Session #1 Abstracts
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Motiliproteus Sediminis Gen. Nov., Sp. Nov., Isolated from Coastal Sediment
Antonie van Leeuwenhoek (2014) 106:615–621 DOI 10.1007/s10482-014-0232-2 ORIGINAL PAPER Motiliproteus sediminis gen. nov., sp. nov., isolated from coastal sediment Zong-Jie Wang • Zhi-Hong Xie • Chao Wang • Zong-Jun Du • Guan-Jun Chen Received: 3 April 2014 / Accepted: 4 July 2014 / Published online: 20 July 2014 Ó Springer International Publishing Switzerland 2014 Abstract A novel Gram-stain-negative, rod-to- demonstrated that the novel isolate was 93.3 % similar spiral-shaped, oxidase- and catalase- positive and to the type strain of Neptunomonas antarctica, 93.2 % facultatively aerobic bacterium, designated HS6T, was to Neptunomonas japonicum and 93.1 % to Marino- isolated from marine sediment of Yellow Sea, China. bacterium rhizophilum, the closest cultivated rela- It can reduce nitrate to nitrite and grow well in marine tives. The polar lipid profile of the novel strain broth 2216 (MB, Hope Biol-Technology Co., Ltd) consisted of phosphatidylethanolamine, phosphatidyl- with an optimal temperature for growth of 30–33 °C glycerol and some other unknown lipids. Major (range 12–45 °C) and in the presence of 2–3 % (w/v) cellular fatty acids were summed feature 3 (C16:1 NaCl (range 0.5–7 %, w/v). The pH range for growth x7c/iso-C15:0 2-OH), C18:1 x7c and C16:0 and the main was pH 6.2–9.0, with an optimum at 6.5–7.0. Phylo- respiratory quinone was Q-8. The DNA G?C content genetic analysis based on 16S rRNA gene sequences of strain HS6T was 61.2 mol %. Based on the phylogenetic, physiological and biochemical charac- teristics, strain HS6T represents a novel genus and The GenBank accession number for the 16S rRNA gene T species and the name Motiliproteus sediminis gen. -
Textile Waste and Microplastic Induce Activity and Development of Unique
bioRxiv preprint doi: https://doi.org/10.1101/2020.02.08.939876; this version posted February 10, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.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 Textile waste and microplastic induce activity and 2 development of unique hydrocarbon-degrading marine 3 bacterial communities 4 5 Elsa B. Girard1, Melanie Kaliwoda2, Wolfgang W. Schmahl1,2,3, Gert Wörheide1,3,4 and 6 William D. Orsi1,3* 7 8 1 Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, 9 80333 Munich, Germany 10 2 SNSB - Mineralogische Staatssammlung München, 80333 München, Germany 11 3 GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, 80333 Munich, Germany 12 4 SNSB - Bayerische Staatssammlung für Paläontologie und Geologie, 80333 Munich, Germany 13 *Corresponding author (e-mail: [email protected]) 14 15 16 17 18 KEYWORDS 19 Microplastic, Fiber, Hydrocarbon-degrading bacteria, Microbial community, Pollution 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.02.08.939876; this version posted February 10, 2020. 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. 22 ABSTRACT 23 Biofilm-forming microbial communities on plastics and textile fibers are of growing interest since 24 they have potential to contribute to disease outbreaks and material biodegradability in the 25 environment. -
Aliagarivorans Marinus Gen. Nov., Sp. Nov. and Aliagarivorans Taiwanensis Sp
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1880–1887 DOI 10.1099/ijs.0.008235-0 Aliagarivorans marinus gen. nov., sp. nov. and Aliagarivorans taiwanensis sp. nov., facultatively anaerobic marine bacteria capable of agar degradation Wen Dar Jean,1 Ssu-Po Huang,2 Tung Yen Liu,2 Jwo-Sheng Chen3 and Wung Yang Shieh2 Correspondence 1Center for General Education, Leader University, No. 188, Sec. 5, An-Chung Rd, Tainan, Wung Yang Shieh Taiwan, ROC [email protected] 2Institute of Oceanography, National Taiwan University, PO Box 23-13, Taipei, Taiwan, ROC 3College of Health Care, China Medical University, No. 91, Shyue-Shyh Rd, Taichung, Taiwan, ROC Two agarolytic strains of Gram-negative, heterotrophic, facultatively anaerobic, marine bacteria, designated AAM1T and AAT1T, were isolated from seawater samples collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. Cells grown in broth cultures were straight rods that were motile by means of a single polar flagellum. The two isolates required NaCl for growth and grew optimally at about 25–30 6C, in 2–4 % NaCl and at pH 8. They grew aerobically and could achieve anaerobic growth by fermenting D-glucose or other sugars. The major isoprenoid quinone was Q-8 (79.8–92.0 %) and the major cellular fatty acids were summed feature 3 (C16 : 1v7c and/or iso-C15 : 0 2-OH; 26.4–35.6 %), C18 : 1v7c (27.1–31.4 %) and C16 : 0 (14.8–16.3 %) in the two strains. Strains AAM1T and AAT1T had DNA G+C contents of 52.9 and 52.4 mol%, respectively. -
Bowmanella Pacifica Sp. Nov., Isolated from a Pyrene-Degrading Consortium
International Journal of Systematic and Evolutionary Microbiology (2009), 59, 1579–1582 DOI 10.1099/ijs.0.001826-0 Bowmanella pacifica sp. nov., isolated from a pyrene-degrading consortium Qiliang Lai,13 Jun Yuan,1,23 Baojiang Wang,1 Fengqin Sun,1 Nan Qiao,1 Tianling Zheng2 and Zongze Shao1 Correspondence 1Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Zongze Shao Administration, Xiamen 361005, PR China [email protected] 2MOE of Key Lab for Coast and Wetland Ecosystem, School of Life Sciences, Xiamen University, Tianling Zheng Xiamen 361005, PR China [email protected] A taxonomic study was carried out on a strain, designated W3-3AT, which was isolated from a pyrene-degrading consortium, enriched from sediment of the Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain W3-3AT belonged to the genus Bowmanella, with the highest sequence similarity (99.0 %) with Bowmanella denitrificans BD1T, whereas sequence similarities with other species were less than 93 %. The nucleotide sequence similarity of both gyrB and rpoD genes of strain W3-3AT and B. denitrificans BD1T was 81.1 %. However, the protein sequence similarities of the gyrB and rpoD genes of strain W3-3AT and B. denitrificans BD1T were 96.1 % and 91.0 %, respectively. Phylogenetic trees based on these housekeeping genes showed that strain W3-3AT and B. denitrificans BD1T formed a distinct lineage in the Gammaproteobacteria. The DNA–DNA hybridization value between strain W3-3AT and B. denitrificans BD1T was 43 %. Strain W3-3AT could also be differentiated from B. denitrificans BD1T based on the repetitive extragenic palindromic DNA-PCR fingerprint. -
Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas Joobiniege Gen, Nov, Sp
J. Microbiol. Biotechnol. (2013), 23(11), 1509–1518 http://dx.doi.org/10.4014/jmb.1308.08007 Research Article jmb Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea Won-Jae Chi1, Jae-Seon Park1, Min-Jung Kwak2, Jihyun F. Kim3, Yong-Keun Chang4, and Soon-Kwang Hong1* 1Division of Biological Science and Bioinformatics, Myongji University, Yongin 449-728, Republic of Korea 2Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350, Republic of Korea 3Department of Systems Biology, Yonsei University, Seoul 120-749, Republic of Korea 4Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea Received: August 2, 2013 Revised: August 14, 2013 An agar-degrading bacterium, designated as strain G7T, was isolated from a coastal seawater Accepted: August 20, 2013 sample from Gaya Island (Gayado in Korean), Republic of Korea. The isolated strain G7T is gram-negative, rod shaped, aerobic, non-motile, and non-pigmented. A similarity search based on its 16S rRNA gene sequence revealed that it shares 95.5%, 90.6%, and 90.0% T First published online similarity with the 16S rRNA gene sequences of Catenovulum agarivorans YM01, Algicola August 22, 2013 sagamiensis, and Bowmanella pacifica W3-3AT, respectively. Phylogenetic analyses demonstrated T *Corresponding author that strain G7 formed a distinct monophyletic clade closely related to species of the family Phone: +82-31-330-6198; Alteromonadaceae in the Alteromonas-like Gammaproteobacteria. The G+C content of strain Fax: +82-31-335-8249; G7T was 41.12 mol%. -
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. -
Identification and Classification of Marine Bacteria Associated with Poly(Ethylene Terephthalate) Degradation
Identification and classification of marine bacteria associated with poly(ethylene terephthalate) degradation Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy by Hooi Jun Ng Department of Chemistry and Biotechnology School of Science Faculty of Science, Engineering and Technology Swinburne University of Technology November 2014 Abstract Poly(ethylene terephthalate) (PET) is manmade synthetic polymer that has been widely used over the past few decades due to its low manufacturing cost, together with desirable properties. The high production and usage of PET, together with the inappropriate handling of resultant wastes are becoming a major global environmental issue, especially in the marine environment due to the fact that PET is fairly stable and not easily degraded in the environment. The waste handling methods that are currently available, such as burying, incineration and recycling, have their own drawbacks and limitations. Biodegradation represents an environmentally friendly, cost effective and potentially more efficient method for the management of PET, as can be concluded historical instances where microorganisms have been shown to be capable remediating and biodegrading environmental pollutants. The potential with which microorganisms could adapt to mineralize PET has previously been reported, however, none of the studies have identified the potential of marine bacteria to biodegrade of PET. In this project, a collection of marine bacteria belonging to two phylotypes, Alpha- and Gammaproteobacteria, which might have the potential to biodegrade PET, have been investigated to examine their ability to degrade PET. One strain, affiliated to the genus Marinobacter, and designated as A3d10T, was identified to have the ability to hydrolyze bis(benzoyloxyethyl) terephthalate, a trimer of PET. -
Biodiversidad Bacteriana Marina: Nuevos Taxones Cultivables
Departamento de Microbiología y Ecología Colección Española de Cultivos Tipo Doctorado en Biotecnología Biodiversidad bacteriana marina: nuevos taxones cultivables Directores de Tesis David Ruiz Arahal Mª Jesús Pujalte Domarco Mª Carmen Macián Rovira Teresa Lucena Reyes Tesis Doctoral Valencia, 2012 Dr. David Ruiz Arahal , Profesor Titular del Departamento de Microbiología y Ecología de la Universidad de Valencia, Dra. María Jesús Pujalte Domarco , Catedrática del Departamento de Microbiología y Ecología de la Universidad de Valencia, y Dra. Mª Carmen Macián Rovira , Técnico Superior de Investigación de la Colección Española de Cultivos Tipo de la Universidad de Valencia, CERTIFICAN: Que Teresa Lucena Reyes, Licenciada en Ciencias Biológicas por la Universidad de Valencia, ha realizado bajo su dirección el trabajo titulado “Biodiversidad bacteriana marina: nuevos taxones cultivables”, que presenta para optar al grado de Doctor en Ciencias Biológicas por la Universidad de Valencia. Y para que conste, en el cumplimiento de la legislación vigente, firman el presente certificado en Valencia, a. David Ruiz Arahal Mª Jesús Pujalte Domarco Mª Carmen Macián Rovira Relación de publicaciones derivadas de la presente Tesis Doctoral Lucena T , Pascual J, Garay E, Arahal DR, Macián MC, Pujalte MJ (2010) . Haliea mediterranea sp. nov., a marine gammaproteobacterium. Int J Syst Evol Microbiol 60 , 1844-8. Lucena T, Pascual J, Giordano A, Gambacorta A, Garay E, Arahal DR, Macián MC, Pujalte MJ (2010) . Euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae . Int J Syst Evol Microbiol 60 , 2871-6. Lucena T, Ruvira MA, Pascual J, Garay E, Macián MC, Arahal DR, Pujalte MJ (2011) . Photobacterium aphoticum sp. -
Viral Regulation of Nutrient Assimilation by Algae and Prokaryotes
Viral regulation of nutrient assimilation by algae and prokaryotes Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - dem Fachbereich Geowissenschaften der Universität Bremen vorgelegt von Abdul Rahiman Sheik Bremen, Oktober 2012 Die vorliegende Arbeit wurde in der Zeit von April 2009 bis September 2012 am Max Planck Institut für Marine Mikrobiologie angefertigt. 1. Gutachter: Prof. Dr. Marcel Kuypers 2. Gutachterin: Dr. Corina Brussaard Tag des Promotionskolloquiums: 10. Dezember 2012 Summary Viruses are the most abundant entities in the ocean and represent a large portion of ‘lifes’ genetic diversity. As mortality agents, viruses catalyze transformations of particulate matter to dissolved forms. This viral catalytic activity may influence the microbial community structure and affect the flow of critical elements in the sea. However, the extent to which viruses mediate bacterial diversity and biogeochemical processes is poorly studied. The current thesis, using a single cell approach, provides rare and novel insights in to how viral infections of algae influence host carbon assimilation. Furthermore this thesis details how cell lysis by viruses regulates the temporal bacterial community structure and their subsequent uptake of algal viral lysates. Chapter 2 shows how viruses impair the release of the star-like structures of virally infected Phaeocystis globosa cells. The independent application of high resolution single cells techniques using atomic force microscopy (AFM) visualized the unique host morphological feature due to viral infection and nanoSIMS imaging quantified the impact of viral infection on the host carbon assimilation. Prior to cell lysis, substantial amounts of newly produced viruses (~ 68%) were attached to P. globosa cells. The hypothesis that impediment of star-like structures in infected P. -
Evaluation of FISH for Blood Cultures Under Diagnostic Real-Life Conditions
Original Research Paper Evaluation of FISH for Blood Cultures under Diagnostic Real-Life Conditions Annalena Reitz1, Sven Poppert2,3, Melanie Rieker4 and Hagen Frickmann5,6* 1University Hospital of the Goethe University, Frankfurt/Main, Germany 2Swiss Tropical and Public Health Institute, Basel, Switzerland 3Faculty of Medicine, University Basel, Basel, Switzerland 4MVZ Humangenetik Ulm, Ulm, Germany 5Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Hamburg, Germany 6Institute for Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Rostock, Germany Received: 04 September 2018; accepted: 18 September 2018 Background: The study assessed a spectrum of previously published in-house fluorescence in-situ hybridization (FISH) probes in a combined approach regarding their diagnostic performance with incubated blood culture materials. Methods: Within a two-year interval, positive blood culture materials were assessed with Gram and FISH staining. Previously described and new FISH probes were combined to panels for Gram-positive cocci in grape-like clusters and in chains, as well as for Gram-negative rod-shaped bacteria. Covered pathogens comprised Staphylococcus spp., such as S. aureus, Micrococcus spp., Enterococcus spp., including E. faecium, E. faecalis, and E. gallinarum, Streptococcus spp., like S. pyogenes, S. agalactiae, and S. pneumoniae, Enterobacteriaceae, such as Escherichia coli, Klebsiella pneumoniae and Salmonella spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Bacteroides spp. Results: A total of 955 blood culture materials were assessed with FISH. In 21 (2.2%) instances, FISH reaction led to non-interpretable results. With few exemptions, the tested FISH probes showed acceptable test characteristics even in the routine setting, with a sensitivity ranging from 28.6% (Bacteroides spp.) to 100% (6 probes) and a spec- ificity of >95% in all instances. -
10 the Family Colwelliaceae John P
10 The Family Colwelliaceae John P. Bowman Food Safety Centre, Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia Taxonomy, Historical, and Current Short Description Taxonomy, Historical, and Current Short of the Family Colwelliaceae Ivanova Description of the Family Colwelliaceae VP et al. 2004, 1773VP .........................................179 Ivanova et al. 2004, 1773 Molecular Analyses . ..................................180 Col.well.i0a.ce.ae. N.L. fem. n. Colwellia, type genus of the fam- ily; suff. -aceae, ending to denote a family; N.L. fem. pl. n. Phenotypic Properties . ..................................181 Colwelliaceae, the Colwellia family. The family Colwelliaceae was first described by Ivanova and Genus Colwellia Deming et al. 1988, 328AL ...............181 colleagues (2004) as part of an effort to create taxonomic har- mony within a large clade of almost exclusively marine bacteria Genus Thalassomonas Macia´n et al. 2001, 1283 . 187 located within class Gammaproteobacteria. This clade now rep- resents the order Alteromonadales (Bowman and McMeekin Enrichment, Isolation, and Maintenance Procedures . 187 2005) and consists of at least 22 genera as of late 2012. In addition to the genera Colwellia and Thalassomonas, Genome-Based and Genetic Studies . .....................191 the other members of the order include Aesturaiibacter, Agarivorans, Algicola, Aliagarivorans, Alkalimonas, Ecology . ...............................................192 Alishewanella, Alteromonas, Bowmanella, Catenovulum, -
Bowmanella Denitrificans Gen. Nov., Sp. Nov., a Denitrifying Bacterium
International Journal of Systematic and Evolutionary Microbiology (2006), 56, 2463–2467 DOI 10.1099/ijs.0.64306-0 Bowmanella denitrificans gen. nov., sp. nov., a denitrifying bacterium isolated from seawater from An-Ping Harbour, Taiwan Wen Dar Jean,1 Jwo-Sheng Chen,2 Yu-Te Lin3 and Wung Yang Shieh3 Correspondence 1Center for General Education, Leader University, No. 188, Sec. 5, An-Chung Road, Tainan, Wung Yang Shieh Taiwan [email protected] 2School of Medicine, China Medical University, No. 91, Shyue-Shyh Road, Taichung, Taiwan 3Institute of Oceanography, National Taiwan University, PO Box 23-13, Taipei, Taiwan A heterotrophic, non-fermentative, denitrifying isolate, designated strain BD1T, was obtained from a seawater sample collected in the shallow coastal region of An-Ping Harbour, Tainan, Taiwan. The cells of strain BD1T were Gram-negative. Cells grown in broth cultures were curved rods that were motile by means of a single polar flagellum. Growth occurred between 10 and 40 6C, with an optimum at 30–35 6C. Strain BD1T grew in NaCl levels of 0–10 %, with better growth occurring at 1–3 %. It grew aerobically and could achieve anaerobic growth by adopting a denitrifying metabolism with nitrate or nitrous oxide as the terminal electron acceptor. The major fatty acids were C16 : 0,C18 : 1v7c and summed feature 3 (C16 : 1v7c and/or C15 : 0 iso 2-OH). The polar lipids consisted of phosphatidylethanolamine (56?6 %) and phosphatidylglycerol (43?4 %). The isoprenoid quinones were Q-8 (81?5 %), Q-9 (11?1 %) and Q-10 (7?4 %). The DNA G+C content was 50?0 mol%.