DOCSLIB.ORG

Chryseobacterium Oleae Sp. Nov., an Efficient Plant

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Chryseobacterium Oleae Sp. Nov., an Efficient Plant Systematic and Applied Microbiology 37 (2014) 342–350 Contents lists available at ScienceDirect Systematic and Applied Microbiology j ournal homepage: www.elsevier.de/syapm Short communication Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense a,b,∗∗ a c Maria del Carmen Montero-Calasanz , Markus Göker , Manfred Rohde , a a d e Cathrin Spröer , Peter Schumann , Hans-Jürgen Busse , Michael Schmid , a a,∗ b Hans-Peter Klenk , Brian J. Tindall , Maria Camacho a Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany b IFAPA-Instituto de Investigación y Formación Agraria y Pesquera, Centro Las Torres-Tomejil, Ctra, Sevilla-Cazalla de la Sierra, Km 12.2, Alcalá del Río, 41200 Sevilla, Spain c HZI – Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany d Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria e Research Unit Microbe-Plant Interactions, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany a r t i c l e i n f o a b s t r a c t T Article history: A novel non-motile, Gram-staining-negative, yellow-pigmented bacterium, designated CT348 , isolated Received 5 November 2013 from the ectorhizosphere of an organic olive tree in Spain and characterised as an efficient plant growth Received in revised form 21 February 2014 promoting bacterium, was investigated to determine its taxonomic status. The isolate grew best in a Accepted 22 April 2014 ◦ temperature range of 5–35 C, at pH 5.0–8.0 and with 0–1% (w/v) NaCl. Chemotaxonomic and molecular characteristics of the isolate matched those described for members of the genus Chryseobacterium. The Keywords: DNA G + C content of the novel strain was 38.2 mol%. The strain contained a polyamine pattern with Bacteriodetes sym-homospermidine as the major compound and produced flexirubin-type pigments. MK-6 was the Flavobacteriaceae ␻ Taxonomy dominant menaquinone and the major cellular fatty acids were iso-C15:0, C17:1 9c, iso-C17:0 3-OH and PGPB iso-C15:0 2-OH. The main polar lipids were phosphatidylethanolamine and several unidentified lipids and Indole-3-acetic acid aminolipids. The 16S rRNA gene showed 92.2–97.8% sequence identity with the members of the genus Chyseobacterium. Based on the phenotypic traits and DNA–DNA hybridizations with the type strains of the most closely related species, the isolate is shown to represent a novel species, Chyseobacterium oleae, T type strain CT348 (=DSM 25575 =CCUG 63020). Emended descriptions of the genus Chryseobacterium and C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense are also proposed. © 2014 Elsevier GmbH. All rights reserved. The genus Chryseobacterium [58] whose type species is members of the genus Chryseobacterium based on the interpre- Chryseobacterium gleum [21,58] is included within the family tation of the list of all validly published names within this genus Flavobacteriaceae (emended by Bernardet et al. [4]), the main according to the “List of Prokaryotic Names with Standing in bacterial lineage in the phylum Bacteroidetes. At the time of writing Nomenclature” (http://www.bacterio.net/). Members of the genus 76 species with validly published names were considered to be Chryseobacterium can be found in a wide variety of environments, including freshwater [50], soil [32], rhizosphere [9], phyllosphere [3], sludge [43], fish [68–70], midgut of insects [26], raw dairy ∗ products [19], raw chicken [11], faeces of millipede [27], industrial Corresponding author. Tel.: +49 0531 26 16 224; fax: +49 0531 26 16 418. ∗∗ plants [20] and clinical samples [67]. Corresponding author. Tel.: +49 0531 26 16 210; fax: +49 0531 26 16 418. Based on previous studies, it is known that members of the E-mail addresses: [email protected] (M.d.C. Montero-Calasanz), [email protected] (B.J. Tindall). genus Chryseobacterium are considered to be an important bacterial http://dx.doi.org/10.1016/j.syapm.2014.04.004 0723-2020/© 2014 Elsevier GmbH. All rights reserved. M.d.C. Montero-Calasanz et al. / Systematic and Applied Microbiology 37 (2014) 342–350 343 group associated with plants [1,7,31] and currently there is strong were performed as described in Tindall et al. [55]. The utilisation evidence to show that strains of plant-associated Chryseobacterium of carbon compounds and acid production were determined using species exhibit plant-growth promoting activities [10,38]. API 20NE and API 20E strips (bioMérieux) according to the manu- ◦ During the characterisation of organisms isolated from the rhi- factures instructions, incubated at 28 C as well as using GEN III zosphere of an organically farmed olive grove (Olea europaea L. Microplates incubated in an Omnilog device (BIOLOG Inc., Hay- ◦ cv. arbequina) in Mairena del Aljarafe, Seville, Spain (37 20 18.97 ward, CA, USA). The GEN III Microplates were inoculated with a ◦ N, 6 5 8.61 W), in 2006, for application in alternative systems to cell suspension made in “gelling” inoculating fluid (IF) A at a cell T produce organically grown olive plants, strain CT348 was recov- density of 90% transmittance, yielding a running time of 4 days ◦ ered. This study based on a polyphasic approach in agreement with in Phenotype Microarray mode at 28 C. The exported data were the recommended minimal standards for describing new taxa of further analysed with the opm package for R [56,57] v.0.9.23., the family Flavobacteriaceae [4] refers the taxonomic position of using its functionality for merging subsequent measurements of a plant growth promoting bacterial (PGPB) strain representing a the same plate, statistically estimating parameters from the res- novel species within the genus Chryseobacterium isolated from the piration curves such as the maximum height, and automatically ectorhizosphere of an organically farmed olive tree. “discretizing” these values into negative and positive reactions. T Ectorhizospheric soil samples were suspended and Strain CT348 in comparison with the reference strains Chryseobac- T homogenised in sterile mineral buffer [59]. Serial dilutions terium daecheongense DSM 15235 , Chryseobacterium defluvii DSM TM T T were inoculated on Plate Count Agar (PCA; Difco ) diluted at 50% 14219 , Chryseobacterium gambrini DSM 18014 , Chryseobacterium T T supplemented with cycloheximide (100 mg/l), adjusted at pH 7.0, gleum DSM 16776 , Chryseobacterium gregarium DSM 19109 , Chry- ◦ T T at 28 C for 5 days. Strain CT348 was firstly isolated based on seobacterium indologenes DSM 16777 , Chryseobacterium joostei T T colony morphology, purified by sub-culturing on Trypticase Soy DSM 16927 , Chryseobacterium jejuense DSM 19299 , Chryseobac- TM T T Agar (TSA; Difco ) diluted at 10% and then selected by its ability terium luteum DSM 18605 , Chryseobacterium shigense DSM 17126 , T to produce indole-3-acetic acid (IAA) and siderophores, desirable Chryseobacterium taiwanense JCM 21767 , Chryseobacterium ure- T T PGPR features, and to promote rooting in model plants and olive ilyticum DSM 18017 Chryseobacterium vrystaatense DSM 25206 T cuttings [37]. The culture was suspended in 0.5% peptone and 15% and Chryseobacterium wanjuense DSM 17724 was just studied in ◦ (w/v) glycerol for storage at −80 C. the GEN III Microplates, in two independent determinations. Reac- T The colony morphology and pigmentation of strain CT348 tions that gave contradictory results between the two repetitions were observed on TSB agar after 24 and 72 h under a binocular were regarded as ambiguous. microscope according to Pelczar [42]. Exponentially growing bac- The extraction and analysis of cellular fatty acids was carried ◦ terial cultures were observed with an optical microscope (Zeiss out from biomass grown on TSA plates held at 28 C for 24 h and AxioScope A1) with a 100-fold magnification and phase-contrast harvested always from the same sector (the last quadrant streak). illumination. Micrographs of bacterial cells grown on Trypticase Analysis was conducted using the Microbial Identification System Soy Broth (TSB) for 48 h were taken with a field-emission scanning (MIDI) Sherlock Version 6.1 (results evaluated against the TSBA40 electron microscope (FE-SEM Merlin, Zeiss, Germany). Gram stain- peak naming table database) as described by Sasser [46]. The fatty ing was performed according to Halebian et al. [15] and checked by acid extracts obtained using the standard MIDI protocol were sub- the KOH test [14]. Anaerobic respiration was investigated by incu- jected to further analysis by GC–MS. GC–MS experiments were TM ◦ bation in an anaerobic pouch (Merck ) for 7 days at 28 C on 1% carried out using a Varian CP-3800 gas chromatograph, fitted with casitone, 0.3% yeast extract broth and 0.2% nitrate and 0.2% nitrite a Varian CP-8400 autosampler, coupled to a Varian 320-MS mass as terminal electron acceptors [65]. Activity of oxidase was ana- spectrometer. The gas chromatograph was fitted with a 30 m Varian lysed using filter-paper disks (Sartorius grade 388) impregnated VF-5 ms capillary column, internal diameter 0.25 mm, film thick- ◦ with 1% solution of N,N,N ,N -tetramethyl-p-phenylenediamine ness 0.25 ␮m. The run conditions were injector temperature 250 C, ◦ ◦ ◦ (Sigma–Aldrich); a positive test was indicated by the immediate transfer line 260 C, ion source 250 C, column temperature 130 C ◦ ◦ development of a blue-purple colour after applying biomass on the to 250 C at a rate of 4 C per minute, carrier gas helium at a con- filter paper. Catalase activity was tested by the observation of bub- stant flow rate of 1.3 ml/min.
Load more

Recommended publications
  • High Quality Permanent Draft Genome Sequence of Chryseobacterium Bovis DSM 19482T, Isolated from Raw Cow Milk
    Lawrence Berkeley National Laboratory Recent Work Title High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk. Permalink https://escholarship.org/uc/item/4b48v7v8 Journal Standards in genomic sciences, 12(1) ISSN 1944-3277 Authors Laviad-Shitrit, Sivan Göker, Markus Huntemann, Marcel et al. Publication Date 2017 DOI 10.1186/s40793-017-0242-6 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Laviad-Shitrit et al. Standards in Genomic Sciences (2017) 12:31 DOI 10.1186/s40793-017-0242-6 SHORT GENOME REPORT Open Access High quality permanent draft genome sequence of Chryseobacterium bovis DSM 19482T, isolated from raw cow milk Sivan Laviad-Shitrit1, Markus Göker2, Marcel Huntemann3, Alicia Clum3, Manoj Pillay3, Krishnaveni Palaniappan3, Neha Varghese3, Natalia Mikhailova3, Dimitrios Stamatis3, T. B. K. Reddy3, Chris Daum3, Nicole Shapiro3, Victor Markowitz3, Natalia Ivanova3, Tanja Woyke3, Hans-Peter Klenk4, Nikos C. Kyrpides3 and Malka Halpern1,5* Abstract Chryseobacterium bovis DSM 19482T (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. C. bovis is a member of the Flavobacteriaceae, a family within the phylum Bacteroidetes. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The C. bovis genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.
    [Show full text]
  • Table S5. the Information of the Bacteria Annotated in the Soil Community at Species Level
    Table S5. The information of the bacteria annotated in the soil community at species level No. Phylum Class Order Family Genus Species The number of contigs Abundance(%) 1 Firmicutes Bacilli Bacillales Bacillaceae Bacillus Bacillus cereus 1749 5.145782459 2 Bacteroidetes Cytophagia Cytophagales Hymenobacteraceae Hymenobacter Hymenobacter sedentarius 1538 4.52499338 3 Gemmatimonadetes Gemmatimonadetes Gemmatimonadales Gemmatimonadaceae Gemmatirosa Gemmatirosa kalamazoonesis 1020 3.000970902 4 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas indica 797 2.344876284 5 Firmicutes Bacilli Lactobacillales Streptococcaceae Lactococcus Lactococcus piscium 542 1.594633558 6 Actinobacteria Thermoleophilia Solirubrobacterales Conexibacteraceae Conexibacter Conexibacter woesei 471 1.385742446 7 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas taxi 430 1.265115184 8 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas wittichii 388 1.141545794 9 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas sp. FARSPH 298 0.876754244 10 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sorangium cellulosum 260 0.764953367 11 Proteobacteria Deltaproteobacteria Myxococcales Polyangiaceae Sorangium Sphingomonas sp. Cra20 260 0.764953367 12 Proteobacteria Alphaproteobacteria Sphingomonadales Sphingomonadaceae Sphingomonas Sphingomonas panacis 252 0.741416341
    [Show full text]
  • Structural Basis of Mammalian Mucin Processing by the Human Gut O
    ARTICLE https://doi.org/10.1038/s41467-020-18696-y OPEN Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila ✉ ✉ Beatriz Trastoy 1,4, Andreas Naegeli2,4, Itxaso Anso 1,4, Jonathan Sjögren 2 & Marcelo E. Guerin 1,3 Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness 1234567890():,; and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila,anO-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also con- tribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins. 1 Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain. 2 Genovis AB, Box 790, 22007 Lund, Sweden. 3 IKERBASQUE, Basque Foundation for Science, 48013 ✉ Bilbao, Spain. 4These authors contributed equally: Beatriz Trastoy, Andreas Naegeli, Itxaso Anso.
    [Show full text]
  • Emerging Flavobacterial Infections in Fish
    Journal of Advanced Research (2014) xxx, xxx–xxx Cairo University Journal of Advanced Research REVIEW Emerging flavobacterial infections in fish: A review Thomas P. Loch a, Mohamed Faisal a,b,* a Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, 174 Food Safety and Toxicology Building, Michigan State University, East Lansing, MI 48824, USA b Department of Fisheries and Wildlife, College of Agriculture and Natural Resources, Natural Resources Building, Room 4, Michigan State University, East Lansing, MI 48824, USA ARTICLE INFO ABSTRACT Article history: Flavobacterial diseases in fish are caused by multiple bacterial species within the family Received 12 August 2014 Flavobacteriaceae and are responsible for devastating losses in wild and farmed fish stocks Received in revised form 27 October 2014 around the world. In addition to directly imposing negative economic and ecological effects, Accepted 28 October 2014 flavobacterial disease outbreaks are also notoriously difficult to prevent and control despite Available online xxxx nearly 100 years of scientific research. The emergence of recent reports linking previously uncharacterized flavobacteria to systemic infections and mortality events in fish stocks of Keywords: Europe, South America, Asia, Africa, and North America is also of major concern and has Flavobacterium highlighted some of the difficulties surrounding the diagnosis and chemotherapeutic treatment Chryseobacterium of flavobacterial fish diseases. Herein, we provide a review of the literature that focuses on Fish disease Flavobacterium and Chryseobacterium spp. and emphasizes those associated with fish. Coldwater disease ª 2014 Production and hosting by Elsevier B.V. on behalf of Cairo University. Flavobacteriosis Mohamed Faisal D.V.M., Ph.D., is currently a Thomas P.
    [Show full text]
  • The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights Into the Evolution of Gene Structure and Organization
    microorganisms Article The Histidine Biosynthetic Genes in the Superphylum Bacteroidota-Rhodothermota-Balneolota-Chlorobiota: Insights into the Evolution of Gene Structure and Organization Sara Del Duca , Christopher Riccardi , Alberto Vassallo , Giulia Fontana, Lara Mitia Castronovo, Sofia Chioccioli and Renato Fani * Department of Biology, University of Florence, Via Madonna del Piano 6, Sesto Fiorentino, 50019 Florence, Italy; sara.delduca@unifi.it (S.D.D.); christopher.riccardi@unifi.it (C.R.); alberto.vassallo@unifi.it (A.V.); [email protected]fi.it (G.F.); [email protected] (L.M.C.); sofia.chioccioli@unifi.it (S.C.) * Correspondence: renato.fani@unifi.it; Tel.: +39-055-4574742 Abstract: One of the most studied metabolic routes is the biosynthesis of histidine, especially in enterobacteria where a single compact operon composed of eight adjacent genes encodes the complete set of biosynthetic enzymes. It is still not clear how his genes were organized in the genome of the last universal common ancestor community. The aim of this work was to analyze the structure, organization, phylogenetic distribution, and degree of horizontal gene transfer (HGT) of his genes in the Bacteroidota-Rhodothermota-Balneolota-Chlorobiota superphylum, a group of phylogenetically close bacteria with different surviving strategies. The analysis of the large variety of his gene structures and organizations revealed different scenarios with genes organized in more Citation: Del Duca, S.; Riccardi, C.; or less compact—heterogeneous or homogeneous—operons, in suboperons, or in regulons. The Vassallo, A.; Fontana, G.; Castronovo, organization of his genes in the extant members of the superphylum suggests that in the common L.M.; Chioccioli, S.; Fani, R.
    [Show full text]
  • Bacteria Associated with Vascular Wilt of Poplar
    Bacteria associated with vascular wilt of poplar Hanna Kwasna ( [email protected] ) Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu https://orcid.org/0000-0001- 6135-4126 Wojciech Szewczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Marlena Baranowska Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Jolanta Behnke-Borowczyk Poznan University of Life Sciences: Uniwersytet Przyrodniczy w Poznaniu Research Article Keywords: Bacteria, Pathogens, Plantation, Poplar hybrids, Vascular wilt Posted Date: May 27th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-250846/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/30 Abstract In 2017, the 560-ha area of hybrid poplar plantation in northern Poland showed symptoms of tree decline. Leaves appeared smaller, turned yellow-brown, and were shed prematurely. Twigs and smaller branches died. Bark was sunken and discolored, often loosened and split. Trunks decayed from the base. Phloem and xylem showed brown necrosis. Ten per cent of trees died in 1–2 months. None of these symptoms was typical for known poplar diseases. Bacteria in soil and the necrotic base of poplar trunk were analysed with Illumina sequencing. Soil and wood were colonized by at least 615 and 249 taxa. The majority of bacteria were common to soil and wood. The most common taxa in soil were: Acidobacteria (14.757%), Actinobacteria (14.583%), Proteobacteria (36.872) with Betaproteobacteria (6.516%), Burkholderiales (6.102%), Comamonadaceae (2.786%), and Verrucomicrobia (5.307%).The most common taxa in wood were: Bacteroidetes (22.722%) including Chryseobacterium (5.074%), Flavobacteriales (10.873%), Sphingobacteriales (9.396%) with Pedobacter cryoconitis (7.306%), Proteobacteria (73.785%) with Enterobacteriales (33.247%) including Serratia (15.303%) and Sodalis (6.524%), Pseudomonadales (9.829%) including Pseudomonas (9.017%), Rhizobiales (6.826%), Sphingomonadales (5.646%), and Xanthomonadales (11.194%).
    [Show full text]
  • Epidemiological and Phylogenetic Analysis Reveals Flavobacteriaceae As Potential Ancestral Source of Tigecycline Resistance Gene Tet(X)
    ARTICLE https://doi.org/10.1038/s41467-020-18475-9 OPEN Epidemiological and phylogenetic analysis reveals Flavobacteriaceae as potential ancestral source of tigecycline resistance gene tet(X) Rong Zhang 1,5, Ning Dong2,5, Zhangqi Shen3,5, Yu Zeng1, Jiauyue Lu1, Congcong Liu1, Hongwei Zhou1, Yanyan Hu1, Qiaoling Sun1, Qipeng Cheng2,4, Lingbing Shu1, Jiachang Cai1, Edward Wai-Chi Chan4, ✉ ✉ Gongxiang Chen 1 & Sheng Chen 2 1234567890():,; Emergence of tigecycline-resistance tet(X) gene orthologues rendered tigecycline ineffective as last-resort antibiotic. To understand the potential origin and transmission mechanisms of these genes, we survey the prevalence of tet(X) and its orthologues in 2997 clinical E. coli and K. pneumoniae isolates collected nationwide in China with results showing very low pre- valence on these two types of strains, 0.32% and 0%, respectively. Further surveillance of tet (X) orthologues in 3692 different clinical Gram-negative bacterial strains collected during 1994–2019 in hospitals in Zhejiang province, China reveals 106 (2.7%) tet(X)-bearing strains with Flavobacteriaceae being the dominant (97/376, 25.8%) bacteria. In addition, tet(X)s are found to be predominantly located on the chromosomes of Flavobacteriaceae and share similar GC-content as Flavobacteriaceae. It also further evolves into different orthologues and transmits among different species. Data from this work suggest that Flavobacteriaceae could be the potential ancestral source of the tigecycline resistance gene tet(X). 1 Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, ZhejiangHangzhou, China. 2 Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.
    [Show full text]
  • Apibacter Adventoris Gen. Nov., Sp. Nov., a Member of the Phylum Bacteroidetes Isolated from Honey Bees Waldan K
    International Journal of Systematic and Evolutionary Microbiology (2016), 66, 1323–1329 DOI 10.1099/ijsem.0.000882 Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees Waldan K. Kwong1,2 and Nancy A. Moran2 Correspondence 1Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA Waldan K. Kwong 2Department of Integrative Biology, University of Texas, Austin, TX, USA [email protected] Honey bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29–31 mol%. They had ,87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T (5NRRL B-65307T5NCIMB 14986T). Bacteria from the phylum Bacteroidetes are often constitu- In July and August of 2014, samples of the Asian honey bee ents of animal microbiotas.
    [Show full text]
  • Genome-Based Taxonomic Classification Of
    ORIGINAL RESEARCH published: 20 December 2016 doi: 10.3389/fmicb.2016.02003 Genome-Based Taxonomic Classification of Bacteroidetes Richard L. Hahnke 1 †, Jan P. Meier-Kolthoff 1 †, Marina García-López 1, Supratim Mukherjee 2, Marcel Huntemann 2, Natalia N. Ivanova 2, Tanja Woyke 2, Nikos C. Kyrpides 2, 3, Hans-Peter Klenk 4 and Markus Göker 1* 1 Department of Microorganisms, Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 Department of Energy Joint Genome Institute (DOE JGI), Walnut Creek, CA, USA, 3 Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia, 4 School of Biology, Newcastle University, Newcastle upon Tyne, UK The bacterial phylum Bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes from Bacteroidetes and closely related phyla for Edited by: assessing their taxonomy based on the principles of phylogenetic classification and Martin G. Klotz, Queens College, City University of trees inferred from genome-scale data. No significant conflict between 16S rRNA gene New York, USA and whole-genome phylogenetic analysis is found, whereas many but not all of the Reviewed by: involved taxa are supported as monophyletic groups, particularly in the genome-scale Eddie Cytryn, trees. Phenotypic and phylogenomic features support the separation of Balneolaceae Agricultural Research Organization, Israel as new phylum Balneolaeota from Rhodothermaeota and of Saprospiraceae as new John Phillip Bowman, class Saprospiria from Chitinophagia.
    [Show full text]
  • Diversity of Multidrug-Resistant Bacteria in an Urbanized River: a Case Study of the Potential Risks from Combined Sewage Overflows
    water Article Diversity of Multidrug-Resistant Bacteria in an Urbanized River: A Case Study of the Potential Risks from Combined Sewage Overflows Gabriella Balasa, Enjolie S. Levengood, Joseph M. Battistelli and Rima B. Franklin * Laboratory of Microbial Ecology, Department of Biology, Virginia Commonwealth University, 1000 West Cary Street, Richmond, VA 23284, USA; [email protected] (G.B.); [email protected] (E.S.L.); [email protected] (J.M.B.) * Correspondence: [email protected] Abstract: Wastewater contamination and urbanization contribute to the spread of antibiotic resistance in aquatic environments. This is a particular concern in areas receiving chronic pollution of untreated waste via combined sewer overflow (CSO) events. The goal of this study was to expand knowledge of CSO impacts, with a specific focus on multidrug resistance. We sampled a CSO-impacted seg- ment of the James River (Virginia, USA) during both clear weather and an active overflow event and compared it to an unimpacted upstream site. Bacteria resistant to ampicillin, streptomycin, and tetracycline were isolated from all samples. Ampicillin resistance was particularly abundant, especially during the CSO event, so these isolates were studied further using disk susceptibility tests to assess multidrug resistance. During a CSO overflow event, 82% of these isolates were resistant to five or more antibiotics, and 44% were resistant to seven or more. The latter statistic contrasts Citation: Balasa, G.; Levengood, E.S.; starkly with the upstream reference site, where only 4% of isolates displayed resistance to more Battistelli, J.M.; Franklin, R.B. Diversity than seven antibiotics. DNA sequencing (16S rRNA gene) revealed that ~35% of our isolates were of Multidrug-Resistant Bacteria in an opportunistic pathogens, comprised primarily of the genera Stenotrophomonas, Pseudomonas, and Urbanized River: A Case Study of the Potential Risks from Combined Sewage Chryseobacterium.
    [Show full text]
  • Structural and Functional Diversity of the Diazotrophic Community in Xeric Ecosystems: Response to Nitrogen Availability
    UNIVERSIDADE DE LISBOA FACULDADE DE CIÊNCIAS DEPARTAMENTO BIOLOGIA VEGETAL Structural and functional diversity of the diazotrophic community in xeric ecosystems: response to nitrogen availability Carolina Cristiano de Almeida Mestrado em Microbiologia Aplicada Dissertação orientada por: Prof. Cristina Maria Nobre Sobral de Vilhena da Cruz Houghton Prof. Rogério Paulo de Andrade Tenreiro 2019 This Dissertation was fully performed at Plant Soil Ecology at cE3c under the direct co-supervision of Prof. Cristina Maria Nobre Sobral de Vilhena da Cruz Houghton Professor Rogério Paulo de Andrade Tenreiro was the internal supervisor designated in the scope of the Master in Applied Microbiology of the Faculty of Sciences of the University of Lisbon ACKNOWLEDGMENTS This dissertation arose from the collaboration between the Plant Soil Ecology group at cE3c and the Laboratory of Microbiology and Biotechnology at BioISI. This work would not be possible without the assistance and commitment of the individuals involved. First, I would like to express my greatest gratefulness to Professor Cristina Cruz, for the opportunity that was given to me. Thank you for the knowledge shared and for always having an enthusiastic perspective which is contagious. To Professor Rogério Tenreiro, thank you for welcoming me, for always pushing me to see further and for helping me to build more critical thinking. Thank you for all the knowledge shared with me, and for the ideas that help my work to go beyond what I thought was possible. I would also like to thank all members of the PSE group for their contribution, especially to Teresa Dias who has made possible this work with the samples used as well as every soil characteristic.
    [Show full text]
  • Identification of Novel Flavobacteria from Michigan and Assessment of Their Impacts on Fish Health
    IDENTIFICATION OF NOVEL FLAVOBACTERIA FROM MICHIGAN AND ASSESSMENT OF THEIR IMPACTS ON FISH HEALTH By Thomas P. Loch A DISSERTATION Submitted to Michigan State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Pathology 2012 1 ABSTRACT IDENTIFICATION OF NOVEL FLAVOBACTERIA FROM MICHIGAN AND ASSESSMENT OF THEIR IMPACTS ON FISH HEALTH By Thomas P. Loch Flavobacteriosis poses a serious threat to wild and propagated fish stocks alike, accounting for more fish mortality in the State of Michigan, USA, and its associated hatcheries than all other pathogens combined. Although this consortium of fish diseases has primarily been attributed to Flavobacterium psychrophilum, F. columnare, and F. branchiophilum, herein I describe a diverse assemblage of Flavobacterium spp. and Chryseobacterium spp. recovered from diseased, as well as apparently healthy wild, feral, and famed fishes of Michigan. Among 254 fish-associated flavobacterial isolates recovered from 21 fish species during 2003-2010, 211 of these isolates were Flavobacterium spp., and 43 were Chryseobacterium spp. according to ribosomal RNA partial gene sequencing and phylogenetic analysis. Both F. psychrophilum and F. columnare were indeed associated with multiple fish epizootics, but the majority of isolates were either most similar to recently described Flavobacterium and Chryseobacterium spp. that have not been reported within North America, or they did not cluster with any described species. Many of these previously uncharacterized flavobacteria were recovered from systemically infected fish that showed overt signs of disease and were highly proteolytic to multiple substrates in protease assays. Polyphasic characterization, which included extensive physiological, morphological, and biochemical analyses, fatty acid profiling, and phylogenetic analyses using Bayesian and neighbor-joining methodologies, confirmed that there were at least eight clusters of isolates that belonged to the genera Chryseobacterium and Flavobacterium, which represented eight novel species.
    [Show full text]