The Algal Microbiome: Friends and Foes

Livrables

D7.1 All ESRs to have completed 3 postgraduate courses and attended 1 scientific conference, as per their PCDP

D7.2 All ESRs to have completed 3 postgraduate courses and attended 1 scientific conference, as per their PCDP

D2.2 [ESR4] Fungal bioassay, transcriptomics and metabolomics of Saccharina and endophyte pathogens
D6.4 PhD awarded to all ALFF ESRs
D3.8 [ESR9] Comparison of the data obtained by the mutant-driven approach with data generated my mass spectrometric identification of signalling molecules
D5.1 [ESR13] strategies for the storage and analysis of temporally- or spatially-resolved metagenomics data.
Supervisory Board of the network
D1.7 [ESR3] Test correlation between Pseudo-nitschzia infections, interrannual variation & toxicity events
D5.6 [ESR15] novel insights into Ectocarpus-Eurychasma interactions and potential effectors

D5.7 [ESR15] novel insights into Ectocarpus-Eurychasma interactions and potential effectors

D3.7 [ESR9] Transposon tagging bacterial mutants failing to induce diatom growth or carbohydrate secretion

D37ESR9 Transposon tagging bacterial mutants failing to induce diatom growth or carbohydrate secretion

D2.6 [ESR6] Functional study of eukaryotic-bacterial interactions using DNA stable-isotope probing
D4.3 [ESR10] Bacterial localization, transcriptomic & metabolomic profiling along a salinity gradient
Attendance to ALFF courses

"All ESRs to have attended the 6 courses organised by ALFF beneficiaries on 1) Algal Cutluring from the field to the lab; 2) ""Commercial Algal Culturing: technologies, markets and business skills""; 3) ""Metabolomics and experimental design in chemical ecology""; 4) ""Systems biology and bioinformatics""; 5) ""Regulatory Water Quality Monitoring""; 6) ""Science into business""."

D2.7 [ESR6] Insights in the ecological/evolutionary principles underlying the assembly & structure of complex microbial communities in Caulerpa
D9.1 All outreach events delivered as per Section 3.3.1

D9.1 All outreach events delivered

D4.5 [ESR11] Transcriptomic & metabolomic profiling of young Ulva germlings during biofilm formation

D4.7 [ESR12] Proteomic analysis of Marinobacter–algal cultures
D4.4 [ESR11] Bioassays on algicidal/beneficial microorganism on development and morphogenesis of Ulva

D44ESR11 Bioassays on algicidalbeneficial microorganism on development and morphogenesis of Ulva

D1.2 Integration of transcriptomics and metabolomics to identify Paraphysoderma nutrients requirements [ESR1] and Seminavis robusta / bacteria [ESR2] interactions.

Integration of transcriptomics and metabolomics to identify Paraphysoderma nutrients requirements [ESR1] and Seminavis robusta / bacteria [ESR2] interactions.

D1.5 [ESR2] Mechanisms and first applications of bacterial interference compounds on diatom signalling

D3.9 [ESR9] Mimicking the effects of identified substances on biofilm formation in biofilm growth chambers
D2.5 [ESR6] Metagenomic characterization & localization of communities in native and invasive Caulerpa species

D25ESR6 Metagenomic characterization localization of communities in native and invasive Caulerpa species

D4.1 [ESR10] List of bacterial species and cultures necessary for E. subulatus acclimation to freshwater

D41ESR10 List of bacterial species and cultures necessary for E subulatus acclimation to freshwater

D5.3 [ESR14] effects of bacterial communities on Nannochloropsis pathways
D4.2 [ESR10] Genome (expected nb: 5) sequencing and annotation of Ectocarpus-associated bacteria

D42ESR10 Genome expected nb 5 sequencing and annotation of Ectocarpusassociated bacteria

D3.4 [ESR8] Community composition and chemical nature of biofilms during cultivation of Nannochloropsis and Isochrysis

D34ESR8 Community composition and chemical nature of biofilms during cultivation of Nannochloropsis and Isochrysis

D8.1 Release of ALFF-derived Open Access resources in collaboration with the UNU-INWEH
D5.4 [ESR14] Public release of upgraded ORCAE platform, incl. systems biology tools & all relevant ALFF datasets
D5.5 [ESR15] Extended ORCAE version with integrated tools for variant (e.g. SNP) analysis

D5.6 [ESR15] Extended ORCAE version with integrated tools for variant (e.g. SNP) analysis

Publications

Exploring the Cultivable Ectocarpus Microbiome

Auteurs: Hetty KleinJan, Christian Jeanthon, Catherine Boyen, Simon M. Dittami
Publié dans: Frontiers in Microbiology, Numéro 8, 2017, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2017.02456

Life history determinants of the susceptibility of the blood alga Haematococcu s to infection by Paraphysoderma sedebokerense (Blastocladiomycota)

Auteurs: Céline C. Allewaert, Noreen Hiegle, Martina Strittmatter, Reinhoud de Blok, Tiago Guerra, Claire M.M. Gachon, Wim Vyverman
Publié dans: Algal Research, Numéro 31, 2018, Page(s) 282-290, ISSN 2211-9264
Éditeur: Elsevier BV
DOI: 10.1016/j.algal.2018.02.015

Biofilm interactions – bacteria modulate sexual reproduction success of the diatom Seminavis robusta

Auteurs: Emilio Cirri, Wim Vyverman, Georg Pohnert
Publié dans: FEMS Microbiology Ecology, 2018, ISSN 0168-6496
Éditeur: Blackwell
DOI: 10.1093/femsec/fiy161

Genetic mapping of the <i>qSBN7</i> locus, a QTL controlling secondary branch number per panicle in rice

Auteurs: Sheng-Shan Wang, Rong-Kuen Chen, Kai-Yi Chen, Chu-Yin Liu, Shu-Min Kao, Chia-Lin Chung
Publié dans: Breeding Science, Numéro 67/4, 2017, Page(s) 340-347, ISSN 1344-7610
Éditeur: Japanese Society of Breeding
DOI: 10.1270/jsbbs.17007

Insights into the Evolution of Multicellularity from the Sea Lettuce Genome

Auteurs: Olivier De Clerck, Shu-Min Kao, Kenny A. Bogaert, Jonas Blomme, Fatima Foflonker, Michiel Kwantes, Emmelien Vancaester, Lisa Vanderstraeten, Eylem Aydogdu, Jens Boesger, Gianmaria Califano, Benedicte Charrier, Rachel Clewes, Andrea Del Cortona, Sofie D’Hondt, Noe Fernandez-Pozo, Claire M. Gachon, Marc Hanikenne, Linda Lattermann, Frederik Leliaert, Xiaojie Liu, Christine A. Maggs, Zoë A. Popper
Publié dans: Current Biology, Numéro 28/18, 2018, Page(s) 2921-2933.e5, ISSN 0960-9822
Éditeur: Cell Press
DOI: 10.1016/j.cub.2018.08.015

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Auteurs: Joshua C. Stein, Yeisoo Yu, Dario Copetti, Derrick J. Zwickl, Li Zhang, Chengjun Zhang, Kapeel Chougule, Dongying Gao, Aiko Iwata, Jose Luis Goicoechea, Sharon Wei, Jun Wang, Yi Liao, Muhua Wang, Julie Jacquemin, Claude Becker, Dave Kudrna, Jianwei Zhang, Carlos E. M. Londono, Xiang Song, Seunghee Lee, Paul Sanchez, Andrea Zuccolo, Jetty S. S. Ammiraju, Jayson Talag, Ann Danowitz, Luis F. Rivera,
Publié dans: Nature Genetics, Numéro 50/2, 2018, Page(s) 285-296, ISSN 1061-4036
Éditeur: Nature Publishing Group
DOI: 10.1038/s41588-018-0040-0

Analysis of Allelic Imbalance in Rice Hybrids Under Water Stress and Association of Asymmetrically Expressed Genes with Drought-Response QTLs

Auteurs: Nelzo C. Ereful, Li-Yu Liu, Eric Tsai, Shu-Min Kao, Shalabh Dixit, Ramil Mauleon, Katrina Malabanan, Michael Thomson, Antonio Laurena, David Lee, Ian Mackay, Andy Greenland, Wayne Powell, Hei Leung
Publié dans: Rice, Numéro 9/1, 2016, ISSN 1939-8425
Éditeur: Springer Pub. Co.,
DOI: 10.1186/s12284-016-0123-4

Microspongium alariae in Alaria esculenta: a widely-distributed non-parasitic brown algal endophyte that shows cell modifications within its host

Auteurs: Pedro Murúa, Frithjof C. Küpper, Liliana A. Muñoz, Miriam Bernard, Akira F. Peters
Publié dans: Botanica Marina, Numéro 61/4, 2018, Page(s) 343-354, ISSN 0006-8055
Éditeur: Walter de Gruyter GmbH & Co. KG
DOI: 10.1515/bot-2017-0095

A gene transfer event suggests a long-term partnership between eustigmatophyte algae and a novel lineage of endosymbiotic bacteria

Auteurs: Tatiana Yurchenko, Tereza Ševčíková, Pavel Přibyl, Khalid El Karkouri, Vladimír Klimeš, Raquel Amaral, Veronika Zbránková, Eunsoo Kim, Didier Raoult, Lilia M. A. Santos, Marek Eliáš
Publié dans: The ISME Journal, Numéro 12/9, 2018, Page(s) 2163-2175, ISSN 1751-7362
Éditeur: Nature Publishing Group
DOI: 10.1038/s41396-018-0177-y

Identification of Metallophores and Organic Ligands in the Chemosphere of the Marine Macroalga Ulva (Chlorophyta) and at Land-Sea Interfaces

Auteurs: Thomas Wichard
Publié dans: Frontiers in Marine Science, Numéro 3, 2016, ISSN 2296-7745
Éditeur: Frontiers in Marine Science
DOI: 10.3389/fmars.2016.00131

Novel species of the oomycete Olpidiopsis potentially threaten European red algal cultivation

Auteurs: Yacine Badis, Tatyana A. Klochkova, Martina Strittmatter, Andrea Garvetto, Pedro Murúa, J. Craig Sanderson, Gwang Hoon Kim, Claire M. M. Gachon
Publié dans: Journal of Applied Phycology, 2018, ISSN 0921-8971
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10811-018-1641-9

Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation

Auteurs: Andrea Garvetto, Elisabeth Nézan, Yacine Badis, Gwenael Bilien, Paola Arce, Eileen Bresnan, Claire M. M. Gachon, Raffaele Siano
Publié dans: Frontiers in Microbiology, Numéro 9, 2018, ISSN 1664-302X
Éditeur: Frontiers Media
DOI: 10.3389/fmicb.2018.02918

Rediscovering Zygorhizidium affluens Canter: Molecular Taxonomy, Infectious Cycle, and Cryopreservation of a Chytrid Infecting the Bloom-Forming Diatom Asterionella formosa

Auteurs: Cecilia Rad-Menéndez, Mélanie Gerphagnon, Andrea Garvetto, Paola Arce, Yacine Badis, Télesphore Sime-Ngando, Claire M. M. Gachon
Publié dans: Applied and Environmental Microbiology, Numéro 84/23, 2018, ISSN 0099-2240
Éditeur: American Society for Microbiology
DOI: 10.1128/aem.01826-18

Diversity, biogeography and host specificity of kelp endophytes with a focus on the genera Laminarionema and Laminariocolax (Ectocarpales, Phaeophyceae)

Auteurs: Miriam S. Bernard, Martina Strittmatter, Pedro Murúa, Svenja Heesch, Ga Youn Cho, Catherine Leblanc, Akira F. Peters
Publié dans: European Journal of Phycology, Numéro 54/1, 2018, Page(s) 39-51, ISSN 0967-0262
Éditeur: Taylor & Francis
DOI: 10.1080/09670262.2018.1502816

Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts

Auteurs: Tereza Ševčíková, Tatiana Yurchenko, Karen P Fawley, Raquel Amaral, Hynek Strnad, Lilia M A Santos, Marvin W Fawley, Marek Eliáš
Publié dans: Genome Biology and Evolution, Numéro 11/2, 2019, Page(s) 362-379, ISSN 1759-6653
Éditeur: Oxford University Press
DOI: 10.1093/gbe/evz004

A community perspective on the concept of marine holobionts: state-of-the-art, challenges, and future directions

Auteurs: Simon M Dittami, Enrique Arboleda, Jean-Christophe Auguet, Arite Bigalke, Enora Briand, Paco Cárdenas, Ulisse Cardini, Johan Decelle, Aschwin Engelen, Damien Eveillard, Claire M.M. Gachon, Sarah Griffiths, Tilmann Harder, Ehsan Kayal, Elena Kazamia, François H Lallier, Mónica Media, Ezequiel M. Marzinelli, Teresa Morganti, Laura Núñez Pons, Soizic Prado, José Pintado, Mahasweta Saha, Marc
Publié dans: Peer J, 2019, ISSN 2167-8359
Éditeur: PeerJ
DOI: 10.7287/peerj.preprints.27519v1

qPCR-based relative quantification of the brown algal endophyte Laminarionema elsbetiae in Saccharina latissima: variation and dynamics of host—endophyte interactions

Auteurs: Miriam Bernard, Sylvie Rousvoal, Bertrand Jacquemin, Marion Ballenghien, Akira F. Peters, Catherine Leblanc
Publié dans: Journal of Applied Phycology, Numéro 30/5, 2018, Page(s) 2901-2911, ISSN 0921-8971
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10811-017-1367-0

N -Acyl Homoserine Lactone Derived Tetramic Acids Impair Photosynthesis in Phaeodactylum tricornutum

Auteurs: Frederike Stock, Michail Syrpas, Shiri Graff van Creveld, Simon Backx, Lander Blommaert, Lachlan Dow, Willem Stock, Ewout Ruysbergh, Bernard Lepetit, Benjamin Bailleul, Koen Sabbe, Norbert De Kimpe, Anne Willems, Peter G. Kroth, Assaf Vardi, Wim Vyverman, Sven Mangelinckx
Publié dans: ACS Chemical Biology, Numéro 14/2, 2019, Page(s) 198-203, ISSN 1554-8929
Éditeur: American Chemical Society
DOI: 10.1021/acschembio.8b01101

Time Course Exo-Metabolomic Profiling in the Green Marine Macroalga Ulva (Chlorophyta) for Identification of Growth Phase-Dependent Biomarkers

Auteurs: Taghreed Alsufyani, Anne Weiss, Thomas Wichard
Publié dans: Marine Drugs, Numéro 15/1, 2017, Page(s) 14, ISSN 1660-3397
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/md15010014

A solid phase extraction based non-disruptive sampling technique to investigate the surface chemistry of macroalgae

Auteurs: Emilio Cirri, Katharina Grosser, Georg Pohnert
Publié dans: Biofouling, Numéro 32/2, 2016, Page(s) 145-153, ISSN 0892-7014
Éditeur: Taylor & Francis
DOI: 10.1080/08927014.2015.1130823

The plastid genome of some eustigmatophyte algae harbours a bacteria-derived six-gene cluster for biosynthesis of a novel secondary metabolite

Auteurs: Tatiana Yurchenko, Tereza Ševčíková, Hynek Strnad, Anzhelika Butenko, Marek Eliáš
Publié dans: Open Biology, Numéro 6/11, 2016, Page(s) 160249, ISSN 2046-2441
Éditeur: Royal Society Publishing
DOI: 10.1098/rsob.160249

Macroalgal-bacterial interactions: Role of dimethylsulfoniopropionate in microbial gardening by Ulva (Chlorophyta)

Auteurs: Kessler, Ralf W.; Weiss, Anne; Kuegler, Stefan; Hermes, Cornelia; Wichard, Thomas
Publié dans: Molecular Ecology, Numéro 2, 2018, ISSN 1365-294X
Éditeur: Wiley
DOI: 10.5281/zenodo.2580629

Protocols for Macroalgae Research

Auteurs: Emilio Cirri, Georg Pohnert
Publié dans: Protocols for Macroalgae Research, 2018, Page(s) 31-321, ISBN 9781-351132954
Éditeur: Taylor & Francis
DOI: 10.1201/b21460

Preparation of axenic cultures in Ulva (Chlorophyta)

Auteurs: Gianmaria Califano, Thomas Wichard
Publié dans: Protocols for Macroalgae Research, 2018
Éditeur: Francis & Taylor Group
DOI: 10.5281/zenodo.2578236

Metabolomics of intra- and extracellular metabolites from micro- and macroalgae using GC-MS and LC-MS

Auteurs: C Kuhlisch, G Califano, T Wichard, G Pohnert
Publié dans: Protocols for Macroalgae Research, 2018
Éditeur: Francis & Taylor Group
DOI: 10.5281/zenodo.2578249

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