Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan
A novel thermophilic phototrophic purple sulphur bacterium was isolated from microbial mats (56 °C) at Nakabusa hot springs, Nagano prefecture, Japan. Cells were motile, rod-shaped, stain Gram-negative and stored sulphur globules intracellularly. Bacteriochlorophyll a and carotenoids of the normal spirilloxanthin series were the major pigments. Dense liquid cultures were red in colour. Strain No.7T was able to grow photoautotrophically using sulfide, thiosulfate, sulfite and hydrogen (in the presence of sulfide) as electron donors and bicarbonate as the sole carbon source. Optimum growth occurred under anaerobic conditions in the light at 50 °C (range, 40–56 °C) and pH 7.2 (range, pH 7–8). Major fatty acids were C16 : 0 (46.8 %), C16 : 1 ω7c (19.9 %), C18 : 1 ω7c (21.1 %), C14 : 0 (4.6 %) and C18 : 0 (2.4 %). The polar lipid profile showed phosphatidylglycerol and unidentified aminophospholipids to be the major lipids. The only quinone detected was ubiquinone-8. 16S rRNA gene sequence comparisons indicated that the novel bacterium is only distantly related to Thermochromatium tepidum with a nucleotide identity of 90.4 %. The phylogenetic analysis supported the high novelty of strain No.7T with a long-branching phylogenetic position within the Chromatiaceae next to Thermochromatium tepidum. The genome comprised a circular chromosome of 2.99 Mbp (2 989 870 bp), included no plasmids and had a DNA G+C content of 61.2 mol%. Polyphasic taxonomic analyses of the isolate suggested strain No.7T is a novel genus within the Chromatiaceae. The proposed genus name of the second truly thermophilic purple sulphur bacterium is Caldichromatium gen. nov. with the type species Caldichromatium japonicum sp. nov. (DSM 110881=JCM 39101).
PfennigN, TrüperHG et al. The family Chromatiaceae. In BalowsA, TrüperHG, DworkinM, HarderW, SchleiferK-H et al. (editors) The Prokaryotes. a Handbook on the Biology of Bacteria. Ecophysiology, Isolation, Identification, Applications, 2nd ed. Berlin: Heidelberg & New York: Springer; 1992 pp 3200–3221
StompM, HuismanJ, StalLJ, MatthijsHCP. Colorful niches of phototrophic microorganisms shaped by vibrations of the water molecule. Isme J2007; 1:271–282 [View Article]
ImhoffJF. Diversity of anaerobic anoxygenic phototrophic purple bacteria. In HallenbeckP. editor Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects Springer International Publishing; 2017 pp 47–85
MadiganMT, JungDO. An overview of purple bacteria: systematics, physiology, and habitats. In HunterCN, DaldalF, ThurnauerMC, BeattyJT. (editors) The Purple Phototrophic Bacteria. Advances in Photosynthesis and Respiration, Vol. 28, The Purple Phototrophic Bacteria Dordrecht: Springer; 2009 pp 1–15
TankM, ThielV, WardDM, BryantDA. A panoply of phototrophs: an overview of the thermophilic chlorophototrophs of the microbial mats of alkaline siliceous hot springs in Yellowstone National Park, WY, USA. In HallenbeckP. editor Modern Topics in the Phototrophic Prokaryotes: Environmental and Applied Aspects Springer International Publishing; 2017 pp 87–137
MadiganMT. Chromatium tepidum sp. nov., a thermophilic photosynthetic bacterium of the family Chromatiaceae. Int J Syst Bacteriol1986; 36:222–227 [View Article]
MartinezJN, NishiharaA, LichtenbergM, TrampeE, KawaiS et al. Vertical distribution and diversity of phototrophic bacteria within a hot spring microbial mat (Nakabusa hot springs, Japan). Microb Environ2019; 34:374–387 [View Article]
KimuraY, LyuS, OkoshiA, OkazakiK, NakamuraN et al. Effects of calcium ions on the thermostability and spectroscopic properties of the LH1-RC complex from a new thermophilic purple bacterium Allochromatium tepidum. J Phys Chem B2017; 121:5025–5032 [View Article]
KampfC, PfennigN. Capacity of Chromatiaceae for chemotrophic growth. specific respiration rates of Thiocystis violacea and Chromatium vinosum. Arch Microbiol1980; 127:125–135 [View Article]
FrigaardN-U, TakaichiS, HirotaM, ShimadaK, MatsuuraK. Quinones in chlorosomes of green sulfur bacteria and their role in the redox-dependent fluorescence studied in chlorosome-like bacteriochlorophyll c aggregates. Arch Microbiol1997; 167:343–349 [View Article]
BieblH, DrewsG. Das in-vivo-Spektrum als taxonomisches Merkmal bei Untersuchungen zur Verbreitung von Athiorhodaceae. Zentralb. Bakterio. Parasitenkd Infektionskr Hyg Abt1969; 2:425–452
GlaeserJ, OvermannJ. Selective enrichment and characterization of Roseospirillum parvum, gen. nov. and sp. nov., a new purple nonsulfur bacterium with unusual light absorption properties. Arch Microbiol1999; 171:405–416 [View Article]
ImanishiM, TakenouchiM, TakaichiS, NakagawaS, SagaY et al. A dual role for Ca 2+ in expanding the spectral diversity and stability of light-harvesting 1 reaction center photocomplexes of purple phototrophic bacteria. Biochemistry2019; 58:2844–2852 [View Article]
KimuraY, HiranoY, YuL-J, SuzukiH, KobayashiM et al. Calcium ions are involved in the unusual red shift of the light-harvesting 1 Qy transition of the core complex in thermophilic purple sulfur bacterium Thermochromatium tepidum. J Biol Chem2008; 283:13867–13873 [View Article]
MinnikinDE, CollinsMD, GoodfellowM. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol1979; 47:87–95 [View Article]
Núñez-CardonaMT. Fatty acids analysis of photosynthetic sulfur bacteria by gas chromatography. In SalihB. editor Gas Chromatography - Biochemicals, Narcotics and Essential Oils InTech; 2012 pp 117–138
ParksDH, ImelfortM, SkennertonCT, HugenholtzP, TysonGW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res2015; 25:1043–1055 [View Article]
OverbeekR, OlsonR, PuschGD, OlsenGJ, DavisJJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res2014; 42:D206–D214 [View Article]
BrettinT, DavisJJ, DiszT, EdwardsRA, GerdesS et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep2015; 5:8365 [View Article]
GloFO, RichterM, RossellR. Genome analysis JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics2016; 32:929–931
TankM, ThielV, ImhoffJF. Phylogenetic relationship of phototrophic purple sulfur bacteria according to pufL and pufM genes. Int Microbiol2009; 12:175–185
WrightES, YilmazLS, NogueraDR. Decipher, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol2012; 78:717–725 [View Article]
YilmazP, ParfreyLW, YarzaP, GerkenJ, PruesseE, LudwigW et al. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Res2014; 42:D643–D648 [View Article]
KimuraM. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol1980; 16:111–120 [View Article]
Caldichromatium japonicum gen. nov., sp. nov., a novel thermophilic phototrophic purple sulphur bacterium of the Chromatiaceae isolated from Nakabusa hot springs, Japan