Enhanced Degradation of Polycyclic Aromatic Hydrocarbons (Pahs) in the Rhizosphere of Sudangrass (Sorghum Drummondii)

Total Page:16

File Type:pdf, Size:1020Kb

Enhanced Degradation of Polycyclic Aromatic Hydrocarbons (Pahs) in the Rhizosphere of Sudangrass (Sorghum � Drummondii) Chemosphere 234 (2019) 789e795 Contents lists available at ScienceDirect Chemosphere journal homepage: www.elsevier.com/locate/chemosphere Enhanced degradation of polycyclic aromatic hydrocarbons (PAHs) in the rhizosphere of sudangrass (Sorghum  drummondii) * John Jewish A. Dominguez a, , Hernando P. Bacosa a, b, Mei-Fang Chien a, Chihiro Inoue a a Graduate School of Environmental Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai, 980-8579, Japan b Department of Marine Sciences, Texas A&M University at Galveston, Galveston, TX, United States highlights graphical abstract Sudangrass emerged superior in removing PAHs in soil than other previously reported grasses. Sudangrass specially enriched Sphingomonadales, a potent PAHs degrader, in its rhizosphere. The abundance of PAHs degradation biomarker genes, PAH-RHDa and nidA, was highest in soil planted with sudangrass. article info abstract Article history: Grasses are advantageous in the removal of polycyclic aromatic hydrocarbons (PAHs) in soil because of Received 30 January 2019 their fibrous root, high tolerance to environmental stress, and low nutritional requirements. In this study, Received in revised form a pot experiment was conducted to test the ability of four grasses to remove PAHs in the soil, and to 21 May 2019 investigate the corresponding bacterial community shift in the rhizosphere of each. Sudangrass achieved Accepted 30 May 2019 the maximum removal of PAHs at 98% dissipation rate after 20 days. Polymerase chain reaction- Available online 3 June 2019 denaturing gradient gel electrophoresis (PCR-DGGE) and next-generation sequencing revealed that su- Handling Editor: T. Cutright dangrass specially enriched the growth of a known PAHs degrader, Sphingomonadales, regardless of the presence or absence of PAHs in the soil. Moreover, the gene copy numbers of PAHs catabolic genes, PAH- Keywords: RHDa and nidA, as measured by real time-PCR (RT-PCR) were highest in the soil planted with sudangrass. Polycyclic aromatic hydrocarbons Overall, this study suggested that sudangrass further enhanced the dissipation of PAHs by enriching Phytoremediation Sphingomonadales in its rhizosphere. Rhizodegradation © 2019 Elsevier Ltd. All rights reserved. Sphingomonadales Rhizosphere effect 1. Introduction carcinogenic, teratogenic, mutagenic, and eco-toxic (Abdel-shafy and Mansour, 2016; Brown et al., 2017; Samanta et al., 2002; Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants Wang et al., 2018). Once released into the environment, PAHs tend known to pose risks to both ecological and human health. It is to adsorb in soil humic contents in the topsoil where they tend to concentrate (Kanu and Anyanwu, 2005; Okere and Semple, 2012). In order to remove PAHs with low cost and environmental burden, one method is to use living organisms such as plant, bacteria or * Corresponding author. Inoue Laboratory, Graduate School of Environmental both (Abdel Ghany et al., 2015; Gan et al., 2009; Shukla et al., 2013). Studies, Tohoku University, Aoba 6-6-20, Aramaki, Aoba-ku, Sendai, 980-8579, In particular, rhizoremediation is proposed to be the approach with Japan. E-mail address: [email protected] (J.J.A. Dominguez). most potential in remediating PAHs in soil (Shukla et al., 2013). https://doi.org/10.1016/j.chemosphere.2019.05.290 0045-6535/© 2019 Elsevier Ltd. All rights reserved. 790 J.J.A. Dominguez et al. / Chemosphere 234 (2019) 789e795 Rhizoremediation is the process in which plants indirectly 30 seeds of Italian ryegrass, tall fescue, and perennial ryegrass were degrade PAHs by stimulating the microbial community in its root accordingly dispersed in each pot and covered with 3 cm of soil. (Dzantor, 2007). This can be achieved in multiple ways, namely: 1) Sudangrass seeds are bigger than the other grasses. The average plant provides aeration to the soil and microbes thereby enhancing germination rate for sudangrass was 86%, 85% for tall fescue, 88% aerobic reactions (Anderson et al., 1993; Bisht et al., 2015); 2) plants for perennial rye grass, and 90% for Italian ryegrass. The soil secrete organic compounds (i.e. sugar, organic acids, secondary moisture content was maintained to 20% throughout the plant metabolites) that can stimulate microbial growth, select experiment. PAHs-degrading bacteria, and induce PAHs catabolic reactions Depending on the plant used, five experimental treatments (Anderson et al., 1993; Balasubramaniyam, 2015; Rohrbacher and were prepared with (1) or without (0) the addition of PAHs solution St-Arnaud, 2016); and finally, plants can increase the bioavail- (Table 1). The treatments include the following: unplanted control ability of PAHs through physical and chemical means (Lefevre et al., (H1, H0); tall fescue (T1, T0); sudangrass (S1, S0); perennial ryegrass 2013; Rohrbacher and St-Arnaud, 2016; Zhu et al., 2009). (P1, P0); lastly, Italian ryegrass (I1, I0). Each treatment was prepared Plants under the family Poaceae, collectively known as grasses, in triplicate. After 20 days of cultivation at room temperature, soil are often employed in rhizoremediation studies due to their fast samples were stored in 4 C until extraction. growth, tolerance to PAHs, deep and fibrous roots, resistance to environmental stress, and low nutritional requirements 2.3. Analytical procedure (Balasubramaniyam, 2015; Sivaram et al., 2018a). Furthermore, in a study conducted by Olson et al. (2007), grasses emerged as the The remaining PAHs in the soil were extracted using methods most effective in dissipating PAHs in soil among the eight families from Lee et al. (2008). Briefly, 10 g fresh weight of soil were ho- tested. Thus, it is not surprising that numerous PAHs rhizor- mogenized and transferred to 50 mL centrifuge tube and shaken emediation studies have been conducted using grasses (Fu et al., vertically with 25 mL of dichloromethane at 300 rpm for 1 h. The 2012; Gaskin and Bentham, 2010; Khan et al., 2009; Kuiper et al., tubes were then centrifuged at 5000 rpm and the supernatant was 2001). decanted and stored in 4 C until analysis. PAHs were analyzed Of particular interest in this study is sudangrass (Sorghum x using GC-4000 gas chromatography (GL Sciences Inc., Tokyo, Japan) drummondii). Despite reports of superior PAHs dissipation equipped with flame ionization detector (FID) and an InertCap 17 enhancing ability (Reilley et al., 1996; Sivaram et al., 2018b; Su et al., MS column. The column temperature was held at 80 C for 2 min, 2008), sudangrass remained relatively not studied and the infor- then increased to a maximum temperature of 300 C at the rate of mation about how the plant influences its rhizosphere during rhi- 10 C/min. The injector and detector temperatures were main- zoremediation is lacking. Among the four plants tested in a study tained at 350 C. Helium was used as a carrier gas. The concentra- conducted by Su et al. (2008), sudangrass dissipated most of pyrene tion of PAHs was calculated based on a five-point standard curve. but enriched the soil microbial population the least. Hence, it is worth investigating how sudangrass possibly achieve dissipation of 2.4. Microbial community analyses PAHs with respect to its rhizosphere microbial community. fl In this study, the ability of sudangrass to dissipate PAHs ( uo- Total DNA was extracted from the soil using Powersoil DNA fl rene, phenanthrene, uoranthene, and anthracene) in soil and the extraction Kit (Qiagen, Inc., Hilde, Germany) based on the manu- corresponding changes in the bacterial community of the rhizo- facturer's protocol. The extracted DNA was used as template for sphere soil was investigated. Furthermore, known PAHs degrada- polymerase chain reaction-denaturing gel gradient electrophoresis a tion biomarkers such as PAH-RHD and nidA genes were analyzed (PCR-DGGE). Briefly, the V3 region of 16s rRNA gene was amplified in parallel. These were conducted together with other grasses by PCR using universal primers 341F-GC (50-CGC CCG CCG CGC GCG previously reported to enhance PAHs degradation, namely: tall GCG GGC GGG GCG GGG GCA CGG GGG GCC TAC GGG AGG CAG fescue (Festuca arundinacea), perennial ryegrass (Lolium perenne) CAG-30) and 518R (50-ATT ACC GCG GCT GCT GG-30). PCR was per- fl and Italian ryegrass (Lolium multi orum). formed in reaction mixtures composed of 25 ml of Promega Master Mix (Promega Corp., WI, USA), 2 mL(10mM) each of forward and 2. Materials and methods reverse primers, approximately 10 ng of DNA extract and filled with DNAse free water to a volume of 50 mL. The amplification conditions 2.1. Chemicals and plant samples in the 2720 Thermal Cycler (Applied Biosystems, Foster, CA, USA) were as follows: initial denaturation at 94 C for 5 min, followed by fl fl Analytical grade uorene, phenanthrene, uoranthene, and 30 cycles of 94 C for 30 s, 55 C for 30s and 72 C for 30s, and a final pyrene were procured from Wako Chemicals, Ltd. (Osaka, Japan). extension step at 72 C for 7 min. The presence of PCR products was Four grasses were used in the study, namely: tall fescue (Festuca confirmed by gel electrophoresis. arundinacea), sudangrass (Sorghum x drummondii), perennial DGGE was performed using the DCode Universal Mutation fl ryegrass (Lolium perenne), and Italian ryegrass (Lolium multi orum). Detection System (Bio-Rad, California, USA). An 8% polyacrylamide & The seeds were purchased from Takii Co., Ltd (Miyagi, Japan). gel with a 30e70% gradient was prepared using urea and form- amide as denaturants. The samples were then loaded and run at a 2.2. Biodegradation experiment constant voltage of 70V and constant temperature of 60 C for 16 h. For the soil, four bags of lawn soil with unknown composition (Daisin Co., Ltd., Miyagi, Japan) were thoroughly mixed to achieve a Table 1 homogenous soil composition. The PAHs in the lawn soil were Experimental set-up employed in the biodegradation experiment. below detection limit. Four hundred grams of the soil was weighed, Soil with 400 ppm PAHs No PAHs added fl sprayed with PAHs solution (1 mg/mL each of uorene, phenan- Unplanted control H1 H0 threne, fluoranthene, and pyrene) to a final concentration of Tall fescue T1 T0 400 mg/kg, and mixed thoroughly using a hand mixer.
Recommended publications
  • Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline
    marine drugs Article Diversity and Antimicrobial Potential of Predatory Bacteria from the Peruvian Coastline Luis Linares-Otoya 1,2,5, Virginia Linares-Otoya 3,5 ID , Lizbeth Armas-Mantilla 3, Cyntia Blanco-Olano 3, Max Crüsemann 2 ID , Mayar L. Ganoza-Yupanqui 3 ID , Julio Campos-Florian 3 ID , Gabriele M. König 2,4 and Till F. Schäberle 1,2,4,* 1 Institute for Insect Biotechnology, Justus Liebig University of Giessen, 5392 Giessen, Germany; [email protected] 2 Institute for Pharmaceutical Biology, University of Bonn, 3115 Bonn, Germany; [email protected] (M.C.); [email protected] (G.M.K.) 3 Department of Pharmacology, Faculty of Pharmacy and Biochemistry, National University of Trujillo, 13011 Trujillo, Peru; [email protected] (V.L.-O.); [email protected] (L.A.-M.); [email protected] (C.B.-O.); [email protected] (M.L.G.-Y.); [email protected] (J.C.-F.) 4 German Centre for Infection Research (DZIF) Partner Site Bonn/Cologne, Bonn 53115, Germany 5 Research Centre for Sustainable Development Uku Pacha, 13011 Uku Pacha, Peru * Correspondence: [email protected]; Tel.: +49-641-99-37140 Received: 6 September 2017; Accepted: 9 October 2017; Published: 12 October 2017 Abstract: The microbiome of three different sites at the Peruvian Pacific coast was analyzed, revealing a lower bacterial biodiversity at Isla Foca than at Paracas and Manglares, with 89 bacterial genera identified, as compared to 195 and 173 genera, respectively. Only 47 of the bacterial genera identified were common to all three sites. In order to obtain promising strains for the putative production of novel antimicrobials, predatory bacteria were isolated from these sampling sites, using two different bait organisms.
    [Show full text]
  • Analysis of 1000 Type-Strain Genomes Improves
    Lawrence Berkeley National Laboratory Recent Work Title Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Permalink https://escholarship.org/uc/item/5pg6w486 Authors García-López, Marina Meier-Kolthoff, Jan P Tindall, Brian J et al. Publication Date 2019 DOI 10.3389/fmicb.2019.02083 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 23 September 2019 doi: 10.3389/fmicb.2019.02083 Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes Marina García-López 1, Jan P. Meier-Kolthoff 1, Brian J. Tindall 1, Sabine Gronow 1, Tanja Woyke 2, Nikos C. Kyrpides 2, Richard L. Hahnke 1 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States Edited by: Although considerable progress has been made in recent years regarding the Martin G. Klotz, classification of bacteria assigned to the phylum Bacteroidetes, there remains a Washington State University, United States need to further clarify taxonomic relationships within a diverse assemblage that Reviewed by: includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes Maria Chuvochina, classification has proved to be difficult, not least when taxonomic decisions rested University of Queensland, Australia Vera Thiel, heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number Tokyo Metropolitan University, Japan of phenotypic features. Here, draft genome sequences of a greatly enlarged collection David W. Ussery, of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used University of Arkansas for Medical Sciences, United States to infer phylogenetic trees from genome-scale data using the principles drawn from Ilya V.
    [Show full text]
  • Genome-Based Taxonomic Classification Of
    ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia.
    [Show full text]
  • Diversity of Marine Gliding Bacteria in Thailand and Their Cytotoxicity
    Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.12 No.3, Issue of July 15, 2009 © 2009 by Pontificia Universidad Católica de Valparaíso -- Chile Received October 7, 2008 / Accepted March 29, 2009 DOI: 10.2225/vol12-issue3-fulltext-13 RESEARCH ARTICLE Diversity of marine gliding bacteria in Thailand and their cytotoxicity Yutthapong Sangnoi Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Pornpoj Srisukchayakul Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Vullapa Arunpairojana Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Akkharawit Kanjana-Opas* Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Tel: 66 74286373 Fax: 66 74212889 E-mail: [email protected] Financial support: Thailand Research Fund (MRG4880153) and a Biodiversity Research and Training Grant (BRTR_149011). Scholarship for YS from the Graduate School, Prince of Songkla University. Keywords: Aureispira marina, Aureispira maritime, Fulvivirga kasyanovii, human cell lines, Rapidithrix thailandica, Tenacibaculum mesophilum. Abbreviations: CFB: Cytophaga-Flavobacterium-Bacteriodes HeLa: cervical cancer HT-29: colon cancer KB: oral cancer MCF-7: breast adenocarcinoma PCR: polymerase chain reaction SK: skim milk medium SRB: sulphorodamine B Eighty-four marine gliding bacteria were isolated from thailandica, Aureispira marina and Aureispira maritima specimens collected in the Gulf of Thailand and the respectively. The isolates were cultivated in four Andaman Sea. All exhibited gliding motility and swarm different cultivation media (Vy/2, RL 1, CY and SK) colonies on cultivation plates and they were purified by and the crude extracts were submitted to screen subculturing and micromanipulator techniques.
    [Show full text]
  • Mooreia Alkaloidigena Gen. Nov., Sp. Nov. and Catalinimonas Alkaloidigena Gen
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 1219–1228 DOI 10.1099/ijs.0.043752-0 Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes Eun Ju Choi, Deanna S. Beatty, Lauren A. Paul, William Fenical and Paul R. Jensen Correspondence Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University Paul R. Jensen of California San Diego, La Jolla, CA 92093-0204, USA [email protected] Bacterial strains CNX-216T and CNU-914T were isolated from marine sediment samples collected from Palmyra Atoll and off Catalina Island, respectively. Both strains were Gram- negative and aerobic and produce deep-orange to pink colonies and alkaloid secondary metabolites. Cells of strain CNX-216T were short, non-motile rods, whereas cells of strain CNU- 914T were short, curved rods with gliding motility. The DNA G+C contents of CNX-216T and CNU-914T were respectively 57.7 and 44.4 mol%. Strains CNX-216T and CNU-914T contained MK-7 as the predominant menaquinone and iso-C15 : 0 and C16 : 1v5c as the major fatty acids. Phylogenetic analyses revealed that both strains belong to the order Cytophagales in the phylum Bacteroidetes. Strain CNX-216T exhibited low 16S rRNA gene sequence identity (87.1 %) to the nearest type strain, Cesiribacter roseus 311T, and formed a well-supported lineage that is outside all currently described families in the order Cytophagales. Strain CNU-914T shared 97.6 % 16S rRNA gene sequence identity with ‘Porifericola rhodea’ N5EA6-3A2B and, together with ‘Tunicatimonas pelagia’ N5DB8-4 and four uncharacterized marine bacteria isolated as part of this study, formed a lineage that is clearly distinguished from other families in the order Cytophagales.
    [Show full text]
  • Characterisation of Opportunistic Bacterial Pathogens of the Marine Macroalga Delisea Pulchra Vipra Kumar Doctor of Philosophy
    Characterisation of opportunistic bacterial pathogens of the marine macroalga Delisea pulchra Vipra Kumar A thesis in fulfilment of the requirements for the degree of Doctor of Philosophy School of Biotechnology and Biomolecular Sciences Faculty of Science The University of New South Wales Sydney, Australia August 2015 THE UNIVERSITY OF NEW SOUTH WALES Thesis/Dissertation Sheet Surname or Family name: Kumar First name: Vipra Other name/s: Nandani Abbreviation for degree as given in the University calendar: PhD School: Biotechnology and Biomolecular Sciences Faculty: Science Title: Characterisation of opportunistic bacterial pathogens of the marine macroalga Delisea pulchra Abstract Macroalgae, the major habitat-formers of temperate marine ecosystems are susceptible to disease, yet in many cases the aetiological agent/s remain unknown. The red macroalga Delisea pulchra suffers from a bleaching disease, which can be induced by the bacteria Nautella italica R11 and Phaeobacter sp. LSS9 under laboratory conditions. However recent analyses suggest that these strains are not representative of the dominant pathogens in the environment. Therefore, the aim of this thesis was to determine if multiple pathogens of D. pulchra exist and to further understand the microbial dynamics of bleaching in D. pulchra. To achieve this aim, a culture collection of bacterial strains present on bleached and adjacent-to-bleached tissues of D. pulchra was generated. Bacterial strains that were also overrepresented in previous culture independent studies were subsequently assessed for virulence-related traits, including motility, biofilm-formation, resistance to chemical defences of D. pulchra and the degradation of algal polysaccharides. Ten bacterial isolates with the broadest range of virulence traits were thereafter tested for the ability to induce in vivo bleaching of D.
    [Show full text]
  • Cazymes in Maribacter Dokdonensis 62-1 from the Patagonian Shelf: Genomics
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416198; this version posted December 8, 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. CAZymes in Maribacter dokdonensis 62-1 from the Patagonian shelf: Genomics and physiology compared to related flavobacteria and a co-occurring Alteromonas strain Laura A. Wolter1,2, Maximilian Mitulla1, Jovan Kalem3, Rolf Daniel4, Meinhard Simon1 and Matthias Wietz1,5* 1Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany 2JST ERATO Nomura Project, Faculty of Life and Environmental Sciences, Tsukuba, Japan 3University of Belgrade, Serbia 4Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University, Göttingen, Germany 5Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany *Corresponding author HGF-MPG Joint Research Group for Deep-Sea Ecology and Technology Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Am Handelshafen 12 27570 Bremerhaven Germany Email: [email protected] Telephone: +49-471-48311454 bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416198; this version posted December 8, 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. ABSTRACT Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides.
    [Show full text]
  • A Report of 28 Unrecorded Bacterial Species, Phylum Bacteroidetes, in Korea
    Journal104 of Species Research 7(2):104-113, 2018JOURNAL OF SPECIES RESEARCH Vol. 7, No. 2 A report of 28 unrecorded bacterial species, phylum Bacteroidetes, in Korea Soohyun Maeng1, Chaeyun Baek1, Jin-Woo Bae2, Chang-Jun Cha3, Kwang-Yeop Jahng4, Ki-seong Joh5, Wonyong Kim6, Chi Nam Seong7, Soon Dong Lee8, Jang-Cheon Cho9 and Hana Yi1,10,* 1Department of Public Health Sciences, Graduate School, Korea University, Seoul 02841, Republic of Korea 2Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea 3Department of Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea 4Department of Life Sciences, Chonbuk National University, Jeonju 54896, Republic of Korea 5Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yongin 17035, Republic of Korea 6Department of Microbiology, Chung-Ang University College of Medicine, Seoul 06973, Republic of Korea 7Department of Biology, Sunchon National University, Suncheon 57922, Republic of Korea 8Faculty of Science Education, Jeju National University, Jeju 63243, Republic of Korea 9Department of Biological Sciences, Inha University, Incheon 22201, Republic of Korea 10School of Biosystem and Biomedical Science, Korea University, Seoul 02841, Republic of Korea *Correspondent: [email protected] In order to investigate indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined. Isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species, but not reported in Korea, were selected as unrecorded species. 28 unrecorded bacterial species belonging to the phylum Bacteroidetes were discovered from various habitats including wastewater, freshwater, freshwater sediment, wet land, reclaimed land, plant root, bird feces, seawater, sea sand, tidal flat sediment, a scallop, marine algae, and seaweed.
    [Show full text]
  • Diversity of Marine Gliding Bacteria in Thailand and Their Cytotoxicity
    Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.12 No.3, Issue of July 15, 2009 © 2009 by Pontificia Universidad Católica de Valparaíso -- Chile Received October 7, 2008 / Accepted March 29, 2009 DOI: 10.2225/vol12-issue3-fulltext-13 RESEARCH ARTICLE Diversity of marine gliding bacteria in Thailand and their cytotoxicity Yutthapong Sangnoi Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Pornpoj Srisukchayakul Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Vullapa Arunpairojana Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Akkharawit Kanjana-Opas* Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Tel: 66 74286373 Fax: 66 74212889 E-mail: [email protected] Financial support: Thailand Research Fund (MRG4880153) and a Biodiversity Research and Training Grant (BRTR_149011). Scholarship for YS from the Graduate School, Prince of Songkla University. Keywords: Aureispira marina, Aureispira maritime, Fulvivirga kasyanovii, human cell lines, Rapidithrix thailandica, Tenacibaculum mesophilum. Abbreviations: CFB: Cytophaga-Flavobacterium-Bacteriodes HeLa: cervical cancer HT-29: colon cancer KB: oral cancer MCF-7: breast adenocarcinoma PCR: polymerase chain reaction SK: skim milk medium SRB: sulphorodamine B Eighty-four marine gliding bacteria were isolated from thailandica, Aureispira marina and Aureispira maritima specimens collected in the Gulf of Thailand and the respectively. The isolates were cultivated in four Andaman Sea. All exhibited gliding motility and swarm different cultivation media (Vy/2, RL 1, CY and SK) colonies on cultivation plates and they were purified by and the crude extracts were submitted to screen subculturing and micromanipulator techniques.
    [Show full text]
  • Genome-Based Taxonomic Classification of Bacteroidetes
    Lawrence Berkeley National Laboratory Recent Work Title Genome-Based Taxonomic Classification of Bacteroidetes. Permalink https://escholarship.org/uc/item/2fs841cf Journal Frontiers in microbiology, 7(DEC) ISSN 1664-302X Authors Hahnke, Richard L Meier-Kolthoff, Jan P García-López, Marina et al. Publication Date 2016 DOI 10.3389/fmicb.2016.02003 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G.
    [Show full text]
  • Supplementary Material Integrated 'Omic' Analyses Provide
    Supplementary Material Integrated ‘omic’ analyses provide evidence that a Ca. Accumulibacter phosphatis strain performs denitrification under micro-aerobic conditions Pamela Y. Camejo1, Ben O. Oyserman1, Katherine D. McMahon1,2, Daniel R. Noguera1,* 1Department of Civil and Environmental Engineering, University of Wisconsin - Madison, Madison, WI, USA 2Department of Bacteriology, University of Wisconsin - Madison, Madison, WI, USA 1 Supplementary Figures 66-26 83.5 83.2 82.7 82.7 82.4 82.4 82.7 83.0 83.1 83.2 83.1 83.1 83.1 83.2 83.2 83.3 83.0 83.7 84.0 83.2 UBA704 9.4 82.4 82.7 82.6 82.5 82.5 82.0 82.6 82.5 82.4 82.7 82.5 82.7 82.3 82.2 82.2 82.2 82.2 82.2 82.5 UW−1 (IIA) 10.9 2.9 84.8 84.9 84.7 84.7 85.1 84.1 85.0 85.0 84.1 83.8 84.0 83.7 83.8 83.8 83.9 83.7 83.9 83.7 SK−01 (IIC) 6.2 1.5 21.7 99.7 93.6 93.6 90.4 83.8 83.8 84.0 83.6 83.5 83.7 83.5 83.8 84.9 84.4 83.5 84.0 83.4 UBA5574 (IIC) 7.2 1.9 25.2 91.0 93.7 93.6 90.5 83.9 83.8 84.0 83.7 83.6 83.7 83.4 83.4 83.4 83.6 83.4 83.6 83.5 HKU-2 (IIC) 6.4 1.6 22.1 70.2 72.3 99.3 89.8 83.9 83.8 83.9 83.6 83.5 83.6 83.2 83.2 83.3 83.2 83.2 83.3 83.3 SK−02 (IIC) 6.6 1.6 22.0 69.8 69.4 77.7 89.8 84.0 83.8 83.9 83.5 83.4 83.7 87.0 87.1 88.0 84.6 84.0 84.6 84.1 BA−91 (IIC) 5.6 1.3 19.8 53.2 54.5 54.4 58.5 84.4 83.7 83.9 83.8 83.6 83.7 83.7 83.7 83.7 84.0 84.9 84.3 83.9 BA−94 (IIF) 13.0 3.0 22.6 16.1 16.5 14.3 15.7 12.5 88.7 88.5 88.4 88.4 88.4 84.1 84.2 84.1 84.0 83.9 83.9 83.8 UBA2327 (IIF) 11.6 2.8 22.9 16.0 16.0 14.3 15.6 12.1 41.4 99.6 88.1 87.7 87.9 83.5 83.7 83.6 83.8 83.5 83.5 83.6 SK−11
    [Show full text]
  • Redalyc.Diversity of Marine Gliding Bacteria in Thailand and Their Cytotoxicity
    Electronic Journal of Biotechnology E-ISSN: 0717-3458 [email protected] Pontificia Universidad Católica de Valparaíso Chile Sangnoi, Yutthapong; Srisukchayakul, Pornpoj; Arunpairojana, Vullapa; Kanjana-Opas, Akkharawit Diversity of marine gliding bacteria in Thailand and their cytotoxicity Electronic Journal of Biotechnology, vol. 12, núm. 3, julio, 2009, pp. 1-8 Pontificia Universidad Católica de Valparaíso Valparaíso, Chile Available in: http://www.redalyc.org/articulo.oa?id=173313803003 How to cite Complete issue Scientific Information System More information about this article Network of Scientific Journals from Latin America, the Caribbean, Spain and Portugal Journal's homepage in redalyc.org Non-profit academic project, developed under the open access initiative Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.12 No.3, Issue of July 15, 2009 © 2009 by Pontificia Universidad Católica de Valparaíso -- Chile Received October 7, 2008 / Accepted March 29, 2009 DOI: 10.2225/vol12-issue3-fulltext-13 RESEARCH ARTICLE Diversity of marine gliding bacteria in Thailand and their cytotoxicity Yutthapong Sangnoi Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Pornpoj Srisukchayakul Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Vullapa Arunpairojana Thailand Institute of Scientific and Technological Research 35 Moo 3, Technopolis, Khlong 5, Khlong Luang Pathum Thani 12120, Thailand Akkharawit Kanjana-Opas* Department of Industrial Biotechnology Faculty of Agro-Industry Prince of Songkla University Hat Yai, Songkhla 90112, Thailand Tel: 66 74286373 Fax: 66 74212889 E-mail: [email protected] Financial support: Thailand Research Fund (MRG4880153) and a Biodiversity Research and Training Grant (BRTR_149011).
    [Show full text]