DOCSLIB.ORG

Polaromonas Eurypsychrophila Sp. Nov., Isolated from an Ice Core

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Polaromonas Eurypsychrophila Sp. Nov., Isolated from an Ice Core International Journal of Systematic and Evolutionary Microbiology (2016), 66, 2497–2501 DOI 10.1099/ijsem.0.001079 Polaromonas eurypsychrophila sp. nov., isolated from an ice core Tingting Xing,1 Tandong Yao,2,3 Yongqin Liu,2,3 Ninglian Wang,2,4 Bainqing Xu,2,3 Liang Shen,1 Zhengquan Gu,1 Bixi Gu,1 Hongcan Liu5 and Yuguang Zhou5 Correspondence 1Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Yongqin Liu Chinese Academy of Sciences, Beijing 100101, China [email protected] 2CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing 100101, China 3Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing 100101, China 4College of Urban and Environmental Science, Northwest University, Xi’an 710000, China 5Institute of Microbiology, China General Microbiological Culture Collection Center, Chinese Academy of Sciences, Beijing 100101, China A Gram-stain-negative, aerobic, rod-shaped, beige bacterium, strain B717-2T, was isolated from an ice core drilled from Muztagh Glacier on the Tibetan Plateau, China. According to phylogenetic analyses based on 16S rRNA gene sequences, the novel strain was related most closely to Polaromonas vacuolataand shared 97.7 % similarity with the type strain of this species. It grew optimally at pH 7, at 15 C and with 2 % (w/v) NaCl. Major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The major fatty acids were summed feature 3 (C16 : 1!7c and/or iso-C15 : 0 2-OH), summed feature 8 (C18 : 1!7c, C18 : 1!6c) and C16 : 0. The sole respiratory quinone was Q-8. The DNA G+C content was 63.4 mol %. In DNA–DNA hybridization tests, strain B717-2T shared 37.0±1.9, 30.0±1.7, 26.0±0.9, 23.4±0.5 and 18.4±1.9 % DNA–DNA relatedness with Polaromonas jejuensisJS12-13T, P. vacuolata 34-PT, Polaromonas aquatica CCUG 39402T, Polaromonas glacialisCr4-12T and Polaromonas cryoconitiCr4-35T, respectively. Based on the phenotypic, phylogenetic and genetic characteristics, strain B717-2T represents a novel species of the genus Polaromonas, for which the name Polaromonaseurypsychrophila sp. nov. is proposed. The type strain is B717- 2T (=CGMCC 1.15322T=JCM 31171T). The genus Polaromonas was first proposed by Irgens et al. (Irgens et al., 1996), tap water (K€ampfer et al., 2006), soil (1996) for a psychrophilic, marine bacterium isolated from (Weon et al., 2008; Sizova & Panikov, 2007), sediment Antarctica, Polaromonas vacuolata. At the time of writing, (Jeon et al., 2004) and glacier cryoconite (Margesin et al., this genus comprised seven recognized species: Polaromonas 2012). A novel bacterial strain, B717-2T, was isolated from naphthalenivorans (Jeon et al., 2004), Polaromonas aquatica an ice core at a depth of 38 m. The whole ice core was € (Kampfer et al., 2006), Polaromonas hydrogenivorans (Sizova 120 m in length drilled from Muztagh Glacier (83.7 E & Panikov, 2007), Polaromonas jejuensis (Weon et al., 26.4 N) on the Tibetan Plateau, China. Climate on the gla- 2008), Polaromonas glacialis (Margesin et al., 2012), Polaro- cier is extremely cold. Therefore, bacteria recovered from monas cryoconiti (Margesin et al., 2012) and the type species, P. vacuolata (Irgens et al., 1996). this area may survive in an inactive state at low temperature. The taxonomic position of the novel strain was investigated Members of the genus Polaromonas have been isolated from by using a polyphasic approach. various environmental sources, such as marine water The ice core was preserved at À20 C before analysis. The ice core was cut into 5 cm long sections using a band saw The GenBank/EMBL/DDJB accession number for the 16S rRNA gene within walk-in freezers. All samples were decontaminated sequence of strain B717-2T is KP013181. by cutting away an outer annulus of about 4 mm with a 001079 ã 2016 IUMS Printed in Great Britain 2497 Downloaded from www.microbiologyresearch.org by IP: 124.16.145.97 On: Sat, 08 Oct 2016 08:31:15 T. Xing and others sterilized saw tooth knife, before rinsing the remaining phylogenetic position of the novel strain was reconstructed inner cores with cold ethanol (95 %) and finally with cold by treeing using the software package MEGA 5.0.5 (Tamura autoclaved water. No particulate sterile suits were worn et al., 2011). A phylogenetic tree was reconstructed using the during the sampling process. All work was done in a sterile neighbour-joining and maximum-likelihood methods with operating room. The samples were then melted in sterile bootstrap values based on 1000 replications (Fig. 1). In the Nalgene bottles at 4 C. We subsequently incubated 200 µl neighbour-joining phylogenetic tree, strain B717-2T formed of meltwater at 4 C for 30 days on an R2A agar plate (con- a distinct cluster in a phyletic line with P. vacuolata 34-PT, taining 0.05 % yeast extract, 0.05 % peptone, 0.05 % Casa- and the maximum-likelihood tree displayed a similar topol- mino acids, 0.05 % glucose, 0.05 % starch, 0.03 % sodium ogy (Fig. 1). DNA–DNA hybridization experiments were pyruvate, 0.03 % K2HPO4, 0.005 % MgSO4, 1.5 % agar; pH carried out applying the optical renaturation method (De 7.2) (Reasoner & Geldreich, 1985), and several bacterial col- Ley et al., 1970; Huß et al., 1983; Jahnke, 1992). The geno- onies were recovered. mic DNA G+C content of strain B717-2T, which was esti- mated from the midpoint value (T ) of the thermal DNA of the novel strain was extracted according to the m denaturation profile, was 63.4 mol% (Mandel et al., 1970). method of Marmur (1961) from cells grown on R2A agar The temperature used in the optical renaturation method for 10 days at 15 C. Purity was assessed using a NanoDrop was 79 C. Mean levels of DNA–DNA relatedness between spectrophotometer (2000c; Thermo). PCR amplification strain B717-2T and P. jejuensis JS12-13T, P. vacuolata 34-PT, was via universal primers 27F (5¢-AGAGTTTGATCCTGGC P. aquatica CCUG 39402T, P. glacialis Cr4-12T and P. cryoco- TCAG-3¢) and 1492R (5¢-CGGTTACCTTGTTACGACTT- niti Cr4-35T were 37.0±1.9, 30.0±1.7, 26.0±0.9, 23.4±0.5 3¢) (Embley, 1991), and the PCR products were sequenced and 18.4±1.9 %, respectively. These data again indicate that at Sangon using an ABI PRISM 3730xl sequencer. The strain B717-2T may represent a novel species of the genus sequence was then analysed against the GenBank database Polaromonas. with the BLAST program (NCBI) and EzBioCloud (http:// www.ezbiocloud.net/eztaxon) (Kim et al., 2012) to reveal To further determine the taxonomic position of the novel the most similar sequences deposited in GenBank. In isolate, a series of phenotypic and genotypic approaches comparisons with the type strains of Polaromonas species, were used. Cell morphology was examined by transmission strain B717-2T appeared to be related most closely to P. electron microscopy (JEM-1230; JEOL) (Fig. 2), using cells vacuolata 34-PT, with a 16S rRNA gene sequence similarity that had been grown on R2A agar at 15 C. Gram staining of 97.7 %, followed by similarities of 97.4, 97.4, 97.1 and and catalase activity tests were conducted according to the 97.1 % with P. jejuensis JS12-13T, P. aquatica CCUG 39402T, methods described by Smibert & Krieg (1994). Physiologi- P. glacialis Cr4-12T and P. cryoconiti Cr4-35T, respectively. cal and biochemical characteristics and other enzyme activ- Based on the threshold value of 98.65 % (Kim et al, 2014), ities were determined by using API 20E, API 20NE and strain B717-2T may thus represent a novel species. The API ZYM systems (bioMerieux) at 15 C. All tests were 63 Variovorax boronicumulans BAM-48 T(AB 300597) 64 Variovorax paradoxus IAM 12373T(D 88006) 0.01 99 Variovorax ginsengisoli Gsoil 3165 T(AB 245358) Variovorax defluvii 2C1-b T (HQ 385753) 86 88 Variovorax soli GH 9-3T(DQ 432053) Pseudorhodoferax aquiterrae NAFc-7T(GU 721026) T 100 Pseudorhodoferax caeni SB1 (AJ 606333) 100 Pseudorhodoferax soli TBEA3T(EU 825700) 98 B717-2T(KP 013181) Polaromonas vacuolata 34-PT(U 14585) T 100 Polaromonas jejuensis JS12-13 (EU 030285) Polaromonas cryoconiti Cr4-35 T(HM 583567) 42 Polaromonas glacialis Cr4-12T(HM 583568) 87 T 49 Polaromonas hydrogenivorans DSM 17735 (DQ 094183) 100 Polaromonas naphthalenivorans CJ2T(CP 000529) Roseateles terrae CCUG 52222T(AM 501445) Fig. 1. Neighbour-joining phylogenetic tree, based on 16S rRNA gene sequences, showing the position of strain B717-2T. Numbers at nodes indicate bootstrap percentages (based on 1000 replications). Bar, 0.01 accumulated changes per nucleo- tide. Filled circles indicate that the corresponding nodes were also obtained in the maximum-likelihood tree. 2498 International Journal of Systematic and Evolutionary Microbiology 66 Downloaded from www.microbiologyresearch.org by IP: 124.16.145.97 On: Sat, 08 Oct 2016 08:31:15 Polaromonas eurypsychrophila sp. nov. carried out simultaneously with strain B717-2T and the seven reference strains. P. vacuolata 34-PT, P. aquatica CCUG 39402T, P. hydrogenivorans DSM 17735T and P. jejuensis JS12-13T were obtained from China General Microbiological Culture Collection Center, while P. naph- thalenivorans CJ2T, P. glacialis Cr4-12T and P. cryoconiti Cr4-35T were obtained from Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures. Growth at various temperatures (0–35 C) was tested in R2A broth at increments of 5 C. The pH range (5.0–11.0) for growth was determined in R2A broth at 15 C. The pH values of <6, 6–9 and >9 were obtained by using sodium acetate/acetic acid, Tris/HCl and Na2CO3 buffers, respec- tively.
Load more

Recommended publications
  • Novel Copper-Containing Membrane Monooxygenases (Cummos) Encoded by Alkane- Utilizing Betaproteobacteria
    Lawrence Berkeley National Laboratory Recent Work Title Novel copper-containing membrane monooxygenases (CuMMOs) encoded by alkane- utilizing Betaproteobacteria. Permalink https://escholarship.org/uc/item/8z48x96q Journal The ISME journal, 14(3) ISSN 1751-7362 Authors Rochman, Fauziah F Kwon, Miye Khadka, Roshan et al. Publication Date 2020-03-01 DOI 10.1038/s41396-019-0561-2 Peer reviewed eScholarship.org Powered by the California Digital Library University of California 1 1 2 1Novel copper-containing membrane monooxygenases 2(CuMMOs) encoded by alkane-utilizing Betaproteobacteria 3 4Running title: Novel CuMMOs in Betaproteobacteria 5 6Fauziah F. Rochman1, Miye Kwon2, Roshan Khadka1, Ivica Tamas1,3, Azriel 7Abraham Lopez-Jauregui1,4, Andriy Sheremet1, Angela Smirnova1, Rex R. 8Malmstrom5, Sukhwan Yoon2, Tanja Woyke5, Peter F. Dunfield1*, Tobin J. 9Verbeke1 10 111 Department of Biological Sciences, University of Calgary, 2500 University 12Dr. NW Calgary AB Canada T2N 1N4 132 Department of Civil and Environmental Engineering, Korea Advanced 14Institute of Science and Technology, Daejeon, Korea 153Department of Biology and Ecology, University of Novi Sad Novi Sad, Serbia 164 Instituto Tecnologico y de Estudios Superiores de Monterrey, Chihuahua, 17Mexico 185 Department of Energy Joint Genome Institute, Walnut Creek, California, 19USA. 20 21*Corresponding author: [email protected]; 403-220-2469 22 3 2 4 23Competing interests: The authors declare that they have no competing 24interests. 5 3 6 25Abstract 26Copper-containing membrane monooxygenases (CuMMOs) are encoded by 27xmoCAB(D) gene clusters and catalyze the oxidation of methane, ammonia, 28or some short chain alkanes and alkenes. In a metagenome constructed from 29an oilsands tailings pond we detected an xmoCABD gene cluster with <59% 30derived amino acid identity to genes from known bacteria.
    [Show full text]
  • Virulence Determinants, Drug Resistance and Mobile Genetic
    Lau et al. Cell & Bioscience 2011, 1:17 http://www.cellandbioscience.com/content/1/1/17 Cell & Bioscience RESEARCH Open Access Virulence determinants, drug resistance and mobile genetic elements of Laribacter hongkongensis: a genome-wide analysis Susanna KP Lau1,2,3,4*†, Gilman KM Wong4†, Alan KL Tsang4†, Jade LL Teng4, Rachel YY Fan4, Herman Tse1,2,3,4, Kwok-Yung Yuen1,2,3,4 and Patrick CY Woo1,2,3,4* Abstract Background: Laribacter hongkongensis is associated with community-acquired gastroenteritis and traveler’s diarrhea. In this study, we performed an in-depth annotation of the genes in its genome related to the various steps in the infective process, drug resistance and mobile genetic elements. Results: For acid and bile resistance, L. hongkongensis possessed a urease gene cassette, two arc gene clusters and bile salt efflux systems. For intestinal colonization, it possessed a putative adhesin of the autotransporter family homologous to those of diffusely adherent Escherichia coli (E. coli) and enterotoxigenic E. coli. To evade from host defense, it possessed superoxide dismutase and catalases. For lipopolysaccharide biosynthesis, it possessed the same set of genes that encode enzymes for synthesizing lipid A, two Kdo units and heptose units as E. coli, but different genes for its symmetrical acylation pattern, and nine genes for polysaccharide side chains biosynthesis. It contained a number of CDSs that encode putative cell surface acting (RTX toxin and hemolysins) and intracellular cytotoxins (patatin-like proteins) and enzymes for invasion (outer membrane phospholipase A). It contained a broad variety of antibiotic resistance-related genes, including genes related to b-lactam (n = 10) and multidrug efflux (n = 54).
    [Show full text]
  • Isolation, Characterization, and Applications of Rhizobiophages
    University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2014-10-02 Isolation, characterization, and applications of rhizobiophages Halmillawewa, Anupama Halmillawewa, A. (2014). Isolation, characterization, and applications of rhizobiophages (Unpublished doctoral thesis). University of Calgary, Calgary, AB. doi:10.11575/PRISM/26680 http://hdl.handle.net/11023/1912 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Isolation, characterization, and applications of rhizobiophages by Anupama P. Halmillawewa A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF BIOLOGICAL SCIENCES CALGARY, ALBERTA AUGUST, 2014 © Anupama Halmillawewa 2014 Abstract Rhizobiophages are the group of bacteriophages that infect rhizobia. The rhizobia constitute a bacterial group that includes members of several different genera and are capable of nodulating legume plant roots, and providing a source of fixed nitrogen for the plant. Rhizobiophages can play a vital role in the Rhizobium-legume symbiosis by altering the population dynamics of the rhizobia present in the rhizosphere, which can be used in agriculture to improve the efficacy of commercial Rhizobium inoculants and mitigate the Rhizobium competition problem. As a prerequisite for the application of such technology, a thorough understanding of rhizobiophage biology is required.
    [Show full text]
  • Microbial Ecology of Full-Scale Wastewater Treatment Systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi
    www.nature.com/scientificreports OPEN Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Received: 28 November 2017 Accepted: 21 January 2018 Bacteria and Fungi Published: xx xx xxxx Alejandro Gonzalez-Martinez1, Maija Sihvonen1, Barbara Muñoz-Palazon2, Alejandro Rodriguez-Sanchez2, Anna Mikola1 & Riku Vahala1 Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in infuent and bioreactors were classifed as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassifed Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All infuents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors. Undoubtedly, microbial ecology of bioprocesses is a factor of major importance for the functioning of biopro- cesses, especially wastewater treatment (WWT) systems1.
    [Show full text]
  • Ecogenomics and Genome Landscapes of Marine Pseudoalteromonas Phage H105/1
    The ISME Journal (2010), 1–15 & 2010 International Society for Microbial Ecology All rights reserved 1751-7362/10 $32.00 www.nature.com/ismej ORIGINAL ARTICLE Ecogenomics and genome landscapes of marine Pseudoalteromonas phage H105/1 Melissa Beth Duhaime1,2, Antje Wichels3, Jost Waldmann1, Hanno Teeling1 and Frank Oliver Glo¨ckner1,2 1Microbial Genomics Group, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, Bremen, Germany; 2School of Engineering and Sciences, Jacobs University, Bremen, Germany and 3Biosciences Division, Alfred Wegener Institute for Polar and Marine Research, BAH, Helgoland, Germany Marine phages have an astounding global abundance and ecological impact. However, little knowledge is derived from phage genomes, as most of the open reading frames in their small genomes are unknown, novel proteins. To infer potential functional and ecological relevance of sequenced marine Pseudoalteromonas phage H105/1, two strategies were used. First, similarity searches were extended to include six viral and bacterial metagenomes paired with their respective environmental contextual data. This approach revealed ‘ecogenomic’ patterns of Pseudoalteromo- nas phage H105/1, such as its estuarine origin. Second, intrinsic genome signatures (phylogenetic, codon adaptation and tetranucleotide (tetra) frequencies) were evaluated on a resolved intra- genomic level to shed light on the evolution of phage functional modules. On the basis of differential codon adaptation of Phage H105/1 proteins to the sequenced Pseudoalteromonas spp., regions of the phage genome with the most ‘host’-adapted proteins also have the strongest bacterial tetra signature, whereas the least ‘host’-adapted proteins have the strongest phage tetra signature. Such a pattern may reflect the evolutionary history of the respective phage proteins and functional modules.
    [Show full text]
  • Dynamics of Bacterial Communities in Two Unpolluted Soils After Spiking with Phenanthrene: Soil Type Specific and Common Responders
    ORIGINAL RESEARCH ARTICLE published: 21 August 2012 doi: 10.3389/fmicb.2012.00290 Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders Guo-Chun Ding, Holger Heuer and Kornelia Smalla* Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Braunschweig, Germany Edited by: Considering their key role for ecosystem processes, it is important to understand the Matthew Fields, Montana State response of microbial communities in unpolluted soils to pollution with polycyclic aro- University, USA matic hydrocarbons (PAH). Phenanthrene, a model compound for PAH, was spiked to a Reviewed by: Uwe Strotmann, Fachhochschule Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and con- Gelsenkirchen, Germany trol soils collected on days 0, 21, and 63 were analyzed based on PCR-amplified 16S Yingying Wang, Nankai University, rRNA gene fragments. Denaturing gradient gel electrophoresis (DGGE) fingerprints of China bacterial communities increasingly deviated with time between spiked and control soils. *Correspondence: In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacte- Kornelia Smalla, Julius Kühn-Institut, Federal Research Centre for ria became only detectable after 63 days, while significant effects on Betaproteobacteria Cultivated Plants, Messeweg 11-12, were detectable in both soils after 21 days. Comparison of the taxonomic distribution of D-38104 Braunschweig, Germany. bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil e-mail: [email protected] type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta-, or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils.
    [Show full text]
  • Gene Transfers from Diverse Bacteria Compensate for Reductive Genome Evolution in the Chromatophore of Paulinella Chromatophora
    Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora Eva C. M. Nowacka,b,1, Dana C. Pricec, Debashish Bhattacharyad, Anna Singerb, Michael Melkoniane, and Arthur R. Grossmana aDepartment of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; bDepartment of Biology, Heinrich-Heine-Universität Düsseldorf, 40225 Dusseldorf, Germany; cDepartment of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; dDepartment of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; and eBiozentrum, Universität zu Köln, 50674 Koln, Germany Edited by John M. Archibald, Dalhousie University, Halifax, Canada, and accepted by Editorial Board Member W. Ford Doolittle September 6, 2016 (received for review May 19, 2016) Plastids, the photosynthetic organelles, originated >1 billion y ago horizontal gene transfers (HGTs) from cooccurring intracellular via the endosymbiosis of a cyanobacterium. The resulting prolifer- bacteria also supplied genes that facilitated plastid establishment ation of primary producers fundamentally changed global ecology. (6). However, the extent and sources of HGTs and their impor- Endosymbiotic gene transfer (EGT) from the intracellular cyanobac- tance to organelle evolution remain controversial topics (7, 8). terium to the nucleus is widely recognized as a critical factor in the The chromatophore of the cercozoan amoeba Paulinella evolution of photosynthetic eukaryotes. The contribution of hori- chromatophora (Rhizaria) represents the only known case of zontal gene transfers (HGTs) from other bacteria to plastid estab- acquisition of a photosynthetic organelle other than the primary lishment remains more controversial. A novel perspective on this endosymbiosis that gave rise to the Archaeplastida (9).
    [Show full text]
  • Polaromonas Vacuolata Gen
    INTERNATIONALJOURNAL OF SYSTEMATICBACTERIOLOGY, July 1996, p. 822-826 Vol. 46, No. 3 0020-7713/96/$04.00+0 Copyright 0 1996, International Union of Microbiological Societies Polaromonas vacuolata gen. nov., sp. nov., a Psychrophilic, Marine, Gas Vacuolate Bacterium from Antarctica R. L. IRGENS, J. J. GOSINK, AND J. T. STALEY" Department of Microbiology (357242), University of Washington, Seattle, Washington 981 95 Several strains of a novel heterotrophic gas vacuolate bacterium were isolated from antarctic marine waters. The results of phylogenetic analyses in which 16s ribosomal DNA sequencing was used, coupled with pheno- typic tests, indicated that strain 34-PT (T = type strain) belongs to a new genus and species of the beta subgroup of the Proteobacteria, for which the name Polaromonas vacuolutu is proposed. Although the other four strains studied probably belong to this new species, DNA-DNA hybridization tests were not conducted. The closest phylogenetic relatives of P. vacuolata are the photosynthetic nonsulfur purple bacterium Rhoduferax fernentans and the hydrogen autotroph Vuriovorax puradoms. Although gas vacuolate heterotrophic bacteria are well- ATCC 1701lT (D16213), Brachymonas denitrificans JCM known inhabitants of aquatic ecosystems, until recently none of 9216T (D14320), Comamonas testosteroni ATCC 11996T these organisms had been observed in or isolated from marine (M11224), Stripa-derived bacterium (L2081l), Variovorax habitats. In 1989 several types of gas vacuolate bacteria were paradoxus IAM 12373T (D30793), str. PAD44 (D26231), Rho- found in Antarctica growing in association with the sea ice doferax fermentans JCM 781gT (D16211), Alcaligenes faecalis microbial community (9, 13). Sequencing and analyses of 16s ATCC 8750T (M22508), and Bordetella parapertussis ATCC ribosomal DNAs (rDNAs) of a variety of these Antarctic gas 15311T (U04949).
    [Show full text]
  • Microbial Oxidation of Arsenite in a Subarctic
    Osborne et al. BMC Microbiology 2010, 10:205 http://www.biomedcentral.com/1471-2180/10/205 RESEARCH ARTICLE Open Access Microbial oxidation of arsenite in a subarctic environment: diversity of arsenite oxidase genes and identification of a psychrotolerant arsenite oxidiser Thomas H Osborne1, Heather E Jamieson2, Karen A Hudson-Edwards3, D Kirk Nordstrom4, Stephen R Walker2, Seamus A Ward5, Joanne M Santini1* Abstract Background: Arsenic is toxic to most living cells. The two soluble inorganic forms of arsenic are arsenite (+3) and arsenate (+5), with arsenite the more toxic. Prokaryotic metabolism of arsenic has been reported in both thermal and moderate environments and has been shown to be involved in the redox cycling of arsenic. No arsenic metabolism (either dissimilatory arsenate reduction or arsenite oxidation) has ever been reported in cold environments (i.e. < 10°C). Results: Our study site is located 512 kilometres south of the Arctic Circle in the Northwest Territories, Canada in an inactive gold mine which contains mine waste water in excess of 50 mM arsenic. Several thousand tonnes of arsenic trioxide dust are stored in underground chambers and microbial biofilms grow on the chamber walls below seepage points rich in arsenite-containing solutions. We compared the arsenite oxidisers in two subsamples (which differed in arsenite concentration) collected from one biofilm. ‘Species’ (sequence) richness did not differ between subsamples, but the relative importance of the three identifiable clades did. An arsenite-oxidising bacterium (designated GM1) was isolated, and was shown to oxidise arsenite in the early exponential growth phase and to grow at a broad range of temperatures (4-25°C).
    [Show full text]
  • Gene Transfers from Diverse Bacteria Compensate for Reductive Genome Evolution in the Chromatophore of Paulinella Chromatophora
    Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora Eva C. M. Nowacka,b,1, Dana C. Pricec, Debashish Bhattacharyad, Anna Singerb, Michael Melkoniane, and Arthur R. Grossmana aDepartment of Plant Biology, Carnegie Institution for Science, Stanford, CA 94305; bDepartment of Biology, Heinrich-Heine-Universität Düsseldorf, 40225 Dusseldorf, Germany; cDepartment of Plant Biology and Pathology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; dDepartment of Ecology, Evolution and Natural Resources, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901; and eBiozentrum, Universität zu Köln, 50674 Koln, Germany Edited by John M. Archibald, Dalhousie University, Halifax, Canada, and accepted by Editorial Board Member W. Ford Doolittle September 6, 2016 (received for review May 19, 2016) Plastids, the photosynthetic organelles, originated >1 billion y ago horizontal gene transfers (HGTs) from cooccurring intracellular via the endosymbiosis of a cyanobacterium. The resulting prolifer- bacteria also supplied genes that facilitated plastid establishment ation of primary producers fundamentally changed global ecology. (6). However, the extent and sources of HGTs and their impor- Endosymbiotic gene transfer (EGT) from the intracellular cyanobac- tance to organelle evolution remain controversial topics (7, 8). terium to the nucleus is widely recognized as a critical factor in the The chromatophore of the cercozoan amoeba Paulinella evolution of photosynthetic eukaryotes. The contribution of hori- chromatophora (Rhizaria) represents the only known case of zontal gene transfers (HGTs) from other bacteria to plastid estab- acquisition of a photosynthetic organelle other than the primary lishment remains more controversial. A novel perspective on this endosymbiosis that gave rise to the Archaeplastida (9).
    [Show full text]
  • Prezentace Aplikace Powerpoint
    Figure S2. Microarray comparisons of bacterial communities between PW and UP water (A), PW water and PW ETBE- enrichments (B), UP water and UP ETBE-enrichments (C), and PW ETBE-enrichments and UW ETBE-enrichments (D). The probes whose signals cumulatively contributed to up to 50% differences in bacterial community composition between each pair of compaired groups according to SIMPER and statistically differed between the two groups according to Wilcoxon rank sum tests (P < 0.05), are shown together with their targets. The probe signal intensities are indicated by a heatmap. A Taxonomical affiliation Probe target Probe PW_VI/08 PW_XI/08 PW_III/09 PW_IV/09 UW_VI/08 UW_XI/08 UW_III/09 UW_IV/09 Alphaproteobacteria Rhizobiaceae, Brucellaceae, Bartonella, Phyllobacteriaceae, Rzbc1247 0,0 0,9 0,7 0,9 3,3 2,2 3,1 2,9 Blastochloris, Azospirillum irakense and amazonense Agrobacterium genomospecies G1, G3, G4, and G7, A. rubi, A. B6-603 0,0 0,0 0,0 0,0 1,4 0,7 1,4 1,8 larrymoorei, some Rhizobium and some Brevundimonas Xanthobacter Xan 0,0 0,0 0,0 0,0 2,1 1,0 1,4 1,7 Cowdria Cow1 1,8 1,5 1,3 1,3 3,5 2,1 3,1 2,9 Betaproteobacteria Azoarcus Arcus1 1,8 1,1 4,8 4,0 0,0 0,0 0,0 0,0 Azoarcus Arcus2 2,5 1,5 5,4 4,3 0,0 0,0 0,0 0,0 few Azoarcus spp. AZA463 1,8 0,7 4,5 2,9 0,0 0,0 0,0 0,0 Most Nitrosospira Nit1A 2,3 3,2 4,1 3,0 0,8 0,6 1,0 0,0 Some Nitrosospira Nit1C 4,4 5,9 6,5 6,0 1,7 4,2 3,2 1,9 Acidovorax cattleyae, Acidovorax citrulli, Acidovorax avenae Acave3 1,5 1,7 3,2 2,5 0,0 0,0 0,7 0,0 Acidovorax cattleyae, Acidovorax citrulli, Acidovorax avenae
    [Show full text]
  • Microbiota Assembly and Dissolved Organic Matter Diversity in Natural Mineral Waters Celine C
    Lesaulnier et al. Microbiome (2017) 5:126 DOI 10.1186/s40168-017-0344-9 RESEARCH Open Access Bottled aqua incognita: microbiota assembly and dissolved organic matter diversity in natural mineral waters Celine C. Lesaulnier1†, Craig W. Herbold1†, Claus Pelikan1, David Berry1, Cédric Gérard4, Xavier Le Coz4, Sophie Gagnot4, Jutta Niggemann3, Thorsten Dittmar3, Gabriel A. Singer2† and Alexander Loy1* Abstract Background: Non-carbonated natural mineral waters contain microorganisms that regularly grow after bottling despite low concentrations of dissolved organic matter (DOM). Yet, the compositions of bottled water microbiota and organic substrates that fuel microbial activity, and how both change after bottling, are still largely unknown. Results: We performed a multifaceted analysis of microbiota and DOM diversity in 12 natural mineral waters from six European countries. 16S rRNA gene-based analyses showed that less than 10 species-level operational taxonomic units (OTUs) dominated the bacterial communities in the water phase and associated with the bottle wall after a short phase of post-bottling growth. Members of the betaproteobacterial genera Curvibacter, Aquabacterium, and Polaromonas (Comamonadaceae) grew in most waters and represent ubiquitous, mesophilic, heterotrophic aerobes in bottled waters. Ultrahigh-resolution mass spectrometry of DOM in bottled waters and their corresponding source waters identified thousands of molecular formulae characteristic of mostly refractory, soil-derived DOM. Conclusions: The bottle environment, including source water physicochemistry, selected for growth of a similar low-diversity microbiota across various bottled waters. Relative abundance changes of hundreds of multi-carbon molecules were related to growth of less than ten abundant OTUs. We thus speculate that individual bacteria cope with oligotrophic conditions by simultaneously consuming diverse DOM molecules.
    [Show full text]