Abt+Et+Al Final.Pdf

Total Page:16

File Type:pdf, Size:1020Kb

Abt+Et+Al Final.Pdf Complete genome sequence of Leadbetterella byssophila type strain (4M15). Item Type Article Authors Abt, Birte; Teshima, Hazuki; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Rohde, Manfred; Göker, Markus; Tindall, Brian J; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C Citation Complete genome sequence of Leadbetterella byssophila type strain (4M15). 2011, 4 (1):2-12 Stand Genomic Sci DOI 10.4056/sigs.1413518 Journal Standards in genomic sciences Rights Archived with thanks to Standards in genomic sciences Download date 06/10/2021 16:29:06 Link to Item http://hdl.handle.net/10033/216992 This is an Open Access-journal’s PDF published in Abt, B., Teshima, H., Lucas, S., Lapidus, A., del Rio, T.G., Nolan, M., Tice, H., Cheng, J.-F., Pitluck, S., Liolios, K., Pagani, I., Ivanova, N., Mavromatis, K., Pati, A., Tapia, R., Han, C., Goodwin, L., Chen, A., Palaniappan, K., Land, M., Hauser, L., Chang, Y.-J., Jeffries, C.D., Rohde, M., Göker, M., Tindall, B.J., Detter, J.C., Woyke, T., Bristow, J., Eisen, J.A., Markowitz, V., Hugenholtz, P., Klenk, H.-P., Kyrpides, N.C. Complete genome sequence of leadbetterella byssophila type strain (4M15T) (2011) Standards in Genomic Sciences, 4 (1), pp. 2-12. Standards in Genomic Sciences (2011) 4:2-12 DOI:10.4056/sigs.1413518 Complete genome sequence of Leadbetterella byssophila type strain (4M15T) Birte Abt1, Hazuki Teshima2,3, Susan Lucas2, Alla Lapidus2, Tijana Glavina Del Rio2, Matt Nolan2, Hope Tice2, Jan-Fang Cheng2, Sam Pitluck2, Konstantinos Liolios2, Ioanna Pagani2, Natalia Ivanova2, Konstantinos Mavromatis2, Amrita Pati2, Roxane Tapia2,3, Cliff Han2,3, Lynne Goodwin2,3, Amy Chen4, Krishna Palaniappan4, Miriam Land2,5, Loren Hauser2,5, Yun-Juan Chang2,5, Cynthia D. Jeffries2,5, Manfred Rohde6, Markus Göker1, Brian J. Tindall1, John C. Detter2,3, Tanja Woyke2, James Bristow2, Jonathan A. Eisen2,7, Victor Markowitz4, Philip Hugenholtz2,8, Hans-Peter Klenk1, and Nikos C. Kyrpides2* 1 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 2 DOE Joint Genome Institute, Walnut Creek, California, USA 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Lawrence Livermore National Laboratory, Livermore, California, USA 6 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 7 University of California Davis Genome Center, Davis, California, USA 8 Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia *Corresponding author: Nikos C. Kyrpides Keywords: non-motile, non-sporulating, aerobic, mesophile, Gram-negative, flexirubin, Cy- tophagaceae, GEBA Leadbetterella byssophila Weon et al. 2005 is the type species of the genus Leadbetterella of the family Cytophagaceae in the phylum Bacteroidetes. Members of the phylum Bacteroi- detes are widely distributed in nature, especially in aquatic environments. They are of special interest for their ability to degrade complex biopolymers. L. byssophila occupies a rather iso- lated position in the tree of life and is characterized by its ability to hydrolyze starch and ge- latine, but not agar, cellulose or chitin. Here we describe the features of this organism, to- gether with the complete genome sequence, and annotation. L. byssophila is already the 16th member of the family Cytophagaceae whose genome has been sequenced. The 4,059,653 bp long single replicon genome with its 3,613 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. Introduction Strain 4M15T (= DSM 17132 = JCM 16389 = KACC saccharides. The CFB group consists of many bac- 11308) is the type strain of the species Leadbette- terial strains isolated from marine environments rella byssophila, which is the type species of the and hypersaline lakes; but only a few were iso- genus Leadbetterella. Currently L. byssophila is the lated from other habitats such as soil. Various tax- only validly named species in this genus. The type onomic treatments have placed L. byssophila ei- strain was isolated by Weon et al. [1] from cotton- ther in the family 'Flexibacteraceae' or the family waste compost soil used as mushroom cultivation Cytophagaceae. This is most probably due to a in Suwon, South Korea. L. byssophila is described number of nomenclatural problems. The family as aerobic, rod shaped and non-motile. The spe- 'Flexibacteraceae' as outlined in TOBA7.7 [3] cies belongs to the Cytophaga-Flavobacterium- would include Cytophaga hutchinsonii, which is Bacteroides (CFB) group, also known as the phy- the type species of the genus Cytophaga, which in lum Bacteroidetes [2], which comprises organisms turn is the type of the family Cytophagaceae, a associated with the degradation of complex poly- name that may not be replaced by the family name The Genomic Standards Consortium Abt et al. 'Flexibacteraceae' as long as Cytophaga hutchinso- The highest-scoring environmental sequence was nii is one of the included species. A similar prob- HM238135 ('structure full-scale air pig facility bio- lem arises with the placement of Spirosoma lin- filter treating waste gas clone FF 92'), which guale in the higher taxonomic ranks and has been showed an identity of 93.1% and a HSP coverage of discussed previously [4]. Here we present a sum- 96.0%. The five most frequent keywords within the mary classification and a set of features for L. bys- labels of environmental samples which yielded hits sophila 4M15T, together with the description of were 'lake' (4.8%), 'litholog/stream' (4.5%), the complete genomic sequencing and annotation. 'biofilm' (3.3%), 'microbi' (2.9%) and 'site' (2.5%) (170 hits in total). The five most frequent keywords Classification and features within the labels of environmental samples which L. byssophila 4M15T is very isolated in the tree of yielded hits of a higher score than the highest scor- life, with no other species allocated to the same ge- ing species were 'soil' (5.1%), 'biofilm/oxid' nus and with the type strains of the members of the (5.1%), 'air, biofilt, facil, full-scal, pig, structur, treat, genus Emticicia [5,6] sharing the highest degree of wast' (2.7%), 'forest, ghat, ground, india, mangrov, 16S rRNA sequence identity (88.3-88.9%) [7], fol- nich, prokaryt, select, studi, swab, western' (2.7%) lowed by Sporocytophaga myxococcoides (85.2%) and 'cold, spring' (2.6%) (5 hits in total). [8] and Siphonobacter aquaeclarae (85.0%) [9]. No Figure 1 shows the phylogenetic neighborhood of L. other cultured strain belonging to the species or byssophila 4M15T in a 16S rRNA based tree. The genus has been described. Only one 16S rRNA se- sequences of the three 16S rRNA gene copies in the quence from a moderately related (95% sequence genome do not differ from each other, and do not identity) uncultivated clone, W4S69 (GU560170), differ from the previously published 16S rRNA se- identified by Xu and colleagues in pharmaceutical quence (AY854022). wastewater biofilms, was reported in GenBank. Cells of L. byssophila stain Gram-negative and are Neither environmental screenings nor genomic non-motile, rod shaped with a width of 0.6-0.9 µm surveys produced any sequence that could be and a length of 2-7 µm (Figure 2 and Table 1). Co- linked to the species L. byssophila or the genus lonies are circular, 1-2 mm in diameter, smooth, Leadbetterella, indicating that members of the spe- light orange, shiny and convex with entire margin cies are not heavily represented in the so far when grown on trypticase soy agar. After pro- screened habitats (status November 2010). longed incubation colonies become dark orange. A representative genomic 16S rRNA sequence of L. Strain 4M15T grows under aerobic conditions at byssophila 4M15T was compared using NCBI BLAST temperatures of 15-45°C and at a pH range of 6.0- under default settings (e.g., considering only the 8.0. The strain grows in the presence of 1% (w/v) high-scoring segment pairs (HSPs) from the best NaCl, but not at 3% NaCl [1]. Growth on carbohy- 250 hits) with the most recent release of the drates (API 20NE) was observed for glucose, arabi- Greengenes database [10] and the relative frequen- nose, mannose, N-acetylglucosamine and maltose cies, weighted by BLAST scores, of taxa and key- but not for mannitol. Strain 4M15T was positive for words (reduced to their stem [11]) were deter- -galactosidase, and nega- mined. The five most frequent genera were Pedo- tive for nitrate reduction and arginine dihydrolase bacter (35.1%), Flectobacillus (11.4%), Leadbette- indole(API 20N productionE). Enzymatic and βactivity was detected for rella (9.4%), Algoriphagus (8.6%) and Arcicella alkaline phosphatase, leucine arylamidase, valine (6.8%) (80 hits in total). Regarding the single hit to arylamidase, trypsin, acid phosphatase, naphthol- sequences from members of the species, the aver- AS-BI- - - age identity within HSPs was 100.0%, whereas the glucosidase, N-acetyl- - - average coverage by HSPs was 97.9%. Among all fucosidase;phosphohydrolase, weak enzymatic actα ivityglucosidase, was ob servedβ other species, the one yielding the highest score - β glucosaminidase-galactosidase (API and ZYM). α was 'Kaistomonas ginsengisoli', which corres- L. byssophila produces catalase and urease [1]. ponded to an identity of 92.2% and a HSP coverage Whereasfor α galactosidase starch, gelatin, and β aesculin and tyrosine are of 49.8%. The name 'Kaistomonas ginsengisoli' hydrolyzed; agar, casein, cellulose and chitin are (strain Gsoil 085, AB245370) is also to be found in not. Strain 4M15T is sensitive to ampicillin, carben- a number of publications [12-14], but that has since cillin, lincomycin, streptomycin and tetracycline become the type strain of Emticicia ginsengisoli [6].
Recommended publications
  • Taxonomy JN869023
    Species that differentiate periods of high vs. low species richness in unattached communities Species Taxonomy JN869023 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 JN674641 Bacteria; Bacteroidetes; [Saprospirae]; [Saprospirales]; Chitinophagaceae; Sediminibacterium JN869030 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales; ACK-M1 U51104 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae; Limnohabitans JN868812 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae JN391888 Bacteria; Planctomycetes; Planctomycetia; Planctomycetales; Planctomycetaceae; Planctomyces HM856408 Bacteria; Planctomycetes; Phycisphaerae; Phycisphaerales GQ347385 Bacteria; Verrucomicrobia; [Methylacidiphilae]; Methylacidiphilales; LD19 GU305856 Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales; Pelagibacteraceae GQ340302 Bacteria; Actinobacteria; Actinobacteria; Actinomycetales JN869125 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae New.ReferenceOTU470 Bacteria; Cyanobacteria; ML635J-21 JN679119 Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Comamonadaceae HM141858 Bacteria; Acidobacteria; Holophagae; Holophagales; Holophagaceae; Geothrix FQ659340 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; auto67_4W AY133074 Bacteria; Elusimicrobia; Elusimicrobia; Elusimicrobiales FJ800541 Bacteria; Verrucomicrobia; [Pedosphaerae]; [Pedosphaerales]; R4-41B JQ346769 Bacteria; Acidobacteria; [Chloracidobacteria]; RB41; Ellin6075
    [Show full text]
  • Ice-Nucleating Particles Impact the Severity of Precipitations in West Texas
    Ice-nucleating particles impact the severity of precipitations in West Texas Hemanth S. K. Vepuri1,*, Cheyanne A. Rodriguez1, Dimitri G. Georgakopoulos4, Dustin Hume2, James Webb2, Greg D. Mayer3, and Naruki Hiranuma1,* 5 1Department of Life, Earth and Environmental Sciences, West Texas A&M University, Canyon, TX, USA 2Office of Information Technology, West Texas A&M University, Canyon, TX, USA 3Department of Environmental Toxicology, Texas Tech University, Lubbock, TX, USA 4Department of Crop Science, Agricultural University of Athens, Athens, Greece 10 *Corresponding authors: [email protected] and [email protected] Supplemental Information 15 S1. Precipitation and Particulate Matter Properties S1.1 Precipitation Categorization In this study, we have segregated our precipitation samples into four different categories, such as (1) snows, (2) hails/thunderstorms, (3) long-lasted rains, and (4) weak rains. For this categorization, we have considered both our observation-based as well as the disdrometer-assigned National Weather Service (NWS) 20 code. Initially, the precipitation samples had been assigned one of the four categories based on our manual observation. In the next step, we have used each NWS code and its occurrence in each precipitation sample to finalize the precipitation category. During this step, a precipitation sample was categorized into snow, only when we identified a snow type NWS code (Snow: S-, S, S+ and/or Snow Grains: SG). Likewise, a precipitation sample was categorized into hail/thunderstorm, only when the cumulative sum of NWS codes for hail was 25 counted more than five times (i.e., A + SP ≥ 5; where A and SP are the codes for soft hail and hail, respectively).
    [Show full text]
  • Fibrisoma Limi Gen. Nov., Sp. Nov., an Orange Pigmented Filamentous Bacterium of the Family Cytophagaceae Isolated from North Sea Tidal Flats
    http://www.ncbi.nlm.nih.gov/pubmed/20601484. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. University of Zurich http://www.zora.uzh.ch Zurich Open Repository and Archive Originally published at: Filippini, M; Kaech, A; Ziegler, U; Bagheri, H C (2011). Fibrisoma limi gen. nov., sp. nov., an orange pigmented filamentous bacterium of the family Cytophagaceae isolated from North Sea tidal flats. International Journal of Systematic and Evolutionary Microbiology, 61(6):1418-1424. Winterthurerstr. 190 CH-8057 Zurich http://www.zora.uzh.ch Year: 2011 Fibrisoma limi gen. nov., sp. nov., an orange pigmented filamentous bacterium of the family Cytophagaceae isolated from North Sea tidal flats Filippini, M; Kaech, A; Ziegler, U; Bagheri, H C http://www.ncbi.nlm.nih.gov/pubmed/20601484. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: Filippini, M; Kaech, A; Ziegler, U; Bagheri, H C (2011). Fibrisoma limi gen. nov., sp. nov., an orange pigmented filamentous bacterium of the family Cytophagaceae isolated from North Sea tidal flats. International Journal of Systematic and Evolutionary Microbiology, 61(6):1418-1424. Fibrisoma limi gen. nov., sp. nov., an orange pigmented filamentous bacterium of the family Cytophagaceae isolated from North Sea tidal flats Abstract An orange pigmented Gram-staining-negative, non motile, filament forming rod-shaped bacterium (BUZ 3T) was isolated from a coastal mud sample from the North Sea (Fedderwardersiel, Germany) and characterized taxonomically using a polyphasic approach.
    [Show full text]
  • Conserved and Reproducible Bacterial Communities Associate with Extraradical Hyphae of Arbuscular Mycorrhizal Fungi
    The ISME Journal (2021) 15:2276–2288 https://doi.org/10.1038/s41396-021-00920-2 ARTICLE Conserved and reproducible bacterial communities associate with extraradical hyphae of arbuscular mycorrhizal fungi 1,2 1,3 1 Bryan D. Emmett ● Véronique Lévesque-Tremblay ● Maria J. Harrison Received: 21 September 2020 / Revised: 21 January 2021 / Accepted: 29 January 2021 / Published online: 1 March 2021 © The Author(s) 2021. This article is published with open access Abstract Extraradical hyphae (ERH) of arbuscular mycorrhizal fungi (AMF) extend from plant roots into the soil environment and interact with soil microbial communities. Evidence of positive and negative interactions between AMF and soil bacteria point to functionally important ERH-associated communities. To characterize communities associated with ERH and test controls on their establishment and composition, we utilized an in-growth core system containing a live soil–sand mixture that allowed manual extraction of ERH for 16S rRNA gene amplicon profiling. Across experiments and soils, consistent enrichment of members of the Betaproteobacteriales, Myxococcales, Fibrobacterales, Cytophagales, Chloroflexales, and Cellvibrionales was observed on ERH samples, while variation among samples from different soils was observed primarily 1234567890();,: 1234567890();,: at lower taxonomic ranks. The ERH-associated community was conserved between two fungal species assayed, Glomus versiforme and Rhizophagus irregularis, though R. irregularis exerted a stronger selection and showed greater enrichment for taxa in the Alphaproteobacteria and Gammaproteobacteria. A distinct community established within 14 days of hyphal access to the soil, while temporal patterns of establishment and turnover varied between taxonomic groups. Identification of a conserved ERH-associated community is consistent with the concept of an AMF microbiome and can aid the characterization of facilitative and antagonistic interactions influencing the plant-fungal symbiosis.
    [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]
  • Pontibacter Diazotrophicus Sp. Nov., a Novel Nitrogen- Fixing Bacterium of the Family Cytophagaceae
    Pontibacter diazotrophicus sp. nov., a Novel Nitrogen- Fixing Bacterium of the Family Cytophagaceae Linghua Xu1,2, Xian-Chun Zeng1*, Yao Nie1, Xuesong Luo3*, Enmin Zhou4, Lingli Zhou1, Yunfan Pan1, Wenjun Li4 1 State Key Laboratory of Biogeology and Environmental Geology & Department of Biological Science and Technology, School of Environmental Studies, China University of Geosciences (Wuhan), Wuhan, China, 2 School of Chemical and Material Engineering, Hubei Polytechnic University, Huangshi, China, 3 State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China, 4 Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, and Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, China Abstract Few diazotrophs have been found to belong to the family Cytophagaceae so far. In the present study, a Gram-negative, rod- shaped bacterium that forms red colonies, was isolated from sands of the Takalamakan desert. It was designated H4XT. Phylogenetic and biochemical analysis indicated that the isolate is a new species of the genus Pontibacter. The 16S rRNA gene of H4XT displays 94.2–96.8% sequence similarities to those of other strains in Pontibacter. The major respiratory quinone is menaquinone-7 (MK-7). The DNA G+C content is 46.6 mol%. The major cellular fatty acids are iso-C15:0,C16:1v5c, summed feature 3 (containing C16:1v6c and/or C16:1v7c) and summed feature 4 (comprising anteiso-C17:1B and/or iso-C17:1I). The major polar lipids are phosphatidylethanolamine (PE), one aminophospholipid (APL) and some unknown phospholipids (PLs). It is interesting to see that this bacterium can grow very well in a nitrogen-free medium.
    [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]
  • Pontibacter Indicus Sp. Nov., Isolated from Hexachlorocyclohexane-Contaminated Soil
    International Journal of Systematic and Evolutionary Microbiology (2014), 64, 254–259 DOI 10.1099/ijs.0.055319-0 Pontibacter indicus sp. nov., isolated from hexachlorocyclohexane-contaminated soil Amit Kumar Singh,1 Nidhi Garg,1 Pushp Lata,1 Roshan Kumar,1 Vivek Negi,1 Surendra Vikram2 and Rup Lal1 Correspondence 1Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi-110007, India Rup Lal 2IMTECH-Institute of Microbial Technology, Sector-39A, Chandigarh-160036, India [email protected] An orange-pigmented bacterial strain, designated LP100T, was isolated from hexachlorocyclohexane-contaminated soil (Lucknow, India). A neighbour-joining tree based on 16S rRNA gene sequences showed that strain LP100T occupied a distinct phylogenetic position in the Pontibacter species cluster, showing highest similarity with Pontibacter lucknowensis DM9T (97.4 %). Levels of similarity to strains of other Pontibacter species ranged between 94.0 and 96.8 %. Strain LP100T contained MK-7 as the predominant menaquinone and sym- homospermidine was the major polyamine in the cell. The major cellular fatty acids of strain T T LP100 were anteiso-C17 : 0 A, iso-C15 : 0 and iso-C18 : 1 H. The polar lipid profile of strain LP100 showed the presence of phosphatidylethanolamine, an unidentified aminophospholipid, three unknown aminolipids and two unknown polar lipids. The G+C content of strain LP100T was 58.2 mol%. The results of DNA–DNA hybridization, biochemical and physiological tests clearly distinguish the novel strain from closely related species of the genus Pontibacter. Therefore, strain LP100T represents a novel species of the genus Pontibacter for which the name Pontibacter indicus is proposed. The type strain is LP100T (5CCM8435T5MCC2027T).
    [Show full text]
  • Spirosoma Linguale Type Strain (1T)
    Lawrence Berkeley National Laboratory Recent Work Title Complete genome sequence of Spirosoma linguale type strain (1). Permalink https://escholarship.org/uc/item/5pg186v8 Journal Standards in genomic sciences, 2(2) ISSN 1944-3277 Authors Lail, Kathleen Sikorski, Johannes Saunders, Elizabeth et al. Publication Date 2010-03-30 DOI 10.4056/sigs.741334 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Standards in Genomic Sciences (2010) 2:176-185 DOI:10.4056/sigs.741334 Complete genome sequence of Spirosoma linguale type strain (1T) Kathleen Lail1, Johannes Sikorski2, Elizabeth Saunders3, Alla Lapidus1, Tijana Glavina Del Rio1, Alex Copeland1, Hope Tice1, Jan-Fang Cheng1, Susan Lucas1, Matt Nolan1, David Bruce1,3, Lynne Goodwin1,3, Sam Pitluck1, Natalia Ivanova1, Konstantinos Mavromatis1, Galina Ovchinnikova1, Amrita Pati1, Amy Chen4, Krishna Palaniappan4, Miriam Land1,5, Loren Hauser1,5, Yun-Juan Chang1,5, Cynthia D. Jeffries1,5, Patrick Chain1,6, Thomas Brettin1,3, John C. Detter1,3, Andrea Schütze2, Manfred Rohde7, Brian J. Tindall2, Markus Göker2, Jim Bristow1, Jonathan A. Eisen1,8, Victor Markowitz4, Philip Hugenholtz1, Nikos C. Kyrpides1*, Hans-Peter Klenk2, and Feng Chen1 1 DOE Joint Genome Institute, Walnut Creek, California, USA 2 DSMZ – German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany 3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA 4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA 5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 6 Lawrence Livermore National Laboratory, Livermore, California, USA 7 HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany 8 University of California Davis Genome Center, Davis, California, USA *Corresponding author: Nikos C.
    [Show full text]
  • Fibrella Aestuarina Gen. Nov., Sp. Nov., a Filamentous Bacterium of the Family Cytophagaceae Isolated from a Tidal Flat, and Emended Description of the Genus Rudanella Weon Et Al. 2008
    Filippini, M; Svercel, M; Laczko, E; Kaech, A; Ziegler, U; Bagheri, H C (2011). Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008. International Journal of Systematic and Evolutionary Microbiology, 61(Pt 1):184-189. Postprint available at: University of Zurich http://www.zora.uzh.ch Zurich Open Repository and Archive Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: Winterthurerstr. 190 International Journal of Systematic and Evolutionary Microbiology 2011, 61(Pt 1):184-189. CH-8057 Zurich http://www.zora.uzh.ch Year: 2011 Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008 Filippini, M; Svercel, M; Laczko, E; Kaech, A; Ziegler, U; Bagheri, H C Filippini, M; Svercel, M; Laczko, E; Kaech, A; Ziegler, U; Bagheri, H C (2011). Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008. International Journal of Systematic and Evolutionary Microbiology, 61(Pt 1):184-189. Postprint available at: http://www.zora.uzh.ch Posted at the Zurich Open Repository and Archive, University of Zurich. http://www.zora.uzh.ch Originally published at: International Journal of Systematic and Evolutionary Microbiology 2011, 61(Pt 1):184-189. 1 Int. J. Syst. Evol. Microbiol. in press, PubMed ID 20190021 2 Fibrella aestuarina gen.
    [Show full text]
  • Pontibacter Locisalis Sy30t Sp. Nov. Isolated from Soil Collected from an Abandoned Saltern
    Antonie van Leeuwenhoek (2016) 109:415–420 DOI 10.1007/s10482-016-0646-0 ORIGINAL PAPER Pontibacter locisalis Sy30T sp. nov. isolated from soil collected from an abandoned saltern Yan-Xia Zhou . Zhi-Hong Xie . Jin-Xin Zhao . Zong-Jun Du . Guan-Jun Chen Received: 26 June 2015 / Accepted: 4 January 2016 / Published online: 29 January 2016 Ó Springer International Publishing Switzerland 2016 Abstract A novel Gram-stain negative, red, rod- phenotypic, chemotaxonomic and phylogenetic anal- shaped, non-motile and aerobic bacterial strain, desig- ysis, strain Sy30T represents a novel species of the nated Sy30T, was isolated from dry soils of an genus Pontibacter in the family Cytophagaceae, abandoned marine saltern at Weihai, China. 16S rRNA phylum Bacteroidetes, for which the name Pontibacter sequence analysis indicated that strain Sy30T belongs locisalis sp. nov. is proposed. The type strain is Sy30T to the genus Pontibacter in the family Cytophagaceae, (=KCTC 42498T = CICC AB 2015060T). with sequence similarities ranging from 93.3 to 96.4 % with other type species of the genus Pontibacter. The Keywords Pontibacter locisalis Á 16S rRNA gene predominant cellular fatty acids were iso-C15:0 and sequence Á Polyphasic taxonomy summed feature 4 (iso-C17:1 I and/or anteiso-C17:1 B). The major menaquinone was MK-7. The major polyamine was sym-homospermidine. The DNA G?C content was 47.7 mol%. The major polar lipids Introduction consisted of phosphatidylethanolamine, phospho- aminolipid and two unidentified polar lipid. Based on The genus Pontibacter belongs to the family Cytopha- gaceae within the phylum Bacteroidetes, and was first described by Nedashkovskaya et al.
    [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]