1
|
Coe LSY, Fei C, Weston J, Amin SA. Phycobacter azelaicus gen. nov. sp. nov., a diatom symbiont isolated from the phycosphere of Asterionellopsis glacialis. Int J Syst Evol Microbiol 2023; 73. [PMID: 37889154 DOI: 10.1099/ijsem.0.006104] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
A diatom-associated bacterium, designated as strain F10T, was isolated from a pure culture of the pennate diatom Asterionellopsis glacialis A3 and has since been used to characterize molecular mechanisms of symbiosis between phytoplankton and bacteria, including interactions using diatom-derived azelaic acid. Its origin from a hypersaline environment, combined with its capacity for quorum sensing, biofilm formation, and potential for dimethylsulfoniopropionate methylation/cleavage, suggest it is within the family Roseobacteraceae. Initial phylogenetic analysis of the 16S rRNA gene sequence placed this isolate within the Phaeobacter genus, but recent genomic and phylogenomic analyses show strain F10T is a separate lineage diverging from the genus Pseudophaeobacter. The genomic DNA G+C content is 60.0 mol%. The predominant respiratory quinone is Q-10. The major fatty acids are C18 : 1 ω7c and C16 : 0. Strain F10T also contains C10 : 03-OH and the furan-containing fatty acid 10,13-epoxy-11-methyl-octadecadienoate (9-(3-methyl-5-pentylfuran-2-yl)nonanoic acid). The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. Based on genomic, phylogenomic, phenotypic and chemotaxonomic characterizations, strain F10T represents a novel genus and species with the proposed name, Phycobacter azelaicus gen. nov. sp. nov. The type strain is F10T (=NCMA B37T=NCIMB 15470T=NRIC 2002T).
Collapse
Affiliation(s)
- Lisa S Y Coe
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| | - Cong Fei
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| | - James Weston
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| | - Shady A Amin
- Marine Microbiomics Laboratory, Biology Program, New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
- Arabian Center for Climate and Environmental Sciences (ACCESS), New York University Abu Dhabi, Abu Dhabi, PO Box 129188, UAE
| |
Collapse
|
2
|
Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW. Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005286] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains (GL-11-2T and ZH2-Y79) were isolated from the seawater collected from the West Pacific Ocean and the East China Sea, respectively. Cells were Gram-stain-negative, strictly aerobic, non-motile and rod-shaped. Cells grew in the medium containing 0.5–7.5 % NaCl (w/v, optimum, 1.0–3.0 %), at pH 6.0–8.0 (optimum, pH 6.5–7.0) and at 4–40 °C (optimum, 30 °C). H2S production occurred in marine broth supplemented with sodium thiosulphate. The almost-complete 16S rRNA gene sequences of the two isolates were identical, and exhibited the highest similarity to
Pseudoruegeria aquimaris
JCM 13603T (97.5 %), followed by
Ruegeria conchae
TW15T (97.2%),
Shimia aestuarii
DSM 15283T (97.1 %) and
Ruegeria lacuscaerulensis
ITI-1157T (97.0 %). Phylogenetic analysis revealed that the isolates were affiliated with the family
Roseobacteraceae
and represented an independent lineage. The sole isoprenoid quinone was ubiquinone 10. The principal fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c) and cyclo-C19 : 0
ω8c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and diphosphatidylglycerol. The DNA G+C content was 62.3 mol%. The orthologous average nucleotide identity, in silico DNA–DNA hybridization and average amino acid identity values among the genomes of strain GL-11-2T and the reference strains were 73.2–79.0, 20.3–22.5 and 66.0–80.8 %, respectively. Strains GL-11-2ᵀ and ZH2-Y79 possessed complete metabolic pathways for thiosulphate oxidation, dissimilatory nitrate reduction and denitrification. Phylogenetic distinctiveness, chemotaxonomic differences and phenotypic properties revealed that the isolates represent a novel genus and species of the family
Roseobacteraceae
, belonging to the class
Alphaproteobacteria
, for which the name Thiosulfatihalobacter marinus gen. nov., sp. nov. (type strain, GL-11–2T=KCTC 82723T=MCCC M20691T) is proposed.
Collapse
Affiliation(s)
- Yuehong Wu
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
| | - Wen-Ting Ren
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Ying-Wen Zhong
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Li-Li Guo
- College of Life and Environmental Science, Hunan University of Arts and Science, Changde 415000, PR China
| | - Peng Zhou
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| | - Xue-Wei Xu
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Key Laboratory of Marine Ecosystem Dynamics, Ministry of Natural Resources & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, PR China
| |
Collapse
|
3
|
Electrochemical Bacterial Enrichment from Natural Seawater and Its Implications in Biocorrosion of Stainless-Steel Electrodes. MATERIALS 2020; 13:ma13102327. [PMID: 32438636 PMCID: PMC7288148 DOI: 10.3390/ma13102327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/29/2020] [Accepted: 05/09/2020] [Indexed: 11/17/2022]
Abstract
Microbial electrochemical technologies have revealed the opportunity of electrochemical enrichment for specific bacterial groups that are able to catalyze reactions of interest. However, there are unsolved challenges towards their application under aggressive environmental conditions, such as in the sea. This study demonstrates the impact of surface electrochemical potential on community composition and its corrosivity. Electrochemical bacterial enrichment was successfully carried out in natural seawater without nutrient amendments. Experiments were carried out for ten days of exposure in a closed-flow system over 316L stainless steel electrodes under three different poised potentials (−150 mV, +100 mV, and +310 mV vs. Ag/AgCl). Weight loss and atomic force microscopy showed a significant difference in corrosion when +310 mV (vs. Ag/AgCl) was applied in comparison to that produced under the other tested potentials (and an unpoised control). Bacterial community analysis conducted using 16S rRNA gene profiles showed that poised potentials are more positive as +310 mV (vs. Ag/AgCl) resulted in strong enrichment for Rhodobacteraceae and Sulfitobacter. Hence, even though significant enrichment of the known electrochemically active bacteria from the Rhodobacteraceae family was accomplished, the resultant bacterial community could accelerate pitting corrosion in 316 L stainless steel, thereby compromising the durability of the electrodes and the microbial electrochemical technologies.
Collapse
|
4
|
Complete Genome Sequence of Leisingera aquamixtae R2C4, Isolated from a Self-Regenerating Biocathode Consortium. Microbiol Resour Announc 2019; 8:8/36/e00833-19. [PMID: 31488535 PMCID: PMC6728645 DOI: 10.1128/mra.00833-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present the complete genome sequence of Leisingera aquamixtae R2C4, isolated from the electroautotrophic microbial consortium biocathode MCL (Marinobacter-Chromatiaceae-Labrenzia). As an isolate of a current-producing system, the genome sequence of L. aquamixtae will yield insights regarding electrode-associated microorganisms and communities. A dark pigment is also observed during cultivation. Here, we present the complete genome sequence of Leisingera aquamixtae R2C4, isolated from the electroautotrophic microbial consortium biocathode MCL (Marinobacter-Chromatiaceae-Labrenzia). As an isolate of a current-producing system, the genome sequence of L. aquamixtae will yield insights regarding electrode-associated microorganisms and communities. A dark pigment is also observed during cultivation.
Collapse
|
5
|
The influence of surface microbial diversity and succession on microbiologically influenced corrosion of steel in a simulated marine environment. Arch Microbiol 2018; 200:1447-1456. [DOI: 10.1007/s00203-018-1559-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/03/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
|
6
|
Lee MD, Kling JD, Araya R, Ceh J. Jellyfish Life Stages Shape Associated Microbial Communities, While a Core Microbiome Is Maintained Across All. Front Microbiol 2018; 9:1534. [PMID: 30050517 PMCID: PMC6052147 DOI: 10.3389/fmicb.2018.01534] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022] Open
Abstract
The key to 650 million years of evolutionary success in jellyfish is adaptability: with alternating benthic and pelagic generations, sexual and asexual reproductive modes, multitudes of body forms and a cosmopolitan distribution, jellyfish are likely to have established a plenitude of microbial associations. Here we explored bacterial assemblages in the scyphozoan jellyfish Chrysaora plocamia (Lesson 1832). Life stages involved in propagation through cyst formation, i.e., the mother polyp, its dormant cysts (podocysts), and polyps recently excysted (excysts) from podocysts – were investigated. Associated bacterial assemblages were assessed using MiSeq Illumina paired-end tag sequencing of the V1V2 region of the 16S rRNA gene. A microbial core-community was identified as present through all investigated life stages, including bacteria with closest relatives known to be key drivers of carbon, nitrogen, phosphorus, and sulfur cycling. Moreover, the fact that half of C. plocamia’s core bacteria were also present in life stages of the jellyfish Aurelia aurita, suggests that this bacterial community might represent an intrinsic characteristic of scyphozoan jellyfish, contributing to their evolutionary success.
Collapse
Affiliation(s)
- Michael D Lee
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Joshua D Kling
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Rubén Araya
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile
| | - Janja Ceh
- Instituto de Ciencias Naturales Alexander von Humboldt, Universidad de Antofagasta, Antofagasta, Chile.,Laboratory of Microbial Complexity and Functional Ecology, Institute of Antofagasta, University of Antofagasta, Antofagasta, Chile.,Centre for Biotechnology and Bioengineering, Universidad de Chile, Santiago, Chile
| |
Collapse
|
7
|
Cho K, Jeong D, Lee S, Bae H. Chlorination caused a shift in marine biofilm niches on microfiltration/ultrafiltration and reverse osmosis membranes and UV irradiation effectively inactivated a chlorine-resistant bacterium. Appl Microbiol Biotechnol 2018; 102:7183-7194. [DOI: 10.1007/s00253-018-9111-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 04/16/2018] [Accepted: 05/16/2018] [Indexed: 01/30/2023]
|
8
|
Sonnenschein EC, Phippen CBW, Bentzon-Tilia M, Rasmussen SA, Nielsen KF, Gram L. Phylogenetic distribution of roseobacticides in the Roseobacter group and their effect on microalgae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2018; 10:383-393. [PMID: 29624899 DOI: 10.1111/1758-2229.12649] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/21/2018] [Accepted: 04/02/2018] [Indexed: 06/08/2023]
Abstract
The Roseobacter-group species Phaeobacter inhibens produces the antibacterial tropodithietic acid (TDA) and the algaecidal roseobacticides with both compound classes sharing part of the same biosynthetic pathway. The purpose of this study was to investigate the production of roseobacticides more broadly in TDA-producing roseobacters and to compare the effect of producers and non-producers on microalgae. Of 33 roseobacters analyzed, roseobacticide production was a unique feature of TDA-producing P. inhibens, P. gallaeciensis and P. piscinae strains. One TDA-producing Phaeobacter, 27-4, did not produce roseobacticides, possibly due to a transposable element. TDA-producing Ruegeria and Pseudovibrio did not produce roseobacticides. Addition of roseobacticide-containing bacterial extracts affected the growth of the microalgae Rhodomonas salina, Thalassiosira pseudonana and Emiliania huxleyi, while growth of Tetraselmis suecica was unaffected. During co-cultivation, growth of E. huxleyi was initially stimulated by the roseobacticide producer DSM 17395, while the subsequent decline in algal cell numbers during senescence was enhanced. Strain 27-4 that does not produce roseobacticides had no effect on algal growth. Both bacterial strains, DSM 17395 and 27-4, grew during co-cultivation presumably utilizing algal exudates. Furthermore, TDA-producing roseobacters have potential as probiotics in marine larviculture and it is promising that the live feed Tetraselmis was unaffected by roseobacticides-containing extracts.
Collapse
Affiliation(s)
- Eva C Sonnenschein
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | | | - Mikkel Bentzon-Tilia
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Silas Anselm Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Kristian Fog Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| | - Lone Gram
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Anker Engelundsvej 301, DK-2800 Kgs, Lyngby, Denmark
| |
Collapse
|
9
|
Paraphaeobacter pallidus gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2017; 67:2520-2526. [DOI: 10.1099/ijsem.0.001935] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
|
10
|
Antibacterial activity of aquatic gliding bacteria. SPRINGERPLUS 2016; 5:116. [PMID: 26885469 PMCID: PMC4742450 DOI: 10.1186/s40064-016-1747-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 01/28/2016] [Indexed: 11/10/2022]
Abstract
The study aimed to screen and isolate strains of freshwater aquatic gliding bacteria, and to investigate their antibacterial activity against seven common pathogenic bacteria. Submerged specimens were collected and isolated for aquatic gliding bacteria using four different isolation media (DW, MA, SAP2, and Vy/2). Gliding bacteria identification was performed by 16S rRNA gene sequencing and phylogenetic analysis. Crude extracts were obtained by methanol extraction. Antibacterial activity against seven pathogenic bacteria was examined by agar-well diffusion assay. Five strains of aquatic gliding bacteria including RPD001, RPD008, RPD018, RPD027 and RPD049 were isolated. Each submerged biofilm and plastic specimen provided two isolates of gliding bacteria, whereas plant debris gave only one isolate. Two strains of gliding bacteria were obtained from each DW and Vy/2 isolation medium, while one strain was obtained from the SAP2 medium. Gliding bacteria strains RPD001, RPD008 and RPD018 were identified as Flavobacterium anhuiense with 96, 82 and 96 % similarity, respectively. Strains RPD049 and RPD027 were identified as F. johnsoniae and Lysobacter brunescens, respectively, with similarity equal to 96 %. Only crude extract obtained from RPD001 inhibited growth of Listeria monocytogenes (MIC 150 µg/ml), Staphylococcus aureus (MIC 75 µg/ml) and Vibrio cholerae (MIC 300 µg/ml), but showed weak inhibitory effect on Salmonella typhimurium (MIC > 300 µg/ml). Gliding bacterium strain RPD008 should be considered to a novel genus separate from Flavobacterium due to its low similarity value. Crude extract produced by RPD001 showed potential for development as a broad antibiotic agent.
Collapse
|
11
|
Rodrigo-Torres L, Pujalte MJ, Arahal DR. Draft genome of Leisingera aquaemixtae CECT 8399(T), a member of the Roseobacter clade isolated from a junction of fresh and ocean water in Jeju Island, South Korea. GENOMICS DATA 2016; 7:233-6. [PMID: 26981415 PMCID: PMC4778666 DOI: 10.1016/j.gdata.2016.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/08/2016] [Accepted: 01/14/2016] [Indexed: 10/26/2022]
Abstract
We report the draft genome sequence and annotation of Leisingera aquaemixtae CECT 8399(T) (DDBJ/EMBL/GenBank accession number CYSR00000000) which comprises 4,614,060 bp, 4313 protein coding genes, 54 tRNA coding genes and 7 rRNA coding genes. General findings of the annotated genome, such as pigment indigoidine operon, phenylacetate oxidation genes or predictable number of replicons, are commented in comparison to other Leisingera species. Average Nucleotide Identity between available genomes of type strains of species of Leisingera and Phaeobacter genera has been calculated to evaluate its current classification.
Collapse
Affiliation(s)
- Lidia Rodrigo-Torres
- Departamento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - María J Pujalte
- Departamento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| | - David R Arahal
- Departamento de Microbiología y Ecología, Universidad de Valencia, Valencia, Spain
| |
Collapse
|
12
|
Abstract
A Gram-negative, aerobic, non-spore-forming, motile and ovoid or rod-shaped bacterial strain, designated MA2-16(T), was isolated from ark shell (Scapharca broughtonii) collected from the South Sea, South Korea. Strain MA2-16(T) was found to grow optimally at 30°C, at pH 7.0-8.0 and in the presence of 2.0% (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences revealed that strain MA2-16(T) clustered with the type strain of Sedimentitalea nanhaiensis. The novel strain exhibited a 16S rRNA gene sequence similarity value of 97.1% to the type strain of S. nanhaiensis. In the neighbour-joining phylogenetic tree based on gyrB sequences, strain MA2-16(T) formed an evolutionary lineage independent of those of other taxa. Strain MA2-16(T) contained Q-10 as the predominant ubiquinone and C18:1 ω7c and 11-methyl C18:1 ω7c as the major fatty acids. The major polar lipids of strain MA2-16(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, an unidentified aminolipid and an unidentified lipid. The DNA G+C content of strain MA2-16(T) was 57.7 mol% and its DNA-DNA relatedness values with the type strains of S. nanhaiensis and some phylogenetically related species of the genera Leisingera and Phaeobacter were 13-24%. On the basis of the data presented, strain MA2-16(T) is considered to represent a novel genus and novel species within the family Rhodobacteraceae, for which the name Aliisedimentitalea scapharcae gen. nov., sp. nov. is proposed. The type strain is MA2-16(T) (=KCTC 42119(T) =CECT 8598(T)).
Collapse
|
13
|
Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade. Appl Environ Microbiol 2015; 80:4725-37. [PMID: 24858085 DOI: 10.1128/aem.00719-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since genome analysis did not allow unambiguous reconstruction of transport, catabolism, and substrate-specific regulation for several important carbohydrates in Phaeobacter inhibens DSM 17395, proteomic and metabolomic analyses of N-acetylglucosamine-, mannitol-, sucrose-, glucose-, and xylose-grown cells were carried out to close this knowledge gap. These carbohydrates can pass through the outer membrane via porins identified in the outer membrane fraction. For transport across the cytoplasmic membrane, carbohydrate-specific ABC transport systems were identified. Their coding genes mostly colocalize with the respective "catabolic" and "regulatory" genes. The degradation of N-acetylglucosamine proceeds via N-acetylglucosamine-6-phosphate and glucosamine-6-phosphate directly to fructose-6-phosphate; two of the three enzymes involved were newly predicted and identified. Mannitol is catabolized via fructose, sucrose via fructose and glucose, glucose via glucose-6-phosphate, and xylose via xylulose-5-phosphate. Of the 30 proteins predicted to be involved in uptake, regulation, and degradation, 28 were identified by proteomics and 19 were assigned to their respective functions for the first time. The peripheral degradation pathways feed into the Entner-Doudoroff (ED) pathway, which is connected to the lower branch of the Embden-Meyerhof-Parnas (EMP) pathway. The enzyme constituents of these pathways displayed higher abundances in P. inhibens DSM 17395 cells grown with any of the five carbohydrates tested than in succinate-grown cells. Conversely, gluconeogenesis is turned on during succinate utilization. While tricarboxylic acid (TCA) cycle proteins remained mainly unchanged, the abundance profiles of their metabolites reflected the differing growth rates achieved with the different substrates tested. Homologs of the 74 genes involved in the reconstructed catabolic pathways and central metabolism are present in various Roseobacter clade members.
Collapse
|
14
|
Lee MH, Song EJ, Seo MJ, Hyun DW, Bae JW, Lee SY, Roh SW, Nam YD. Phaeobacter marinintestinus sp. nov., isolated from the intestine of a sea cucumber (Apostichopus japonicus). Antonie van Leeuwenhoek 2014; 107:209-16. [PMID: 25355001 DOI: 10.1007/s10482-014-0318-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 10/24/2014] [Indexed: 11/26/2022]
Abstract
A Gram-negative, strictly aerobic, non-motile, and rod-shaped bacterial strain designated UB-M7(T) was isolated from the intestine of a sea cucumber (Apostichopus japonicus) collected from Pohang in South Korea. Strain UB-M7(T) displayed optimal growth at 25 °C, pH 7.0-7.5, and with 2.0-3.0 % (w/v) NaCl. Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain UB-M7(T) clustered with Phaeobacter arcticus DSM 23566(T), Phaeobacter inhibens DSM 16374(T), Phaeobacter gallaeciensis BS107(T), and Phaeobacter leonis 306(T), exhibiting 16S rRNA gene sequence similarity values of 96.8, 96.6, 96.4, and 96.2 %, respectively. Strain UB-M7(T) was found to exhibit the highest gyrB sequence similarity value of 80.6 % to the type strain of P. arcticus. The major respiratory quinone of strain UB-M7(T) was found to be ubiquinone 10 (Q-10). The major cellular fatty acids (>5 % of the total fatty acids) are summed features 8 (comprising C18:1 ω7c and/or C18:1 ω6c), 11-methyl C18:1 ω7c, and cyclo C19:0 ω8c. The DNA G+C content was found to be 58.5 mol% and DNA-DNA relatedness value with P. arcticus JCM 14644(T) was 17.2 ± 2.4 %. The major polar lipids of strain UB-M7(T) were identified as phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine; one phospholipid, and three other lipids remain unidentified. Based on its phenotypic, phylogenetic, and chemotaxonomic properties it is concluded that strain UB-M7(T) represents a novel species in the genus Phaeobacter, for which the name Phaeobacter marinintestinus sp. nov. is proposed. The type strain is UB-M7(T) (=KCCM 43045(T) = JCM 19926(T)).
Collapse
Affiliation(s)
- Mi-Hwa Lee
- Fermentation Research Group, Korea Food Research Institute (KFRI), Sungnam, 463-746, Republic of Korea
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Breider S, Scheuner C, Schumann P, Fiebig A, Petersen J, Pradella S, Klenk HP, Brinkhoff T, Göker M. Genome-scale data suggest reclassifications in the Leisingera-Phaeobacter cluster including proposals for Sedimentitalea gen. nov. and Pseudophaeobacter gen. nov. Front Microbiol 2014; 5:416. [PMID: 25157246 PMCID: PMC4127530 DOI: 10.3389/fmicb.2014.00416] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/22/2014] [Indexed: 11/13/2022] Open
Abstract
Earlier phylogenetic analyses of the marine Rhodobacteraceae (class Alphaproteobacteria) genera Leisingera and Phaeobacter indicated that neither genus might be monophyletic. We here used phylogenetic reconstruction from genome-scale data, MALDI-TOF mass-spectrometry analysis and a re-assessment of the phenotypic data from the literature to settle this matter, aiming at a reclassification of the two genera. Neither Phaeobacter nor Leisingera formed a clade in any of the phylogenetic analyses conducted. Rather, smaller monophyletic assemblages emerged, which were phenotypically more homogeneous, too. We thus propose the reclassification of Leisingera nanhaiensis as the type species of a new genus as Sedimentitalea nanhaiensis gen. nov., comb. nov., the reclassification of Phaeobacter arcticus and Phaeobacter leonis as Pseudophaeobacter arcticus gen. nov., comb. nov. and Pseudophaeobacter leonis comb. nov., and the reclassification of Phaeobacter aquaemixtae, Phaeobacter caeruleus, and Phaeobacter daeponensis as Leisingera aquaemixtae comb. nov., Leisingera caerulea comb. nov., and Leisingera daeponensis comb. nov. The genera Phaeobacter and Leisingera are accordingly emended.
Collapse
Affiliation(s)
- Sven Breider
- Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of OldenburgOldenburg, Germany
| | - Carmen Scheuner
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Peter Schumann
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Anne Fiebig
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Jörn Petersen
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Silke Pradella
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Hans-Peter Klenk
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| | - Thorsten Brinkhoff
- Department of Biology of Geological Processes - Aquatic Microbial Ecology, Institute for Chemistry and Biology of the Marine Environment (ICBM), University of OldenburgOldenburg, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell CulturesBraunschweig, Germany
| |
Collapse
|
16
|
Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment. Stand Genomic Sci 2014; 9:687-703. [PMID: 25197454 PMCID: PMC4148953 DOI: 10.4056/sigs.3828824] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Leisingera nanhaiensis DSM 24252T is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252T possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
Collapse
Affiliation(s)
- Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Brian J Tindall
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| |
Collapse
|
17
|
Liu C, Zhang XY, Su HN, Zhou MY, Chen B, Li H, Chen XL, Zhao DL, Zhou BC, Shi M, Zhang YZ. Puniceibacterium antarcticum gen. nov., sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2014; 64:1566-1572. [DOI: 10.1099/ijs.0.057695-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain SM1211T, was isolated from Antarctic seawater. The isolate grew at 4–35 °C and with 0–10 % (w/v) NaCl. It could produce bacteriochlorophyll a, but did not reduce nitrate to nitrite or hydrolyse DNA. Phylogenetic analysis of 16S rRNA gene sequences revealed that strain SM1211T constituted a distinct phylogenetic line within the family
Rhodobacteraceae
and was closely related to species in the genera
Litorimicrobium
,
Leisingera
,
Seohaeicola
and
Phaeobacter
with 95.1–96.0 % similarities. The predominant cellular fatty acid was C18 : 1ω7c. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid and two unidentified phospholipids. The genomic DNA G+C content of strain SM1211T was 60.7 mol%. Based on the phylogenetic, chemotaxonomic and phenotypic data obtained in this study, strain SM1211T is considered to represent a novel species in a new genus within the family
Rhodobacteraceae
, for which the name Puniceibacterium antarcticum gen. nov., sp. nov. is proposed. The type strain of Puniceibacterium antarcticum is SM1211T ( = CCTCC AB 2013147T = KACC 16875T).
Collapse
Affiliation(s)
- Chang Liu
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xi-Ying Zhang
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Hai-Nan Su
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Ming-Yang Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Bo Chen
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai 200136, PR China
| | - Hai Li
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Xiu-Lan Chen
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Dian-Li Zhao
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Bai-Cheng Zhou
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Mei Shi
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| | - Yu-Zhong Zhang
- Marine Biotechnology Research Center, Shandong University, Jinan 250100, PR China
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, PR China
| |
Collapse
|
18
|
Chen Z, Liu Y, Liu LZ, Zhong ZP, Liu ZP, Liu Y. Cribrihabitans marinus gen. nov., sp. nov., isolated from a biological filter in a marine recirculating aquaculture system. Int J Syst Evol Microbiol 2014; 64:1257-1263. [DOI: 10.1099/ijs.0.059576-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative bacterium, strain CZ-AM5T, was isolated from an aerated biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic position was investigated by using a polyphasic approach. Cells of strain CZ-AM5T were non-spore-forming rods, 0.5–0.8 µm wide and 1.2–2.0 µm long, and motile by means of one or two polar or lateral flagella. Strain CZ-AM5T was strictly aerobic, heterotrophic, oxidase-negative and catalase-positive. Growth occurred at 15–40 °C (optimum, 30–35 °C), at pH 6.5–10.5 (optimum, pH 7.0–7.5) and in the presence of 0–12.0 % (w/v) NaCl (optimum, 4.0 %). The predominant fatty acid was C18 : 1ω7c (80.3 %). Ubiquinone 10 (Q-10) was the sole respiratory quinone. The polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. The DNA G+C content was 60.4 mol%. Strain CZ-AM5T showed the highest 16S rRNA gene sequence similarity (96.5 %) to
Phaeobacter caeruleus
LMG 24369T; it exhibited 16S rRNA gene sequence similarity of 95.0–96.5, 95.2–96.3, 96.2, 94.6–95.7 and 94.8–95.8 % to members of the genera
Phaeobacter
,
Ruegeria
,
Citreimonas
,
Leisingera
and
Donghicola
, respectively. However, phylogenetic trees based on 16S rRNA gene sequences showed that strain CZ-AM5T did not join any of the above genera, but formed a distinct lineage in the trees. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain CZ-AM5T is considered to represent a novel genus and species of the family
Rhodobacteraceae
, for which the name Cribrihabitans marinus gen. nov., sp. nov. is proposed. The type strain of Cribrihabitans marinus is CZ-AM5T ( = CGMCC 1.13219T = JCM 19401T).
Collapse
Affiliation(s)
- Zhu Chen
- R&D Center of Marine Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| | - Ying Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Liang-Zi Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Ping Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zhi-Pei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ying Liu
- R&D Center of Marine Biotechnology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, PR China
| |
Collapse
|
19
|
Park S, Park DS, Bae KS, Yoon JH. Phaeobacter aquaemixtae sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2014; 64:1378-1383. [PMID: 24449788 DOI: 10.1099/ijs.0.057646-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, aerobic, non-spore-forming, non-motile and rod-shaped or ovoid bacterial strain, designated SSK6-1(T), was isolated from the zone where the ocean and a freshwater spring meet at Jeju island, South Korea. Strain SSK6-1(T) grew optimally at 30 °C, at pH 7.0-7.5 and in the presence of 2.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences revealed that strain SSK6-1(T) clustered with Phaeobacter daeponensis TF-218(T) and Phaeobacter caeruleus LMG 24369(T), exhibiting sequence similarities of 98.6 and 98.3 %, respectively. The novel strain exhibited sequence similarities of 94.6-97.8 % to the type strains of other recognized species of the genera Phaeobacter and Leisingera. Strain SSK6-1(T) contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and 11-methyl C18 : 1ω7c as the major fatty acids. The major polar lipids of strain SSK6-1(T) were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain SSK6-1(T) was 64.6 mol% and its DNA-DNA relatedness values with P. daeponensis TF-218(T) and P. caeruleus were 21 and 25 %, respectively. The differential phenotypic properties, together with phylogenetic and genetic distinctiveness, revealed that strain SSK6-1(T) is separate from recognized Phaeobacter species. On the basis of the data presented, strain SSK6-1(T) is considered to represent a novel species of the genus Phaeobacter, for which the name Phaeobacter aquaemixtae sp. nov. is proposed. The type strain is SSK6-1(T) ( = KCTC 32538(T) = CECT 8399(T)).
Collapse
Affiliation(s)
- Sooyeon Park
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| | - Doo-Sang Park
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, South Korea
| | - Kyung Sook Bae
- Biological Resources Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, South Korea
| | - Jung-Hoon Yoon
- Department of Food Science and Biotechnology, Sungkyunkwan University, Jangan-gu, Suwon, South Korea
| |
Collapse
|
20
|
Dogs M, Voget S, Teshima H, Petersen J, Davenport K, Dalingault H, Chen A, Pati A, Ivanova N, Goodwin LA, Chain P, Detter JC, Standfest S, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Klenk HP, Göker M, Brinkhoff T. Genome sequence of Phaeobacter inhibens type strain (T5(T)), a secondary metabolite producing representative of the marine Roseobacter clade, and emendation of the species description of Phaeobacter inhibens. Stand Genomic Sci 2013; 9:334-50. [PMID: 24976890 PMCID: PMC4062626 DOI: 10.4056/sigs.4448212] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Strain T5(T) is the type strain of the species Phaeobacter inhibens Martens et al. 2006, a secondary metabolite producing bacterium affiliated to the Roseobacter clade. Strain T5(T) was isolated from a water sample taken at the German Wadden Sea, southern North Sea. Here we describe the complete genome sequence and annotation of this bacterium with a special focus on the secondary metabolism and compare it with the genomes of the Phaeobacter inhibens strains DSM 17395 and DSM 24588 (2.10), selected because of the close phylogenetic relationship based on the 16S rRNA gene sequences of these three strains. The genome of strain T5(T) comprises 4,130,897 bp with 3.923 protein-coding genes and shows high similarities in genetic and genomic characteristics compared to P. inhibens DSM 17395 and DSM 24588 (2.10). Besides the chromosome, strain T5(T) possesses four plasmids, three of which show a high similarity to the plasmids of the strains DSM 17395 and DSM 24588 (2.10). Analysis of the fourth plasmid suggested horizontal gene transfer. Most of the genes on this plasmid are not present in the strains DSM 17395 and DSM 24588 (2.10) including a nitrous oxide reductase, which allows strain T5(T) a facultative anaerobic lifestyle. The G+C content was calculated from the genome sequence and differs significantly from the previously published value, thus warranting an emendation of the species description.
Collapse
Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Sonja Voget
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Karen Davenport
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Lynne A. Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C. Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Sonja Standfest
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Manfred Rohde
- HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Oldenburg, Germany
| |
Collapse
|
21
|
Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis. Stand Genomic Sci 2013; 9:142-59. [PMID: 24501652 PMCID: PMC3910554 DOI: 10.4056/sigs.4287962] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
TF-218T is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218T contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218T possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
Collapse
Affiliation(s)
- Marco Dogs
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Hazuki Teshima
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Hajnalka Dalingault
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| |
Collapse
|
22
|
Nishiyama M, Yamamoto S, Kurosawa N. Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches. J Microbiol 2013; 51:413-22. [PMID: 23990291 DOI: 10.1007/s12275-013-2419-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 03/07/2013] [Indexed: 11/29/2022]
Abstract
Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.
Collapse
Affiliation(s)
- Minako Nishiyama
- Department of Environmental Engineering for Symbiosis, Faculty of Engineering, Soka University, Tokyo 192-8577, Japan
| | | | | |
Collapse
|
23
|
Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564T), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 2013. [DOI: 10.4056/sigs.3927626] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
24
|
Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, Brinkhoff T. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade. Stand Genomic Sci 2013; 8:403-19. [PMID: 24501626 PMCID: PMC3910702 DOI: 10.4056/sigs.3927623] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564T was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.
Collapse
Affiliation(s)
- Paul G Beyersmann
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
| | - Olga Chertkov
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - Jörn Petersen
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Anne Fiebig
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Amy Chen
- Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amrita Pati
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | | | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Lynne A Goodwin
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Patrick Chain
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA
| | - John C Detter
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico, USA ; DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Manfred Rohde
- HZI - Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabine Gronow
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California, USA
| | - Meinhard Simon
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment (ICMB), Oldenburg, Germany
| |
Collapse
|
25
|
Zech H, Hensler M, Koßmehl S, Drüppel K, Wöhlbrand L, Trautwein K, Hulsch R, Maschmann U, Colby T, Schmidt J, Reinhardt R, Schmidt-Hohagen K, Schomburg D, Rabus R. Adaptation of Phaeobacter inhibens DSM 17395 to growth with complex nutrients. Proteomics 2013; 13:2851-68. [PMID: 23613352 DOI: 10.1002/pmic.201200513] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 02/06/2013] [Accepted: 02/23/2013] [Indexed: 12/19/2022]
Abstract
Phaeobacter inhibens DSM 17395, a member of the Roseobacter clade, was studied for its adaptive strategies to complex and excess nutrient supply, here mimicked by cultivation with Marine Broth (MB). During growth in process-controlled fermenters, P. inhibens DSM 17395 grew faster (3.6-fold higher μmax ) and reached higher optical densities (2.2-fold) with MB medium, as compared to the reference condition of glucose-containing mineral medium. Apparently, in the presence of MB medium, metabolism was tuned to maximize growth rate at the expense of efficiency. Comprehensive proteomic analysis of cells harvested at ½ ODmax identified 1783 (2D DIGE, membrane and extracellular protein-enriched fractions, shotgun) different proteins (50.5% coverage), 315 (based on 2D DIGE) of which displayed differential abundance profiles. Moreover, 145 different metabolites (intra- and extracellular combined) were identified, almost all of which (140) showed abundance changes. During growth with MB medium, P. inhibens DSM 17395 specifically formed the various proteins required for utilization of phospholipids and several amino acids, as well as for gluconeogenesis. Metabolic tuning on amino acid utilization is also reflected by massive discharge of urea to dispose the cell of excess ammonia. Apparently, P. inhibens DSM 17395 modulated its metabolism to simultaneously utilize diverse substrates from the complex nutrient supply.
Collapse
Affiliation(s)
- Hajo Zech
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Lee DH, Cho SJ, Kim SM, Lee SB. Sagittula marina sp. nov., isolated from seawater and emended description of the genus
Sagittula. Int J Syst Evol Microbiol 2013; 63:2101-2107. [DOI: 10.1099/ijs.0.040766-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel bacterium, designated strain F028-2T, was isolated from seawater at Damupo beach in Pohang, Korea, and investigated in a taxonomic study using a polyphasic approach. This novel strain was strictly aerobic, non-motile, Gram-stain-negative and rod-shaped, and occasionally formed aggregates. The temperature, pH and NaCl ranges for growth were 4–30 °C, pH 6.5–9.0 and 1–7 % (w/v), respectively. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain F028-2T formed a lineage within the family
Rhodobacteraceae
of the class
Alphaproteobacteria
, and was closely related to members of the genera
Sagittula
and
Antarctobacter
with 96.3–96.4 % sequence similarities. The polar lipid profile of strain F028-2T comprised diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, one unidentified phospholipid and six unidentified lipids. The predominant cellular fatty acids were C18 : 1ω7c and C12 : 1 3-OH. The genomic DNA G+C content of strain F028-2T was 61.6 mol% and the major respiratory quinone was Q-10. Based on phenotypic, phylogenetic and genotypic data, strain F028-2T is considered to represent a novel species in the genus
Sagittula
, for which the name Sagittula marina sp. nov. is proposed. The type strain is F028-2T ( = KCTC 23543T = JCM 17627T). An emended description of the genus Sagittula is also proposed.
Collapse
Affiliation(s)
- Dong-Heon Lee
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| | - Sun Ja Cho
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| | - Suk Min Kim
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| | - Sun Bok Lee
- Gyeongbuk Sea Grant Institute, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-Dong, Pohang 790-784, Republic of Korea
| |
Collapse
|
27
|
Gaboyer F, Tindall BJ, Ciobanu MC, Duthoit F, Le Romancer M, Alain K. Phaeobacter leonis sp. nov., an alphaproteobacterium from Mediterranean Sea sediments. Int J Syst Evol Microbiol 2013; 63:3301-3306. [PMID: 23475346 DOI: 10.1099/ijs.0.046128-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-stain-negative, strictly aerobic, heterotrophic bacterium, designated 306(T), was isolated from near-surface (109 cm below the sea floor) sediments of the Gulf of Lions, in the Mediterranean Sea. Strain 306(T) grew at temperatures between 4 and 32 °C (optimum 17-22 °C), from pH 6.5 to 9.0 (optimum 8.0-9.0) and between 0.5 and 6.0% (w/v) NaCl (optimum 2.0%). Its DNA G+C content was 58.8 mol%. On the basis of 16S rRNA gene sequence similarity, the novel isolate belongs to the class Alphaproteobacteria and is related to the genus Phaeobacter. It shares 98.7% 16S rRNA sequence identity with Phaeobacter arcticus, its closest phylogenetic relative. It contained Q-10 as the only respiratory quinone, C(18:1)ω7c and C(16:0) as major fatty acids (>5%) and phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, two unidentified lipids and an aminolipid as polar lipids. The chemotaxonomic data are consistent with the affiliation of strain 306(T) to the genus Phaeobacter. Results of physiological experiments, biochemical tests and DNA-DNA hybridizations (with P. arcticus) indicate that strain 306(T) is genetically and phenotypically distinct from the five species of the genus Phaeobacter with validly published names. Strain 306(T) therefore represents a novel species, for which the name Phaeobacter leonis sp. nov. is proposed. The type strain is 306(T) ( =DSM 25627(T) =CIP 110369(T) =UBOCC 3187(T)).
Collapse
Affiliation(s)
- Frédéric Gaboyer
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Brian J Tindall
- DSMZ - Deutsche Sammlung von Mikroorganismem und Zellkulturen Gmbh. Inhoffenstr. 7bN D-38124 Braunschweig. Germany
| | - Maria-Cristina Ciobanu
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Frédérique Duthoit
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Marc Le Romancer
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| | - Karine Alain
- Ifremer, UMR6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, F-29280 Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France.,Université de Bretagne Occidentale (UBO, UEB), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Place Nicolas Copernic, F-29280 Plouzané, France
| |
Collapse
|
28
|
Cude WN, Mooney J, Tavanaei AA, Hadden MK, Frank AM, Gulvik CA, May AL, Buchan A. Production of the antimicrobial secondary metabolite indigoidine contributes to competitive surface colonization by the marine roseobacter Phaeobacter sp. strain Y4I. Appl Environ Microbiol 2012; 78:4771-80. [PMID: 22582055 PMCID: PMC3416362 DOI: 10.1128/aem.00297-12] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/25/2012] [Indexed: 11/20/2022] Open
Abstract
Members of the Roseobacter lineage of marine bacteria are prolific surface colonizers in marine coastal environments, and antimicrobial secondary metabolite production has been hypothesized to provide a competitive advantage to colonizing roseobacters. Here, we report that the roseobacter Phaeobacter sp. strain Y4I produces the blue pigment indigoidine via a nonribosomal peptide synthase (NRPS)-based biosynthetic pathway encoded by a novel series of genetically linked genes: igiBCDFE. A Tn5-based random mutagenesis library of Y4I showed a perfect correlation between indigoidine production by the Phaeobacter strain and inhibition of Vibrio fischeri on agar plates, revealing a previously unrecognized bioactivity of this molecule. In addition, igiD null mutants (igiD encoding the indigoidine NRPS) were more resistant to hydrogen peroxide, less motile, and faster to colonize an artificial surface than the wild-type strain. Collectively, these data provide evidence for pleiotropic effects of indigoidine production in this strain. Gene expression assays support phenotypic observations and demonstrate that igiD gene expression is upregulated during growth on surfaces. Furthermore, competitive cocultures of V. fischeri and Y4I show that the production of indigoidine by Y4I significantly inhibits colonization of V. fischeri on surfaces. This study is the first to characterize a secondary metabolite produced by an NRPS in roseobacters.
Collapse
Affiliation(s)
- W. Nathan Cude
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jason Mooney
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Arash A. Tavanaei
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Mary K. Hadden
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - Ashley M. Frank
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | | | - Amanda L. May
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Alison Buchan
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| |
Collapse
|
29
|
Jin HM, Lee HJ, Kim JM, Park MS, Lee K, Jeon CO. Litorimicrobium taeanense gen. nov., sp. nov., isolated from a sandy beach. Int J Syst Evol Microbiol 2010; 61:1392-1396. [PMID: 20639225 DOI: 10.1099/ijs.0.025007-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative, strictly aerobic, non-motile bacterium, designated strain G4(T), was isolated from a sandy beach of Taean in South Korea. Cells were ovoid rods and were catalase- and oxidase-positive. Growth of strain G4(T) was determined at 15-35 °C (optimum 25-30 °C) and pH 6-8 (optimum pH 6.5-7.5). Strain G4(T) contained Q-10 as the predominant isoprenoid quinone and C(18 : 1)ω7c (59.0 %), C(18 : 1)ω7c 11-methyl (11.3 %) and C(12 : 1) 3-OH (9.8 %) as the major fatty acids. The major cellular polar lipids were identified as phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified amino lipid, an unidentified phospholipid and an unidentified lipid. The DNA G+C content was 62.4 mol%. Phylogenetic and comparative analysis based on 16S rRNA gene sequences indicated that strain G4(T) fell within the family Rhodobacteraceae of Alphaproteobacteria and was most closely related to members of the genera Marinovum, Leisingera and Phaeobacter with 95.5-96.4 % sequence similarities. On the basis of phenotypic, chemotaxonomic and molecular properties, strain G4(T) represents a novel species of a novel genus within the family Rhodobacteraceae, for which the name Litorimicrobium taeanense gen. nov., sp. nov. is proposed. The type strain is G4(T) ( = KACC 13706(T) = DSM 22007(T)).
Collapse
Affiliation(s)
- Hyun Mi Jin
- Department of Life Science and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Hyo Jung Lee
- Department of Life Science and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Jeong Myeong Kim
- Department of Life Science and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Moon Su Park
- Department of Life Science and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Kangseok Lee
- Department of Life Science and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| | - Che Ok Jeon
- Department of Life Science and Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul 156-756, Republic of Korea
| |
Collapse
|
30
|
Yoon JH, Kang SJ, Lee SY, Oh KH, Oh TK. Seohaeicola saemankumensis gen. nov., sp. nov., isolated from a tidal flat. Int J Syst Evol Microbiol 2009; 59:2675-9. [PMID: 19625441 DOI: 10.1099/ijs.0.011312-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-negative, non-motile and rod-, oval- or coccoid-shaped bacterial strain, SD-15(T), was isolated from a tidal flat of the Yellow Sea, Korea. The novel strain, which was phylogenetically closely related to the genera Phaeobacter, Leisingera and Marinovum, was studied using a polyphasic taxonomic approach. Strain SD-15(T) grew optimally at pH 7.0-8.0 and 30 degrees C in the presence of 2 % (w/v) NaCl. It contained Q-10 as the predominant ubiquinone and C(18 : 1)omega7c and 11-methyl C(18 : 1)omega7c as the major fatty acids. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content was 63.4 mol%. Strain SD-15(T) exhibited the highest 16S rRNA gene sequence similarity values (95.1-96.4 %) to the type strains of species of the genus Phaeobacter, Leisingera methylohalidivorans MB2(T) and Marinovum algicola ATCC 51440(T). Strain SD-15(T) could be differentiated from members of the genera Phaeobacter, Leisingera and Marinovum by differences in the contents of some fatty acids, by the absence of aminolipid and by differences in some phenotypic properties. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain SD-15(T) represents a new genus and novel species, for which the name Seohaeicola saemankumensis gen. nov., sp. nov. is proposed. The type strain of the type species is Seohaeicola saemankumensis SD-15(T) (=KCTC 22175(T)=CCUG 55328(T)).
Collapse
Affiliation(s)
- Jung-Hoon Yoon
- Korea Research Institute of Bioscience and Biotechnology, Yusong, Taejon, Republic of Korea.
| | | | | | | | | |
Collapse
|