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Arxiv:2105.11503V2 [Physics.Bio-Ph] 26 May 2021 3.1 Geometry and Swimming Speeds of the Cells
The Bank Of Swimming Organisms at the Micron Scale (BOSO-Micro) Marcos F. Velho Rodrigues1, Maciej Lisicki2, Eric Lauga1,* 1 Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, United Kingdom. 2 Faculty of Physics, University of Warsaw, Warsaw, Poland. *Email: [email protected] Abstract Unicellular microscopic organisms living in aqueous environments outnumber all other creatures on Earth. A large proportion of them are able to self-propel in fluids with a vast diversity of swimming gaits and motility patterns. In this paper we present a biophysical survey of the available experimental data produced to date on the characteristics of motile behaviour in unicellular microswimmers. We assemble from the available literature empirical data on the motility of four broad categories of organisms: bacteria (and archaea), flagellated eukaryotes, spermatozoa and ciliates. Whenever possible, we gather the following biological, morphological, kinematic and dynamical parameters: species, geometry and size of the organisms, swimming speeds, actuation frequencies, actuation amplitudes, number of flagella and properties of the surrounding fluid. We then organise the data using the established fluid mechanics principles for propulsion at low Reynolds number. Specifically, we use theoretical biophysical models for the locomotion of cells within the same taxonomic groups of organisms as a means of rationalising the raw material we have assembled, while demonstrating the variability for organisms of different species within the same group. The material gathered in our work is an attempt to summarise the available experimental data in the field, providing a convenient and practical reference point for future studies. Contents 1 Introduction 2 2 Methods 4 2.1 Propulsion at low Reynolds number . -
Genomic Encyclopedia of Sugar Utilization Pathways in The
Rodionov et al. BMC Genomics 2010, 11:494 http://www.biomedcentral.com/1471-2164/11/494 RESEARCH ARTICLE Open Access Genomic encyclopedia of sugar utilization pathways in the Shewanella genus Dmitry A Rodionov1,2, Chen Yang1,3, Xiaoqing Li1, Irina A Rodionova1, Yanbing Wang4, Anna Y Obraztsova4,7, Olga P Zagnitko5, Ross Overbeek5, Margaret F Romine6, Samantha Reed6, James K Fredrickson6, Kenneth H Nealson4,7, Andrei L Osterman1,5* Abstract Background: Carbohydrates are a primary source of carbon and energy for many bacteria. Accurate projection of known carbohydrate catabolic pathways across diverse bacteria with complete genomes constitutes a substantial challenge due to frequent variations in components of these pathways. To address a practically and fundamentally important challenge of reconstruction of carbohydrate utilization machinery in any microorganism directly from its genomic sequence, we combined a subsystems-based comparative genomic approach with experimental validation of selected bioinformatic predictions by a combination of biochemical, genetic and physiological experiments. Results: We applied this integrated approach to systematically map carbohydrate utilization pathways in 19 genomes from the Shewanella genus. The obtained genomic encyclopedia of sugar utilization includes ~170 protein families (mostly metabolic enzymes, transporters and transcriptional regulators) spanning 17 distinct pathways with a mosaic distribution across Shewanella species providing insights into their ecophysiology and adaptive evolution. Phenotypic -
Hal 89-106 Alimuddin Enzim
Microbial community of black band disease on infection ... (Ofri Johan) MICROBIAL COMMUNITY OF BLACK BAND DISEASE ON INFECTION, HEALTHY, AND DEAD PART OF SCLERACTINIAN Montipora sp. COLONY AT SERIBU ISLANDS, INDONESIA Ofri Johan*)#, Dietriech G. Bengen**), Neviaty P. Zamani**), Suharsono***), David Smith****), Angela Mariana Lusiastuti*****), and Michael J. Sweet******) *) Research and Development Institute for Ornamental Fish Culture, Jakarta **) Department of Marine Science and Technology, Faculty of Fisheries and Marine Science, Bogor Agricultural University ***) Research Center for Oceanography, The Indonesian Institute of Science ****) School of Biology, Newcastle University, NE1 7RU, United Kingdom *****) Center for Aquaculture Research and Development ******) Biological Sciences Research Group, University of Derby, Kedleston Road, Derby, DE22 1GB, United Kingdom (Received 19 March 2014; Final revised 12 September 2014; Accepted 10 November 2014) ABSTRACT It is crucial to understand the microbial community associated with the host when attempting to discern the pathogen responsible for disease outbreaks in scleractinian corals. This study determines changes in the bacterial community associated with Montipora sp. in response to black band disease in Indonesian waters. Healthy, diseased, and dead Montipora sp. (n = 3 for each sample type per location) were collected from three different locations (Pari Island, Pramuka Island, and Peteloran Island). DGGE (Denaturing Gradient Gel Electrophoresis) was carried out to identify the bacterial community associated with each sample type and histological analysis was conducted to identify pathogens associated with specific tissues. Various Desulfovibrio species were found as novelty to be associated with infection samples, including Desulfovibrio desulfuricans, Desulfovibrio magneticus, and Desulfovibrio gigas, Bacillus benzoevorans, Bacillus farraginis in genus which previously associated with pathogenicity in corals. -
Genes for Transport and Metabolism of Spermidine in Ruegeria Pomeroyi DSS-3 and Other Marine Bacteria
Vol. 58: 311–321, 2010 AQUATIC MICROBIAL ECOLOGY Published online February 11 doi: 10.3354/ame01367 Aquat Microb Ecol Genes for transport and metabolism of spermidine in Ruegeria pomeroyi DSS-3 and other marine bacteria Xiaozhen Mou1,*, Shulei Sun2, Pratibha Rayapati2, Mary Ann Moran2 1Department of Biological Sciences, Kent State University, Kent, Ohio 44242, USA 2Department of Marine Sciences, University of Georgia, Athens, Georgia 30602, USA ABSTRACT: Spermidine, putrescine, and other polyamines are sources of labile carbon and nitrogen in marine environments, yet a thorough analysis of the functional genes encoding their transport and metabolism by marine bacteria has not been conducted. To begin this endeavor, we first identified genes that mediate spermidine processing in the model marine bacterium Ruegeria pomeroyi and then surveyed their abundance in other cultured and uncultured marine bacteria. R. pomeroyi cells were grown on spermidine under continuous culture conditions. Microarray-based transcriptional profiling and reverse transcription-qPCR analysis were used to identify the operon responsible for spermidine transport. Homologs from 2 of 3 known pathways for bacterial polyamine degradation were also identified in the R. pomeroyi genome and shown to be upregulated by spermidine. In an analysis of genome sequences of 109 cultured marine bacteria, homologs to polyamine transport and degradation genes were found in 55% of surveyed genomes. Likewise, analysis of marine meta- genomic data indicated that up to 32% of surface ocean bacterioplankton contain homologs for trans- port or degradation of polyamines. The degradation pathway genes puuB (γ-glutamyl-putrescine oxi- dase) and spuC (putrescine aminotransferase), which are part of the spermidine degradation pathway in R. -
Enhanced Eicosapentaenoic Acid Production by a New Deep-Sea Marine Bacterium Shewanella Electrodiphila MAR441T
RESEARCH ARTICLE Enhanced eicosapentaenoic acid production by a new deep-sea marine bacterium Shewanella electrodiphila MAR441T Jinwei Zhang1,2, J. Grant Burgess2* 1 Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, Hatherly Laboratory, Exeter, United Kingdom, 2 School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom * [email protected] a1111111111 a1111111111 Abstract a1111111111 a1111111111 Omega-3 fatty acids are products of secondary metabolism, essential for growth and impor- a1111111111 tant for human health. Although there are numerous reports of bacterial production of omega-3 fatty acids, less information is available on the biotechnological production of these compounds from bacteria. The production of eicosapentaenoic acid (EPA, 20:5ω3) by a new species of marine bacteria Shewanella electrodiphila MAR441T was investigated OPEN ACCESS under different fermentation conditions. This strain produced a high percentage (up to 26%) Citation: Zhang J, Burgess JG (2017) Enhanced of total fatty acids and high yields (mg / g of biomass) of EPA at or below the optimal growth eicosapentaenoic acid production by a new deep- temperature. At higher growth temperatures these values decreased greatly. The amount of sea marine bacterium Shewanella electrodiphila MAR441T. PLoS ONE 12(11): e0188081. https:// EPA produced was affected by the carbon source, which also influenced fatty acid composi- + doi.org/10.1371/journal.pone.0188081 tion. This strain required Na for growth and EPA synthesis and cells harvested at late expo- Editor: Yoshiaki Taniyama, Osaka University nential or early stationary phase had a higher EPA content. Both the highest amounts (20 -1 Graduate School of Medicine, JAPAN mg g ) and highest percent EPA content (18%) occurred with growth on L-proline and -1 Received: January 12, 2017 (NH4)2SO4. -
Bioactivity of Serratiochelin A, a Siderophore Isolated from a Co-Culture of Serratia Sp
microorganisms Article Bioactivity of Serratiochelin A, a Siderophore Isolated from a Co-Culture of Serratia sp. and Shewanella sp. 1, , 1, , 2 1 Yannik Schneider * y , Marte Jenssen * y , Johan Isaksson , Kine Østnes Hansen , Jeanette Hammer Andersen 1 and Espen H. Hansen 1 1 Marbio, Faculty for Fisheries, Biosciences and Economy, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; [email protected] (K.Ø.H.); [email protected] (J.H.A.); [email protected] (E.H.H.) 2 Department of Chemistry, Faculty of Natural Sciences, UiT—The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; [email protected] * Correspondence: [email protected] (Y.S.); [email protected] (M.J.); Tel.: +47-7764-9267 (Y.S.); +47-7764-9275 (M.J.) These authors contributed equally to the work. y Received: 15 June 2020; Accepted: 10 July 2020; Published: 14 July 2020 Abstract: Siderophores are compounds with high affinity for ferric iron. Bacteria produce these compounds to acquire iron in iron-limiting conditions. Iron is one of the most abundant metals on earth, and its presence is necessary for many vital life processes. Bacteria from the genus Serratia contribute to the iron respiration in their environments, and previously several siderophores have been isolated from this genus. As part of our ongoing search for medicinally relevant compounds produced by marine microbes, a co-culture of a Shewanella sp. isolate and a Serratia sp. isolate, grown in iron-limited conditions, was investigated, and the rare siderophore serratiochelin A (1) was isolated with high yields. -
Comparative Genomic Reconstruction of Transcriptional Networks Controlling Central Metabolism in the Shewanella Genus
Lawrence Berkeley National Laboratory Recent Work Title Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. Permalink https://escholarship.org/uc/item/11c6359g Journal BMC genomics, 12 Suppl 1(SUPPL. 1) ISSN 1471-2164 Authors Rodionov, Dmitry A Novichkov, Pavel S Stavrovskaya, Elena D et al. Publication Date 2011-06-15 DOI 10.1186/1471-2164-12-s1-s3 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Rodionov et al. BMC Genomics 2011, 12(Suppl 1):S3 http://www.biomedcentral.com/1471-2164/12/S1/S3 RESEARCH Open Access Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus Dmitry A Rodionov1,2*†, Pavel S Novichkov3†, Elena D Stavrovskaya2,4, Irina A Rodionova1, Xiaoqing Li1, Marat D Kazanov1,2, Dmitry A Ravcheev1,2, Anna V Gerasimova3, Alexey E Kazakov2,3, Galina Yu Kovaleva2, Elizabeth A Permina5, Olga N Laikova5, Ross Overbeek6, Margaret F Romine7, James K Fredrickson7, Adam P Arkin3, Inna Dubchak3,8, Andrei L Osterman1,6, Mikhail S Gelfand2,4 Abstract Background: Genome-scale prediction of gene regulation and reconstruction of transcriptional regulatory networks in bacteria is one of the critical tasks of modern genomics. The Shewanella genus is comprised of metabolically versatile gamma-proteobacteria, whose lifestyles and natural environments are substantially different from Escherichia coli and other model bacterial species. The comparative genomics approaches and computational identification of regulatory sites are useful for the in silico reconstruction of transcriptional regulatory networks in bacteria. Results: To explore conservation and variations in the Shewanella transcriptional networks we analyzed the repertoire of transcription factors and performed genomics-based reconstruction and comparative analysis of regulons in 16 Shewanella genomes. -
For Peer Review
Extremophiles Draft Manuscript for Review Microbial diversity and adaptation to high hydrostatic pressure in deep sea hydrothermal vents prokaryotes Journal:For Extremophiles Peer Review Manuscript ID: EXT-15-Feb-0030.R1 Manuscript Type: Review Date Submitted by the Author: n/a Complete List of Authors: jebbar, mohamed; Université de Bretagne Occidentale, Institut Universitaire Europeen de la Mer Franzetti, Bruno; CNRS, Institut de Biologie Structurale Girard, Eric; CNRS, Institut de Biologie Structurale Oger, Phil; Laboratoire de Sciences de la Terre, Ecole Normale Superieure (Extreme) thermophilic microorganisms and their enzymology, Anaerobes, Keyword: Archaea, Hyperthermophiles, Piezophiles, Enzymes, Deep sea vent microbiology, Ecology, phylogeny, physiology of thermophiles Page 1 of 82 Extremophiles 1 2 3 1 Microbial diversity and adaptation to high hydrostatic pressure in deep sea 4 5 2 hydrothermal vents prokaryotes 6 7 3 Mohamed Jebbar 1,2, 3*, Bruno Franzetti 4,5,6, Eric Girard 4,5,6, and Philippe Oger 7 8 9 10 4 11 1 12 5 Université de Bretagne Occidentale, UMR 6197-Laboratoire de Microbiologie des 13 14 6 Environnements Extrêmes (LM2E), Institut Universitaire Européen de la Mer (IUEM), 15 16 7 rue Dumont d’Urville, 29 280 Plouzané, France 17 18 8 2 CNRS, UMRFor 6197-Laboratoire Peer de MicrobiologieReview des Environnements Extrêmes 19 20 21 9 (LM2E), Institut Universitaire Européen de la Mer (IUEM), rue Dumont d’Urville, 29 22 23 10 280 Plouzané, France 24 25 11 3 Ifremer, UMR 6197-Laboratoire de Microbiologie des Environnements -
Characteristics of Deep-Sea Environments and Biodiversity of Piezophilic Organisms - Kato, Chiaki, Horikoshi, Koki
EXTREMOPHILES – Vol. III - Characteristics of Deep-Sea Environments and Biodiversity of Piezophilic Organisms - Kato, Chiaki, Horikoshi, Koki CHARACTERISTICS OF DEEP-SEA ENVIRONMENTS AND BIODIVERSITY OF PIEZOPHILIC ORGANISMS Kato, Chiaki Department of Marine Ecosystems Research, Japan Marine Science and Technology Center, Japan Horikoshi, Koki Department of Engineering, Toyo University, Japan Keywords: Biodiversity, deep sea, gene expression, high pressure, piezophiles, respiratory chain components, transcription Contents 1. Investigation of Life in a High-Pressure Environment 2. JAMSTEC Exploration of the Deep-Sea High-Pressure Environment 3. Taxonomic Identification of Piezophilic Bacteria 3.1. Isolation of Piezophiles and their Growth Properties 3.2 Taxonomic Characterization and Phylogenetic Relations 4. Biodiversity of Piezophiles in the Ocean Environment 4.1. Microbial Diversity of the Deep-Sea Environment at Different Depths 4.2 Changes in Microbial Diversity under High-Pressure Cultivation 4.3. Diversity of Deep-Sea Shewanella Is Related to Deep Ocean Circulation 4.3.1. Diversity, Phylogenetic Relationships, and Growth Properties of Shewanella Species Under Pressure Conditions 4.3.2. Relations between Shewanella Phylogenetic Structure and Deep Ocean Circulation 5. Molecular Mechanisms of Adaptation to the High-Pressure Environment 5.1. Mechanisms of Transcriptional Regulation under Pressure Conditions in Piezophiles 5.1.1. Pressure-Regulated Promoter of S. violacea Strain DSS12 5.1.2. Analysis of the Region Upstream From The Pressure-Regulated Genes 5.1.3. Possible Model of Molecular Mechanisms of Pressure-Regulated Transcription By The Sigma 54 Factor 5.2. EffectUNESCO of Pressure on Respiratory Chain – ComponentsEOLSS in Piezophiles 5.2.1. Respiratory Systems In S. violacea Strain DSS12 5.2.2. -
Shewanella Algae Relatives Capable of Generating Electricity From
Microbes Environ. Vol. 35, No. 2, 2020 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME19161 Shewanella algae Relatives Capable of Generating Electricity from Acetate Contribute to Coastal-Sediment Microbial Fuel Cells Treating Complex Organic Matter Yoshino Inohana1, Shohei Katsuya1, Ryota Koga1, Atsushi Kouzuma1, and Kazuya Watanabe1* 1School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432–1 Horinouchi, Hachioji 192–0392, Tokyo, Japan (Received December 6, 2019—Accepted January 28, 2020—Published online March 6, 2020) To identify exoelectrogens involved in the generation of electricity from complex organic matter in coastal sediment (CS) microbial fuel cells (MFCs), MFCs were inoculated with CS obtained from tidal flats and estuaries in the Tokyo bay and supplemented with starch, peptone, and fish extract as substrates. Power output was dependent on the CS used as inocula and ranged between 100 and 600 mW m–2 (based on the projected area of the anode). Analyses of anode microbiomes using 16S rRNA gene amplicons revealed that the read abundance of some bacteria, including those related to Shewanella algae, positively correlated with power outputs from MFCs. Some fermentative bacteria were also detected as major populations in anode microbiomes. A bacterial strain related to S. algae was isolated from MFC using an electrode plate-culture device, and pure-culture experiments demonstrated that this strain exhibited the ability to generate electricity from organic acids, including acetate. These results suggest that acetate-oxidizing S. algae relatives generate electricity from fermentation products in CS-MFCs that decompose complex organic matter. Key words: coastal sediment, microbial fuel cell, metabarcoding, exoelectrogen, electrode-plate culture A microbial fuel cell (MFC) is a type of bioelectrochemi‐ trogens (Kouzuma et al., 2018). -
Bacterial Diversity and Bioprospecting for Cold-Active Hydrolytic Enzymes from Culturable Bacteria Associated with Sediment from Nella Fjord, Eastern Antarctica
Mar. Drugs 2011, 9, 184-195; doi:10.3390/md9020184 OPEN ACCESS Marine Drugs ISSN 1660-3397 www.mdpi.com/journal/marinedrugs Article Bacterial Diversity and Bioprospecting for Cold-Active Hydrolytic Enzymes from Culturable Bacteria Associated with Sediment from Nella Fjord, Eastern Antarctica Yong Yu *, Hui-Rong Li, Yin-Xin Zeng and Bo Chen SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, 200136, China; E-Mails: [email protected] (H.-R.L.); [email protected] (Y.-X.Z.); [email protected] (B.C.) * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +86-21-58717207; Fax: +86-21-58711663. Received: 17 December 2010; in revised form: 4 January 2011 / Accepted: 14 January 2011 / Published: 31 January 2011 Abstract: The diversity and cold-active hydrolytic enzymes of culturable bacteria associated with sandy sediment from Nella Fjord, Eastern Antarctica (69°22′6″ S, 76°21′45″ E) was investigated. A total of 33 aerobic heterotrophic bacterial strains were isolated at 4 °C. These bacterial isolates could be sorted into 18 phylotypes based on the 16S rRNA gene sequence belonging to four phyla, namely Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Actinobacteria. Only seven isolates were psychrophilic, 15 isolates were moderately psychrophilic, and 11 isolates were psychrotolerant. More than 72% of the isolates required sodium chloride to grow. Esterase, -glucosidase and proteases activities at 4 °C were detected in more than 45% of the strains while approximately 21%, 15% and 12% of the strains possessed lipase, amylase and chitinase, respectively. These results indicate that a relatively high culturable bacterial diversity is present within marine sediment of Nella Fjord and it could serve as an ideal candidate region for bioprospecting. -
Biological Composition and Microbial Dynamics of Sinking Particulate Organic Matter at Abyssal Depths in the Oligotrophic Open Ocean
Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean Dominique Boeufa,1, Bethanie R. Edwardsa,1,2, John M. Eppleya,1, Sarah K. Hub,3, Kirsten E. Poffa, Anna E. Romanoa, David A. Caronb, David M. Karla, and Edward F. DeLonga,4 aDaniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Manoa, Honolulu, HI 96822; and bDepartment of Biological Sciences, University of Southern California, Los Angeles, CA 90089 Contributed by Edward F. DeLong, April 22, 2019 (sent for review February 21, 2019; reviewed by Eric E. Allen and Peter R. Girguis) Sinking particles are a critical conduit for the export of organic sample both suspended as well as slowly sinking POM. Because material from surface waters to the deep ocean. Despite their filtration methods can be biased by the volume of water filtered importance in oceanic carbon cycling and export, little is known (21), also collect suspended particles, and may under-sample about the biotic composition, origins, and variability of sinking larger, more rapidly sinking particles, it remains unclear how well particles reaching abyssal depths. Here, we analyzed particle- they represent microbial communities on sinking POM in the associated nucleic acids captured and preserved in sediment traps deep sea. Sediment-trap sampling approaches have the potential at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9- to overcome some of these difficulties because they selectively month time-series, Bacteria dominated both the rRNA-gene and capture sinking particles. rRNA pools, followed by eukaryotes (protists and animals) and trace The Hawaii Ocean Time-series Station ALOHA is an open- amounts of Archaea.