & dr. G. Straatsma Plant Research International B.V., Wageningen December 2007 Rapport nummer 2007-10 © 2007 Wageningen, Plant Research International B.V. Alle rechten voorbehouden. Niets uit deze uitgave mag worden verveelvoudigd, opgeslagen in een geautomatiseerd gegevensbestand, of openbaar gemaakt, in enige vorm of op enige wijze, hetzij elektronisch, mechanisch, door fotokopieën, opnamen of enige andere manier zonder voorafgaande schriftelijke toestemming van Plant Research International B.V. Exemplaren van dit rapport kunnen bij de (eerste) auteur worden besteld. Bij toezending wordt een factuur toegevoegd; de kosten (incl. verzend- en administratiekosten) bedragen € 50 per exemplaar. Plant Research International B.V. Adres : Droevendaalsesteeg 1, Wageningen : Postbus 16, 6700 AA Wageningen Tel. : 0317 - 47 70 00 Fax : 0317 - 41 80 94 E-mail : [email protected] Internet : www.pri.wur.nl Inhoudsopgave pagina 1. Samenvatting 1 2. Inleiding 3 3. Methodiek 8 Algemene werkwijze 8 Bestudeerde monsters 8 Monsters uit praktijkteelten 8 Monsters uit proefteelten 9 Alternatieve analyse m.b.v. DGGE 10 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 11 4. Resultaten 13 Monsters uit praktijkteelten 13 Monsters uit proefteelten 16 Alternatieve analyse m.b.v. DGGE 23 Vaststellen van verschillen tussen de bacterie-gemeenschappen op myceliumstrengen en in de omringende dekaarde. 25 5. Discussie 28 6. Conclusies 33 7. Suggesties voor verder onderzoek 35 8. Gebruikte literatuur. 37 Bijlage I. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit commerciële teelten I-1 Bijlage II. Bacteriesoorten geïsoleerd uit dekaarde en van mycelium uit experimentele teelten II-1 1 1. -
Biodiversité Microbienne Dans Les Milieux Extrêmes Salés Du Nord-Est Algérien
اﻟﺟﻣﮭورﯾﺔ اﻟﺟزاﺋرﯾﺔ اﻟدﯾﻣﻘراطﯾﺔ اﻟﺷﻌﺑﯾﺔ République Algérienne Démocratique et Populaire وزارة اﻟتــﻋﻠﯾم اﻟﻊــــاﻟﻲ و اﻟبـــﺣث اﻟﻊـــﻟﻣﻲ Ministère de l’Enseignement Supérieur et de la Recherche Scientifique جـــاﻣﻌﺔ ﺑـﺎﺗـﻧـــــــــــــــﺔ Université Mustapha Ben Boulaid- Batna 2 2 كــــﻟﯾــــــﺔ عـــــﻟوم اﻟطــﺑﯾﻌـــــــﺔ ـوالحــــﯾﺎة Faculté des Sciences de la Nature et de la Vie ﻗـــﺳم اﻟﻣﯾﻛروﺑﯾوﻟوﺟﯾـــــــﺎ و اﻟﺑﯾوﻛﯾﻣﯾـــــــﺎء Département de Microbiologie et Biochimie Réf : …………………………… اﻟﻣـرﺟﻊ :………………….…… Thèse présentée par Taha MENASRIA En vue de l’obtention du diplôme de Doctorat en ScienceS Filière : Sciences Biologiques Spécialité : Microbiologie Appliquée Thème Biodiversité microbienne dans les milieux extrêmes salés du Nord-Est Algérien Devant le jury composé de : Président : Dr. Kamel AISSAT (Professeur) Univ. de Batna 2 Directeur de thèse : Dr. Hocine HACÈNE (Professeur) Univ. d’Alger (USTHB) Co-directeur de thèse : Dr. Abdelkrim SI BACHIR (Professeur) Univ. de Batna 2 Examinateur : Dr. Yacine BENHIZIA (Professeur) Univ. de Constantine 1 Examinateur : Dr. Mahmoud KITOUNI (Professeur) Univ. de Constantine 1 Examinateur : Dr. Lotfi LOUCIF (Maître de conférences ‘A’) Univ. de Batna 2 Membre invité : Dr. Ammar AYACHI (Professeur) Univ. de Batna 1 Année universitaire : 2019-2020 Remerciements C’est un devoir d’exprimer mes remerciements et reconnaissances à travers cette thèse à tous ceux qui par leurs aides, encouragements et leurs conseils ont facilité, de près ou de loin, à l’élaboration et à la réalisation de ce modeste travail. Mes remerciements vont en premier ordre et particulièrement à : Dr. Hocine HACÈNE (Professeur à l’Université d’USTHB, Alger) pour le grand honneur qu’il m’a fait en acceptant de diriger ce travail, pour ses conseils et ses encouragements durant la réalisation de cette thèse.