A Genomic View of the Microbiome of Coral Reef Demosponges
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Metaproteogenomic Insights Beyond Bacterial Response to Naphthalene
ORIGINAL ARTICLE ISME Journal – Original article Metaproteogenomic insights beyond bacterial response to 5 naphthalene exposure and bio-stimulation María-Eugenia Guazzaroni, Florian-Alexander Herbst, Iván Lores, Javier Tamames, Ana Isabel Peláez, Nieves López-Cortés, María Alcaide, Mercedes V. del Pozo, José María Vieites, Martin von Bergen, José Luis R. Gallego, Rafael Bargiela, Arantxa López-López, Dietmar H. Pieper, Ramón Rosselló-Móra, Jesús Sánchez, Jana Seifert and Manuel Ferrer 10 Supporting Online Material includes Text (Supporting Materials and Methods) Tables S1 to S9 Figures S1 to S7 1 SUPPORTING TEXT Supporting Materials and Methods Soil characterisation Soil pH was measured in a suspension of soil and water (1:2.5) with a glass electrode, and 5 electrical conductivity was measured in the same extract (diluted 1:5). Primary soil characteristics were determined using standard techniques, such as dichromate oxidation (organic matter content), the Kjeldahl method (nitrogen content), the Olsen method (phosphorus content) and a Bernard calcimeter (carbonate content). The Bouyoucos Densimetry method was used to establish textural data. Exchangeable cations (Ca, Mg, K and 10 Na) extracted with 1 M NH 4Cl and exchangeable aluminium extracted with 1 M KCl were determined using atomic absorption/emission spectrophotometry with an AA200 PerkinElmer analyser. The effective cation exchange capacity (ECEC) was calculated as the sum of the values of the last two measurements (sum of the exchangeable cations and the exchangeable Al). Analyses were performed immediately after sampling. 15 Hydrocarbon analysis Extraction (5 g of sample N and Nbs) was performed with dichloromethane:acetone (1:1) using a Soxtherm extraction apparatus (Gerhardt GmbH & Co. -
Microbiome Exploration of Deep-Sea Carnivorous Cladorhizidae Sponges
Microbiome exploration of deep-sea carnivorous Cladorhizidae sponges by Joost Theo Petra Verhoeven A Thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology Memorial University of Newfoundland March 2019 St. John’s, Newfoundland and Labrador ABSTRACT Members of the sponge family Cladorhizidae are unique in having replaced the typical filter-feeding strategy of sponges by a predatory lifestyle, capturing and digesting small prey. These carnivorous sponges are found in many different environments, but are particularly abundant in deep waters, where they constitute a substantial component of the benthos. Sponges are known to host a wide range of microbial associates (microbiome) important for host health, but the extent of the microbiome in carnivorous sponges has never been extensively investigated and their importance is poorly understood. In this thesis, the microbiome of two deep-sea carnivorous sponge species (Chondrocladia grandis and Cladorhiza oxeata) is investigated for the first time, leveraging recent advances in high-throughput sequencing and through custom developed bioinformatic and molecular methods. Microbiome analyses showed that the carnivorous sponges co-occur with microorganisms and large differences in the composition and type of associations were observed between sponge species. Tissues of C. grandis hosted diverse bacterial communities, similar in composition between individuals, in stark contrast to C. oxeata where low microbial diversity was found with a high host-to-host variability. In C. grandis the microbiome was not homogeneous throughout the host tissue, and significant shifts occured within community members across anatomical regions, with the enrichment of specific bacterial taxa in particular anatomical niches, indicating a potential symbiotic role of such taxa within processes like prey digestion and chemolithoautotrophy. -
Sponge Fauna in the Sea of Marmara
www.trjfas.org ISSN 1303-2712 Turkish Journal of Fisheries and Aquatic Sciences 16: 51-59 (2016) DOI: 10.4194/1303-2712-v16_1_06 RESEARCH PAPER Sponge Fauna in the Sea of Marmara Bülent Topaloğlu1,*, Alper Evcen2, Melih Ertan Çınar2 1 Istanbul University, Department of Marine Biology, Faculty of Fisheries, 34131 Vezneciler, İstanbul, Turkey. 2 Ege University, Department of Hydrobiology, Faculty of Fisheries, 35100 Bornova, İzmir, Turkey. * Corresponding Author: Tel.: +90.533 2157727; Fax: +90.512 40379; Received 04 December 2015 E-mail: [email protected] Accepted 08 February 2016 Abstract Sponge species collected along the coasts of the Sea of the Marmara in 2012-2013 were identified. A total of 30 species belonging to 21 families were found, of which four species (Ascandra contorta, Paraleucilla magna, Raspailia (Parasyringella) agnata and Polymastia penicillus) are new records for the eastern Mediterranean, while six species [A. contorta, P. magna, Chalinula renieroides, P. penicillus, R. (P.) agnata and Spongia (Spongia) nitens] are new records for the marine fauna of Turkey and 12 species are new records for the Sea of Marmara. Sponge specimens were generally collected in shallow water, but two species (Thenea muricata and Rhizaxinella elongata) were found at depths deeper than 100 m. One alien species (P. magna) was found at 10 m depth at station K18 (Büyükada). The morphological and distributional features of the species that are new to the Turkish marine fauna are presented. Keywords: Porifera, Benthos, Invertebrate, Turkish Straits System. Marmara Denizi Sünger Faunası Özet Bu çalışmada, Marmara Denizi ve kıyılarında 2012-2013 yılları arasında toplanan Sünger örnekleri tanımlanmıştır. -
Seasearch Seasearch Wales 2012 Summary Report Summary Report
Seasearch Wales 2012 Summary Report report prepared by Kate Lock, South and West Wales coco----ordinatorordinator Liz MorMorris,ris, North Wales coco----ordinatorordinator Chris Wood, National coco----ordinatorordinator Seasearch Wales 2012 Seasearch is a volunteer marine habitat and species surveying scheme for recreational divers in Britain and Ireland. It is coordinated by the Marine Conservation Society. This report summarises the Seasearch activity in Wales in 2012. It includes summaries of the sites surveyed and identifies rare or unusual species and habitats encountered. These include a number of Welsh Biodiversity Action Plan habitats and species. It does not include all of the detailed data as this has been entered into the Marine Recorder database and supplied to Natural Resources Wales for use in its marine conservation activities. The data is also available on-line through the National Biodiversity Network. During 2012 we continued to focus on Biodiversity Action Plan species and habitats and on sites that had not been previously surveyed. Data from Wales in 2012 comprised 192 Observation Forms, 154 Survey Forms and 1 sea fan record. The total of 347 represents 19% of the data for the whole of Britain and Ireland. Seasearch in Wales is delivered by two Seasearch regional coordinators. Kate Lock coordinates the South and West Wales region which extends from the Severn estuary to Aberystwyth. Liz Morris coordinates the North Wales region which extends from Aberystwyth to the Dee. The two coordinators are assisted by a number of active Seasearch Tutors, Assistant Tutors and Dive Organisers. Overall guidance and support is provided by the National Seasearch Coordinator, Chris Wood. -
Porifera: Demospongiae
Journal of the Marine Biological Association of the United Kingdom, 2018, 98(6), 1273–1335. # Marine Biological Association of the United Kingdom, 2017. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. doi:10.1017/S0025315417000285 Polymastiidae (Porifera: Demospongiae) of the Nordic and Siberian Seas alexander plotkin1, elena gerasimova2 and hans tore rapp1,3,4 1Department of Biology, University of Bergen, Postbox 7803, 5020 Bergen, Norway, 2Ra˚dgivende Biologer AS, Bredsga˚rden, Bryggen, 5003 Bergen, Norway, 3Centre for Geobiology, University of Bergen, Postbox 7803, 5020 Bergen, Norway, 4Uni Environment, Uni Research AS, Postbox 7810, 5020 Bergen, Norway Polymastiidae (Porifera: Demospongiae) of the Nordic and Siberian Seas are revised and compared with the related species of the North Atlantic based on the morphological data from the type and comparative material and the molecular data from fresh samples. Twenty species from six polymastiid genera are recorded. Two species, Polymastia svenseni from Western Norway and Spinularia njordi from the Norwegian Sea, are new to science. One species, Polymastia andrica, is new to the Nordic Seas and two species, Polymastia cf. bartletti and P. penicillus, are new to the Scandinavian Coast. Distribution of the polymastiids in the North Atlantic and Arctic is discussed -
Supplementary Information
Supplementary Information Comparative Microbiome and Metabolome Analyses of the Marine Tunicate Ciona intestinalis from Native and Invaded Habitats Caroline Utermann 1, Martina Blümel 1, Kathrin Busch 2, Larissa Buedenbender 1, Yaping Lin 3,4, Bradley A. Haltli 5, Russell G. Kerr 5, Elizabeta Briski 3, Ute Hentschel 2,6, Deniz Tasdemir 1,6* 1 GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany 2 Research Unit Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker Weg 20, 24105 Kiel, Germany 3 Research Group Invasion Ecology, Research Unit Experimental Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Duesternbrooker Weg 20, 24105 Kiel, Germany 4 Chinese Academy of Sciences, Research Center for Eco-Environmental Sciences, 18 Shuangqing Rd., Haidian District, Beijing, 100085, China 5 Department of Chemistry, University of Prince Edward Island, 550 University Avenue, Charlottetown, PE C1A 4P3, Canada 6 Faculty of Mathematics and Natural Sciences, Kiel University, Christian-Albrechts-Platz 4, Kiel 24118, Germany * Corresponding author: Deniz Tasdemir ([email protected]) This document includes: Supplementary Figures S1-S11 Figure S1. Genotyping of C. intestinalis with the mitochondrial marker gene COX3-ND1. Figure S2. Influence of the quality filtering steps on the total number of observed read pairs from amplicon sequencing. Figure S3. Rarefaction curves of OTU abundances for C. intestinalis and seawater samples. Figure S4. Multivariate ordination plots of the bacterial community associated with C. intestinalis. Figure S5. Across sample type and geographic origin comparison of the C. intestinalis associated microbiome. -
S & W Wales Summary 2019
Seasearch South and West Wales 2019 Summary Report Blaise Bullimore Report prepared by Kate Lock, South and West Wales Co-ordinator 1 Seasearch De a Gorllewin Cymru 2019 Mae Seasearch yn gynllun cynnal arolygon o gynefinoedd a rhywogaethau morol i wirfoddolwyr sy’n ddeifwyr a snorcelwyr ym Mhrydain ac Iwerddon. Mae'n cael ei gydlynu gan y Gymdeithas Gadwraeth Forol. Mae'r adroddiad hwn yn crynhoi prif ganfyddiadau Seasearch yn ne a gorllewin Cymru yn 2019. Mae'n cynnwys crynodebau o'r safleoedd lle cynhaliwyd arolygon ac yn nodi rhywogaethau a chynefinoedd prin neu anarferol sydd wedi cael eu gweld. Mae'r rhain yn cynnwys nifer o gynefinoedd a rhywogaethau â blaenoriaeth yng Nghymru. Nid yw'r adroddiad hwn yn cynnwys yr holl ddata manwl am fod yr wybodaeth hon wedi cael ei mewnbynnu i gronfa ddata'r Cofnodwr Morol a'i rhoi i Cyfoeth Naturiol Cymru er mwyn ei defnyddio yn ei weithgareddau cadwraeth forol. Mae data ar y rhywogaethau ar gael ar-lein hefyd drwy’r Rhwydwaith Bioamrywiaeth Cenedlaethol. Yn 2019, gwnaeth Seasearch yng Nghymru barhau i ganolbwyntio ar rywogaethau a chynefinoedd â blaenoriaeth yn ogystal â chasglu gwybodaeth am wely'r môr a bywyd morol mewn safleoedd lle nad oedd arolygon wedi cael eu cynnal cyn hyn. Mae data a gasglwyd o dde a gorllewin Cymru yn 2019 yn cynnwys cyfanswm o 57 o ffurflenni arolygwyr a 42 o ffurflenni gwylwyr, sef cyfanswm o 99 o ffurflenni. Yn 2019, mae’r rhaglen Seasearch yn ne a gorllewin Cymru – ardal sy’n ymestyn o aber afon Hafren i Aberystwyth – wedi cael ei chynnal gan gydlynydd rhanbarthol Seasearch, Kate Lock. -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Sponge Biodiversity of the United Kingdom
Sponge Biodiversity of the United Kingdom A report from the Sponge Biodiversity of the United Kingdom project May 2008-May 2011 Claire Goodwin & Bernard Picton National Museums Northern Ireland Sponge Biodiversity of the United Kingdom Contents Page 1. Introduction 2 1.1 Project background 2 1.2 Project aims 2 1.3 Project outputs 2 2. Methods 3 2.1 Survey methodology 3 2.2 Survey locations 4 2.2.1 Firth of Lorn and Sound of Mull , Scotland 6 2.2.2 Pembrokeshire , Wales 6 2.2.3 Firth of Clyde , Scotland 6 2.2.4 Isles of Scilly , England 8 2.2.5 Sark, Channel Isles 8 2.2.6 Plymouth , England 8 2.3 Laboratory methodology 10 2.3.1 The identifi cation process 10 2.4 Data handling 11 3. Results 13 3.1 Notes on UK sponge communities 13 3.1.1 Scotland 13 3.1.2 Wales 13 3.1.3 Isles of Scilly 13 3.1.4 Sark 13 3.1.5 Sponge biogeography 15 3.2 Species of particular interest 15 4. Publications 34 4.1 Manuscripts in preparation 34 4.2 Published/accepted manuscripts 37 5. Publicity 37 5.1 Academic conference presentations 37 5.2 Public talks/events 38 5.3 Press coverage 38 6. Training Courses 39 7. Collaborations with other Organisations 42 8. Conclusions 44 8.1 Ulster Museum, National Museums Northern Ireland – a centre of excellence for sponge 44 taxonomy 8.2 Future work 44 8.2.1. Species requiring further work 45 9. Acknowledgements 46 10. -
Atlas De La Faune Marine Invertébrée Du Golfe Normano-Breton. Volume
350 0 010 340 020 030 330 Atlas de la faune 040 320 marine invertébrée du golfe Normano-Breton 050 030 310 330 Volume 7 060 300 060 070 290 300 080 280 090 090 270 270 260 100 250 120 110 240 240 120 150 230 210 130 180 220 Bibliographie, glossaire & index 140 210 150 200 160 190 180 170 Collection Philippe Dautzenberg Philippe Dautzenberg (1849- 1935) est un conchyliologiste belge qui a constitué une collection de 4,5 millions de spécimens de mollusques à coquille de plusieurs régions du monde. Cette collection est conservée au Muséum des sciences naturelles à Bruxelles. Le petit meuble à tiroirs illustré ici est une modeste partie de cette très vaste collection ; il appartient au Muséum national d’Histoire naturelle et est conservé à la Station marine de Dinard. Il regroupe des bivalves et gastéropodes du golfe Normano-Breton essentiellement prélevés au début du XXe siècle et soigneusement référencés. Atlas de la faune marine invertébrée du golfe Normano-Breton Volume 7 Bibliographie, Glossaire & Index Patrick Le Mao, Laurent Godet, Jérôme Fournier, Nicolas Desroy, Franck Gentil, Éric Thiébaut Cartographie : Laurent Pourinet Avec la contribution de : Louis Cabioch, Christian Retière, Paul Chambers © Éditions de la Station biologique de Roscoff ISBN : 9782951802995 Mise en page : Nicole Guyard Dépôt légal : 4ème trimestre 2019 Achevé d’imprimé sur les presses de l’Imprimerie de Bretagne 29600 Morlaix L’édition de cet ouvrage a bénéficié du soutien financier des DREAL Bretagne et Normandie Les auteurs Patrick LE MAO Chercheur à l’Ifremer -
Integrative and Comparative Biology Advance Access Published June 10, 2013 Integrative and Comparative Biology Integrative and Comparative Biology, Pp
Integrative and Comparative Biology Advance Access published June 10, 2013 Integrative and Comparative Biology Integrative and Comparative Biology, pp. 1–19 doi:10.1093/icb/ict065 Society for Integrative and Comparative Biology SYMPOSIUM Molecular Phylogenies Support Homoplasy of Multiple Morphological Characters Used in the Taxonomy of Heteroscleromorpha (Porifera: Demospongiae) Christine C. Morrow,1,* Niamh E. Redmond,† Bernard E. Picton,‡ Robert W. Thacker,§ Allen G. Collins,† Christine A. Maggs,* Julia D. Sigwart* and A. Louise Allcockô *School of Biological Sciences, MBC, 97 Lisburn Road, Queen’s University, Belfast BT9 7BL, UK; †National Systematics Laboratory, National Museum of Natural History, MRC-153, Smithsonian Institution, P.O. Box 37012, Washington, DC ‡ 20013-7012, USA; National Museums Northern Ireland, 153 Bangor Road, Holywood BT18 0EU, Northern Ireland, UK; Downloaded from §Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA; ôSchool of Natural Science and Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland From the symposium ‘‘Assembling the Poriferan Tree of Life’’ presented at the annual meeting of the Society for Integrative and Comparative Biology, January 3–7, 2013 at San Francisco, California. http://icb.oxfordjournals.org/ 1E-mail: [email protected] Synopsis Sponge classification has long been based mainly on morphocladistic analyses but is now being greatly chal- lenged by more than 12 years of accumulated analyses of molecular data analyses. The current study used phylogenetic hypotheses based on sequence data from 18S rRNA, 28S rRNA, and the CO1 barcoding fragment, combined with morphology to justify the resurrection of the order Axinellida Le´vi, 1953. Axinellida occupies a key position in different at smithsonia3 on June 10, 2013 morphologically derived topologies. -
Abstract Tracing Hydrocarbon
ABSTRACT TRACING HYDROCARBON CONTAMINATION THROUGH HYPERALKALINE ENVIRONMENTS IN THE CALUMET REGION OF SOUTHEASTERN CHICAGO Kathryn Quesnell, MS Department of Geology and Environmental Geosciences Northern Illinois University, 2016 Melissa Lenczewski, Director The Calumet region of Southeastern Chicago was once known for industrialization, which left pollution as its legacy. Disposal of slag and other industrial wastes occurred in nearby wetlands in attempt to create areas suitable for future development. The waste creates an unpredictable, heterogeneous geology and a unique hyperalkaline environment. Upgradient to the field site is a former coking facility, where coke, creosote, and coal weather openly on the ground. Hydrocarbons weather into characteristic polycyclic aromatic hydrocarbons (PAHs), which can be used to create a fingerprint and correlate them to their original parent compound. This investigation identified PAHs present in the nearby surface and groundwaters through use of gas chromatography/mass spectrometry (GC/MS), as well as investigated the relationship between the alkaline environment and the organic contamination. PAH ratio analysis suggests that the organic contamination is not mobile in the groundwater, and instead originated from the air. 16S rDNA profiling suggests that some microbial communities are influenced more by pH, and some are influenced more by the hydrocarbon pollution. BIOLOG Ecoplates revealed that most communities have the ability to metabolize ring structures similar to the shape of PAHs. Analysis with bioinformatics using PICRUSt demonstrates that each community has microbes thought to be capable of hydrocarbon utilization. The field site, as well as nearby areas, are targets for habitat remediation and recreational development. In order for these remediation efforts to be successful, it is vital to understand the geochemistry, weathering, microbiology, and distribution of known contaminants.