Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm.


Journal

Antonie van Leeuwenhoek
ISSN: 1572-9699
Titre abrégé: Antonie Van Leeuwenhoek
Pays: Netherlands
ID NLM: 0372625

Informations de publication

Date de publication:
24 Apr 2024
Historique:
received: 13 12 2023
accepted: 18 04 2024
medline: 25 4 2024
pubmed: 25 4 2024
entrez: 24 4 2024
Statut: epublish

Résumé

The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62

Identifiants

pubmed: 38658407
doi: 10.1007/s10482-024-01971-z
pii: 10.1007/s10482-024-01971-z
doi:

Substances chimiques

RNA, Ribosomal, 16S 0
DNA, Bacterial 0
Bacteriochlorophyll A 0

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

70

Subventions

Organisme : MEXT Grants-in-Aid for Young Scientists
ID : 80635839
Organisme : JSPS KAKENHI
ID : JP19H04263

Informations de copyright

© 2024. The Author(s), under exclusive licence to Springer Nature Switzerland AG.

Références

Adachi M, Kanno T, Okamoto R et al (2004) Jannaschia cystaugens sp. nov., an Alexandrium (Dinophyceae) cyst formation-promoting bacterium from Hiroshima Bay Japan. Int J Syst Evol Microbiol 54:1687–1692. https://doi.org/10.1099/ijs.0.03029-0
doi: 10.1099/ijs.0.03029-0 pubmed: 15388729
Arai W, Taniguchi T, Goto S et al (2018) MAPLE 2.3.0:an improved system for evaluating the functinomes of genomes and metagenomes. Biosci Biotech Biochem 82:1515–1517. https://doi.org/10.1080/09168451.2018.1476122
doi: 10.1080/09168451.2018.1476122
Asnicar F, Thomas AM, Beghini F et al. (2020) Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun 11:2500. https://doi.org/10.1038/s41467-020-16366-7
Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
doi: 10.1089/cmb.2012.0021 pubmed: 22506599 pmcid: 3342519
Bauer AW, Kirby WM, Sherris JC et al (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496
doi: 10.1093/ajcp/45.4_ts.493 pubmed: 5325707
Beatty JT (2002) On the natural selection and evolution of the aerobic phototrophic bacteria. Photosyn Res 73:109–114. https://doi.org/10.1023/A:1020493518379
doi: 10.1023/A:1020493518379
Chen S, He M, Lai Q et al (2021) Jannaschia marina sp. nov., isolated from the gut of a gastropod, Onchidium reevesii. Int J Syst Evol Microbiol 71:004756. https://doi.org/10.1099/ijsem.0.004756
Choi DH, Yi H, Chun J et al (2006) Jannaschia seosinensis sp. nov., isolated from hypersaline water of a solar saltern in Korea. Int J Syst Evol Microbiol 56:45–49. https://doi.org/10.1099/ijs.0.63835-0
doi: 10.1099/ijs.0.63835-0 pubmed: 16403865
Cottrell MT, Kirchman DL (2009) Photoheterotrophic microbes in the arctic ocean in summer and winter. Appl Environ Microbiol 75:4958–4966. https://doi.org/10.1128/AEM.00117-09
doi: 10.1128/AEM.00117-09 pubmed: 19502441 pmcid: 2725502
Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368–376
doi: 10.1007/BF01734359 pubmed: 7288891
Felsenstein J (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783
doi: 10.2307/2408678 pubmed: 28561359
Goris J, Konstantinidis KT, Klappenbach JA et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
doi: 10.1099/ijs.0.64483-0 pubmed: 17220447
Hirose S, Matsuura K, Haruta S (2016) Phylogenetically diverse aerobic anoxygenic phototrophic bacteria isolated from epilithic biofilms in Tama River, Japan. Microb Environ 31:299–306. https://doi.org/10.1264/jsme2.ME15209
doi: 10.1264/jsme2.ME15209
Jung YT, Yoon JH (2014) Jannaschia faecimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 64:945–951. https://doi.org/10.1099/ijs.0.057984-0
doi: 10.1099/ijs.0.057984-0 pubmed: 24425817
Kim BY, Yoo SH, Weon HY, Jeon YA, Hong SB et al (2008) Jannaschia pohangensis sp. nov., isolated from seashore sand in Korea. Int J Syst Evol Microbiol 58:496–499. https://doi.org/10.1099/ijs.0.65167-0
doi: 10.1099/ijs.0.65167-0 pubmed: 18218956
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
doi: 10.1007/BF01731581 pubmed: 7463489
Kolber ZS, Plumley FG, Lang AS, Beatty JT, Blankenship RE et al (2001) Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean. Science 292:2492–2495. https://doi.org/10.1126/science.1059707
doi: 10.1126/science.1059707 pubmed: 11431568
Lami R, Cottrell MT, Ras J et al (2007) High abundances of aerobic anoxygenic photosynthetic bacteria in the South Pacific Ocean. Appl Environ Microbiol 73:4198–4205. https://doi.org/10.1128/AEM.02652-06
doi: 10.1128/AEM.02652-06 pubmed: 17496136 pmcid: 1932784
Lamy D, Jeanthon C, Cottrell MT et al (2011) Ecology of aerobic anoxygenic phototrophic bacteria along an oligotrophic gradient in the Mediterranean Sea. Biogeosciences 8:973–985. https://doi.org/10.5194/bg-8-973-2011
doi: 10.5194/bg-8-973-2011
Luo C, Rodriguez-R LM, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42:e7312. https://doi.org/10.1093/nar/gku169
doi: 10.1093/nar/gku169
Macián MC, Arahal DR, Garay E et al (2005) Jannaschia rubra sp. nov., a red-pigmented bacterium isolated from sea water. Int J Syst Evol Microbiol 55:649–653. https://doi.org/10.1099/ijs.0.63412-0
doi: 10.1099/ijs.0.63412-0 pubmed: 15774638
Meier-Kolthoff JP, Auch AF, Klenk HP et al (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60. http://www.biomedcentral.com/1471-2105/14/60
Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95
doi: 10.1111/j.1365-2672.1979.tb01172.x
Park S, Yoon JH (2012) Jannaschia aquimarina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 62:2631–2636. https://doi.org/10.1099/ijs.0.038448-0
doi: 10.1099/ijs.0.038448-0 pubmed: 22199214
Park S, Choi SJ, Won SM et al (2018) Jannaschia confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 68:669–674. https://doi.org/10.1099/ijsem.0.002564
doi: 10.1099/ijsem.0.002564 pubmed: 29388543
Parte AC, Sardà Carbasse J, Meier-Kolthoff JP et al (2020) List of Prokaryotic Names with Standing in Nomenclature (LPSN) moves to DSMZ. Int J Syst Evol Microbiol 70:5607–5612. https://doi.org/10.1099/ijsem.0.004332
doi: 10.1099/ijsem.0.004332 pubmed: 32701423 pmcid: 7723251
Ritchie AE, Johnson ZI (2012) Abundance and genetic diversity of aerobic anoxygenic phototrophic bacteria of coastal regions of the pacific ocean. Appl Environ Microbiol 78:2858–2866. https://doi.org/10.1128/AEM.06268-11
doi: 10.1128/AEM.06268-11 pubmed: 22307290 pmcid: 3318826
Rodriguez-R LM, Konstantinidis KT (2014) Bypassing cultivation to identify bacterial species. Microbe 9:111–118
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. Epub ahead of print 1987. https://doi.org/10.1093/oxfordjournals.molbev.a040454 .
Sato-Takabe Y, Nakao H, Kataoka T et al (2016) Abundance of common aerobic anoxygenic phototrophic bacteria in a coastal aquaculture area. Front Microbiol 7:1996. https://doi.org/10.3389/fmicb.2016.01996
doi: 10.3389/fmicb.2016.01996 pubmed: 28018324 pmcid: 5156720
Sato-Takabe Y, Nakajima Y, Suzuki S et al (2021) Draft genome sequences of putative aerobic anoxygenic phototrophic bacterial strains Jannaschia sp. strains AI_61 and AI_62, isolated from seawater around a coastal aquaculture area. Microbiol Resour Announc 10:e00491-e521. https://doi.org/10.1128/mra.00491-21
doi: 10.1128/mra.00491-21 pubmed: 34264117 pmcid: 8281076
Seemann T (2014) Prokka: Rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. https://doi.org/10.1093/bioinformatics/btu153
doi: 10.1093/bioinformatics/btu153 pubmed: 24642063
Tamura K, Stecher G, Kumar S (2021) MEGA 11: Molecular evolutionary genetics analysis version 11. Mol Biol Evol 38:3022–3027. https://doi.org/10.1093/molbev/msab120
doi: 10.1093/molbev/msab120 pubmed: 33892491 pmcid: 8233496
Takami H (2019) MAPLE enables functional assessment of Microbiota in various enviroonments. In: Gojobori T, Wada T, Kobayashi T. Mineta K (eds). Marine metagenomisc-technological aspects and applications. (Springer) pp 85–119. https://doi.org/10.1007/978-981-13-8134-8_7
Wagner-Döbler I, Rheims H, Felske A et al (2003) Jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine Roseobacter clade from the North Sea. Int J Syst Evol Microbiol 53:731–738. https://doi.org/10.1099/ijs.0.02377-0
doi: 10.1099/ijs.0.02377-0 pubmed: 12807194
Watanabe K, Morohoshi S, Kunihiro T et al (2020) Fluviibacter phosphoraccumulans gen. nov., sp. nov., a polyphosphate-accumulating bacterium of Fluviibacteraceae fam. nov., isolated from surface river water. Int J Syst Evol Microbiol 70:5551–5560. https://doi.org/10.1099/ijsem.0.004446
doi: 10.1099/ijsem.0.004446 pubmed: 32915122
Yoon JH, Kang SJ, Park S et al (2007) Jannaschia donghaensis sp. nov., isolated from seawater of the East Sea. Korea Int J Syst Evol Microbiol 57:2132–2136. https://doi.org/10.1099/ijs.0.65026-0
doi: 10.1099/ijs.0.65026-0 pubmed: 17766886
Yoon JH, Kang SJ, Park S et al (2010) Jannaschia seohaensis sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 60:191–195. https://doi.org/10.1099/ijs.0.011270-0
doi: 10.1099/ijs.0.011270-0 pubmed: 19648318
Yurkov V, Csotonyi JT (2008) New Light on Aerobic Anoxygenic Phototrophs. In: The Purple Phototrophic Bacteria. Advances in Photosynthesis and Respiration. Springer, Dordrecht. C. Neil HunterFevzi DaldalMarion C. ThurnauerJ. Thomas Beatty. pp. 31–55.
Yurkov V, Hughes E (2017) Aerobic anoxygenic phototrophs: Four decades of mystery. In: Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects. Springer, pp. 193–214.
Zeng Y, Feng F, Medová H et al (2014) Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes. Proc Natl Acad Sci USA 111:7795–7800. https://doi.org/10.1073/pnas.1400295111
doi: 10.1073/pnas.1400295111 pubmed: 24821787 pmcid: 4040607
Zhang R, Wang C, Wang XT et al (2019) Jannaschia formosa sp. nov., isolated from marine saltern sediment. Int J Syst Evol Microbiol 69:2037–2042. https://doi.org/10.1099/ijsem.0.003424
doi: 10.1099/ijsem.0.003424 pubmed: 31066657
Zobell CE (1941) Studies on marine bacteria. I-The cultural requirements of heterotrophic aerobes. J Mar Res 4:42–75

Auteurs

Koyo Kuwata (K)

Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-Ku, Tokyo, 113-8657, Japan.

Yuki Sato-Takabe (Y)

Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8564, Japan. yukitakabe@isc.senshu-u.ac.jp.
School of Economics, Senshu University, 2-1-1 Higashi-Mita, Tama-Ku, Kawasaki-Shi, Kanagawa, 214-8580, Japan. yukitakabe@isc.senshu-u.ac.jp.

Ryosuke Nakai (R)

Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu-Higashi, Toyohira-Ku, Sapporo, 062-8517, Japan.

Yuya Sugimura (Y)

Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan.

Nozomi Tazato (N)

Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan.

Tadao Kunihiro (T)

Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan.

Sho Morohoshi (S)

Technical Department, TechnoSuruga Laboratory Co., Ltd, 388-1 Nagasaki, Shimizu-Ku, Shizuoka, 424-0065, Japan.

Mitsunori Iwataki (M)

Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-Ku, Tokyo, 113-8657, Japan.

Koji Hamasaki (K)

Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8564, Japan.
Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8564, Japan.
Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan.

Takuhei Shiozaki (T)

Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8564, Japan.

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