Sequence from B4 Sponge with (A) the First BLAST Hit Asbestopluma Lycopodium and (B) the Sequence of M
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Supplementary Materials: Patterns of Sponge Biodiversity in the Pilbara, Northwestern Australia
Diversity 2016, 8, 21; doi:10.3390/d8040021 S1 of S3 9 Supplementary Materials: Patterns of Sponge Biodiversity in the Pilbara, Northwestern Australia Jane Fromont, Muhammad Azmi Abdul Wahab, Oliver Gomez, Merrick Ekins, Monique Grol and John Norman Ashby Hooper 1. Materials and Methods 1.1. Collation of Sponge Occurrence Data Data of sponge occurrences were collated from databases of the Western Australian Museum (WAM) and Atlas of Living Australia (ALA) [1]. Pilbara sponge data on ALA had been captured in a northern Australian sponge report [2], but with the WAM data, provides a far more comprehensive dataset, in both geographic and taxonomic composition of sponges. Quality control procedures were undertaken to remove obvious duplicate records and those with insufficient or ambiguous species data. Due to differing naming conventions of OTUs by institutions contributing to the two databases and the lack of resources for physical comparison of all OTU specimens, a maximum error of ± 13.5% total species counts was determined for the dataset, to account for potentially unique (differently named OTUs are unique) or overlapping OTUs (differently named OTUs are the same) (157 potential instances identified out of 1164 total OTUs). The amalgamation of these two databases produced a complete occurrence dataset (presence/absence) of all currently described sponge species and OTUs from the region (see Table S1). The dataset follows the new taxonomic classification proposed by [3] and implemented by [4]. The latter source was used to confirm present validities and taxon authorities for known species names. The dataset consists of records identified as (1) described (Linnean) species, (2) records with “cf.” in front of species names which indicates the specimens have some characters of a described species but also differences, which require comparisons with type material, and (3) records as “operational taxonomy units” (OTUs) which are considered to be unique species although further assessments are required to establish their taxonomic status. -
Sponges of the Caribbean: Linking Sponge Morphology and Associated Bacterial Communities Ericka Ann Poppell
University of Richmond UR Scholarship Repository Master's Theses Student Research 5-2011 Sponges of the Caribbean: linking sponge morphology and associated bacterial communities Ericka Ann Poppell Follow this and additional works at: http://scholarship.richmond.edu/masters-theses Part of the Biology Commons Recommended Citation Poppell, Ericka Ann, "Sponges of the Caribbean: linking sponge morphology and associated bacterial communities" (2011). Master's Theses. Paper 847. This Thesis is brought to you for free and open access by the Student Research at UR Scholarship Repository. It has been accepted for inclusion in Master's Theses by an authorized administrator of UR Scholarship Repository. For more information, please contact [email protected]. ABSTRACT SPONGES OF THE CARIBBEAN: LINKING SPONGE MORPHOLOGY AND ASSOCIATED BACTERIAL COMMUNITIES By: Ericka Ann Poppell, B.S. A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science at the University of Richmond University of Richmond, May 2011 Thesis Director: Malcolm S. Hill, Ph.D., Professor, Department of Biology The ecological and evolutionary relationship between sponges and their symbiotic microflora remains poorly understood, which limits our ability to understand broad scale patterns in benthic-pelagic coupling on coral reefs. Previous research classified sponges into two different categories of sponge-microbial associations: High Microbial Abundance (HMA) and Low Microbial Abundance (LMA) sponges. Choanocyte chamber morphology and density was characterized in representatives of HMA and LMA sponges using scanning electron I)licroscopy from freeze-fractured tissue. Denaturing Gradient Gel Electrophoresis was used to examine taxonomic differences among the bacterial communities present in a variety of tropical sponges. -
Ctz 74-00 Pinheiro.Indd
Contributions to Zoology, 74 (3/4) 271-278 (2005) Shallow-water Niphatidae (Haplosclerina, Haplosclerida, Demospongiae) from the São Sebastião Channel and its environs (tropical southwestern At- lantic), with the description of a new species U. S. Pinheiro1, 2, *, R.G.S. Berlinck 3, **, E. Hajdu 2, *** 1Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Rua José Moreira So- brinho, s/n, 45200-000, Jequiezinho, Jequié, BA, Brazil; 2Departamento de Invertebrados, Museu Nacional, Universidade do Brasil, Quinta da Boa Vista, s/n, 20940-040, Rio de Janeiro, RJ, Brazil; 3Instituto de Química de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil; *FAPERJ fellow, e-mail: upinheiro@gmail. com; **CNPq fellow, e-mail: [email protected]; ***CNPq fellow, e-mail: [email protected] Key words: Porifera, Demospongiae, Haplosclerina, Niphatidae, tropical southwestern Atlantic, taxonomy, new species Abstract Comparison of the niphatids collected in the São Sebastião Channel area and its environs with data Two niphatids are described here: Amphimedon viridis and compiled from the literature lead us to identify Am- Pachychalina alcaloidifera sp. nov. Amphimedon viridis is a common and conspicuous species in most of the tropical western phimedon viridis and a new species, Pachychalina Atlantic. Pachychalina alcaloidifera sp. nov. has this far been alcaloidifera sp. nov., to be described below. found only in the coasts of Rio de Janeiro and São Paulo states. Both species are described on the basis of series of specimens observed alive. Material and methods Specimens were collected during a faunistic survey Contents conducted in the area of the São Sebastião Channel and its environs, in the municipalities of São Sebas- Introduction ................................................................................... -
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. -
Two New Haplosclerid Sponges from Caribbean Panama with Symbiotic Filamentous Cyanobacteria, and an Overview of Sponge-Cyanobacteria Associations
PORIFERA RESEARCH: BIODIVERSITY, INNOVATION AND SUSTAINABILITY - 2007 31 Two new haplosclerid sponges from Caribbean Panama with symbiotic filamentous cyanobacteria, and an overview of sponge-cyanobacteria associations Maria Cristina Diaz'12*>, Robert W. Thacker<3), Klaus Rutzler(1), Carla Piantoni(1) (1) Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, D.C. 20560-0163, USA. [email protected] (2) Museo Marino de Margarita, Blvd. El Paseo, Boca del Rio, Margarita, Edo. Nueva Esparta, Venezuela. [email protected] <3) Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294-1170, USA. [email protected] Abstract: Two new species of the order Haplosclerida from open reef and mangrove habitats in the Bocas del Toro region (Panama) have an encrusting growth form (a few mm thick), grow copiously on shallow reef environments, and are of dark purple color from dense populations of the cyanobacterial symbiont Oscillatoria spongeliae. Haliclona (Soestella) walentinae sp. nov. (Chalinidae) is dark purple outside and tan inside, and can be distinguished by its small oscules with radial, transparent canals. The interior is tan, while the consistency is soft and elastic. The species thrives on some shallow reefs, profusely overgrowing fire corals (Millepora spp.), soft corals, scleractinians, and coral rubble. Xestospongia bocatorensis sp. nov. (Petrosiidae) is dark purple, inside and outside, and its oscules are on top of small, volcano-shaped mounds and lack radial canals. The sponge is crumbly and brittle. It is found on live coral and coral rubble on reefs, and occasionally on mangrove roots. The two species have three characteristics that make them unique among the families Chalinidae and Petrosiidae: filamentous, multicellular cyanobacterial symbionts rather than unicellular species; high propensity to overgrow other reef organisms and, because of their symbionts, high rate of photosynthetic production. -
Interactions in Self-Assembled Microbial Communities Saturate with Diversity
bioRxiv preprint doi: https://doi.org/10.1101/347948; this version posted June 16, 2018. 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 4.0 International license. Interactions in self-assembled microbial communities saturate with diversity Xiaoqian Yu1, Martin F. Polz2*, Eric J. Alm2,3,4,5* 1. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 2. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 3. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 4. Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA 5. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA *Correspondence should be addressed to: E.J.A. ([email protected]) or M.F.P. ([email protected]) Abstract How the diversity of organisms competing for or sharing resources influences community production is an important question in ecology but has rarely been explored in natural microbial communities. These generally contain large numbers of species making it difficult to disentangle how the effects of different interactions scale with diversity. Here, we show that changing diversity affects measures of community function in relatively simple communities but that increasing richness beyond a threshold has little detectable effect. We generated self-assembled communities with a wide range of diversity by growth of cells from serially diluted seawater on brown algal leachate. We subsequently isolated the most abundant taxa from these communities via dilution-to-extinction in order to compare productivity functions of the entire community to those of individual taxa. -
Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S Rrna) and Mitochondrial (Cox1, Nad1) Gene Sequence Data
Phylogenetic Relationships of the Marine Haplosclerida (Phylum Porifera) Employing Ribosomal (28S rRNA) and Mitochondrial (cox1, nad1) Gene Sequence Data Niamh E. Redmond1,2, Jean Raleigh2, Rob W. M. van Soest3, Michelle Kelly4, Simon A. A. Travers5, Brian Bradshaw2, Salla Vartia2, Kelly M. Stephens2, Grace P. McCormack2* 1 Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington D. C., United States of America, 2 Zoology, National University of Ireland, Galway, Ireland, 3 Zoological Museum, University of Amsterdam, Amsterdam, The Netherlands, 4 National Centre for Aquatic Biodiversity and Biosecurity, National Institute of Water and Atmospheric Research, Auckland, New Zealand, 5 South African National Bioinformatics Institute, University of Western Cape, Bellville, South Africa Abstract The systematics of the poriferan Order Haplosclerida (Class Demospongiae) has been under scrutiny for a number of years without resolution. Molecular data suggests that the order needs revision at all taxonomic levels. Here, we provide a comprehensive view of the phylogenetic relationships of the marine Haplosclerida using many species from across the order, and three gene regions. Gene trees generated using 28S rRNA, nad1 and cox1 gene data, under maximum likelihood and Bayesian approaches, are highly congruent and suggest the presence of four clades. Clade A is comprised primarily of species of Haliclona and Callyspongia, and clade B is comprised of H. simulans and H. vansoesti (Family Chalinidae), Amphimedon queenslandica (Family Niphatidae) and Tabulocalyx (Family Phloeodictyidae), Clade C is comprised primarily of members of the Families Petrosiidae and Niphatidae, while Clade D is comprised of Aka species. The polyphletic nature of the suborders, families and genera described in other studies is also found here. -
Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology
crossmark Marine Bacterial and Archaeal Ion-Pumping Rhodopsins: Genetic Diversity, Physiology, and Ecology Jarone Pinhassi,a Edward F. DeLong,b,c Oded Béjà,d José M. González,e Carlos Pedrós-Alióf Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Swedena; Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USAb; Department of Biological Engineering and Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USAc; Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israeld; Department of Microbiology, University of La Laguna, La Laguna, Spaine; Systems Biology Program, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spainf SUMMARY ..................................................................................................................................................929 Downloaded from INTRODUCTION ............................................................................................................................................930 TYPE I RHODOPSIN CONSERVATION AND DIVERSITY .....................................................................................................931 Rhodopsin Types .........................................................................................................................................931 Phylogenetic Distribution of Microbial Rhodopsins According to Biochemical Functions ...............................................................933 -
Horizontal Gene Transfer in the Sponge Amphimedon Queenslandica
Horizontal gene transfer in the sponge Amphimedon queenslandica Simone Summer Higgie BEnvSc (Honours) A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 School of Biological Sciences Abstract Horizontal gene transfer (HGT) is the nonsexual transfer of genetic sequence across species boundaries. Historically, HGT has been assumed largely irrelevant to animal evolution, though widely recognised as an important evolutionary force in bacteria. From the recent boom in whole genome sequencing, many cases have emerged strongly supporting the occurrence of HGT in a wide range of animals. However, the extent, nature and mechanisms of HGT in animals remain poorly understood. Here, I explore these uncertainties using 576 HGTs previously reported in the genome of the demosponge Amphimedon queenslandica. The HGTs derive from bacterial, plant and fungal sources, contain a broad range of domain types, and many are differentially expressed throughout development. Some domains are highly enriched; phylogenetic analyses of the two largest groups, the Aspzincin_M35 and the PNP_UDP_1 domain groups, suggest that each results from one or few transfer events followed by post-transfer duplication. Their differential expression through development, and the conservation of domains and duplicates, together suggest that many of the HGT-derived genes are functioning in A. queenslandica. The largest group consists of aspzincins, a metallopeptidase found in bacteria and fungi, but not typically in animals. I detected aspzincins in representatives of all four of the sponge classes, suggesting that the original sponge aspzincin was transferred after sponges diverged from their last common ancestor with the Eumetazoa, but before the contemporary sponge classes emerged. -
Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia
molecules Article Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia Nadezhda Chernysheva, Evgeniya Bystritskaya, Galina Likhatskaya , Olga Nedashkovskaya and Marina Isaeva * G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 159, Pr. 100 let Vladivostoku, 690022 Vladivostok, Russia; [email protected] (N.C.); [email protected] (E.B.); [email protected] (G.L.); [email protected] (O.N.) * Correspondence: [email protected]; Tel.: +7-423-231-1168 Abstract: We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus- specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs. Keywords: Zobellia; genomes; polysaccharide lyase family 7; alginate utilization system; paralogs; orthologs Citation: Chernysheva, N.; Bystritskaya, E.; Likhatskaya, G.; Nedashkovskaya, O.; Isaeva, M. Genome-Wide Analysis of PL7 1. Introduction Alginate Lyases in the Genus Zobellia. Marine algal polysaccharides are an important nutrient source for marine bacteria. To Molecules 2021, 26, 2387. -
The Mannitol Utilization System of the Marine Bacterium Zobellia Galactanivorans Agnès Groisillier, Aurore Labourel, Gurvan Michel, Thierry Tonon
The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans Agnès Groisillier, Aurore Labourel, Gurvan Michel, Thierry Tonon To cite this version: Agnès Groisillier, Aurore Labourel, Gurvan Michel, Thierry Tonon. The Mannitol Utilization System of the Marine Bacterium Zobellia galactanivorans. Applied and Environmental Microbiology, Ameri- can Society for Microbiology, 2015, 81, pp.1799 - 1812. 10.1128/AEM.02808-14. hal-01116467 HAL Id: hal-01116467 https://hal.archives-ouvertes.fr/hal-01116467 Submitted on 13 Feb 2015 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. 1 1 The mannitol utilization system of the marine bacterium Zobellia galactanivorans 2 3 4 Agnès Groisillier,a,b, Aurore Labourel,a,b,*, Gurvan Michel,a,b and Thierry Tonona,b,# 5 6 Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine 7 Models, Station Biologique de Roscoff, Francea; CNRS, UMR 8227, Integrative Biology of 8 Marine Models, Station Biologique de Roscoff, Franceb 9 10 Running title: Mannitol degradation by Zobellia galactanivorans 11 12 #Address correspondence to Thierry Tonon, [email protected] 13 14 *Present address: University of Newcastle, Cell and Molecular Biosciences, Medical School, 15 Cookson Bidg, Framligton Place, NE2 4HH Newcastle upon Tyne, United Kingdom 16 17 A.G. -
Table S8. Species Identified by Random Forests Analysis of Shotgun Sequencing Data That Exhibit Significant Differences In
Table S8. Species identified by random forests analysis of shotgun sequencing data that exhibit significant differences in their representation in the fecal microbiomes between each two groups of mice. (a) Species discriminating fecal microbiota of the Soil and Control mice. Mean importance of species identified by random forest are shown in the 5th column. Random forests assigns an importance score to each species by estimating the increase in error caused by removing that species from the set of predictors. In our analysis, we considered a species to be “highly predictive” if its importance score was at least 0.001. T-test was performed for the relative abundances of each species between the two groups of mice. P-values were at least 0.05 to be considered statistically significant. Microbiological Taxonomy Random Forests Mean of relative abundance P-Value Species Microbiological Function (T-Test) Classification Bacterial Order Importance Score Soil Control Rhodococcus sp. 2G Engineered strain Bacteria Corynebacteriales 0.002 5.73791E-05 1.9325E-05 9.3737E-06 Herminiimonas arsenitoxidans Engineered strain Bacteria Burkholderiales 0.002 0.005112829 7.1580E-05 1.3995E-05 Aspergillus ibericus Engineered strain Fungi 0.002 0.001061181 9.2368E-05 7.3057E-05 Dichomitus squalens Engineered strain Fungi 0.002 0.018887472 8.0887E-05 4.1254E-05 Acinetobacter sp. TTH0-4 Engineered strain Bacteria Pseudomonadales 0.001333333 0.025523638 2.2311E-05 8.2612E-06 Rhizobium tropici Engineered strain Bacteria Rhizobiales 0.001333333 0.02079554 7.0081E-05 4.2000E-05 Methylocystis bryophila Engineered strain Bacteria Rhizobiales 0.001333333 0.006513543 3.5401E-05 2.2044E-05 Alteromonas naphthalenivorans Engineered strain Bacteria Alteromonadales 0.001 0.000660472 2.0747E-05 4.6463E-05 Saccharomyces cerevisiae Engineered strain Fungi 0.001 0.002980726 3.9901E-05 7.3043E-05 Bacillus phage Belinda Antibiotic Phage 0.002 0.016409765 6.8789E-07 6.0681E-08 Streptomyces sp.