Hemolymph Microbiome of Pacific Oysters in Response to Temperature, Temperature Stress and Infection
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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. -
Colsa Urc Abstract Book
ABSTRACTS FOR ORAL PRESENTATIONS (in order of presentation) 1 CHANGE IN RELATIVE POPULATION ABUNDANCE AND DISTRIBUTION OF HOCHSTETTER’S FROG (LEIOPELMA HOCHSTETTERI) IN MAUNGATAUTARI ECOLOGICAL ISLAND, NEW ZEALAND Heidi Giguere and Ria Brejaart Department of Natural Resources & the Environment, UNH Native New Zealand frogs (Leiopelma spp.) have suffered extinctions since human settlement brought introduced mammalian pests to the country. Since the discovery in 2004 of a population of Hochstetter's frog (Leiopelma hochstetteri) in Maungatautari Ecological Island, a pest-proof fence has been established and all mammalian predators have been eradicated. Mammalian pests are known to prey on native frog species, and can also create habitat instability which has been linked to population declines. With pest eradication, habitat suitability and quality has significantly improved, benefiting the health of the frog population. Results have shown an increase in relative abundance of Hochstetter's frogs, an increase in the proportion of juveniles in the populations, and an increase in spatial distribution within the enclosure. These results suggest that the eradication of pests has had a significant positive effect on this frog population. 2 IN SITU OCEANOGRAPHIC LIDAR AS A TOOL FOR RETRIEVING AND CHARACTERIZING PARTICLE DISTRIBUTIONS IN THE OCEAN Adrien Flouros1 and Richard Zimmerman2 1Department of Natural Resources & the Environment, UNH 2Department of Ocean, Earth, and Atmospheric Sciences, Old Dominion University An in situ LiDAR system (iLiDAR) was deployed from a surface vessel on a cruise in the Chesapeake Bay in June 2015, and the profiles retrieved were compared with other water column optical properties measured in situ. An iLiDAR offers several advantages when compared to airborne or satellite based LiDAR. -
Isolation and Identification of Bacterial Endosymbionts in the Brooding Brittle Star Amphipholis Squamata
University of New Hampshire University of New Hampshire Scholars' Repository Honors Theses and Capstones Student Scholarship Spring 2016 Isolation and identification of bacterial endosymbionts in the brooding brittle star Amphipholis squamata Abbey Rose Tedford University of New Hampshire - Main Campus Follow this and additional works at: https://scholars.unh.edu/honors Part of the Bacteriology Commons, Biodiversity Commons, Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Marine Biology Commons, and the Organismal Biological Physiology Commons Recommended Citation Tedford, Abbey Rose, "Isolation and identification of bacterial endosymbionts in the brooding brittle star Amphipholis squamata" (2016). Honors Theses and Capstones. 273. https://scholars.unh.edu/honors/273 This Senior Honors Thesis is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Honors Theses and Capstones by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. Isolation and identification of bacterial endosymbionts in the brooding brittle star Amphipholis squamata Abbey Rose Tedford, Kathleen M. Morrow, Michael P. Lesser Department of Molecular, Cellular and Biological Sciences, University of New Hampshire, Durham, NH 03824 Abstract: Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. -
A059p283.Pdf
Vol. 59: 283–293, 2010 AQUATIC MICROBIAL ECOLOGY Published online April 21 doi: 10.3354/ame01398 Aquat Microb Ecol High diversity of Rhodobacterales in the subarctic North Atlantic Ocean and gene transfer agent protein expression in isolated strains Yunyun Fu1,*, Dawne M. MacLeod1,*, Richard B. Rivkin2, Feng Chen3, Alison Buchan4, Andrew S. Lang1,** 1Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Ave., St. John’s, Newfoundland A1B 3X9, Canada 2Ocean Sciences Centre, Memorial University of Newfoundland, Marine Lab Road, St. John’s, Newfoundland A1C 5S7, Canada 3Center of Marine Biotechnology, University of Maryland Biotechnology Institute, 236-701 East Pratt St., Baltimore, Maryland 21202, USA 4Department of Microbiology, University of Tennessee, M409 Walters Life Sciences, Knoxville, Tennessee 37914, USA ABSTRACT: Genes encoding gene transfer agent (GTA) particles are well conserved in bacteria of the order Rhodobacterales. Members of this order are abundant in diverse marine environments, fre- quently accounting for as much as 25% of the total bacterial community. Conservation of the genes encoding GTAs allows their use as diagnostic markers of Rhodobacterales in biogeographical stud- ies. The first survey of the diversity of Rhodobacterales based on the GTA major capsid gene was con- ducted in a warm temperate estuarine ecosystem, the Chesapeake Bay, but the biogeography of Rhodobacterales has not been explored extensively. This study investigates Rhodobacterales diver- sity in the cold subarctic water near Newfoundland, Canada. Our results suggest that the subarctic region of the North Atlantic contains diverse Rhodobacterales communities in both winter and sum- mer, and that the diversity of the Rhodobacterales community in the summer Newfoundland coastal water is higher than that found in the Chesapeake Bay, in either the summer or winter. -
Taxonomic Hierarchy of the Phylum Proteobacteria and Korean Indigenous Novel Proteobacteria Species
Journal of Species Research 8(2):197-214, 2019 Taxonomic hierarchy of the phylum Proteobacteria and Korean indigenous novel Proteobacteria species Chi Nam Seong1,*, Mi Sun Kim1, Joo Won Kang1 and Hee-Moon Park2 1Department of Biology, College of Life Science and Natural Resources, Sunchon National University, Suncheon 57922, Republic of Korea 2Department of Microbiology & Molecular Biology, College of Bioscience and Biotechnology, Chungnam National University, Daejeon 34134, Republic of Korea *Correspondent: [email protected] The taxonomic hierarchy of the phylum Proteobacteria was assessed, after which the isolation and classification state of Proteobacteria species with valid names for Korean indigenous isolates were studied. The hierarchical taxonomic system of the phylum Proteobacteria began in 1809 when the genus Polyangium was first reported and has been generally adopted from 2001 based on the road map of Bergey’s Manual of Systematic Bacteriology. Until February 2018, the phylum Proteobacteria consisted of eight classes, 44 orders, 120 families, and more than 1,000 genera. Proteobacteria species isolated from various environments in Korea have been reported since 1999, and 644 species have been approved as of February 2018. In this study, all novel Proteobacteria species from Korean environments were affiliated with four classes, 25 orders, 65 families, and 261 genera. A total of 304 species belonged to the class Alphaproteobacteria, 257 species to the class Gammaproteobacteria, 82 species to the class Betaproteobacteria, and one species to the class Epsilonproteobacteria. The predominant orders were Rhodobacterales, Sphingomonadales, Burkholderiales, Lysobacterales and Alteromonadales. The most diverse and greatest number of novel Proteobacteria species were isolated from marine environments. Proteobacteria species were isolated from the whole territory of Korea, with especially large numbers from the regions of Chungnam/Daejeon, Gyeonggi/Seoul/Incheon, and Jeonnam/Gwangju. -
Genomic Analysis of the Evolution of Phototrophy Among Haloalkaliphilic Rhodobacterales
GBE Genomic Analysis of the Evolution of Phototrophy among Haloalkaliphilic Rhodobacterales Karel Kopejtka1,2,Ju¨rgenTomasch3, Yonghui Zeng4, Martin Tichy1, Dimitry Y. Sorokin5,6,and Michal Koblızek1,2,* 1Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, CAS, Center Algatech, Trebon, Czech Republic 2Faculty of Science, University of South Bohemia, Ceske ´ Budejovice, Czech Republic 3Research Group Microbial Communication, Helmholtz Centre for Infection Research, Braunschweig, Germany 4Aarhus Institute of Advanced Studies, Aarhus, Denmark 5Winogradsky Institute of Microbiology, Research Centre of Biotechnology, Russian Academy of Sciences, Moscow, Russia 6Department of Biotechnology, Delft University of Technology, The Netherlands *Corresponding author: E-mail: [email protected]. Accepted: July 26, 2017 Data deposition: This project has been deposited at NCBI GenBank under the accession numbers: GCA_001870665.1, GCA_001870675.1, GCA_001884735.1. Abstract A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photo- heterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and faculta- tively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter -
Supplement of Biogeosciences, 13, 5527–5539, 2016 Doi:10.5194/Bg-13-5527-2016-Supplement © Author(S) 2016
Supplement of Biogeosciences, 13, 5527–5539, 2016 http://www.biogeosciences.net/13/5527/2016/ doi:10.5194/bg-13-5527-2016-supplement © Author(s) 2016. CC Attribution 3.0 License. Supplement of Seasonal changes in the D / H ratio of fatty acids of pelagic microorganisms in the coastal North Sea Sandra Mariam Heinzelmann et al. Correspondence to: Sandra Mariam Heinzelmann ([email protected]) The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence. Figure legends Supplementary Figure S1 Phylogenetic tree of 16S rRNA gene sequence reads assigned to Bacteroidetes. Scale bar indicates 0.10 % estimated sequence divergence. Groups containing sequences are highlighted. Figure S2 Phylogenetic tree of 16S rRNA gene sequence reads assigned to Alphaproteobacteria. Scale bar indicates 0.10 % estimated sequence divergence. Groups containing sequences are highlighted. Figure S3 Phylogenetic tree of 16S rRNA gene sequence reads assigned to Gammaproteobacteria. Scale bar indicates 0.10 % estimated sequence divergence. Groups containing sequences are highlighted. Figure S4 δDwater versus salinity of North Sea SPM sampled in 2013. Bacteroidetes figS01 group including Prevotellaceae Bacteroidaceae_Bacteroides RH-aaj90h05 RF16 S24-7 gir-aah93ho Porphyromonadaceae_1 ratAN060301C Porphyromonadaceae_2 3M1PL1-52 termite group Porphyromonadaceae_Paludibacter EU460988, uncultured bacterium, red kangaroo feces Porphyromonadaceae_3 009E01-B-SD-P15 Rikenellaceae MgMjR-022 BS11 gut group Rs-E47 termite group group including termite group FTLpost3 ML635J-40 aquatic group group including gut group vadinHA21 LKC2.127-25 Marinilabiaceae Porphyromonadaceae_4 Sphingobacteriia_Sphingobacteriales_1 group including Cytophagales Bacteroidetes Incertae Sedis_Unknown Order_Unknown Family_Prolixibacter WCHB1-32 SB-1 vadinHA17 SB-5 BD2-2 Ika-33 VC2.1 Bac22 Flavobacteria_Flavobacteriales including e.g. -
Biofilm Plasmids with a Rhamnose Operon Are Widely Distributed Determinants of the ‘Swim-Or-Stick’ Lifestyle in Roseobacters
The ISME Journal (2016) 10, 2498–2513 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 OPEN www.nature.com/ismej ORIGINAL ARTICLE Biofilm plasmids with a rhamnose operon are widely distributed determinants of the ‘swim-or-stick’ lifestyle in roseobacters Victoria Michael1, Oliver Frank1, Pascal Bartling, Carmen Scheuner, Markus Göker, Henner Brinkmann and Jörn Petersen Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany Alphaproteobacteria of the metabolically versatile Roseobacter group (Rhodobacteraceae) are abundant in marine ecosystems and represent dominant primary colonizers of submerged surfaces. Motility and attachment are the prerequisite for the characteristic ‘swim-or-stick’ lifestyle of many representatives such as Phaeobacter inhibens DSM 17395. It has recently been shown that plasmid curing of its 65-kb RepA-I-type replicon with 420 genes for exopolysaccharide biosynthesis including a rhamnose operon results in nearly complete loss of motility and biofilm formation. The current study is based on the assumption that homologous biofilm plasmids are widely distributed. We analyzed 33 roseobacters that represent the phylogenetic diversity of this lineage and documented attachment as well as swimming motility for 60% of the strains. All strong biofilm formers were also motile, which is in agreement with the proposed mechanism of surface attachment. We established transposon mutants for the four genes of the rhamnose operon from P. inhibens and proved its crucial role in biofilm formation. In the Roseobacter group, two-thirds of the predicted biofilm plasmids represent the RepA-I type and their physiological role was experimentally validated via plasmid curing for four additional strains. -
Luhtanen Et Al Unihel
FEMS Microbiology Ecology Page 2 of 41 1 2 3 1 Host specificity and temperature adaptation of the first known Antarctic sea- 4 5 2 ice virus isolates 6 7 3 8 1,2,3 1 2 9 4 Anne-Mari Luhtanen , Eeva Eronen-Rasimus , Hanna M. Oksanen , Jean-Louis 10 4 5 6 3,7 5 Tison , Bruno Delille , Gerhard S. Dieckmann , Janne-Markus Rintala and 11 12 6 Dennis H. Bamford2 13 14 7 15 16 8 1Marine Research Centre, Finnish Environment Institute, Helsinki, Finland, 17 18 9 2Programme on molecules, cells and systems, University of Helsinki, Helsinki, 19 3 For Peer Review 20 10 Finland, Tvärminne Zoological Station, University of Helsinki, Hanko, Finland, 21 4 22 11 Laboratoire de Glaciologie, DGES, Université Libre de Bruxelles, Belgium, 23 5 6 24 12 Unité d’Océanographie Chimique, Université de Liège, Belgium, Alfred 25 26 13 Wegener Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, 27 14 7 28 Germany, Department of Environmental Sciences, University of Helsinki, 29 15 Helsinki, Finland 30 31 16 32 33 17 34 35 18 Correspondence: 36 37 19 D.H. Bamford, Programme on molecules, cells and systems, FIN-00014 University 38 39 20 of Helsinki, Finland. Email: [email protected] 40 41 21 42 43 22 Conflict of Interest 44 45 23 The authors declare no conflict of interest. 46 24 47 48 25 49 50 51 52 53 54 55 56 57 58 59 1 60 ScholarOne Support 1-434/964-4100 Page 3 of 41 FEMS Microbiology Ecology 1 2 3 26 Abstract 4 5 27 Viruses are recognized as important actors in ocean ecology and biogeochemical 6 7 28 cycles, but many details are not yet understood. -
Lefse) Analysis of Microbiome in Baseline and 12 Weeks
Figure S1. Linear discriminant analysis effect sized (LEfSE) analysis of microbiome in baseline and 12 weeks. Table S1. Species which showed significant difference (linear discriminant analysis (LDA) score ≥ 2.5) in linear discriminant analysis effect sized (LEfSe) analysis. (A) ASVs of control group which showed significant difference between baseline and 12 weeks. (B) ASVs of test group which showed significant difference between baseline and 12 weeks. u.i, Unidentified (A) Control Mean RA Mean RA in LDA P in Phylum Class Order Family Genus Species ASV Time 12 weeks score value baseline (%) (%) Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae Capnocytophaga u.i ASV110 Baseline 2.4569 0.018 0.05±0.18 0 Fusobacteria Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium u.i ASV225 Baseline 3.0469 0.0047 0.25±0.40 0.06±0.13 Chryseobacteriu 2.25E- Bacteroidetes Flavobacteriia Flavobacteriales Weeksellaceae u.i ASV255 Baseline 2.6588 0.07±0.15 0 m 05 Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Paludibacter u.i ASV213 Baseline 2.3868 0.034 0.04±0.13 0.0024±0.01 (B) Test Mean RA Mean RA in LDA P in Phylum Class Order Family Genus Species ASV Time 12 weeks score value baseline (%) (%) Gammaproteo parainfl 3.55E- Proteobacteria Pasteurellales Pasteurellaceae Haemophilus ASV495 Baseline 4.1743 4.72±5.14 1.57±3.25 bacteria uenzae 05 Betaproteobact Proteobacteria Neisseriales Neisseriaceae ASV309 Baseline 3.4063 0.034 0.03±0.14 0.0007±0.0042 eria Betaproteobact Proteobacteria Neisseriales Neisseriaceae ASV354 -
Proteobacterial Gene Transfer Agents
bioRxiv preprint doi: https://doi.org/10.1101/189738; this version posted October 29, 2017. 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-ND 4.0 International license. 1 Insights into Origin and Evolution of a- 2 proteobacterial Gene Transfer Agents 3 Migun Shakya1,2, Shannon M. Soucy1, and Olga Zhaxybayeva1,3,* 4 1Department of Biological Sciences, Dartmouth College, Hanover NH 03755, USA 5 2Present address: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544 6 3Department of Computer Science, Dartmouth College, Hanover NH 03755, USA 7 *Corresponding author, E-mail: [email protected]; Tel: (603) 646-8616 8 9 Research Paper 10 Keywords: exaptation, domestication, horizontal gene transfer, bacterium-virus co-evolution, 11 bacteriophage 12 1 bioRxiv preprint doi: https://doi.org/10.1101/189738; this version posted October 29, 2017. 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-ND 4.0 International license. 1 Abstract 2 Several bacterial and archaeal lineages produce nanostructures that morphologically resemble 3 small tailed viruses, but, unlike most viruses, contain apparently random pieces of the host 4 genome. Since these elements can deliver the packaged DNA to other cells, they were dubbed 5 Gene Transfer Agents (GTAs). Because many genes involved in GTA production have viral 6 homologs, it has been hypothesized that the GTA ancestor was a virus. -
Supplementary Information 1 2 Population Differentiation Of
1 Supplementary Information 2 3 Population Differentiation of Rhodobacteraceae Along Coral Compartments 4 Danli Luo, Xiaojun Wang, Xiaoyuan Feng, Mengdan Tian, Sishuo Wang, Sen-Lin Tang, Put 5 Ang Jr, Aixin Yan, Haiwei Luo 6 7 8 9 10 11 This PDF file includes: 12 Text 1. Supplementary methods 13 Text 2. Supplementary results 14 Figures S1 to S13 15 Supplementary references 16 17 Text 1. Supplementary methods 18 1.1 Coral sample collection and processing 19 1.2 Bacterial isolation 20 1.3 Genome sequencing, assembly and annotation 21 1.4 Ortholog prediction and phylogenomic tree construction 22 1.5 Analysis of population structure in core genomes 23 1.6 Inference of novel allelic replacement with external lineages in core genomes 24 1.7 Differentiation in the accessory genome and inference of evolutionary history 25 1.8 Identification of pseudogenes in the fla1 flagellar gene cluster 26 1.9 The physiological assays 27 1.10 Test of compartmentalization and dispersal limitation 28 1.11 Estimating the origin time for the Rhodobacteraceae and the Ruegeria populations 29 Text 2. Supplementary results 30 2.1 Population differentiation at the core genomes of the Ruegeria population 31 2.2 The Ruegeria population differentiation at the physiological level 32 2.3 Metabolic potential for utilizing other substrates by the mucus clade of the Ruegeria 33 population 34 2.4 Metabolic potential of the mucus clade in the Ruegeria population underlying 35 microbial interactions in the densely-populated mucus habitat 36 2.5 Adaptation of the skeleton clade in the Ruegeria population to the periodically 37 anoxic skeleton habitat 38 39 40 Text 1.