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Albidoferax, a New Genus of Comamonadaceae and Reclassifi Cation of Rhodoferax Ferrireducens (Finneran Et Al., 2003) As Albidoferax Ferrireducens Comb

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Albidoferax, a New Genus of Comamonadaceae and Reclassifi Cation of Rhodoferax Ferrireducens (Finneran Et Al., 2003) As Albidoferax Ferrireducens Comb J. Gen. Appl. Microbiol., 55, 301‒304 (2009) Short Communication Albidoferax, a new genus of Comamonadaceae and reclassifi cation of Rhodoferax ferrireducens (Finneran et al., 2003) as Albidoferax ferrireducens comb. nov. Chintalapati Venkata Ramana1,* and Chintalapati Sasikala2 1 Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500 046, India 2 Bacterial Discovery Laboratory, Centre for Environment, Institute of Science and Technology, J. N. T. University, Kukatpally, Hyderabad, 500 085, India (Received February 4, 2009; Accepted April 10, 2009) Key Words—Comamonadaceae; comb. nov.; Gammaproteobacteria; purple bacteria; Rhodoferax ferrireducens We propose the reclassifi cation of Rhodoferax ferri- fi cation of a new genus and reclassifi cation. reducens (Finneran et al., 2003) into a new genus, as 16S rRNA gene sequences of two uncultured bacte- the strain does not have the property of anoxygenic rial clones (showing 98‒99% sequence similarity) photosynthesis, which is a genus-specifi c property of along with Rhodoferax ferrireducens and other related the phototrophic Proteobacteria. type strains of the family Comamonadaceae were used The genus-specifi c character of the phototrophic for the phylogenetic analysis. 16S rRNA gene se- Proteobacteria is that they all perform anoxygenic pho- quences were aligned using the CLUSTAL X Program tosynthesis with the help of bacteriochlorophylls and (Thompson et al., 1997) and the alignment was cor- carotenoids, which delineates them from the chemo- rected manually. The alignment fi le was saved with the trophs that are interspersed among them. Thus, “.phy” extenstion. The dendrogram was constructed though Haematobacter massiliensis initially was using the PhyML (Guindon and Gascuel, 2003) pro- placed in the phototrophic genus Rhodobacter (as gram using 100 replicates of non parametric bootstrap Rhodobacter massiliensis; Greub and Raoult, 2003) analysis, the GTR model of nucleotide substitution and based on 16S rRNA gene sequence analysis, lack 4 substitution rate categories. of phototrophy coupled with other differences neces- Phylogenetically based on 16S rRNA gene sequence sitated identifi cation of a new genus and reclassifi - similarity, Rhodoferax ferrireducens has 98.3% and cation (Leta et al., 2007). Rhodoferax ferrireducens is 97.25% sequence similarity with Rhodoferax antarcti- another example of a chemotroph which is placed in cus and Rhodoferax fermentans, respectively, though the photosynthetic genus for which we propose identi- clustered separately from the two species (Fig. 1). Lack of phototrophic growth and photosynthetic pig- ments (Table 1) necessitated the reclassifi cation of this * Address reprint requests to: Dr. Chintalapati Venkata Ra- mana, Department of Plant Sciences, School of Life Sciences, organism into a new genus. This observation is strong- University of Hyderabad, P.O. Central University, Hyderabad ly supported by the whole genome data (http://www. 500 046, India. genome.jp/dbget-bin/www_bget?refseq+NC_ E-mail: [email protected]; [email protected] 007908) which clearly provided evidence for the lack 302 Table 1. Differential characteristics of the genera of Comamonadaceaea. Characteristic 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Cell shape R cvr R-S cr cvr R R C B R R R cvr R R cr R R R R Flagella + + + + - ++- ++++++++++++ Isolated from Aq As So; So; As So; So; Fw As Sw So; Fw As Fw Fw So Fw Fw Fw Pt Fw; Fw; Fw; Fw Fw As; As; As; Cs Pt; Cs Cs Optimum growth 25 25‒ 30 30‒ 30‒ 30 30‒ 30284 30203725353020‒ 50‒ 30‒ 24 temperature (°C) 30 35 35 35 30 55 36 Optimum pH 6.7‒ 6.5‒ 7.0 6.8‒ 7.0‒ nd nd 7 7.5‒ nd nd 7 7 6.5‒ 6.5 6‒ 6.5‒ 7.5‒ 5‒6 6.5 7.1 7.0 7.2 7.5 8.2 7.5 8.5 7.5 8.5 Photosynthetic - + ------------++---- pigments Phototrophic growth - + ------------++---- Autotrophic growth - nd - nd --+ - nd nd - nd - + - nd nd - R AMANA with H2 Anaerobic growth +nd- nd + - nd ----++nd--+ --- andS with nitrate as termi- nal electron acceptor ASIKALA Anaerobic growth + ------------------- with Fe (III) as terminal electron acceptor Denitrifi cation + nd - nd + - nd nd ---nd+nd- nd + --- Mol% G+C of DNA †59.5 60 60‒ 62‒ 63‒ 67‒ 65‒ 61 67 52‒ 67‒ 65‒ 68.1 68‒ 66.2‒ 70.5‒ 69.9 69.7 61‒ 68‒ 69 70 65 90 69 57 69 66 71 66.3 72.4 69 69 Growth modes Co Po, Co Cl, Co Co Cl, Co Co Co Co, Co Co Co Co Pl, Co Clh Cl, Co Co, F Co Co Cl Po, Co Co, F aFor symbols see standard defi nitions. R, rods; B, bean shaped; C, cocci; cr, curved rods; S, spiralla; cvr, cocci to short rods; So, soil; Fw, freshwater; Sw, seawater; As, activated sludge; Pt, plant tissue; Cs, clini- cal samples; Aq, aquifer; Pl, photolithoautotrophy; Po, photoorganoheterotrophy; Cl, chemolithoautotrophy; Clh, chemolithoheterotrophy; Co, chemoorganoheterotrophy; F, fermentation. Strain/species: 1, Albidoferax; 2, Rhodoferax; 3, Comamonas; 4, Acidovorax; 5, Brachymonas; 6, Delftia; 7, Hydrogenophaga; 8, Lampropedia; 9, Macromonas; 10, Polaromo- nas; 11, Variovorax; 12, Aquabacterium; 13, Ideonella; 14, Leptothrix; 15, Roseateles; 16, Rubrivivax; 17, Sphaerotilus; 18, Tepidimonas; 19, Thiomonas and 20, Xylophilus; Data for reference species were taken from Brenner et al. (2005). Cells of all taxa studied divide by binary fi ssion. +, present; -, absent; †, Data for strain DSM 15236T is taken from Vol. 55 Vol. the genome sequence analysis (http://genome.ornl.gov/microbial/rfer/ and http://genamics.com/cgi-bin/genamics/genomes/genomesearch.cgi?fi eld=ID&query=1480); nd, not determined. 2009 Albidoferax ferrireducens comb. nov. 303 T Fig. 1. Phylogenetic tree based on 16S rRNA gene sequences showing the relationship of strain T118 within the family Comamonadaceae. The tree was constructed using the PhyML program. Numbers at nodes are bootstrap values. Bar, two nucleotide substi- tutions per 100 nucleotides. Bootstrap values below 50 are removed from the dendrogram. of photopigment production in this organism. ducens converting to a reduced oxidation state; N.L. part. adj. ferrireducens converting iron to a reduced Description of Albidoferax gen. nov. oxidation state). Albidoferax (Al.bi.do.fe’rax, L. adj. albidus, whitish; L The description is same as that for Rhodoferax ferri- T T adj. ferax fertile; N.L. masc. n. Albidoferax, whitish and reducens strain T118 (=ATCC BAA-621 =DSM fertile). Cells are Gram-negative, short rods and are 15236T; Finneran et al., 2003). Rhodoferax ferrire- motile. Phototrophic or fermentative growth is not pos- ducens is a basonym. sible. No photosynthetic pigments. Facultatively an- aerobic: respires with Fe(III)-NTA, Mn(IV) oxide, fumar- References ate, nitrate and atmospheric oxygen. Organic sub- strates are utilized as electron donors. Habitats are Brenner, D. J., Krieg, N. R., Staley, J. T., and Garrity, G. M. (ed.) coastal aquifer sediments. The type species of the ge- (2005) Bergey’s Manual of Systematic Bacteriology, 2nd ed., Springer, New York, Vol. 2, part C, pp. 686 763. nus is Albidoferax ferrireducens. ‒ Finneran, K. T., Johnsen, C. V., and Lovley, D. R. (2003) Rhod- oferax ferrireducens sp. nov., a psychrotolerant, faculta- Albidoferax ferrireducens Description of comb. tively anaerobic bacterium that oxidizes acetate with the nov. reduction of Fe(III). Int. J. Syst. Evol. Microbiol., 53, 669‒ Albidoferax ferrireducens (Rhodoferax ferrireducens) 673. (fer.ri.re.du’cens. L. n. ferrum iron; L. part. adj. re- Greub, G. and Raoult, D. (2003) Rhodobacter massiliensis sp. 304 RAMANA and SASIKALA Vol. 55 nov., a new amoebae-resistant species isolated from the specimens, and reclassifi cation of Rhodobacter massilien- nose of a patient. Res. Microbiol., 154, 631‒635. sis as Haematobacter massiliensis comb. nov. J. Clin. Mi- Guindon, S. and Gascuel, O. (2003) A simple, fast, and accu- crobiol., 45, 1238‒1243. rate algorithm to estimate large phylogenies by maximum Thompson, J. D., Higgins, D. G., Gibson, T. J., Plewniak, F., likelihood. Syst. Biol., 52, 696‒704. Jeanmougin, F., and Higgins, D. G. (1997) The CLUSTAL_X Leta, O. H., Dannie, H., Arnold, G. S., Roger, E. M., Jean, J., Tin, windows interface: Flexible strategies for multiple sequence A., Jon, R., Deanna, J., Dorothy, T., David, R. L., Jean, B. P., alignment aided by quality analysis tools. Nucleic Acids Maryam, I. D., and Paul, N. L. (2007) Haematobacter, a new Res., 25, 4876‒4882. genus of aerobic Gram-negative rods isolated from clinical .
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