ArticlePublisher preview available

Spongiibacterium fuscum sp. nov., a marine Flavobacteriaceae isolated from the hard coral Galaxea fascicularis

Authors:
Jaewoo Yoon at Keimyung University
Jaewoo Yoon
Mina Yasumoto-Hirose at Tropical Technology Plus
Mina Yasumoto-Hirose
  • Tropical Technology Plus
Hiroaki Kasai at Kitasato University
Hiroaki Kasai
Read publisher preview
Download citation
To read the full-text of this research, you can request a copy directly from the authors.

Abstract and Figures

A novel marine bacterium, designated 04OKA-3-218T, was isolated from the hard coral Galaxea fascicularis L. collected in Japan. The strain was dark-brown-pigmented, Gram-negative, strictly aerobic, curved-rod-shaped and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequence showed the affiliation of the isolate with members of the family Flavobacteriaceae of the phylum Bacteroidetes, with the highest sequence similarity (95.2%) to Spongiibacterium pacificum SW169T. The DNA G+C content was 42.9 mol%; MK-6 was the major menaquinone; with iso-C17:0 3-OH (28.8%), iso-C15:0 (26.8%) and iso-C15:1 H and/or C13:0 3-OH (21.2%) as the main (> 10%) cellular fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phosphoaminolipids and three unidentified lipids. On the basis of distinct phylogenetic and phenotypic evidences, the strain represents a novel species of the genus Spongiibacterium, for which the name Spongiibacterium fuscum sp. nov. is proposed. The type strain of S. fuscum sp. nov. is 04OKA-3-218T (= KCTC 62504T = NBRC 113248T).
Figures - available from: Archives of Microbiology
This content is subject to copyright. Terms and conditions apply.
A preview of this full-text is provided by Springer Nature.
Learn more
Content available from Archives of Microbiology
This content is subject to copyright. Terms and conditions apply.
Vol.:(0123456789)
1 3
Archives of Microbiology (2018) 200:1317–1322
https://doi.org/10.1007/s00203-018-1547-6
ORIGINAL PAPER
Spongiibacterium fuscum sp. nov., amarine Flavobacteriaceae isolated
fromthehard coral Galaxea fascicularis
JaewooYoon1 · MinaYasumoto‑Hirose2,4· HiroakiKasai3
Received: 4 April 2018 / Revised: 29 May 2018 / Accepted: 22 June 2018 / Published online: 28 June 2018
© Springer-Verlag GmbH Germany, par t of Springer Nature 2018
Abstract
A novel marine bacterium, designated 04OKA-3-218T, was isolated from the hard coral Galaxea fascicularis L. collected
in Japan. The strain was dark-brown-pigmented, Gram-negative, strictly aerobic, curved-rod-shaped and non-motile. Phy-
logenetic analysis based on the 16S rRNA gene sequence showed the affiliation of the isolate with members of the family
Flavobacteriaceae of the phylum Bacteroidetes, with the highest sequence similarity (95.2%) to Spongiibacterium pacificum
SW169T. The DNA G+C content was 42.9mol%; MK-6 was the major menaquinone; with iso-C17:0 3-OH (28.8%), iso-
C15:0 (26.8%) and iso-C15:1H and/or C13:0 3-OH (21.2%) as the main (> 10%) cellular fatty acids. The major polar lipid
profile consisted of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phosphoaminolipids and three
unidentified lipids. On the basis of distinct phylogenetic and phenotypic evidences, the strain represents a novel species of
the genus Spongiibacterium, for which the name Spongiibacterium fuscum sp. nov. is proposed. The type strain of S. fuscum
sp. nov. is 04OKA-3-218T (= KCTC 62504T = NBRC 113248T).
Keywords Bacteroidetes· Flavobacteriaceae· Spongiibacterium fuscum sp. nov.· Galaxea fascicularis· 16S rRNA gene·
Polyphasic taxonomy
Introduction
The family Flavobacteriaceae (Jooste 1985) is a major fam-
ily within the phylum Bacteroidetes (Garrity and Holt 2001).
Molecular phylogenetic methods based on small-subunit
rRNA genes revealed that the species of this family com-
prise a large portion of whole bacterial communities in the
marine ecosystem (Glöckner etal. 1999; Cottrell and Kirch-
man 2000; Abell and Bowman 2005). Scleractinian corals
have a variety of different populations of bacteria in their
gastric cavity and tissues and on their surface (Rosenberg
etal. 2007). The hard coral Galaxea fascicularis L. has ena-
bled us to study the taxonomy of many as-yet-uncultivated
marine bacteria. In previous studies, our group identified two
novel flavobacteria, i.e., Aureisphaera galaxeae 04OKA003-
7T (Yoon etal. 2015) and Coraliitalea coralii 04OKA-3-
121T (Yoon etal. 2018), isolated from the hard coral G.
fascicularis L.
Here, we analyzed and characterized a novel marine bac-
terial strain, 04OKA-3-218T, isolated from G. fascicularis L.
using polyphasic taxonomic methods (Colwell 1970) includ-
ing 16S rRNA gene sequence analysis and physiological,
biochemical and chemotaxonomic methods. Based on the
Communicated by Erko Stackebrandt.
The Digital Protologue Database (DPD) number for strain
04OKA-3-218T is TA00366. The GenBank/EMBL/DDBJ
accession number of the 16S rRNA gene sequence of strain
04OKA-3-218T is LC329340.
Electronic supplementary material The online version of this
article (https ://doi.org/10.1007/s0020 3-018-1547-6) contains
supplementary material, which is available to authorized users.
* Jaewoo Yoon
jwyoon@kmu.ac.kr
1 College ofPharmacy, Keimyung University,
1095 Dalgubeoldaero, Dalseo-Gu, Daegu42601,
RepublicofKorea
2 Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi,
Iwate026-0001, Japan
3 Marine Biosciences Kamaishi Research Laboratory, Kitasato
University, 160-4 Utou, Okirai, Sanriku-cho, Ofunato,
Iwate022-0101, Japan
4 Present Address: Tropical Technology Plus, 12-75 Suzaki,
Uruma, Okinawa904-2234, Japan
Content courtesy of Springer Nature, terms of use apply. Rights reserved.
... All assays were performed according to the methodological procedures described previously by Yoon, Yasumoto-Hirose and Kasai (2018) except the determination of temperature range (4,5,8,9,10,15,20,25,30,37,40,41,42,43,44 and 45 • C) for growth. ...
Polyphasic taxonomic analysis of Paracoccus ravus sp. nov., an alphaproteobacterium isolated from marine sediment
Article
  • Aug 2019
  • FEMS MICROBIOL LETT
Polyphasic taxonomic analysis was performed on a novel marine bacterium, designated as strain YJ057T, isolated from marine sediment collected in the Republic of Korea. The strain was Gram-negative, beige-colored, facultatively anaerobic, coccoid or ovoid-shaped and nonmotile. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that this novel marine isolate belongs to the family Rhodobacteraceae of the class Alphaproteobacteria, and has the greatest (96.2%) sequence similarity to Paracoccus aestuariivivens GHD-30T. Major (>10%) fatty acids of strain YJ057T were C16:0 and C18:1 ω7c, G+C content in the genomic DNA of the strain was 63.6 mol% and the sole respiratory quinone was ubiquinone Q-10. It had phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine and some unidentified components (three aminolipids, a glycolipid, a phospholipid and two lipids). As per the distinct phylogenetic position and combination of phenotypic and genotypic traits, the strain is considered a novel species of the genus Paracoccus, and the name Paracoccus ravus sp. nov. is proposed.
View
View
Coraliitalea coralii gen. nov., sp. nov., a Marine Bacterium of the Family Flavobacteriaceae Isolated from the Hard Coral Galaxea fascicularis
Article
Full-text available
  • Apr 2018
  • CURR MICROBIOL
A polyphasic taxonomic study was performed on a novel strain designated as 04OKA-3-121T, which was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. These bacterial cells were observed to be pale-yellow, Gram-stain-negative, strictly aerobic, chemoheterotrophic, non-spore forming, non-motile, and rod-shaped. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel marine isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it shared the highest (93.6%) sequence similarity with Pseudozobellia thermophila KMM 3531T. The strain could be phenotypically differentiated from related members of the family Flavobacteriaceae. Major fatty acids of strain 04OKA-3-121T were iso-C15:0, iso-C15:1 G, and C16:1 ω7c and/or C16:1 ω6c. The DNA G + C content of the strain was determined to be 38.8 mol% and the major respiratory quinone was identified as menaquinone 6 (MK-6). Strain 04OKA-3-121T had phosphatidylethanolamine, two unidentified aminolipids, and eight unidentified lipids as polar lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus in the family Flavobacteriaceae, for which the name Coraliitalea coralii gen. nov., sp. nov. is proposed. The type strain of C. coralii gen. nov., sp. nov. is 04OKA-3-121T (= KCTC 52378T = NBRC 112329T).
View
Muricauda beolgyonensis sp. nov., isolated from a tidal flat
Article
Full-text available
  • Jul 2011
  • INT J SYST EVOL MICR
The taxonomic position of a Gram-staining-negative, non-motile, rod-shaped bacterium, strain BB-My12(T), which was isolated from a sediment sample collected from a tidal flat in Korea, was investigated by using a polyphasic approach. Strain BB-My12(T) grew optimally at 37 °C, at pH 7.0-7.5 and in the presence of 2-3 % (w/v) NaCl. In phylogenetic analyses based on 16S rRNA gene sequences, strain BB-My12(T) fell within the cluster comprising species of the genus Muricauda and appeared most similar to the type strains of Muricauda aquimarina, Muricauda lutimaris and Muricauda ruestringensis (97.5-97.6 % sequence similarity). The DNA G+C content was 45.0 mol%. Strain BB-My12(T) contained MK-6 as the predominant menaquinone and iso-C(15 : 1), iso-C(17 : 0) 3-OH and iso-C(15 : 0) as the major cellular fatty acids. The polar lipids of strain BB-My12(T) were phosphatidylethanolamine and four unidentified lipids. The DNA-DNA relatedness values between strain BB-My12(T) and the type strains of the three species of the genus Muricauda that appeared most closely related were in the range 5-7 %. The genetic distinctiveness and some phenotypic properties indicated that strain BB-My12(T) did not belong to any established species of the genus Muricauda. Strain BB-My12(T) is therefore considered to represent a novel species of the genus Muricauda, for which the name Muricauda beolgyonensis sp. nov. is proposed. The type strain is BB-My12(T) ( = KCTC 23501(T)  = CCUG 60800(T)).
View
Spongiibacterium flavum gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from the marine sponge Halichondria oshoro, and emended descriptions of the genera Croceitalea and Flagellimonas
Article
Full-text available
  • Jul 2011
  • INT J SYST EVOL MICR
A gram-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, yellow-pigmented rod, designated A11(T), was isolated from a marine sponge, Halichondria oshoro, collected on the coastline of Jeju Island, Republic of Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A11(T) was a member of the family Flavobacteriaceae. Its closest relatives were members of the genera Muricauda, Flagellimonas and Croceitalea (94.4-94.8 % 16S rRNA gene sequence similarity). The only polar lipid detected in strain A11(T) was phosphatidylethanolamine. The dominant fatty acids were iso-C(15 : 0) (30.4 %), iso-C(15 : 1) G (26.7 %), iso-C(17 : 0) 3-OH (12.4 %) and iso-C(15 : 0) 3-OH (7.3 %). The DNA G+C content of strain A11(T) was 41.7 mol% and its major respiratory quinone was MK-6. On the basis of combined data from phenotypic and phylogenetic analyses, strain A11(T) represents a novel genus and species within the family Flavobacteriaceae, for which the name Spongiibacterium flavum gen. nov., sp. nov. is proposed. The type strain of the type species is A11(T) ( = KCTC 22665(T) = DSM 22638(T)). Emended descriptions of the genera Croceitalea and Flagellimonas are also given.
View
Cribrihabitans pelagius sp. nov., a marine alphaproteobacterium isolated from seawater
Article
  • May 2016
A Gram-stain-negative, strictly aerobic, cream-coloured, motile, chemoheterotrophic, rod-shaped bacterium, designated strain KMU-32T, was isolated from seawater at Najeong Beach in Korea. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the novel isolate was affiliated with the family Rhodobacteraceae of the class Alphaproteobacteria and that it showed highest sequence similarity (98.2%) to Cribrihabitans neustonicus CC-AMHB-3T. The DNA-DNA relatedness values between strains KMU-32T and C. neustonicus CC-AMHB-3T were 48.5±4%. The DNA G+C content of strain KMU-32T was determined to be 63.7 mol%. Ubiquinone 10 (Q-10) was the sole respiratory quinone. The predominant cellular fatty acid was C18:1 ω7c (73.9%). Strain KMU-32T had diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid as polar lipids. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel species of the genus Cribrihabitans for which the name Cribrihabitans pelagius sp. nov. is proposed. The type strain of C. pelagius sp. nov. is KMU-32T (= KCTC 42981T = NBRC 111834T).
View
Muricauda pacifica sp. nov., isolated from seawater of South Pacific Gyre
Article
  • Aug 2015
  • INT J SYST EVOL MICR
A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase- and catalase-positive, rod-shaped and orange-pigmented bacterium with appendages, designated strain SW027T, was isolated from a surface seawater sample collected from the South Pacific Gyre (26°29' S 137°56' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW027T shared the highest sequence similarity with members of the genus Muricauda (94.3-92.7%), exhibiting 94.3% sequence similarity to Muricauda flavescens SW-62T. Optimal growth occurred in the presence of 3% (w/v) NaCl, at pH 7.0 and at 37°C. The DNA G+C content of strain SW027T was 42.7 mol%. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Enzymatic activity profiles, cell morphology and G+C content differentiated the novel bacterium from the closest related members of the genus Muricauda. On the basis of the polyphasic analyses, strain SW027T is considered to represent a novel species of the genus Muricauda, for which the name Muricauda pacifica sp. nov. is proposed. The type strain is SW027T (=JCM 17861T =LMG 26637T).
View
The Road Map to the Manual
Chapter
  • Jan 2001
The Second Edition of Bergey’s Manual of Systematic Bacteriology represents a major departure from the First Edition, as well as from the Eighth and Ninth Editions of the Manual of Determinative Bacteriology, in that the organization of content follows a phylogenetic framework, based on analysis of the nucleotide sequence of the ribosomal small subunit RNA, rather than a phenotypic structure. The Eighth and Ninth Editions of the Determinative Manual and the First Edition of the Systematic Manual were organized in a non-hierarchical scheme because information about higher taxa was insufficient for construction of a formal hierarchical classification, such as those used in all the previous editions. Instead, the genera were organized into phenotypic groupings, e.g., the Gram-positive cocci, and these groupings were called Parts, Sections, or Groups. By the Ninth Edition of the Determinative Manual, which was based on the information included in the Systematic Manual, there were 35 separate phenotypic groupings.
View
Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis
Article
  • Mar 2015
  • ANTON LEEUW INT J G
A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA003-7(T) was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436(T) and Aureitalea marina S1-66(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7(T) were identified as iso-C15:0 and iso-C17:0 3-OH as defined by the MIDI system. The DNA G+C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7(T) (=KCTC 32993(T) = NBRC 110018(T)).
View
Spongiibacterium pacificum sp. nov., isolated from seawater of South Pacific Gyre and emended description of the genus Spongiibacterium
Article
  • Oct 2014
A Gram-stain-negative, strictly aerobic, non-flagellated, non-gliding, oxidase-positive and rod shaped yellow-pigmented bacterium, designated strain SW169T, was isolated from surface seawater sample collected from the South Pacific Gyre (27°55' S 123°10' W) during the Integrated Ocean Drilling Program (IODP) Expedition 329. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SW169T belonged to the genus Spongiibacterium and showed the highest 16S rRNA gene sequence similarity with Spongiibacterium flavum A11T (95.9%). It showed 93.2-94.8% 16S rRNA gene sequence similarity with respect to members of the genera Croceitalea and Flagellimonas in the family Flavobacteriaceae. Optimal growth occurred in the presence of 3-4% (w/v) NaCl, at pH 8.0 and at 28°C. The DNA G+C content of strain SW169T was 43.3 mol%. The major fatty acids were iso-C15:1 G, iso-C15:0, iso-C17:0 3-OH, iso-C15:0 3-OH and Summed Feature 3 (comprising C16:1 ω7c and/or C16:1 ω6c,). The major respiratory quinone was menaquinone-6. The major polar lipids were phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. On the basis of the polyphasic analyses, strain SW169T is considered to represent a novel species of the genus Spongiibacterium, for which the name Spongiibacterium pacificum sp. nov. is proposed. The type strain is SW169T (=JCM 18379T =LMG 26997T).
View
Improved method for phenotypical characterization of marine bacteria
Article
  • Jul 1991
  • J MICROBIOL METH
A characterization system for marine bacteria using Difco Marine Broth 2216 and disposable 24-well tissue culture plates has been developed. Incubation was performed at desired temperature for up to 4 wk. Where anaerobic conditions were required, the plates were incubated under N2 atmosphere. The majority of tests were based on colorimetric changes in the growth medium, the system allowing accurate reading of the tests, and thus minimizing the degree of subjectivity. This characterization system was compared with two commercial diagnostic kits, API 20E and API 20NE. The multidish system proved to be far more suitable than the commercial kits in characterization of marine bacteria, both fish pathogenic and nonpathogen, and has applications both for numerical taxonomy and for diversity studies of bacterial communities.
View
A numerical taxonomic study of Flavobacterium-Cytophaga strains from dairy sources
Article
  • Oct 1985
  • J Appl Bacteriol
Phenotypic data on 203 Gram-negative non-fermentative bacteria of the Flavobacterium-Cytophaga group isolated from milk and butter were analyzed by numerical taxonomic techniques. Twenty reference strains including species of Flavobacterium, Cytophaga and strains of Pseudomonas paucimobilis were included in the study. Using the matching coefficient of Sokal & Michener with antibiotic susceptibility data included, 189 isolates were recovered in nine clusters. Six of these clusters were linked at or above the 85% S level while three were linked at or above the 79% S level. The largest cluster, representing 46.3% of the isolates, could be equated with Flavobacterium sp. Group IIb. Other clusters could be equated with Flavobacterium sp. L 16/1 (22.7% of isolates), F. balustinum (10.8% of isolates), F. breve (4.4%), F. multivorum (3.5%) and Cytophaga johnsonae (1.5%). The cluster resembling Flavobacterium sp. L 16/1 and a smaller unclassified cluster, were exceptional in being susceptible to the antibiotics cephalothin and penicillin G.
View