Chemical Interactions Between Marine Macroalgae and Bacteria
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University of Copenhagen
Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes Ulvskov, Peter; Paiva, Dionisio Soares; Domozych, David; Harholt, Jesper Published in: P L o S One DOI: 10.1371/journal.pone.0076511 Publication date: 2013 Document version Publisher's PDF, also known as Version of record Citation for published version (APA): Ulvskov, P., Paiva, D. S., Domozych, D., & Harholt, J. (2013). Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes. P L o S One, 8(10), [e76511.]. https://doi.org/10.1371/journal.pone.0076511 Download date: 02. okt.. 2021 Classification, Naming and Evolutionary History of Glycosyltransferases from Sequenced Green and Red Algal Genomes Peter Ulvskov1, Dionisio Soares Paiva1¤, David Domozych2, Jesper Harholt1* 1 Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark, 2 Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York, United States of America Abstract The Archaeplastida consists of three lineages, Rhodophyta, Virideplantae and Glaucophyta. The extracellular matrix of most members of the Rhodophyta and Viridiplantae consists of carbohydrate-based or a highly glycosylated protein-based cell wall while the Glaucophyte covering is poorly resolved. In order to elucidate possible evolutionary links between the three advanced lineages in Archaeplastida, a genomic analysis was initiated. Fully sequenced genomes from -
Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations
fmicb-09-02879 December 1, 2018 Time: 14:0 # 1 ORIGINAL RESEARCH published: 04 December 2018 doi: 10.3389/fmicb.2018.02879 Bacterial Epibiotic Communities of Ubiquitous and Abundant Marine Diatoms Are Distinct in Short- and Long-Term Associations Klervi Crenn, Delphine Duffieux and Christian Jeanthon* CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, France Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community- level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and Edited by: collection cultures, regarded here as short- and long-term associations, respectively. Matthias Wietz, Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning- Alfred Wegener Institut, Germany sequencing of 16S rRNA genes obtained from whole-genome amplification products. Reviewed by: The prevalence of epibiotic bacteria was higher in cultures and dependent of the host Lydia Jeanne Baker, Cornell University, United States species. Culture approaches demonstrated that both diatoms carry distinct bacterial Bryndan Paige Durham, communities in short- and long-term associations. Bacterial epibonts, commonly University of Washington, United States associated with phytoplankton, were repeatedly isolated from cells of diatom collection *Correspondence: cultures but were not recovered from environmental cells. -
Exhaustive Reanalysis of Barcode Sequences from Public
Exhaustive reanalysis of barcode sequences from public repositories highlights ongoing misidentifications and impacts taxa diversity and distribution: a case study of the Sea Lettuce. Antoine Fort1, Marcus McHale1, Kevin Cascella2, Philippe Potin2, Marie-Mathilde Perrineau3, Philip Kerrison3, Elisabete da Costa4, Ricardo Calado4, Maria Domingues5, Isabel Costa Azevedo6, Isabel Sousa-Pinto6, Claire Gachon3, Adrie van der Werf7, Willem de Visser7, Johanna Beniers7, Henrice Jansen7, Michael Guiry1, and Ronan Sulpice1 1NUI Galway 2Station Biologique de Roscoff 3Scottish Association for Marine Science 4University of Aveiro 5Universidade de Aveiro 6University of Porto Interdisciplinary Centre of Marine and Environmental Research 7Wageningen University & Research November 24, 2020 Abstract Sea Lettuce (Ulva spp.; Ulvophyceae, Ulvales, Ulvaceae) is an important ecological and economical entity, with a worldwide distribution and is a well-known source of near-shore blooms blighting many coastlines. Species of Ulva are frequently misiden- tified in public repositories, including herbaria and gene banks, making species identification based on traditional barcoding hazardous. We investigated the species distribution of 295 individual distromatic foliose strains from the North East Atlantic by traditional barcoding or next generation sequencing. We found seven distinct species, and compared our results with all worldwide Ulva spp sequences present in the NCBI database for the three barcodes rbcL, tuf A and the ITS1. Our results demonstrate a large degree of species misidentification in the NCBI database. We estimate that 21% of the entries pertaining to foliose species are misannotated. In the extreme case of U. lactuca, 65% of the entries are erroneously labelled specimens of another Ulva species, typically U. fenestrata. In addition, 30% of U. -
Eelgrass Sediment Microbiome As a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan
Microbes Environ. Vol. 34, No. 1, 13-22, 2019 https://www.jstage.jst.go.jp/browse/jsme2 doi:10.1264/jsme2.ME18103 Eelgrass Sediment Microbiome as a Nitrous Oxide Sink in Brackish Lake Akkeshi, Japan TATSUNORI NAKAGAWA1*, YUKI TSUCHIYA1, SHINGO UEDA1, MANABU FUKUI2, and REIJI TAKAHASHI1 1College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, 252–0880, Japan; and 2Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo, 060–0819, Japan (Received July 16, 2018—Accepted October 22, 2018—Published online December 1, 2018) Nitrous oxide (N2O) is a powerful greenhouse gas; however, limited information is currently available on the microbiomes involved in its sink and source in seagrass meadow sediments. Using laboratory incubations, a quantitative PCR (qPCR) analysis of N2O reductase (nosZ) and ammonia monooxygenase subunit A (amoA) genes, and a metagenome analysis based on the nosZ gene, we investigated the abundance of N2O-reducing microorganisms and ammonia-oxidizing prokaryotes as well as the community compositions of N2O-reducing microorganisms in in situ and cultivated sediments in the non-eelgrass and eelgrass zones of Lake Akkeshi, Japan. Laboratory incubations showed that N2O was reduced by eelgrass sediments and emitted by non-eelgrass sediments. qPCR analyses revealed that the abundance of nosZ gene clade II in both sediments before and after the incubation as higher in the eelgrass zone than in the non-eelgrass zone. In contrast, the abundance of ammonia-oxidizing archaeal amoA genes increased after incubations in the non-eelgrass zone only. Metagenome analyses of nosZ genes revealed that the lineages Dechloromonas-Magnetospirillum-Thiocapsa and Bacteroidetes (Flavobacteriia) within nosZ gene clade II were the main populations in the N2O-reducing microbiome in the in situ sediments of eelgrass zones. -
Genome Analysis of Flaviramulus Ichthyoenteri Th78t in the Family
Zhang et al. BMC Genomics (2015) 16:38 DOI 10.1186/s12864-015-1275-0 RESEARCH ARTICLE Open Access Genome analysis of Flaviramulus ichthyoenteri Th78T in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine Yunhui Zhang1, Jiwen Liu1, Kaihao Tang1, Min Yu1, Tom Coenye2 and Xiao-Hua Zhang1* Abstract Background: Intestinal microbes play significant roles in fish and can be possibly used as probiotics in aquaculture. In our previous study, Flaviramulus ichthyoenteri Th78T, a novel species in the family Flavobacteriaceae, was isolated from fish intestine and showed strong quorum quenching (QQ) ability. To identify the QQ enzymes in Th78T and explore the potential roles of Th78T in fish intestine, we sequenced the genome of Th78T and performed extensive genomic analysis. Results: An N-acyl homoserine lactonase FiaL belonging to the metallo-β-lactamase superfamily was identified and the QQ activity of heterologously expressed FiaL was confirmed in vitro. FiaL has relatively little similarity to the known lactonases (25.2 ~ 27.9% identity in amino acid sequence). Various digestive enzymes including alginate lyases and lipases can be produced by Th78T, and enzymes essential for production of B vitamins such as biotin, riboflavin and folate are predicted. Genes encoding sialic acid lyases, sialidases, sulfatases and fucosidases, which contribute to utilization of mucus, are present in the genome. In addition, genes related to response to different stresses and gliding motility were also identified. Comparative genome analysis shows that Th78T has more specific genes involved in carbohydrate transport and metabolism compared to other two isolates in Flavobacteriaceae, both isolated from sediments. -
High Quality Permanent Draft Genome Sequence of Chryseobacterium Bovis DSM 19482T, Isolated from Raw Cow Milk
Lawrence Berkeley National Laboratory Recent Work Title High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Permalink https://escholarship.org/uc/item/4b48v7v8 Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Laviad-Shitrit, Sivan Göker, Markus Huntemann, Marcel et al. Publication Date 2017 DOI 10.1186/s40793-017-0242-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Laviad-Shitrit et al. Standards in Genomic Sciences (2017) 12:31 DOI 10.1186/s40793-017-0242-6 SHORT GENOME REPORT Open Access High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk Sivan Laviad-Shitrit1, Markus Göker2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, T. B. K. Reddy3, Chris Daum3, Nicole Shapiro3, Victor Markowitz3, Natalia Ivanova3, Tanja Woyke3, Hans-Peter Klenk4, Nikos C. Kyrpides3 and Malka Halpern1,5* Abstract Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study. -
Comparison of Ulva Lactuca and Ulva Clathrata As Ingredients In
International Journal of Fisheries and Aquatic Studies 2021; 9(1): 192-194 E-ISSN: 2347-5129 P-ISSN: 2394-0506 (ICV-Poland) Impact Value: 5.62 Comparison of Ulva lactuca and Ulva clathrata as (GIF) Impact Factor: 0.549 IJFAS 2021; 9(1): 192-194 ingredients in Litopenaeus vannamei feeds © 2021 IJFAS www.fisheriesjournal.com Received: 23-10-2020 Dian Yuni Pratiwi and Fittrie Meyllianawaty Pratiwy Accepted: 02-12-2020 DOI: https://doi.org/10.22271/fish.2021.v9.i1c.2401 Dian Yuni Pratiwi Faculty of Fisheries and Marine Abstract Science, Universitas Ulva lactuca and Ulva clathrata are marine green algae belonging to genera Ulva. These algae have a lot Padjadjaran, Indonesia of nutrient such as protein, carbohydrates, lipids, pigments and others. These nutrient can be used to Fittrie Meyllianawaty Pratiwy improve the growth performance and health of Shrimps. Several studies have shown that U. lactuca and Faculty of Fisheries and Marine U. clathrata have antifungal, antibacterial, antiviral activities. One of popular shrimp among people of Science, Universitas the world is Litopenaeus vannamei. So that, this review article aims to comparing the effect of U. lactuca Padjadjaran, Indonesia and U. clathrata as ingredients in L. vannamei juvenile feeds. This review also summarizes a literature survey of the nutritional content and antimicrobial activity of U. lactuca and U. clathrata. Keywords: Ulva lactuca, Ulva clathrata, Litopenaeus vannamei, growth, health 1. Introduction Shrimps is one of popular seafood commodity among people of the world. The global trade of [1] [2] shrimp achieve 5.10 million tons in 2019 and estimate at USD 28 billion per year . -
Common Benthic Algae and Cyanobacteria in Southern California Tidal Wetlands
Scripps Institution of Oceanography Technical Report Common benthic algae and cyanobacteria in southern California tidal wetlands Christopher N. Janousek Scripps Institution of Oceanography, University of California, San Diego 11 July 2011 Janousek 2011: Algae and cyanobacteria of southern California marine wetlands. 1 Abstract Benthic algae and photosynthetic bacteria are important components of coastal wetlands, contributing to primary productivity, nutrient cycling, and other ecosystem functions. Despite their key roles in mudflat and salt marsh food webs, the extent and patterns of diversity of these organisms is poorly known. Sediments from intertidal marshes in San Diego County, California host a variety of cyanobacteria, diatoms, and multi-cellular algae. This flora describes approximately 40 taxa of common and notable cyanobacteria, microalgae and macroalgae observed in wetland sediments, principally from a small tidal marsh in Mission Bay. Cyanobacteria included coccoid and heterocyte and non-heterocyte bearing filamentous genera. A phylogenetically-diverse assemblage of pennate and centric diatoms, euglenoids, green algae, red algae, tribophytes and brown seaweeds was also observed. Most taxa are illustrated with photographs. Key words alpha diversity • cyanobacteria • diatoms • euglenoids • Kendall-Frost Mission Bay Marsh Reserve • macroalgae • microphytobenthos • salt marsh • Tijuana Estuary • Vaucheria Introduction The sediments of coastal marine wetlands in California are inhabited by a variety of algal and bacterial primary producers in addition to the more conspicuous vascular plants that provide most of the physical structure of coastal salt marshes and seagrass meadows. The non-vascular plant flora includes microscopic cyanobacteria, anoxygenic phototrophic bacteria, diatoms, and euglenoids, often collectively known as “microphytobenthos” (Sullivan and Currin 2000). Larger green algae, red and brown seaweeds, and the macroscopic tribophyte, Vaucheria are also residents of these ecosystems (Barnhardt et al. -
The Essentials of Marine Biotechnology. Frontiers in Marine Science [Online], 8, Article 629629
ROTTER, A., BARBIER, M., BERTONI, F. et al. 2021. The essentials of marine biotechnology. Frontiers in marine science [online], 8, article 629629. Available from: https://doi.org/10.3389/fmars.2021.629629 The essentials of marine biotechnology. ROTTER, A., BARBIER, M., BERTONI, F. et al. 2021 Copyright © 2021 Rotter, Barbier, Bertoni, Bones, Cancela, Carlsson, Carvalho, Cegłowska, Chirivella-Martorell, Conk Dalay, Cueto, Dailianis, Deniz, Díaz-Marrero, Drakulovic, Dubnika, Edwards, Einarsson, Erdoˇgan, Eroldoˇgan, Ezra, Fazi, FitzGerald, Gargan, Gaudêncio, Gligora Udoviˇc, Ivoševi´c DeNardis, Jónsdóttir, Kataržyt˙e, Klun, Kotta, Ktari, Ljubeši´c, Luki´c Bilela, Mandalakis, Massa-Gallucci, Matijošyt˙e, Mazur-Marzec, Mehiri, Nielsen, Novoveská, Overling˙e, Perale, Ramasamy, Rebours, Reinsch, Reyes, Rinkevich, Robbens, Röttinger, Rudovica, Sabotiˇc, Safarik, Talve, Tasdemir, Theodotou Schneider, Thomas, Toru´nska-Sitarz, Varese and Vasquez.. This article was first published in Frontiers in Marine Science on 16.03.2021. This document was downloaded from https://openair.rgu.ac.uk fmars-08-629629 March 10, 2021 Time: 14:8 # 1 REVIEW published: 16 March 2021 doi: 10.3389/fmars.2021.629629 The Essentials of Marine Biotechnology Ana Rotter1*, Michéle Barbier2, Francesco Bertoni3,4, Atle M. Bones5, M. Leonor Cancela6,7, Jens Carlsson8, Maria F. Carvalho9, Marta Cegłowska10, Jerónimo Chirivella-Martorell11, Meltem Conk Dalay12, Mercedes Cueto13, 14 15 16 17 Edited by: Thanos Dailianis , Irem Deniz , Ana R. Díaz-Marrero , Dragana Drakulovic , 18 19 -
Microbial Community Structure and Function on Sinking Particles in the North Pacific Subtropical Gyre
Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Fontanez, Kristina M., John M. Eppley, Ty J. Samo, David M. Karl, and Edward F. DeLong. “Microbial Community Structure and Function on Sinking Particles in the North Pacific Subtropical Gyre.” Frontiers in Microbiology 6 (May 19, 2015). As Published http://dx.doi.org/10.3389/fmicb.2015.00469 Publisher Frontiers Research Foundation Version Final published version Citable link http://hdl.handle.net/1721.1/98187 Terms of Use Creative Commons Attribution Detailed Terms http://creativecommons.org/licenses/by/4.0/ ORIGINAL RESEARCH published: 19 May 2015 doi: 10.3389/fmicb.2015.00469 Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre Kristina M. Fontanez 1, John M. Eppley 1, 2, 3, Ty J. Samo 2, 3, 4, David M. Karl 2, 3 and Edward F. DeLong 1, 2, 3* 1 Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA, 2 Department of Oceanography, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, USA, 3 Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, HI, USA, 4 Lawrence Livermore National Laboratory, Nuclear and Chemical Sciences Division, Livermore, CA, USA Sinking particles mediate the transport of carbon and energy to the deep-sea, yet the specific microbes associated with sedimenting particles in the ocean’s interior remain largely uncharacterized. In this study, we used particle interceptor traps (PITs) Edited by: to assess the nature of particle-associated microbial communities collected at a variety Anton F. -
Biotechnological Potential of Cold Adapted Pseudoalteromonas Spp
marine drugs Article Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from ‘Deep Sea’ Sponges Erik Borchert 1, Stephen Knobloch 2, Emilie Dwyer 1, Sinéad Flynn 1, Stephen A. Jackson 1, Ragnar Jóhannsson 2, Viggó T. Marteinsson 2, Fergal O’Gara 1,3,4 and Alan D. W. Dobson 1,* 1 School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland; [email protected] (E.B.); [email protected] (E.D.); [email protected] (S.F.); [email protected] (S.A.J.); [email protected] (F.O.) 2 Department of Research and Innovation, Matís ohf., Reykjavik 113, Iceland; [email protected] (S.K.); [email protected] (R.J.); [email protected] (V.T.M.) 3 Biomerit Research Centre, University College Cork, National University of Ireland, Cork T12 YN60, Ireland 4 School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth 6102, WA, Australia * Correspondence: [email protected]; Tel.: +353-21-490-2743 Received: 22 February 2017; Accepted: 14 June 2017; Published: 19 June 2017 Abstract: The marine genus Pseudoalteromonas is known for its versatile biotechnological potential with respect to the production of antimicrobials and enzymes of industrial interest. We have sequenced the genomes of three Pseudoalteromonas sp. strains isolated from different deep sea sponges on the Illumina MiSeq platform. The isolates have been screened for various industrially important enzymes and comparative genomics has been applied to investigate potential relationships between the isolates and their host organisms, while comparing them to free-living Pseudoalteromonas spp. from shallow and deep sea environments. -
Labile Dissolved Organic Matter Compound Characteristics Select
http://www.diva-portal.org This is the published version of a paper published in Frontiers in Microbiology. Citation for the original published paper (version of record): Pontiller, B., Martinez-Garcia, S., Lundin, D., Pinhassi, J. (2020) Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription Frontiers in Microbiology, 11: 1-19 https://doi.org/10.3389/fmicb.2020.588778 Access to the published version may require subscription. N.B. When citing this work, cite the original published paper. Permanent link to this version: http://urn.kb.se/resolve?urn=urn:nbn:se:lnu:diva-98814 fmicb-11-588778 September 24, 2020 Time: 19:52 # 1 ORIGINAL RESEARCH published: 25 September 2020 doi: 10.3389/fmicb.2020.588778 Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription Benjamin Pontiller1, Sandra Martínez-García2, Daniel Lundin1 and Jarone Pinhassi1* 1 Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden, 2 Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Vigo, Spain Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced Edited by: changes in bacterial growth, activity, and transcription related to DOM characteristics.