Bioluminescent Fish, Bacteria, and Experiential Learning
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Unlocking the Genomic Taxonomy of the Prochlorococcus Collective
bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Unlocking the genomic taxonomy of the Prochlorococcus collective Diogo Tschoeke1#, Livia Vidal1#, Mariana Campeão1, Vinícius W. Salazar1, Jean Swings1,2, Fabiano Thompson1*, Cristiane Thompson1* 1Laboratory of Microbiology. SAGE-COPPE and Institute of Biology. Federal University of Rio de Janeiro. Rio de Janeiro. Brazil. Av. Carlos Chagas Fo 373, CEP 21941-902, RJ, Brazil. 2Laboratory of Microbiology, Ghent University, Gent, Belgium. *Corresponding authors: E-mail: [email protected] , [email protected] Phone no.: +5521981041035, +552139386567 #These authors contributed equally. ABSTRACT 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.03.09.980698; this version posted March 11, 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 The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 4.0 International license. Prochlorococcus is the most abundant photosynthetic prokaryote on our planet. The extensive ecological literature on the Prochlorococcus collective (PC) is based on the assumption that it comprises one single genus comprising the species Prochlorococcus marinus, containing itself a collective of ecotypes. Ecologists adopt the distributed genome hypothesis of an open pan-genome to explain the observed genomic diversity and evolution patterns of the ecotypes within PC. -
Diverse Deep-Sea Anglerfishes Share a Genetically Reduced Luminous
RESEARCH ARTICLE Diverse deep-sea anglerfishes share a genetically reduced luminous symbiont that is acquired from the environment Lydia J Baker1*, Lindsay L Freed2, Cole G Easson2,3, Jose V Lopez2, Dante´ Fenolio4, Tracey T Sutton2, Spencer V Nyholm5, Tory A Hendry1* 1Department of Microbiology, Cornell University, New York, United States; 2Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, United States; 3Department of Biology, Middle Tennessee State University, Murfreesboro, United States; 4Center for Conservation and Research, San Antonio Zoo, San Antonio, United States; 5Department of Molecular and Cell Biology, University of Connecticut, Storrs, United States Abstract Deep-sea anglerfishes are relatively abundant and diverse, but their luminescent bacterial symbionts remain enigmatic. The genomes of two symbiont species have qualities common to vertically transmitted, host-dependent bacteria. However, a number of traits suggest that these symbionts may be environmentally acquired. To determine how anglerfish symbionts are transmitted, we analyzed bacteria-host codivergence across six diverse anglerfish genera. Most of the anglerfish species surveyed shared a common species of symbiont. Only one other symbiont species was found, which had a specific relationship with one anglerfish species, Cryptopsaras couesii. Host and symbiont phylogenies lacked congruence, and there was no statistical support for codivergence broadly. We also recovered symbiont-specific gene sequences from water collected near hosts, suggesting environmental persistence of symbionts. Based on these results we conclude that diverse anglerfishes share symbionts that are acquired from the environment, and *For correspondence: that these bacteria have undergone extreme genome reduction although they are not vertically [email protected] (LJB); transmitted. -
FDA: "Glowing" Seafood?
FDA: "Glowing" Seafood? http://web.archive.org/web/20080225162926/http://vm.cfsan.fda.gov/~ea... U.S. Food and Drug Administration Seafood Products Research Center July 1998 "GLOWING" SEAFOOD? by Patricia N. Sado* Introduction Seafood that produces a bright, blue-green light in the dark could be a meal from outer space or haute cuisine in a science fiction novel. The U. S. Food and Drug Administration (FDA) has received many consumer complaints about various seafood products "glowing" in the dark. Some of these consumers called their local health departments, poison control centers, and their U.S. Senator because they thought they had been poisoned by radiation. These consumers said they had trouble convincing people that their seafood was emitting light. One consumer took his imitation crabmeat to a local television station. Unfortunately his seafood had dried out and did not glow for the television reporters. Several consumers said that it took them many weeks before they found phone numbers for various government agencies to make inquiries. Several consumers thought their "glowing" seafood was due to phosphorescing phytoplankton, or even fluorescence. The consumers' seafood products "glowing" in the dark were not due to radiation or to fluorescence, which requires an ultraviolet light to trigger the reaction. These seafood products exhibited luminescence due to the presence of certain bacteria that are capable of emitting light. Luminescence by bacteria is due to a chemical reaction catalyzed by luciferase, a protein similar to that found in fireflies. The reaction involves oxidation of a reduced flavin mononucleotide and a long chain aliphatic aldehyde by molecular oxygen to produce oxidized flavin plus fatty acid and light (5, 12). -
Developments in Aquatic Microbiology
INTERNATL MICROBIOL (2000) 3: 203–211 203 © Springer-Verlag Ibérica 2000 REVIEW ARTICLE Samuel P. Meyers Developments in aquatic Department of Oceanography and Coastal Sciences, Louisiana State University, microbiology Baton Rouge, LA, USA Received 30 August 2000 Accepted 29 September 2000 Summary Major discoveries in marine microbiology over the past 4-5 decades have resulted in the recognition of bacteria as a major biomass component of marine food webs. Such discoveries include chemosynthetic activities in deep-ocean ecosystems, survival processes in oligotrophic waters, and the role of microorganisms in food webs coupled with symbiotic relationships and energy flow. Many discoveries can be attributed to innovative methodologies, including radioisotopes, immunofluores- cent-epifluorescent analysis, and flow cytometry. The latter has shown the key role of marine viruses in marine system energetics. Studies of the components of the “microbial loop” have shown the significance of various phagotrophic processes involved in grazing by microinvertebrates. Microbial activities and dissolved organic carbon are closely coupled with the dynamics of fluctuating water masses. New biotechnological approaches and the use of molecular biology techniques still provide new and relevant information on the role of microorganisms in oceanic and estuarine environments. International interdisciplinary studies have explored ecological aspects of marine microorganisms and their significance in biocomplexity. Studies on the Correspondence to: origins of both life and ecosystems now focus on microbiological processes in the Louisiana State University Station. marine environment. This paper describes earlier and recent discoveries in marine Post Office Box 19090-A. Baton Rouge, LA 70893. USA (aquatic) microbiology and the trends for future work, emphasizing improvements Tel.: +1-225-3885180 in methodology as major catalysts for the progress of this broadly-based field. -
The Evolution of Bacterial Shape Complexity by a Curvature-Inducing Module
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.20.954503; this version posted February 20, 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. Title: The evolution of bacterial shape complexity by a curvature-inducing module Authors: Nicholas R. Martin, Edith Blackman, Benjamin P. Bratton, Thomas M. Bartlett†, Zemer Gitai*. Affiliations: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA *Correspondence to: [email protected] †Present address: Department of Microbiology, Harvard Medical School, Boston, MA 02115 Abstract: Bacteria can achieve a staggering diversity of cell shapes that promote critical functions like growth, motility, and virulence1-4. Previous studies suggested that bacteria establish complex shapes by co-opting the core machineries essential for elongation and division5,6. In contrast, we discovered a two-protein module, CrvAB, that can curve bacteria autonomously of the major elongation and division machinery by forming a dynamic, asymmetrically-localized structure in the periplasm. CrvAB is essential for curvature in its native species, Vibrio cholerae, and is sufficient to curve multiple heterologous species spanning 2.5 billion years of evolution. Thus, modular shape determinants can promote the evolution of morphological complexity independently of existing cell shape regulation. Main Text: Cells come in a variety of shapes that contribute to fitness in diverse environments 1,2,7,8. In bacteria, cell curvature can influence motility and host colonization 1,3,4. -
Diversity and Evolution of Bacterial Bioluminescence Genes in the Global Ocean Thomas Vannier, Pascal Hingamp, Floriane Turrel, Lisa Tanet, Magali Lescot, Y
Diversity and evolution of bacterial bioluminescence genes in the global ocean Thomas Vannier, Pascal Hingamp, Floriane Turrel, Lisa Tanet, Magali Lescot, Y. Timsit To cite this version: Thomas Vannier, Pascal Hingamp, Floriane Turrel, Lisa Tanet, Magali Lescot, et al.. Diversity and evolution of bacterial bioluminescence genes in the global ocean. NAR Genomics and Bioinformatics, Oxford University Press, 2020, 2 (2), 10.1093/nargab/lqaa018. hal-02514159 HAL Id: hal-02514159 https://hal.archives-ouvertes.fr/hal-02514159 Submitted on 21 Mar 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Published online 14 March 2020 NAR Genomics and Bioinformatics, 2020, Vol. 2, No. 2 1 doi: 10.1093/nargab/lqaa018 Diversity and evolution of bacterial bioluminescence genes in the global ocean Thomas Vannier 1,2,*, Pascal Hingamp1,2, Floriane Turrel1, Lisa Tanet1, Magali Lescot 1,2,* and Youri Timsit 1,2,* 1Aix Marseille Univ, Universite´ de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France and 2Research / Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022 Tara GOSEE, 3 rue Michel-Ange, Downloaded from https://academic.oup.com/nargab/article-abstract/2/2/lqaa018/5805306 by guest on 21 March 2020 75016 Paris, France Received October 21, 2019; Revised February 14, 2020; Editorial Decision March 02, 2020; Accepted March 06, 2020 ABSTRACT ganisms and is particularly widespread in marine species (7–9). -
The Barracudina Genera Lestidium and Lestrolepis of Taiwan, with Descriptions of Two New Species (Aulopiformes: Paralepididae)
Zootaxa 4702 (1): 114–139 ISSN 1175-5326 (print edition) https://www.mapress.com/j/zt/ Article ZOOTAXA Copyright © 2019 Magnolia Press ISSN 1175-5334 (online edition) https://doi.org/10.11646/zootaxa.4702.1.16 http://zoobank.org/urn:lsid:zoobank.org:pub:DC33157E-E5E9-4CE2-AB3F-27E22F21A954 The barracudina genera Lestidium and Lestrolepis of Taiwan, with descriptions of two new species (Aulopiformes: Paralepididae) HSUAN-CHING HO1,2*, SONG-YU TSAI3 & HSING-HUI LI1,2 1National Museum of Marine Biology & Aquarium, Checheng, Pingtung, Taiwan 2Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan 3Institute of Marine Biology, National Sun-Yet-Son University, Kaohsiung, Taiwan *Corresponding author. E-mail:[email protected] Abstract Two genera of barracudinas with luminescent duct in abdominal cavity, Lestrolepis and Lestidium, collected from around Taiwan are studied. Two species in each genus are recognized in Taiwan, including one new species in each genus. New diagnostic characters are used to distinguish these species. Lestrolepis nigroventralis sp. nov. is similar to Lestrolepis intermedia and can be distinguished by having 32–35 prehaemal vertebrae; dorsal-fin origin slightly in front of midline of distance between origins of pelvic and anal fins, distance between origins of dorsal and pelvic fin 9.8–11.7% SL; and pelvic-fin origin at or slightly behind midline of body, prepelvic length 50.6–52.6% SL. Lestidium orientale sp. nov. is similar to Lestidium atlanticum and can be distinguished by having prehaemal vertebrae 37–40; caudal vertebrae 41–44; a relatively short and deep head, reflected by a shorter snout (9.7–10.4% SL), shorter upper jaw (8.6–10.1% SL), shorter lower jaw (11.9–13.7% SL) and a deeper head (31.2–33.9% HL). -
Revival and Phylogenetic Analysis of the Luminous Bacterial Cultures of MW Beijerinck
RESEARCH ARTICLE Historical microbiology: revival and phylogenetic analysis of the luminous bacterial cultures of M. W. Beijerinck Marian J. Figge1, Lesley A. Robertson2, Jennifer C. Ast3 & Paul V. Dunlap3 1The Netherlands Culture Collection of Bacteria, CBS-KNAW Fungal Biodiversity Centre, Utrecht, The Netherlands; 2Department of Biotechnology, Delft University of Technology, Delft, The Netherlands; and 3Department of Ecological and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA Correspondence: Paul V. Dunlap, Abstract Department of Ecology and Evolutionary Biology, University of Michigan, 830 North Luminous bacteria isolated by Martinus W. Beijerinck were sealed in glass University Ave., Ann Arbor, MI 48109-1048, ampoules in 1924 and 1925 and stored under the names Photobacterium phos- USA. Tel.: +1 734 615 9099; fax: +1 734 phoreum and ‘Photobacterium splendidum’. To determine if the stored cultures 763 0544; e-mail: [email protected] were viable and to assess their evolutionary relationship with currently recog- nized bacteria, portions of the ampoule contents were inoculated into culture Present address: Jennifer C. Ast, medium. Growth and luminescence were evident after 13 days of incubation, Evolutionary Biology Centre, Departments of Molecular Evolution and Limnology, Uppsala indicating the presence of viable cells after more than 80 years of storage. The University, Norbyva¨ gen 18C, 752 36, Beijerinck strains are apparently the oldest bacterial cultures to be revived from Uppsala, Sweden. storage. Multi-locus sequence analysis, based on the 16S rRNA, gapA, gyrB, pyrH, recA, luxA, and luxB genes, revealed that the Beijerinck strains are distant Received 3 May 2011; revised 21 July 2011; from the type strains of P. -
(COVIS) Overview
National Enteric Disease Surveillance: Cholera and Other Vibrio Illness Surveillance (COVIS) Surveillance System Overview: Cholera and Other Vibrio Illness Surveillance (COVIS) Background on infection with species from the family Vibrionaceae Infection with pathogenic species of the family Vibrionaceae can cause two distinct categories of infection: cholera and vibriosis, both of which are nationally notifiable. Cholera is, by definition, caused by infection with toxigenic Vibrio cholerae O1 or O139 and was first reported in the United States in 1832. Infection is characterized by acute, watery diarrhea. An average of 5-10 cases of cholera are reported annually in the United States; most are acquired during international travel, however, on average 1-2 per year are domestically acquired. An increase in the number of cholera cases reported in the United States has occurred when there are cholera outbreaks in the Western Hemisphere, such as Latin America in the 1990s and Haiti in 2010, with almost all attributable to exposures during international travel. CDC annually reports to the World Health Organization all confirmed cholera cases diagnosed in the United States. Vibriosis is caused by infection with any species of the family Vibrionaceae (excluding toxigenic Vibrio cholerae O1 and O139), with an estimated 80,000 cases and 300 deaths annually in the United States (1). The most common clinical manifestations are watery diarrhea, primary septicemia, wound infection, and otitis externa. Risk factors for illness include consumption of shellfish, -
Short Communication Isolation of Bioluminescent Bacteria From
Indian Journal of Geo Marine Sciences Vol. 49 (03), March 2020, pp. 471-476 Short Communication Isolation of bioluminescent bacteria from widely distributed light emitting organisms are marine organisms luminescent bacteria. Such bioluminescent bacteria are either found in planktonic form in the ocean6-12 or Paritosh Parmar, Arpit Shukla, Meenu Saraf & Baldev Patel* in symbiotic relationship with the marine host for instance certain fishes and squids2,8,13-17. Department of Microbiology & Biotechnology, University School of Sciences, Gujarat University, Ahmedabad-380 009, India The reaction which is responsible for emission of *[E-mail: [email protected]] light involves the enzyme luciferase that oxidizes long chain aliphatic aldehyde (RCHO), reduced flavin Received 31 July 2018; 05 October 2018 mononucleotide (FMNH2), and oxygen (O2) to a long chain aliphatic acid (RCOOH), oxidized flavin Bioluminescence is an emission of cold light by enzyme driven reaction within certain living organisms. The most mononucleotide (FMN), and water (H2O). In this abundant and widely distributed light emitting organisms are process, the excess energy is liberated and emitted as luminescent bacteria. Such organisms are either found as free- luminescent blue-green light of 490 nm (Fig. 1)4. All living in the ocean or in symbiotic relationship with the marine luminescent bacteria are distributed among three host. To employ bioluminescence in environmental monitoring, 4,18 isolation of bioluminescent bacteria from the two different marine genera Vibrio, Photobacterium, Xenorhabdus . samples (sea water sample and various organs of squid and fish) However, recently one more genera Kurthia has also were collected from different sites of Veraval seashore and fish been reported to be luminescent19. -
FAMILY Lestidiidae Harry, 1953 - Naked Barracudinas [=Lestidiini] Notes: Lestidiini Harry, 1953:229 [Ref
FAMILY Lestidiidae Harry, 1953 - naked barracudinas [=Lestidiini] Notes: Lestidiini Harry, 1953:229 [ref. 2045] (tribe) Lestidium GENUS Lestidiops Hubbs, 1916 - barracudinas [=Lestidiops Hubbs [C. L.], 1916:154] Notes: [ref. 2225]. Masc. Lestidiops sphyraenopsis Hubbs, 1916. Type by original designation (also monotypic). •Valid as Lestidiops Hubbs, 1916 – (Post 1973:205 [ref. 7182], Post in Whitehead et al. 1984:499 [ref. 13675], Okiyama 1984:207 [ref. 13644], Fujii in Masuda et al. 1984:76 [ref. 6441], Post 1986:275 [ref. 5705], Paxton et al. 1989:246 [ref. 12442], Gomon et al. 1994:271 [ref. 22532], Paxton & Niem 1999:1949 [ref. 24746], Sato & Nakabo 2002:44 [ref. 25953], Mecklenburg et al. 2002:236 [ref. 25968], Thompson 2003:934 [ref. 27003], Paxton et al. 2006:492 [ref. 28995], Gomon 2008:267 [ref. 30616]). Current status: Valid as Lestidiops Hubbs, 1916. Paralepididae. Species Lestidiops affinis (Ege, 1930) - barracudina [=Paralepis affinis Ege [V.], 1930:81, Fig. 21] Notes: [Report on the Danish Oceanographic Expedition 1908-1910 to the Mediterranean and Adjacent Seas.. v. 2 A (no. 13); ref. 16270] Central Atlantic, 12°11'N, 35°49'W, depth about 2000 meters. Current status: Valid as Lestidiops affinis (Ege, 1930). Paralepididae. Distribution: Atlantic. Habitat: marine. Species Lestidiops bathyopteryx (Fowler, 1944) - Fowler's Eastern Pacific barracudina (author) [=Sudis bathyopteryx Fowler [H. W.], 1944:353, Figs. 92-93] Notes: [Monographs of the Academy of Natural Sciences of Philadelphia No. 6; ref. 1448] 300 miles off Acapulco, Mexico (stomach content). Current status: Valid as Lestidiops bathyopteryx (Fowler, 1944). Paralepididae. Distribution: Eastern Pacific. Habitat: marine. Species Lestidiops cadenati Maul, 1962 - Goree barracudina [=Lestidium cadenati Maul [G. -
Characterization of Bacterial Communities of Cold-Smoked Salmon During Storage
foods Article Characterization of Bacterial Communities of Cold-Smoked Salmon during Storage Aurélien Maillet 1,2,* , Pauline Denojean 2, Agnès Bouju-Albert 2 , Erwann Scaon 1 ,Sébastien Leuillet 1, Xavier Dousset 2, Emmanuel Jaffrès 2,Jérôme Combrisson 1 and Hervé Prévost 2 1 Biofortis Mérieux NutriSciences, 3 route de la Chatterie, 44800 Saint-Herblain, France; [email protected] (E.S.); [email protected] (S.L.); [email protected] (J.C.) 2 INRAE, UMR Secalim, Oniris, Route de Gachet, CS 44307 Nantes, France; [email protected] (P.D.); [email protected] (A.B.-A.); [email protected] (X.D.); [email protected] (E.J.); [email protected] (H.P.) * Correspondence: [email protected] Abstract: Cold-smoked salmon is a widely consumed ready-to-eat seafood product that is a fragile commodity with a long shelf-life. The microbial ecology of cold-smoked salmon during its shelf-life is well known. However, to our knowledge, no study on the microbial ecology of cold-smoked salmon using next-generation sequencing has yet been undertaken. In this study, cold-smoked salmon microbiotas were investigated using a polyphasic approach composed of cultivable methods, V3—V4 16S rRNA gene metabarcoding and chemical analyses. Forty-five cold-smoked salmon products processed in three different factories were analyzed. The metabarcoding approach highlighted 12 dominant genera previously reported as fish spoilers: Firmicutes Staphylococcus, Carnobacterium, Lactobacillus, β-Proteobacteria Photobacterium, Vibrio, Aliivibrio, Salinivibrio, Enterobacteriaceae Serratia, Citation: Maillet, A.; Denojean, P.; Pantoea γ Psychrobacter, Shewanella Pseudomonas Bouju-Albert, A.; Scaon, E.; Leuillet, , -Proteobacteria and .