DOCSLIB.ORG

Photosensitivity Responses of Sagittula Stellata Probed by FTIR, fluorescence and Raman Cite This: RSC Adv.,2019,9,27391 Microspectroscopy

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Photosensitivity Responses of Sagittula Stellata Probed by FTIR, fluorescence and Raman Cite This: RSC Adv.,2019,9,27391 Microspectroscopy RSC Advances PAPER View Article Online View Journal | View Issue Photosensitivity responses of Sagittula stellata probed by FTIR, fluorescence and Raman Cite this: RSC Adv.,2019,9,27391 microspectroscopy Marios Papageorgiou, Charalampos Tselios and Constantinos Varotsis* Raman, fluorescence and FTIR experiments of prestine Sagittula stellata and Sagittula stellata–metal ion complexes grown in light and in dark were performed to probe the photosensitivity response of the cellular components in the marine bacterium. In the presence of Cu(II) and Zn(II) the frequency shifts of À PO2 ,C–O–C and C–O–P vibrations indicate metal binding to nucleic acids, carbohydrates and polysaccharides. We assign the observed bands in the 514.1 nm Raman spectra of the prestine S. Stellata and of the extracted carotenoids to the C]C and C–C stretching vibrations. The fluorescence Received 14th May 2019 excitation–emission matrix (EEM) of S. stellata in light, dark and in the presence of metal ions are Accepted 26th August 2019 reported and compared with the Raman and FTIR data. The novel ability of S. stellata although DOI: 10.1039/c9ra03630j Creative Commons Attribution 3.0 Unported Licence. heterotrophic, to show light-dependent metal binding ability may be an important feature property that rsc.li/rsc-advances maintains a stable heterotroph–prototroph interaction and a dynamic system. 1. Introduction compound involved in biogeochemical cycling and in climate control, as a carbon or a sulfur source and oxidize it to DMSO. Marine Roseobacter clade bacteria (RCB) are one of the most DMS is also oxidized photochemically to DMSO which is abundant bacterioplanktonic groups in oceans worldwide.1–3 present in high concentration in seawater in association with RCB are free-living, but they are also oen found in epibiotic phytoplankton and is degraded in anaerobic environments by 8 This article is licensed under a biolms on macro-algae and various invertebrates and are key methanogens and sulfate reductases. Light-stimulated DMSO players in the carbon and sulfur cycles and have a variety of production has led to the hypothesis that phototrophic bacteria mechanisms for obtaining energy. Ecologically, the Roseobacters may use DMS as an energy source in the environment as have been proposed to adapt a strategy that takes advantage of observed in pure cultures. There are reports for utilization of Open Access Article. Published on 30 August 2019. Downloaded 9/26/2021 12:33:12 PM. the microenvironment with elevated nutrient concentrations DMS as a sulfur source with the aid of light by marine hetero- from the seawater. Genome analysis has shown that in addition trophic isolates other that S. stellata that are able to degrade to heterotrophic energy acquisition some members are capable DMS aerobically. The oxidation of DMS to other compounds in of phototrophy. Light utilization involving bacteriochlorophyll the sea plays an important role in sulfur circulation because the a synthesized by Aerobic Anoxygenic Phototrophic (AAP) Rose- oxidation reduces the release of DMS into the air. There are no obacters without producing molecular oxygen is found in four- data available in the literature regarding the photosensitivity teen diverse strains.4 AAP bacteria may alter current models of response of S. stellata and of the intact and extracted the carbon cycle and other biogeochemical processes. The fact carotenoids. that members of the Roseobacter lineage can be cultured in the Trace metals such as iron and copper play important roles in laboratory provides an advantage in efforts to understand their the ocean because they are essential for the growth of marine biology and chemistry as well their biogeochemical properties.5 phytoplankton. These trace metals are also needed for the Sagittula stellata is a heterotrophic member of the alpha growth and survival of photosynthetic organisms. Because the proteobacteria Roseobacter clade typically found in marine speciation of many metals is controlled by pH, a more acidic environments responsible for the degradation of cellulose, ocean will alter the bioavailable fractions of these metals. In the lignin related compounds and for the oxidation of dime- surface ocean, the biochemically signicant metals for micro- thylsulde (DMS) to dimethyl sulfoxide (DMSO) that is coupled organisms are manganese, iron, nickel, cobalt, copper, zinc, to ATP synthesis and other organic sulfur compounds typically and cadmium. On the other hand, metal ions such as Fe(III), found in surface.6,7 Phototrophic bacteria found in marine Cu(II), Mg(II) and Zn(II) have been employed in industrial environments use DMS which is a volatile organosulfur applications and thus are considered as environmental contaminants. There is an increasing concern with respect to Department of Environmental Science and Technology, Cyprus University of their impact and safety in seawaters. Small increases in Technology, Lemesos, Cyprus. E-mail: [email protected]; Fax: +357 25002802 concentration of normally scarce metals o en result in toxic This journal is © The Royal Society of Chemistry 2019 RSC Adv.,2019,9,27391–27397 | 27391 View Article Online RSC Advances Paper effects to organisms unaccustomed to the higher concentra- Agilent Technologies Cary 60 UV-Vis. The bacteria cells in the tions.9,10 This has been observed with the free form of Cu(II) third day of cultivation were centrifuged for 7 min at which are reported to be toxic to marine phytoplankton. 13 200 rpm. The supernatant was removed and sterilized and Although iron is known to be used in chlorophyll production the procedure was repeated twice. All samples were prepared in and nitrogen xation, regulating primary productivity and phosphate buffer (10 mM) and the pH was adjusted to 4.0, 7.0 marine biogeochemical cycles, contributes signicantly in the and 10.0 for FTIR analysis. degradation of b-carotene, photochemical processes in ocean Two bacteria cultures of S. stellata were grown at 28 Cin surface waters produce a number of free radicals that can dark and light conditions respectively. The optical density (OD change the oxidation state of a number of metals. A number of at 600 nm) was between 0.8 and 1.0 for each sample when the researchers have shown that many biologically signicant cells were harvest for carotenoids extraction according to pub- metals form strong complexes with organic ligands in lished procedures.22,23 10 mL of each culture were transferred in seawater.11 Although a large amount of metal ions products are 15 mL tube and centrifuged at 4000 Â g rpm (4 C) for 4 min. released in the environment, the mechanism for the interac- The supernatant was discarded and the remaining bacteria were tions between metal ions and surface-seawaters is poorly centrifuged again at 11 000 Â g rpm (4 C) for 1 min. 200 mlof understood. pre-chilled methanol was added on the pellet and the sample Raman spectroscopy is a non-destructive, structure sensitive was vortexed and sonicated (10 s each). The procedure repeated technique and has been applied in a variety of biological twice with the addition of 200 mL of acetone and dichloro- dynamics studies.12–18 The FTIR technique offers a unique methane. The samples were incubated on ice for 2 min and then advantage to probe and monitor at the molecular scale, in situ, centrifuged at 11 000 Â g rpm (4 C) for 4 min. The procedure non-destructively, in real time, and under different hydrated was performed under dim light. The supernatant was collected conditions, the biochemical composition of bacteria species and used for the UV-Vis and Raman experiments. attached onto surfaces and the interphase between the surfaces 16,19 Creative Commons Attribution 3.0 Unported Licence. and bacteria and between bacteria. Fluorescence spectros- 2.2. FTIR spectroscopy copy is a non-invasive analytical tool in the study of biomole- The S. stellata–CuCl2, –FeCl3, –MgCl2 and –ZnCl2 metal 20,21 cules by virtue of its high sensitivity. complexes (30 mM) were incubated for 5 days with gentle stir- In this study, we have applied a combination of Raman, ring. The FTIR spectra were recorded using a Vertex 70v FTIR uorescence and FTIR spectroscopies towards establishing spectrometer (BRUKER) equipped with a photovoltaic MCT a direct method for monitoring the photosensitivity response in detector. The sample compartment was purged with nitrogen the metal binding properties of S. stellata and establish the gas. The bacterial solutions were centrifuged and the superna- vibrational marker bands for monitoring the functional groups tant was carefully removed. The precipitated was placed on ff a ected by the presence of metal ions at the molecular level. silver uoride window and let to dry out and form a lm. The This article is licensed under a À The 514.1 nm excitation Raman data revealed strong scattering spectral signal was averaged from 100 scans at 4 cm 1 resolu- À from carotenoids and partial and complete photo-degradation tion, and collected from 800–4000 cm 1. in the presence of CuCl2 and FeCl3, respectively. The dynamics of the uorescence excitation–emission matrix (EEM) Open Access Article. Published on 30 August 2019. Downloaded 9/26/2021 12:33:12 PM. 2.3. Raman spectroscopy of S. stellata in the presence of metal ions are reported, dis- cussed and compared with the FTIR and Raman results. To our The 514.1 nm excitation Raman spectra of S. stellata and of the best knowledge this is the rst application of a comprehensive CuCl2, FeCl3, MgCl2 and ZnCl2 complexes (30 mM) were per- spectroscopic study involving Raman, FTIR and uorescence formed with a iHR550 Raman spectrometer equipped with spectroscopies for chemical analysis of the complex bacteria Olympus BX41 microscope and a Synapse CCD Detector matrix formed by the metal ion binding to S. stellata illustrating (Horiba), controlled by Syner JY so ware (Horiba).
Load more

Recommended publications
  • Article-Associated Bac- Teria and Colony Isolation in Soft Agar Medium for Bacteria Unable to Grow at the Air-Water Interface
    Biogeosciences, 8, 1955–1970, 2011 www.biogeosciences.net/8/1955/2011/ Biogeosciences doi:10.5194/bg-8-1955-2011 © Author(s) 2011. CC Attribution 3.0 License. Diversity of cultivated and metabolically active aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea C. Jeanthon1,2, D. Boeuf1,2, O. Dahan1,2, F. Le Gall1,2, L. Garczarek1,2, E. M. Bendif1,2, and A.-C. Lehours3 1Observatoire Oceanologique´ de Roscoff, UMR7144, INSU-CNRS – Groupe Plancton Oceanique,´ 29680 Roscoff, France 2UPMC Univ Paris 06, UMR7144, Adaptation et Diversite´ en Milieu Marin, Station Biologique de Roscoff, 29680 Roscoff, France 3CNRS, UMR6023, Microorganismes: Genome´ et Environnement, Universite´ Blaise Pascal, 63177 Aubiere` Cedex, France Received: 21 April 2011 – Published in Biogeosciences Discuss.: 5 May 2011 Revised: 7 July 2011 – Accepted: 8 July 2011 – Published: 20 July 2011 Abstract. Aerobic anoxygenic phototrophic (AAP) bac- detected in the eastern basin, reflecting the highest diver- teria play significant roles in the bacterioplankton produc- sity of pufM transcripts observed in this ultra-oligotrophic tivity and biogeochemical cycles of the surface ocean. In region. To our knowledge, this is the first study to document this study, we applied both cultivation and mRNA-based extensively the diversity of AAP isolates and to unveil the ac- molecular methods to explore the diversity of AAP bacte- tive AAP community in an oligotrophic marine environment. ria along an oligotrophic gradient in the Mediterranean Sea By pointing out the discrepancies between culture-based and in early summer 2008. Colony-forming units obtained on molecular methods, this study highlights the existing gaps in three different agar media were screened for the production the understanding of the AAP bacteria ecology, especially in of bacteriochlorophyll-a (BChl-a), the light-harvesting pig- the Mediterranean Sea and likely globally.
    [Show full text]
  • Bacteria Are Important Dimethylsulfoniopropionate Producers in Coastal Sediments
    1 Bacteria are important dimethylsulfoniopropionate producers in coastal sediments 2 Beth T. Williams1, Kasha Cowles1, Ana Bermejo Martínez1, Andrew R. J. Curson1, Yanfen 3 Zheng1,2, Jingli Liu1,2, Simone Newton-Payne1, Andrew Hind3, Chun-Yang Li2, Peter Paolo 4 L. Rivera1, Ornella Carrión3, Ji Liu1,2, Lewis G. Spurgin1, Charles A. Brearley1, Brett Wagner 5 Mackenzie5, Benjamin J. Pinchbeck1, Ming Peng4, Jennifer Pratscher6, Xiao-Hua Zhang2, 6 Yu-Zhong Zhang4, J. Colin Murrell3, Jonathan D. Todd1* 7 1School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, 8 NR4 7TJ, UK. 9 2College of Marine Life Sciences, Ocean University of China, 5 Yushan Road, Qingdao 10 266003, China. 11 3School of Environmental Sciences, University of East Anglia, Norwich Research Park, 12 Norwich, NR4 7TJ, UK. 13 4State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, 14 China 15 5Department of Surgery, University of Auckland, Auckland 1142, New Zealand 16 6The Lyell Centre, Heriot-Watt University, Edinburgh, EH14 4AS, UK. 17 *corresponding author 18 Dimethylsulfoniopropionate (DMSP) and its catabolite dimethyl sulfide (DMS) are key 19 marine nutrients1,2, with roles in global sulfur cycling2, atmospheric chemistry3, 20 signalling4,5 and, potentially, climate regulation6,7. DMSP production was previously 21 thought to be an oxic and photic process, mainly confined to the surface oceans. 1 22 However, here we show that DMSP concentrations and DMSP/DMS synthesis rates 23 were higher in surface marine sediment from e.g., saltmarsh ponds, estuaries and the 24 deep ocean than in the overlying seawater. A quarter of bacterial strains isolated from 25 saltmarsh sediment produced DMSP (up to 73 mM), and previously unknown DMSP- 26 producers were identified.
    [Show full text]
  • Sagittula Stellata Gen. Nov., Sp. Nov., a Lignin-Transforming Bacterium from a Coastal Environment
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1997, p. 773-780 Vol. 47, No. 3 0020-7713/97/$04.00+0 Copyright 0 1997, International Union of Microbiological Societies Sagittula stellata gen. nov., sp. nov., a Lignin-Transforming Bacterium from a Coastal Environment J. M. GONZALEZ,' F. MAYER,2 M. A. MORAN,193R. E. HODSON,1,3 AND W. B. WHITMAN1,3* Department of Microbiology,' and Department of Marine Sciences and Institute of Ecology, University of Georgia, Athens, Georgia 30602, and Institut fur Mikrobiologie, Universitat Gottingen, 37077 Gottingen, Germany2 A numerically important member of marine enrichment cultures prepared with lignin-rich, pulp mill emuent was isolated. This bacterium was gram negative and rod shaped, did not form spores, and was strictly aerobic. The surfaces of its cells were covered by blebs or vesicles and polysaccharide fibrils. Each cell also had a holdfast structure at one pole. The cells formed rosettes and aggregates. During growth in the presence of lignocellulose or cellulose particles, cells attached to the surfaces of the particles. The bacterium utilized a variety of monosaccharides, disaccharides, amino acids, and volatile fatty acids for growth. It hydrolyzed cellulose, and synthetic lignin preparations were partially solubilized and mineralized. As determined by 16s rRNA analysis, the isolate was a member of the (Y subclass of the phylum Proteobacteria and was related to the genus Roseobacter. A signature secondary structure of the 16s rRNA is proposed. The guanine-plus-cytosine content of the genomic DNA was 65.0 mol%. On the basis of the results of 16s rRNA sequence and phenotypic characterizations, the isolate was sufficiently different to consider it a member of a new genus.
    [Show full text]
  • ALISON BUCHAN Ecology and Genetics of Aromatic Compound
    ALISON BUCHAN Ecology and Genetics of Aromatic Compound Degradation in the Ecologically Important Roseobacter Lineage of Marine Bacteria (Under the direction of MARY ANN MORAN) The degradation of lignin-related aromatic compounds is an important ecological process in the highly productive salt marshes of the southeastern U. S., yet little is known of the mediating organisms or their catabolic pathways. An initial study of six isolates suggested that members of the roseobacter lineage, a dominant marine clade within the α- Proteobacteria, could degrade aromatic compounds via the β-ketoadipate pathway, a catabolic route that has been well characterized in soil microbes. Four of the roseobacter group isolates had inducible protocatechuate 3,4-dioxygenase activity, a key enzyme in the pathway, in cell-free extracts when grown on p-hydroxybenzoate. The pcaHG genes encoding this ring-cleavage enzyme were cloned and sequenced from two isolates and in both cases the genes could be expressed in E. coli to yield dioxygenase activity. Evidence of genes encoding for protocatechuate 3,4-dioxygenase was found in all six roseobacter isolates by detection of pcaH by Southern hybridization or PCR amplification. These results suggested this ecologically important marine lineage compose a significant fraction of the aromatic compound degrading community in coastal systems. To test this hypothesis we investigated the diversity of pcaH amplified from bacterial communities associated with decaying Spartina alterniflora, the salt marsh grass dominating these coastal systems, as well as from enrichment cultures with aromatic substrates. Sequence analysis of 149 pcaH clones revealed 85 unique sequences. Fifty-eight percent of the clones matched sequences amplified from a collection of 36 bacterial isolates obtained from seawater or from senescent Spartina.
    [Show full text]
  • Dimethylsulphoniopropionate Biosynthesis in Marine Bacteria and Identification of the Key Gene in This Process
    Dimethylsulphoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process Andrew R. J. Curson, Ji Liu, Ana Bermejo Martínez, Robert T. Green, Yohan Chan, Ornella Carrión, Beth T. Williams, Sheng-Hui Zhang, Gui-Peng Yang, Philip C. Bulman Page, Xiao- Hua Zhang, Jonathan D. Todd Supplementary Figures Supplementary Figure 1. LC-MS traces for standards and Rhizobium leguminosarum J391.LC- MS chromatograms for a, Met (m/z 150), MTOB (m/z 147), MTHB (m/z 149), DMSHB (m/z 165) and DMSP (m/z 135) standards, b, MTHB production from R. leguminosarum J391 incubated with Met, MTOB or MTHB, and DMSP production from R. leguminosarum J391 incubated with DMSHB. Supplementary Figure 2. Gene maps showing genomic locations of dsyB in selected dsyB- containing bacteria. a, Gene map for Labrenzia aggregata LZB033 and L. aggregata IAM12614. b, Gene map for Salipiger mucosus DSM16094, Pelagibaca bermudensis HTCC2601, Thalassiobius gelatinovorus DSM5887, Donghicola xiamenensis DSM18339, Antarctobacter heliothermus DSM11445, Pseudooceanicola nanhaiensis DSM18065, Citreicella sp. 357, Citreicella aestuarii DSM22011, Sediminimonas qiaohouensis DSM21189, Roseivivax halodurans JCM10272. Genes encoding protein products predicted to be involved in Fe-S cluster assembly are marked. c, Gene map for Rhizobiales bacterium HL-109. Predicted gene products: 1. tricarboxylate transporter; 2. AraC family transcriptional regulator; 3. nucleotide phosphate sugar epimerase; 4. hypothetical protein; 5. dehydratase; 6. MaoC-like dehydratase; 7. hypothetical protein; 8. agmatinase; 9. acetyltransferase; 10. cob(II)yrinic acid a,c-diamide reductase; 11. adenine phosphoribosyltransferase; 12. S-methyladenosine phosphorylase; 13. hypothetical protein; 14. cytochrome C1; 15. cysteine desulfurase; 16. hypothetical protein; 17. hypothetical protein; 18.
    [Show full text]
  • Mechanisms Driving Genome Reduction of a Novel Roseobacter Lineage Showing
    bioRxiv preprint doi: https://doi.org/10.1101/2021.01.15.426902; this version posted January 16, 2021. 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 Mechanisms Driving Genome Reduction of a Novel Roseobacter Lineage Showing 2 Vitamin B12 Auxotrophy 3 4 Xiaoyuan Feng1, Xiao Chu1, Yang Qian1, Michael W. Henson2a, V. Celeste Lanclos2, Fang 5 Qin3, Yanlin Zhao3, J. Cameron Thrash2, Haiwei Luo1* 6 7 1Simon F. S. Li Marine Science Laboratory, School of Life Sciences and State Key 8 Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong 9 Kong SAR 10 2Department of Biological Sciences, University of Southern California, Los Angeles, CA 11 USA 12 3Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, 13 College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China 14 a Current Affiliation: Department of Geophysical Sciences, University of Chicago, Chicago, 15 Illinois, USA 16 17 *Corresponding author: 18 Haiwei Luo 19 School of Life Sciences, The Chinese University of Hong Kong 20 Shatin, Hong Kong SAR 21 Phone: (+852) 3943-6121 22 Fax: (+852) 2603-5646 23 E-mail: [email protected] 24 25 Keywords: Roseobacter, CHUG, genome reduction, vitamin B12 auxotrophy 26 27 bioRxiv preprint doi: https://doi.org/10.1101/2021.01.15.426902; this version posted January 16, 2021. 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.
    [Show full text]
  • 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.
    [Show full text]
  • 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.
    [Show full text]
  • Alphaproteobacterial Strain HIMB11, the First Cultivated Representative of a Unique Lineage Within the Roseobacter Clade Possessing an Unusually Small Genome
    UC Irvine UC Irvine Previously Published Works Title Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome Permalink https://escholarship.org/uc/item/3r52w0kt Journal Standards in Genomic Sciences, 9(3) ISSN 1944-3277 Authors Durham, Bryndan P Grote, Jana Whittaker, Kerry A et al. Publication Date 2014-03-15 DOI 10.4056/sigs.4998989 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2014) 9:632 -645 DOI:10.4056/sig s.4998989 Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome Bryndan P. Durham1,2, Jana Grote1,3, Kerry A. Whittaker1,4, Sara J. Bender1,5, Haiwei Luo6, Sharon L. Grim 1,7, Julia M. Brown1,8, John R. Casey1,3, Antony Dron1,9, Lennin Florez-Leiva1,10, Andreas Krupke1,11, Catherine M. Luria1,12, Aric H. Mine1,13, Olivia D. Nig ro 1,3, Santhiska Pather1,14, Ag athe Tal armi n 1,15, Emma K. Wear1,16, Thomas S. Weber1,17, Jesse M. Wi lson 1,18, Matthew J. Church 1,3, Edward F. D eLong 1,19, David M. Karl 1,3, Gri eg F. Steward1,3, John M. Eppl ey1,19, Ni kos C. Kyrpides1,20, Stephan Schuster1, and Michael S. Rappé1* 1 Center for Microbial Oceanography: Research and Education, University of Hawaii, Honolulu, Hawaii, USA 2 Department of Microbiology, University of Georgia, Athens, Georgia,
    [Show full text]
  • CGM-18-001 Perseus Report Update Bacterial Taxonomy Final Errata
    report Update of the bacterial taxonomy in the classification lists of COGEM July 2018 COGEM Report CGM 2018-04 Patrick L.J. RÜDELSHEIM & Pascale VAN ROOIJ PERSEUS BVBA Ordering information COGEM report No CGM 2018-04 E-mail: [email protected] Phone: +31-30-274 2777 Postal address: Netherlands Commission on Genetic Modification (COGEM), P.O. Box 578, 3720 AN Bilthoven, The Netherlands Internet Download as pdf-file: http://www.cogem.net → publications → research reports When ordering this report (free of charge), please mention title and number. Advisory Committee The authors gratefully acknowledge the members of the Advisory Committee for the valuable discussions and patience. Chair: Prof. dr. J.P.M. van Putten (Chair of the Medical Veterinary subcommittee of COGEM, Utrecht University) Members: Prof. dr. J.E. Degener (Member of the Medical Veterinary subcommittee of COGEM, University Medical Centre Groningen) Prof. dr. ir. J.D. van Elsas (Member of the Agriculture subcommittee of COGEM, University of Groningen) Dr. Lisette van der Knaap (COGEM-secretariat) Astrid Schulting (COGEM-secretariat) Disclaimer This report was commissioned by COGEM. The contents of this publication are the sole responsibility of the authors and may in no way be taken to represent the views of COGEM. Dit rapport is samengesteld in opdracht van de COGEM. De meningen die in het rapport worden weergegeven, zijn die van de auteurs en weerspiegelen niet noodzakelijkerwijs de mening van de COGEM. 2 | 24 Foreword COGEM advises the Dutch government on classifications of bacteria, and publishes listings of pathogenic and non-pathogenic bacteria that are updated regularly. These lists of bacteria originate from 2011, when COGEM petitioned a research project to evaluate the classifications of bacteria in the former GMO regulation and to supplement this list with bacteria that have been classified by other governmental organizations.
    [Show full text]
  • 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
    [Show full text]
  • 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.
    [Show full text]