DOCSLIB.ORG

Pontibacter Lucknowensis Sp. Nov., Isolated from a Hexachlorocyclohexane Dump Site

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Pontibacter Lucknowensis Sp. Nov., Isolated from a Hexachlorocyclohexane Dump Site International Journal of Systematic and Evolutionary Microbiology (2013), 63, 309–313 DOI 10.1099/ijs.0.040147-0 Pontibacter lucknowensis sp. nov., isolated from a hexachlorocyclohexane dump site Vatsala Dwivedi, Neha Niharika and Rup Lal Correspondence Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India Rup Lal [email protected] A Gram-negative, orange-pigmented, rod-shaped, motile and aerobic bacterial strain designated DM9T was isolated from hexachlorocyclohexane (HCH)-contaminated soil (Lucknow, India) and its taxonomic position was determined using a polyphasic approach. 16S rRNA gene sequence analysis showed that the isolate belonged to the phylum Bacteroidetes and confirmed its placement in the genus Pontibacter, with sequence similarity ranging from 93.92 to 96.21 % with other members of the genus Pontibacter. The major cellular fatty acids of the novel strain were iso- C17 : 0 3-OH (6.00 %), iso-C15 : 0 (21.54 %) and summed feature 4 (comprising C17 : 1 iso I/ anteiso B; 32.3 %). The polar lipid profile of strain DM9T showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, two unknown aminolipids and four unknown polar lipids. Strain DM9T contained MK-7 as the predominant menaquinone and its DNA G+C content was 49.2 mol%. sym-Homospermidine was the major polyamine observed in the cell. The results obtained on the basis of phenotypic characteristics, phylogenetic analysis, biochemical and physiological tests clearly distinguished DM9T from closely related members of the genus Pontibacter. It is proposed that DM9T represents a novel species, Pontibacter lucknowensis sp. nov.; the type strain is DM9T (5CCM 7955T5MTCC 11079T). The genus Pontibacter belongs to the phylum Bacteroidetes agar plates. An orange-coloured colony, designated DM9T, and was first described by Nedashkovskaya et al. (2005). At appeared within 36 h of incubation at 28 uC which was the time of writing, there were seven species with validly picked and purified by streaking on LB agar. A polyphasic published names belonging to this genus, Pontibacter approach (Prakash et al., 2007) was adopted for taxonomic actiniarum (Nedashkovskaya et al., 2005), P. akesuensis classification of strain DM9T. (Zhou et al., 2007), P. korlensis (Zhang et al., 2008), P. 16S rRNA gene sequence determines the phylogenetic niistensis (Dastager et al., 2010), P. roseus (Suresh et al., relationship among bacteria based on its universal 2006), P. xinjiangensis (Wang et al., 2010) and P. populi distribution, highly conserved nature, the fundamental (Xu et al., 2012). In addition, ‘Pontibacter salisaro’ has also role of the ribosome in protein synthesis, no horizontal been described (Joung et al., 2011), but the name is not yet transfer and its rate of evolution, which represents an validly published. The type strains of the recognized species appropriate level of variation between organisms. The 16S of the genus are Gram-negative, rod-shaped, aerobic, rRNA gene sequence analysis of strain DM9T was carried heterotrophic and pigmented. Various species of the genus out as described by Prakash et al. (2007) using a 3100- Pontibacter have been isolated from marine actinians, Avant Genetic Analyzer sequencer at the Department of desert soil, muddy water and forest soil (Nedashkovskaya Zoology, University of Delhi, India. The sequence thus et al., 2005; Zhou et al., 2007; Suresh et al., 2006; Dastager obtained was assembled manually using Sequencing et al., 2010). In our ongoing effort (Kaur et al., 2011) to Analysis version 5.1.1 and Clone Manager software version identify the culturable and unculturable diversity at a 5. A continuous stretch of 1400 bp of the 16S rRNA gene of hexachlorocyclohexane (HCH) dump site, Lucknow, Uttar the strain DM9T was obtained and this sequence was Pradesh in North India (27u009 N and 81u099 E), we subjected to similarity search using the Seqmatch tool describe here a further species of the genus Pontibacter. For of the Ribosomal Database Project (http://rdp.cme.msu. this purpose, soil samples from the HCH dump site were edu/) and BLAST program of the National Centre for collected, serially diluted and plated on Luria–Bertani (LB) Biotechnology Information (http://www.ncbi.nlm.nih.gov/). A non-redundant BLASTN search of full sequences through Abbreviation: HCH, hexachlorocyclohexane. GenBank (Altschul et al., 1990), RDP II (Maidak et al., The GenBank accession number for 16S rRNA gene sequence of strain 2001) and EzTaxon Server version 2.1 (Chun et al., 2007) DM9T (5CCM 7955T5MTCC 11079T) is JN561788 identified its closest relatives. 16S rRNA gene sequence T Two supplementary figures and a supplementary table are available with analysis (1400 bp) revealed that strain DM9 showed T the online version of this paper. highest similarity to P. korlensis X14-1 (96.21 %). The 040147 G 2013 IUMS Printed in Great Britain 309 V. Dwivedi, N. Niharika and R. Lal nearly full-length 16S rRNA gene sequences of all members Cantor (1969) and an evolutionary tree was constructed of the genus Pontibacter were retrieved for the construction using the neighbour-joining method of Saitou & Nei (1987). of a phylogenetic tree. The 16S rRNA gene sequence Statistical evaluation of the tree topology based on 1000 similarity between strain DM9T and member of the genus resamplings was done using the bootstrap option in the T Pontibacter ranged from 93.92 to 96.21 %. Strain DM9T TREECON software (Fig. 1). Strain DM9 , falls in the clade showed highest similarity to P. korlensis X14-1T (96.21 %) containing members exclusively belonging to the genus followed by ‘P. salisaro’ HMC5104 (95.89 %), P. actiniarum Pontibacter. T T KMM 6156 (95.35 %), P. niistensis NII-0905 (95.06 %), P. Cell morphology was examined using light (Eclipse E 600; roseus SRC-1T (94.43 %), P. populi HYL7-15T (94.06 %), P. T T Nikon) and electron microscopes (transmission electron akesuensis AKS 1 (94.01 %) and P. xinjiangensis 311-10 microscope, TEM 269D; Morgagni, FEI) (see Fig. S1 (93.92 %). A phylogenetic tree was constructed using available in IJSEM Online). Microscopic analysis revealed sequences of closely related species selected from GenBank that strain DM9T is non-flagellated. Gliding motility of the and EzTaxon Server version 2.1 (Chun et al., 2007). The 16S organism was tested on a fresh LB broth culture using the rRNA gene sequence of the Reichenbachiella agariperforans hanging-drop method (Bowman et al., 2003) and was T KMM 3525 was used as an outgroup and the selected found to be positive. Colonies of strain DM9T showed sequences were aligned using the program CLUSTAL_X optimum growth on LB agar and marine agar at 28 uC version 1.81b (Thompson et al., 1997). Trimming of within 36 h of incubation. DM9T colonies were orange- terminal nucleotides that were not common to all sequences coloured, circular and smooth. The Gram staining test was was carried out manually. Phylogenetic analysis was carried performed using a Gram staining kit (HiMedia); the strain out using the TREECONW software package version 1.3b (Van was found to be Gram-negative. Antibiotic sensitivity tests de Peer & De Wachter, 1994). The evolutionary distance were performed on Muller-Hinton II medium using matrix was calculated using the distance model of Jukes & Readymade Sensi-discs (HiMedia) with varying amounts T 0.02 757 Hymenobacter xinjiangensis X2-1g (DQ888329) 531 Hymenobacter rigui WPCB131T (DQ089669) T 571 Hymenobacter gelipurpurascens Txg1 (Y18836) Hymenobacter yonginensis HMD1010T (GU808562) Hymenobacter psychrotolerans Tibet-IIU11T (DQ177475) T 999 Hymenobacter aerophilus DSM13606 (EU155008) 552 Hymenobacter actinosclerus CCUG 39621T (Y17356) 756 Hymenobacter psychrophilus BZ33rT (GQ131579) 998 Hymenobacter tibetensis XTM003T(EU382214) 591 Hymenobacter norwichensis NS/50T (AJ549285) Hymenobacter roseosalivarius AA-718T (Y18833) 945 1000 Hymenobacter chitinivorans Txc1T (Y18837) Hymenobacter elongatus VUG-A112T (GQ454797) 981 Hymenobacter daecheongensis Dae14T (EU370958) 1000 1000 Hymenobacter soli PB17T (AB251884) Hymenobacter glaciei VUG-A130T (GQ454806) 1000 Hymenobacter ocellatus Myx 2105T (Y18835) Hymenobacter deserti ZLB-3T (EU325941) 1000 997 Adhaeribacter aerophilus 6424S-25T ( GQ421850) 965 Adhaeribacter aerolatus 6515J-31T (GQ421846) 895 Adhaeribacter aquaticus MBRG1.5T (AJ626894) T 834 Adhaeribacter terreus DNG6 (EU682684) Pontibacter populi HLY7-15T (HQ223078) 1000 Pontibacter xinjiangensis 311-10T (FJ004994) 743 ‘Pontibacter salisaro’ HMC5104 (FJ903180) 513 Pontibacter lucknowensis DM9T (JN561788) 711 T 497 Pontibacter korlensis X14-1 (DQ888330) Pontibacter actiniarum KMM 6156T (AY989908) 611 Pontibacter roseus SRC-1T (AM049256) Pontibacter akesuensis AKS 1T (DQ672723) Pontibacter niistensis NII-0905T (FJ897494) Reichenbachiella agariperforans KMM 3525T (AB058919) Fig. 1. Phylogenetic tree based on nearly complete 16S rRNA gene sequence data showing the evolutionary relationship of strain DM9T and representative members of the genera Pontibacter, Adhaeribacter and Hymenobacter. The tree was constructed by using the neighbour-joining (Jukes & Cantor, 1969) method of TREECONW software and the rooting was done by using Reichenbachiella agariperforans KMM 3525T as the outgroup. Bar, 0.02 nt substitutions per 1000 nt positions. The GenBank accession numbers for the 16S rRNA gene sequences of each strain are shown in parentheses. 310 International Journal of Systematic and Evolutionary Microbiology 63 Pontibacter lucknowensis sp. nov. of antibiotics.
Load more

Recommended publications
  • Microbiome Exploration of Deep-Sea Carnivorous Cladorhizidae Sponges
    Microbiome exploration of deep-sea carnivorous Cladorhizidae sponges by Joost Theo Petra Verhoeven A Thesis submitted to the School of Graduate Studies in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Biology Memorial University of Newfoundland March 2019 St. John’s, Newfoundland and Labrador ABSTRACT Members of the sponge family Cladorhizidae are unique in having replaced the typical filter-feeding strategy of sponges by a predatory lifestyle, capturing and digesting small prey. These carnivorous sponges are found in many different environments, but are particularly abundant in deep waters, where they constitute a substantial component of the benthos. Sponges are known to host a wide range of microbial associates (microbiome) important for host health, but the extent of the microbiome in carnivorous sponges has never been extensively investigated and their importance is poorly understood. In this thesis, the microbiome of two deep-sea carnivorous sponge species (Chondrocladia grandis and Cladorhiza oxeata) is investigated for the first time, leveraging recent advances in high-throughput sequencing and through custom developed bioinformatic and molecular methods. Microbiome analyses showed that the carnivorous sponges co-occur with microorganisms and large differences in the composition and type of associations were observed between sponge species. Tissues of C. grandis hosted diverse bacterial communities, similar in composition between individuals, in stark contrast to C. oxeata where low microbial diversity was found with a high host-to-host variability. In C. grandis the microbiome was not homogeneous throughout the host tissue, and significant shifts occured within community members across anatomical regions, with the enrichment of specific bacterial taxa in particular anatomical niches, indicating a potential symbiotic role of such taxa within processes like prey digestion and chemolithoautotrophy.
    [Show full text]
  • Imperialibacter Roseus Gen. Nov., Sp. Nov., a Novel Bacterium of the Family Flammeovirgaceae Isolated from Permian Groundwater
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 4136–4140 DOI 10.1099/ijs.0.052662-0 Imperialibacter roseus gen. nov., sp. nov., a novel bacterium of the family Flammeovirgaceae isolated from Permian groundwater Hui Wang,1,2,3 Junde Li,1 Tianling Zheng,2 Russell T. Hill3 and Xiaoke Hu1 Correspondence 1Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China Xiaoke Hu 2Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, [email protected] Xiamen University, Xiamen 361005, China 3Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA A novel bacterial strain, designated P4T, was isolated from Permian groundwater and identified on the basis of its phylogenetic, genotypic, chemotaxonomic and phenotypic characteristics. Cells were aerobic, Gram-stain-negative rods. 16S rRNA gene sequence-based phylogenetic analysis revealed that P4T is affiliated with the family Flammeovirgaceae in the phylum Bacteroidetes, but forms a distinct cluster within this family. The DNA G+C content of strain P4T was 45.2 mol%. The predominant cellular fatty acids were C16 : 1v6c/C16 : 1v7c and iso-C15 : 0. MK-7 was the main respiratory quinone. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, unidentified phospholipids, an unidentified aminolipid, unidentified glycoli- pids and unidentified polar lipids. Based on our extensive polyphasic analysis, a novel species in a new genus, Imperialibacter roseus gen. nov., sp. nov., is proposed. The type strain of Imperialibacter roseus is P4T (5CICC 10659T5KCTC 32399T). Bacteria affiliated with the family Flammeovirgaceae of the staining was performed according to the method described phylum Bacteroidetes are widely distributed in various by Gerhardt et al.
    [Show full text]
  • Succession and Cazyme Expression of Marine Bacterial
    bioRxiv preprint doi: https://doi.org/10.1101/2020.12.08.416354; 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. Sweet and magnetic: Succession and CAZyme expression of marine bacterial communities encountering a mix of alginate and pectin particles Carina Bunse1,2,*, Hanna Koch3,4,*, Sven Breider3, Meinhard Simon1,3 and Matthias Wietz2,3# 1Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Germany 2Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Germany 3Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Germany 4Department of Microbiology, Radboud University Nijmegen, The Netherlands *These authors contributed equally to this work. #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/10.1101/2020.12.08.416354; 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 Polysaccharide particles are an important nutrient source and microhabitat for marine bacteria. However, substrate-specific bacterial dynamics in a mixture of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed.
    [Show full text]
  • Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications
    fmicb-11-01636 July 23, 2020 Time: 17:36 # 1 ORIGINAL RESEARCH published: 24 July 2020 doi: 10.3389/fmicb.2020.01636 Evidence of Vent-Adaptation in Sponges Living at the Periphery of Hydrothermal Vent Environments: Ecological and Evolutionary Implications Magdalena N. Georgieva1*, Sergi Taboada1,2,3, Ana Riesgo1, Cristina Díez-Vives1, Fabio C. De Leo4,5, Rachel M. Jeffreys6, Jonathan T. Copley7, Crispin T. S. Little1,8, Pilar Ríos3,9, Javier Cristobo3,10, Jon T. Hestetun11 and Adrian G. Glover1 1 Life Sciences Department, Natural History Museum, London, United Kingdom, 2 Departamento de Biología (Zoología), Universidad Autónoma de Madrid, Madrid, Spain, 3 Departamento de Zoología y Antropología Física, Universidad de Alcalá, Madrid, Spain, 4 Ocean Networks Canada, University of Victoria, Victoria, BC, Canada, 5 Department of Biology, University of Victoria, Victoria, BC, Canada, 6 School of Environmental Sciences, University of Liverpool, Liverpool, United Kingdom, 7 School of Ocean and Earth Science, University of Southampton, Southampton, United Kingdom, 8 School of Earth Edited by: and Environment, University of Leeds, Leeds, United Kingdom, 9 Centro Oceanográfico de Santander, Instituto Español Iliana B. Baums, de Oceanografía, Santander, Spain, 10 Centro Oceanográfico de Gijón, Instituto Español de Oceanografía, Gijón, Spain, Pennsylvania State University (PSU), 11 NORCE Environment, Norwegian Research Centre (NORCE), Bergen, Norway United States Reviewed by: Jillian Petersen, The peripheral areas of deep-sea hydrothermal vents are often inhabited by an University of Vienna, Austria assemblage of animals distinct to those living close to vent chimneys. For many such Peter Deines, University of Kiel, Germany taxa, it is considered that peak abundances in the vent periphery relate to the availability *Correspondence: of hard substrate as well as the increased concentrations of organic matter generated Magdalena N.
    [Show full text]
  • A Robust Metaproteomics Pipeline for a Holistic Taxonomic and Functional
    bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 Title: A robust metaproteomics pipeline for a holistic taxonomic and functional 3 characterization of microbial communities from marine particles 4 Authors: Doreen Schultz,1 Daniela Zühlke,1 Jörg Bernhardt,1 Thomas Ben Francis,2 Dirk 5 Albrecht,1 Claudia Hirschfeld,1 Stephanie Markert,3 and Katharina Riedel 1* 6 7 Addresses: 1 Institute of Microbiology, University of Greifswald, Greifswald, Germany. 8 2 Max-Planck Institute for Marine Microbiology, Bremen, Germany. 9 3 Institute of Pharmacy, University of Greifswald, Greifswald, Germany. 10 11 *Corresponding author mailing address: Institute of Microbiology, Center for Functional 12 Genomics of Microbes (C_FunGene), University of Greifswald, Felix-Hausdorff-Straße 8, DE- 13 17487 Greifswald, Germany. E-mail [email protected]; Tel (+49) 3834 420 5900 14 15 Running title: Metaproteomic pipeline to analyse marine particles 1 bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 16 Originality-Significance Statement 17 Marine particles consist of organic particulate matter (e.g. phyto- or zooplankton) and 18 particle-associated (PA) microbial communities, which are often embedded in a sugary 19 matrix. A significant fraction of the decaying algal biomass in marine ecosystems is expected 20 to be mineralized by PA heterotrophic communities, which are thus greatly contributing to 21 large-scale carbon fluxes.
    [Show full text]
  • Feed Types Driven Differentiation of Microbial Community And
    water Article Feed Types Driven Differentiation of Microbial Community and Functionality in Marine Integrated Multitrophic Aquaculture System Yale Deng 1,2 , Fan Zhou 3, Yunjie Ruan 1,4,*, Bin Ma 5, Xueyan Ding 3, Xiaomei Yue 6, Wenjun Ma 3 and Xuwang Yin 7 1 Institute of Agricultural Bio-Environmental Engineering, College of Bio-Systems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; [email protected] 2 Aquaculture and Fisheries Group, Department of Animal Sciences, Wageningen University, 6708 WD Wageningen, The Netherlands 3 Zhejiang Fisheries Technical Extension Station, Hangzhou 310023, China; [email protected] (F.Z.); [email protected] (X.D.); [email protected] (W.M.) 4 Academy of Rural Development, Zhejiang University, Hangzhou 310058, China 5 Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; [email protected] 6 Business Economics Group, Department of Social Science, Wageningen University, 6706 KN Wageningen, The Netherlands; [email protected] 7 College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; [email protected] * Correspondence: [email protected]; Tel.: +86-571-8898-2373 Received: 2 October 2019; Accepted: 17 December 2019; Published: 26 December 2019 Abstract: Integrated multi trophic aquaculture (IMTA) improves the production of aquatic animals by promoting nutrient utilization through different tropical levels. Microorganisms play an important role in elements cycling, energy flow and farmed-species health. The aim of this study was to evaluate how feed types, fresh frozen fish diet (FFD) or formulated diet (FD), influence the microbial community diversity and functionality in both water and sediment in a marine IMTA system.
    [Show full text]
  • Downloaded the Sequences of UCYN-A1 [42] (Gi|284809060) and UCYN-A2 284 [43](Gi|671395793)
    bioRxiv preprint doi: https://doi.org/10.1101/216978; this version posted March 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Dynamics and interactions of highly resolved marine plankton via automated high 2 frequency sampling 3 4 5 6 7 8 9 10 David M. Needham1, Erin B. Fichot1, Ellice Wang1, Lyria Berdjeb1, Jacob A. Cram1, 11 Cedric G. Fichot2, Jed A. Fuhrman1 12 13 1Department of Biological Sciences, University of Southern California 14 2Earth and Environment, Boston University 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 Conflicts of Interest: The authors declare no conflict of interest. 1 bioRxiv preprint doi: https://doi.org/10.1101/216978; this version posted March 21, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 32 Abstract 33 Short time-scale observations are valuable for understanding microbial ecological 34 processes. We assessed dynamics in relative abundance and potential activities by 35 sequencing the small sub-unit ribosomal RNA gene (rRNA gene) and rRNA 36 molecules (rRNA) of Bacteria, Archaea, and Eukaryota once to twice-daily between 37 March 2014 and May 2014 from the surface ocean off Catalina Island, California. 38 Typically Ostreococcus, Braarudosphaera, Teleaulax, and Synechococcus dominated 39 phytoplankton sequences (including chloroplasts) while SAR11, Sulfitobacter, and 40 Fluviicola dominated non-phytoplankton Bacteria and Archaea. We observed short- 41 lived increases of diatoms, mostly Pseudo-nitzschia and Chaetoceros, with quickly 42 responding Bacteria and Archaea including Flavobacteriaceae (Polaribacter & 43 Formosa), Roseovarius, and Euryarchaeota (MGII), notably the exact amplicon 44 sequence variants we observed responding similarly to another diatom bloom 45 nearby, three years prior.
    [Show full text]
  • Appendix 1. Validly Published Names, Conserved and Rejected Names, And
    Appendix 1. Validly published names, conserved and rejected names, and taxonomic opinions cited in the International Journal of Systematic and Evolutionary Microbiology since publication of Volume 2 of the Second Edition of the Systematics* JEAN P. EUZÉBY New phyla Alteromonadales Bowman and McMeekin 2005, 2235VP – Valid publication: Validation List no. 106 – Effective publication: Names above the rank of class are not covered by the Rules of Bowman and McMeekin (2005) the Bacteriological Code (1990 Revision), and the names of phyla are not to be regarded as having been validly published. These Anaerolineales Yamada et al. 2006, 1338VP names are listed for completeness. Bdellovibrionales Garrity et al. 2006, 1VP – Valid publication: Lentisphaerae Cho et al. 2004 – Valid publication: Validation List Validation List no. 107 – Effective publication: Garrity et al. no. 98 – Effective publication: J.C. Cho et al. (2004) (2005xxxvi) Proteobacteria Garrity et al. 2005 – Valid publication: Validation Burkholderiales Garrity et al. 2006, 1VP – Valid publication: Vali- List no. 106 – Effective publication: Garrity et al. (2005i) dation List no. 107 – Effective publication: Garrity et al. (2005xxiii) New classes Caldilineales Yamada et al. 2006, 1339VP VP Alphaproteobacteria Garrity et al. 2006, 1 – Valid publication: Campylobacterales Garrity et al. 2006, 1VP – Valid publication: Validation List no. 107 – Effective publication: Garrity et al. Validation List no. 107 – Effective publication: Garrity et al. (2005xv) (2005xxxixi) VP Anaerolineae Yamada et al. 2006, 1336 Cardiobacteriales Garrity et al. 2005, 2235VP – Valid publica- Betaproteobacteria Garrity et al. 2006, 1VP – Valid publication: tion: Validation List no. 106 – Effective publication: Garrity Validation List no. 107 – Effective publication: Garrity et al.
    [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]
  • Thermal and Microbial Effects on Brown Macroalgae: Heat
    The University of Maine DigitalCommons@UMaine Electronic Theses and Dissertations Fogler Library Winter 11-19-2018 Thermal and Microbial Effects on Brown Macroalgae: Heat Acclimation and the Biodiversity of the Microbiome Charlotte TC Quigley University of Maine, [email protected] Follow this and additional works at: https://digitalcommons.library.umaine.edu/etd Part of the Bacteriology Commons, Bioinformatics Commons, Computational Biology Commons, Environmental Microbiology and Microbial Ecology Commons, Genetics Commons, Marine Biology Commons, Molecular Biology Commons, and the Molecular Genetics Commons Recommended Citation Quigley, Charlotte TC, "Thermal and Microbial Effects on Brown Macroalgae: Heat Acclimation and the Biodiversity of the Microbiome" (2018). Electronic Theses and Dissertations. 2933. https://digitalcommons.library.umaine.edu/etd/2933 This Open-Access Thesis is brought to you for free and open access by DigitalCommons@UMaine. It has been accepted for inclusion in Electronic Theses and Dissertations by an authorized administrator of DigitalCommons@UMaine. For more information, please contact [email protected]. THERMAL AND MICROBIAL EFFECTS ON BROWN MACROALGAE: HEAT ACCLIMATION AND THE BIODIVERSITY OF THE MICROBIOME By Charlotte Terry Carrigan Quigley B.A. Colby College, 2009 A DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctorate of Philosophy (in Marine Biology) The Graduate School The University of Maine December 2018 Advisory Committee: Susan Brawley, Professor of Marine Sciences, Advisor Nick Brown, Former Director of Center for Cooperative Aquaculture Research Bill Halteman, Professor Emeritus of Mathematics and Statistics Vicki Hertzberg, Professor of Biostatistics and Bioinformatics Benildo de los Reyes, Professor of Plant Genomics John Singer, Professor of Microbiology THERMAL AND MICROBIAL EFFECTS ON BROWN MACROALGAE: HEAT ACCLIMATION AND THE BIODIVERSITY OF THE MICROBIOME By Charlotte Terry Carrigan Quigley Dissertation Advisor: Dr.
    [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]
  • Summer Phyto- and Bacterioplankton Communities During Low and High
    Polar Biology https://doi.org/10.1007/s00300-018-2411-5 ORIGINAL PAPER Summer phyto‑ and bacterioplankton communities during low and high productivity scenarios in the Western Antarctic Peninsula Sebastián Fuentes1,2 · José Ignacio Arroyo1,2 · Susana Rodríguez‑Marconi3,4 · Italo Masotti3 · Tomás Alarcón‑Schumacher1,2 · Martin F. Polz5 · Nicole Trefault6 · Rodrigo De la Iglesia1 · Beatriz Díez1,2 Received: 25 May 2018 / Revised: 25 September 2018 / Accepted: 28 September 2018 © Springer-Verlag GmbH Germany, part of Springer Nature 2018 Abstract Phytoplankton blooms taking place during the warm season drive high productivity in Antarctic coastal seawaters. Impor- tant temporal and spatial variations exist in productivity patterns, indicating local constraints infuencing the phototrophic community. Surface water in Chile Bay (Greenwich Island, South Shetlands) is infuenced by freshwater from the melting of sea ice and surrounding glaciers; however, it is not a widely studied system. The phyto- and bacterioplankton communities in Chile Bay were studied over two consecutive summers; during a low productivity period (chlorophyll a < 0.05 mg m−3) and an ascendant phototrophic bloom (chlorophyll a up to 2.38 mg m−3). Microbial communities were analyzed by 16S rRNA—including plastidial—gene sequencing. Diatoms (mainly Thalassiosirales) were the most abundant phytoplankton, particularly during the ascendant bloom. Bacterioplankton in the low productivity period was less diverse and dominated by a few operational taxonomic units (OTUs), related to Colwellia and Pseudoalteromonas. Alpha diversity was higher during the bloom, where several Bacteroidetes taxa absent in the low productivity period were present. Network analysis indicated that phytoplankton relative abundance was correlated with bacterioplankton phylogenetic diversity and the abundance of several bacterial taxa.
    [Show full text]