Host–Microbe Interactions As a Driver of Acclimation to Salinity Gradients in Brown Algal Cultures
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The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service. -
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. -
Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
The Role of Charcoal and Dietary Crude Protein Supplemented with Probiotic Escherchia Coli Strains UM2 and UM7
Gut microbiome analysis in piglet models infected with Escherchia coli K88: The role of charcoal and dietary crude protein supplemented with probiotic Escherchia coli strains UM2 and UM7. by Shahab Meshkibaf A Thesis submitted to the Faculty of Graduate Studies of The University of Manitoba in partial fulfillment of the requirements of the degree of MASTER OF SCIENCE Department of Medical Microbiology and Infectious Diseases University of Manitoba Winnipeg Copyright © 2011 by Shahab Meshkibaf ABSTRACT Entrotoxigenic Escherichia coli (ETEC) K88 is a causative agent of post-weaning diarrhea (PWD) in early-weaned pigs. This study investigated the efficacy of two alternative diets, charcoal (0.1, 0.5, 1, and 2%) and a low crude protein (CP) diet (17%) supplemented with probiotic E. coli strains (UM2 and UM7), against PWD infection in ETEC K88 challenged piglets. The present study found that charcoal had no effect on the challenged piglets’ performance, ileal and colonic microbiota or their fermentation end products. There was, however, a correlation between charcoal dosage and fecal consistency score. Charcoal reduced the ileal mucosal attached ETEC K88. Feeding a low-CP diet resulted in a lower ileal ammonia concentration. The low-CP diet reduced the E. coli populations in the ileal digesta as well as lowered mRNA expression of the IL-1ß. We concluded that the use of both 1-2% charcoal diet and a low-CP diet supplemented with probiotic E. coli strains were effective in reducing the incidence and severity of PWD infection. ACKNOWLEDGEMENTS I would like to thank all people who have helped and inspired me during my graduate study. -
Feasibility of Bacterial Probiotics for Mitigating Coral Bleaching
Feasibility of bacterial probiotics for mitigating coral bleaching Ashley M. Dungan ORCID: 0000-0003-0958-2177 Thesis submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy September 2020 School of BioSciences The University of Melbourne Declaration This is to certify that: 1. This thesis comprises only of my original work towards the PhD, except where indicated in the preface. 2. Due acknowledgements have been made in the text to all other material used. 3. The thesis is under 100,000 words, exclusive of tables, bibliographies, and appendices. Signed: Date: 11 September 2020 ii General abstract Given the increasing frequency of climate change driven coral mass bleaching and mass mortality events, intervention strategies aimed at enhancing coral thermal tolerance (assisted evolution) are urgently needed in addition to strong action to reduce carbon emissions. Without such interventions, coral reefs will not survive. The seven chapters in my thesis explore the feasibility of using a host-sourced bacterial probiotic to mitigate bleaching starting with a history of reactive oxygen species (ROS) as a biological explanation for bleaching (Chapter 1). In part because of the difficulty to experimentally manipulate corals post-bleaching, I use Great Barrier Reef (GBR)-sourced Exaiptasia diaphana as a model organism for this system, which I describe in Chapter 2. The comparatively high levels of physiological and genetic variability among GBR anemone genotypes make these animals representatives of global E. diaphana diversity and thus excellent model organisms. The ‘oxidative stress theory for coral bleaching’ provides rationale for the development of a probiotic with a high free radical scavenging ability. -
Roseisalinus Antarcticus Gen. Nov., Sp. Nov., a Novel Aerobic Bacteriochlorophyll A-Producing A-Proteobacterium Isolated from Hypersaline Ekho Lake, Antarctica
International Journal of Systematic and Evolutionary Microbiology (2005), 55, 41–47 DOI 10.1099/ijs.0.63230-0 Roseisalinus antarcticus gen. nov., sp. nov., a novel aerobic bacteriochlorophyll a-producing a-proteobacterium isolated from hypersaline Ekho Lake, Antarctica Matthias Labrenz,13 Paul A. Lawson,2 Brian J. Tindall,3 Matthew D. Collins2 and Peter Hirsch1 Correspondence 1Institut fu¨r Allgemeine Mikrobiologie, Christian-Albrechts-Universita¨t, Kiel, Germany Matthias Labrenz 2School of Food Biosciences, University of Reading, PO Box 226, Reading RG6 6AP, UK matthias.labrenz@ 3DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Mascheroder io-warnemuende.de Weg 1b, D-38124 Braunschweig, Germany A Gram-negative, aerobic to microaerophilic rod was isolated from 10 m depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strain was oxidase- and catalase-positive, metabolized a variety of carboxylic acids and sugars and produced lipase. Cells had an absolute requirement for artificial sea water, which could not be replaced by NaCl. A large in vivo absorption band at 870 nm indicated production of bacteriochlorophyll a. The predominant fatty acids of this organism were 16 : 0 and 18 : 1v7c, with 3-OH 10 : 0, 16 : 1v7c and 18 : 0 in lower amounts. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The DNA G+C content was 67 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represents a member of the Roseobacter clade within the a-Proteobacteria. The organism showed no particular relationship to any members of this clade but clustered on the periphery of the genera Jannaschia, Octadecabacter and ‘Marinosulfonomonas’ and the species Ruegeria gelatinovorans. -
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. -
Microbiological Study in Petrol-Spiked Soil
molecules Article Microbiological Study in Petrol-Spiked Soil Agata Borowik , Jadwiga Wyszkowska * and Jan Kucharski Department of Soil Science and Microbiology, University of Warmia and Mazury in Olsztyn, 10-727 Olsztyn, Poland; [email protected] (A.B.); [email protected] (J.K.) * Correspondence: [email protected] Abstract: The pollution of arable lands and water with petroleum-derived products is still a valid problem, mainly due the extensive works aimed to improve their production technology to reduce fuel consumption and protect engines. An example of the upgraded fuels is the BP 98 unleaded petrol with Active technology. A pot experiment was carried out in which Eutric Cambisol soil was polluted with petrol to determine its effect on the microbiological and biochemical properties of this soil. Analyses were carried out to determine soil microbiome composition—with the incubation and metagenomic methods, the activity of seven enzymes, and cocksfoot effect on hydrocarbon degradation. The following indices were determined: colony development index (CD); ecophysiological diversity index (EP); index of cocksfoot effect on soil microorganisms and enzymes (IFG); index of petrol effect on soil microorganisms and enzymes (IFP); index of the resistance of microorganisms, enzymes, and cocksfoot to soil pollution with petrol (RS); Shannon–Weaver’s index of bacterial taxa diversity (H); and Shannon–Weaver’s index of hydrocarbon degradation (IDH). The soil pollution with petrol was found to increase population numbers of bacteria and fungi, and Protebacteria phylum abundance as well as to decrease the abundance of Actinobacteria and Acidobacteria phyla. The cultivation of cocksfoot on the petrol-polluted soil had an especially beneficial effect mainly on the Citation: Borowik, A.; Wyszkowska, bacteria belonging to the Ramlibacter, Pseudoxanthomonas, Mycoplana, and Sphingobium genera. -
The Gut Microbiome of the Sea Urchin, Lytechinus Variegatus, from Its Natural Habitat Demonstrates Selective Attributes of Micro
FEMS Microbiology Ecology, 92, 2016, fiw146 doi: 10.1093/femsec/fiw146 Advance Access Publication Date: 1 July 2016 Research Article RESEARCH ARTICLE The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles Joseph A. Hakim1,†, Hyunmin Koo1,†, Ranjit Kumar2, Elliot J. Lefkowitz2,3, Casey D. Morrow4, Mickie L. Powell1, Stephen A. Watts1,∗ and Asim K. Bej1,∗ 1Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL 35294, USA, 2Center for Clinical and Translational Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA and 4Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, 1918 University Blvd., Birmingham, AL 35294, USA ∗Corresponding authors: Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, CH464, Birmingham, AL 35294-1170, USA. Tel: +1-(205)-934-8308; Fax: +1-(205)-975-6097; E-mail: [email protected]; [email protected] †These authors contributed equally to this work. One sentence summary: This study describes the distribution of microbiota, and their predicted functional attributes, in the gut ecosystem of sea urchin, Lytechinus variegatus, from its natural habitat of Gulf of Mexico. Editor: Julian Marchesi ABSTRACT In this paper, we describe the microbial composition and their predictive metabolic profile in the sea urchin Lytechinus variegatus gut ecosystem along with samples from its habitat by using NextGen amplicon sequencing and downstream bioinformatics analyses. The microbial communities of the gut tissue revealed a near-exclusive abundance of Campylobacteraceae, whereas the pharynx tissue consisted of Tenericutes, followed by Gamma-, Alpha- and Epsilonproteobacteria at approximately equal capacities. -
Ectocarpus: an Evo‑Devo Model for the Brown Algae Susana M
Coelho et al. EvoDevo (2020) 11:19 https://doi.org/10.1186/s13227-020-00164-9 EvoDevo REVIEW Open Access Ectocarpus: an evo-devo model for the brown algae Susana M. Coelho1* , Akira F. Peters2, Dieter Müller3 and J. Mark Cock1 Abstract Ectocarpus is a genus of flamentous, marine brown algae. Brown algae belong to the stramenopiles, a large super- group of organisms that are only distantly related to animals, land plants and fungi. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity. For many years, little information was available concerning the molecular mechanisms underlying multicellular development in the brown algae, but this situation has changed with the emergence of Ectocarpus as a model brown alga. Here we summarise some of the main questions that are being addressed and areas of study using Ectocarpus as a model organism and discuss how the genomic information, genetic tools and molecular approaches available for this organism are being employed to explore developmental questions in an evolutionary context. Keywords: Ectocarpus, Life-cycle, Sex determination, Gametophyte, Sporophyte, Brown algae, Marine, Complex multicellularity, Phaeoviruses Natural habitat and life cycle Ectocarpus is a cosmopolitan genus, occurring world- Ectocarpus is a genus of small, flamentous, multicellu- wide in temperate and subtropical regions, and has been lar, marine brown algae within the order Ectocarpales. collected on all continents except Antarctica [1]. It is pre- Brown algae belong to the stramenopiles (or Heter- sent mainly on rocky shores where it grows on abiotic okonta) (Fig. 1a), a large eukaryotic supergroup that (rocks, pebbles, dead shells) and biotic (other algae, sea- is only distantly related to animals, plants and fungi. -
17, 3203–3222, 2020 © Author(S) 2020
Biogeosciences, 17, 3203–3222, 2020 https://doi.org/10.5194/bg-17-3203-2020 © Author(s) 2020. This work is distributed under the Creative Commons Attribution 4.0 License. The contribution of microbial communities in polymetallic nodules to the diversity of the deep-sea microbiome of the Peru Basin (4130–4198 m depth) Massimiliano Molari1, Felix Janssen1,2, Tobias R. Vonnahme1,a, Frank Wenzhöfer1,2, and Antje Boetius1,2 1Max Planck Institute for Marine Microbiology, Bremen, Germany 2HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany apresent address: UiT the Arctic University of Tromsø, Tromsø, Norway Correspondence: Massimiliano Molari ([email protected]) Received: 16 January 2020 – Discussion started: 3 February 2020 Revised: 27 April 2020 – Accepted: 15 May 2020 – Published: 25 June 2020 Abstract. Industrial-scale mining of deep-sea polymetal- tween the Clarion–Clipperton Fracture Zone (CCZ) and the lic nodules will remove nodules in large areas of the sea Peru Basin suggest that changes in environmental setting floor. The regrowth of the nodules by metal precipita- (e.g. sedimentation rates) also play a significant role in struc- tion is estimated to take millions of years. Thus, for fu- turing the nodule microbiome. ture mining impact studies, it is crucial to understand the role of nodules in shaping microbial diversity and function in deep-sea environments. Here we investigated microbial- community composition based on 16S rRNA gene sequences 1 Introduction retrieved from sediments and nodules of the Peru Basin (4130–4198 m water depth). The nodule field of the Peru Polymetallic nodules (or manganese nodules) occur in Basin showed a typical deep-sea microbiome, with domi- abyssal plains (4000–6000 m water depth) and consist pri- nance of the classes Gammaproteobacteria, Alphaproteobac- marily of manganese and iron as well as many other metals teria, Deltaproteobacteria, and Acidimicrobiia. -
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.