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Rhodobacter Johrii Sp. Nov., an Endospore- Producing Cryptic Species Isolated from Semi-Arid Tropical Soils

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Rhodobacter Johrii Sp. Nov., an Endospore- Producing Cryptic Species Isolated from Semi-Arid Tropical Soils International Journal of Systematic and Evolutionary Microbiology (2010), 60, 2099–2107 DOI 10.1099/ijs.0.011718-0 Rhodobacter johrii sp. nov., an endospore- producing cryptic species isolated from semi-arid tropical soils K. R. Girija,1 Ch. Sasikala,1 Ch. V. Ramana,2 C. Spro¨er,3 S. Takaichi,4 V. Thiel5 and J. F. Imhoff5 Correspondence 1Bacterial Discovery Laboratory and Resource Centre, Centre for Environment, IST, JNT University, Ch. V. Ramana Kukatpally, Hyderabad 500 085, India [email protected] or sasi449@ 2Department of Plant Sciences, School of Life Sciences, University of Hyderabad, PO Central yahoo.ie University, Hyderabad 500 046, India 3DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany 4Department of Biology, Nippon Medical School, Kosugi-cho, Nakahara, Kawasaki 211-0063, Japan 5Leibniz-Institut fu¨r Meereswissenschaften IFM-GEOMAR, Marine Mikrobiologie, Du¨sternbrooker Weg 20, 24105 Kiel, Germany An oval to rod-shaped, phototrophic, purple non-sulfur bacterium, strain JA192T, was isolated from an enrichment culture of a pasteurized rhizosphere soil sample from a field cultivated with jowar (sorghum) collected from Godumakunta village near Hyderabad, India. Strain JA192T is Gram-negative, motile and produces endospores. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that the strain JA192T is closely related to Rhodobacter sphaeroides 2.4.1T (99.9 % sequence similarity), Rba. megalophilus JA194T (99.8 %) and Rba. azotoformans KA25T (98.1 %) and clusters with other species of the genus Rhodobacter of the family Rhodobacteraceae. However, DNA–DNA hybridization with Rba. sphaeroides DSM 158T, Rba. megalophilus JA194T and Rba. azotoformans JCM 9340T showed relatedness of only 38– 57 % with respect to strain JA192T. On the basis of 16S rRNA gene sequence analysis, DNA– DNA hybridization data and morphological, physiological and chemotaxonomic characters, strain JA192T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter johrii sp. nov. is proposed. The type strain is JA192T (5DSM 18678T 5JCM 14543T 5MTCC 8172T). At the time of writing, the genus Rhodobacter comprises 11 soils of Andhra Pradesh, India. According to 16S rRNA recognized species, Rhodobacter capsulatus, Rba. sphaer- gene sequence analysis, the isolate, designated strain oides, Rba. azotoformans, Rba. blasticus, Rba. veldkampii JA192T, clustered within the genus Rhodobacter. On the and six species described by our group, Rhodobacter basis of phenotypic and molecular analysis, it is proposed vinaykumarii (Srinivas et al., 2007), Rba. changlensis (Anil that strain JA192T represents a novel species. Kumar et al., 2007), Rba. ovatus (Srinivas et al., 2008), Rba. In May 2002, a wet rhizosphere soil sample from a field maris (Venkata Ramana et al., 2008), Rba. megalophilus cultivated with jowar (sorghum) was collected from (Arunasri et al., 2008) and Rba. aestuarii (Anil Kumar et al., Godumakunta village, Hyderabad, India (17.28u N 78.35u 2009). In this study, a strain was isolated from semi-arid E), and brought to the laboratory. The soil was first air- dried for 24 h in the laboratory and then pasteurized Abbreviations: ICM, internal cytoplasmic membrane; PHA, poly-b- (80 uC for 30 min in a hot oven) as described previously hydroxyalkanoate. (Madigan, 1992). Pasteurized soil (0.5 g) was added to a The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene mineral medium (Biebl & Pfennig, 1981) with pyruvate sequence of strain JA192T is AM398152. (0.1 %, w/v) and ammonium chloride (0.1 %, w/v) as Further micrographs of strain JA192T, results of FTIR fingerprinting and carbon and nitrogen sources, respectively, in fully filled a whole-cell absorption spectrum are available as supplementary screw-capped tubes (106100 mm) and incubated at 30 uC material with the online version of this paper. and 2400 lx. Olive-green enrichments of heliobacteria 011718 G 2010 IUMS Printed in Great Britain 2099 K. R. Girija and others (identified through whole-cell absorption maxima for cells by the hanging drop technique were assessed bacteriochlorophyll g at 785–790 nm) were observed after according to Skerman (1967). Flagella and internal 7 days. The enrichment culture was streaked on agar test- cytoplasmic membrane (ICM) structures were determined tube slants (256150 mm test tubes sealed with subba seals using transmission electron microscopy by the protocol of and flushed with argon) and after 48 h of incubation only Arunasri et al. (2005). Sizes of vegetative cells and spores of one type of reddish-brown colonies appeared on the slants. strain JA192T were determined from scanning electron The culture was purified by repeated streaking on the agar microscope images after fixing the cells in glutaraldehyde slants to yield a pure culture. The strain was maintained in (2.5 % glutaraldehyde in 0.05 M phosphate buffer, pH 7.2) broth and preserved by lyophilization. for 24 h at 4 uC and post-fixing (2 h) in aqueous (2 %) osmium tetroxide. After a process of dehydration, the air- For 16S rRNA gene amplification by PCR, DNA was dried sample was gold coated and viewed in a JEOL JSM extracted from a single colony by a boiling method (Englen 5600 scanning electron microscope. & Kelley, 2000). PCR amplification was done as described previously (Imhoff et al., 1998b) and 16S rRNA gene Poly-b-hydroxyalkanoate (PHA) granules were observed sequencing was performed using the BigDye Terminator by epifluorescence microscopy after Nile blue A staining version 1.1 sequencing kit (Applied Biosystems) in a 3730 (Ostle & Holt, 1982). Spore staining was done according to DNA Analyzer (Applied Biosystems) as specified by the Schaeffer & Fulton (1933) using a Himedia staining kit. manufacturer. For sequencing, primers 342f (Lane, 1991), Fluorescent staining was done using acridine orange 790f (59-GATACCCTGGTAGTCC-39) and 543r (Muyzer according to the method described by Schichnes et al. et al., 1993) were used. Sequence similarities were (2006). In vivo absorption spectra were measured with a determined using the BLAST 2 SEQUENCES program Spectronic Genesys 2 spectrophotometer in sucrose (Tatusova & Madden, 1999). Sequences were aligned using solution (Tru¨per & Pfennig, 1981). Carotenoid composi- the CLUSTAL_X program (Thompson et al., 1997) using tion was analysed by using HPLC (Takaichi & Shimada, standard settings and the alignment was improved 1992). Fatty acid methyl esters were prepared, separated manually. Phylogenetic trees were reconstructed by the and identified according to the instructions for the neighbour-joining (NJ; Fig. 1) and maximum-parsimony Microbial Identification System (Microbial ID; MIDI; (MP) methods (topologies of the NJ and MP trees were Agilent 6850) (Sasser, 1990); this analysis was carried out very similar) using MEGA 4.0 software (Tamura et al., 2007). by M/s Royal Life Sciences Pt. Ltd (Secunderabad, India). Genomic DNA was extracted and purified according to the Dipicolinic acid (pyridine 2,6-dicarboxylic acid) was method of Marmur (1961) and the G+C content of the extracted from sporulating cells using the protocol of DNA was determined by HPLC (Mesbah et al., 1989). Janssen et al. (1958) and analysed using HPLC. HPLC analysis was performed at room temperature using a Morphological and physiological characteristics were Shimadzu SPD-10AVP isocratic system. Methanol/water/ determined as follows. Gram-staining and motility of the acetonitrile (1 : 1 : 0.25) was used as the solvent at 1.0 ml Fig. 1. Phylogenetic tree based on 16S rRNA gene sequence analysis of members of the Rhodobacteraceae including strain JA192T and all Rhodobacter species with validly published names. The NJ tree was constructed using MEGA 4.0 (Tamura et al., 2007). Numbers at nodes represent bootstrap values (100 replicates). Bar, 2 substitutions per 100 nucleotide positions. 2100 International Journal of Systematic and Evolutionary Microbiology 60 Rhodobacter johrii sp. nov. (a) (c) Fig. 2. Micrographs of cells of strain JA192T. (b) (d) (a) Phase-contrast photomicrograph of veget- ative cells. Bar, 2.5 mm. (b) Phase-contrast photomicrograph of sporulating cells (arrows). ICM ES Bar, 5 mm. (c) Malachite green-stained spor- ulating cells. Bar, 5.5 mm. (d) Transmission electron micrograph showing sporulated cell along with vesicular ICM structures and thick- walled endospore (ES). Bar, 0.39 mm. 21 [ ] min Luna 5m C18 (2) 100A column; 25064.6 mm and temperature controller with in-situ temperature probe compounds were detected using a UV-Vis detector at (Varian). 270 nm. The retention time for calcium dipicolinate was Individual cells of strain JA192T were oval to rod-shaped 2.5 min. Endometabolome (fingerprinting) analysis of (Fig. 2a), 0.8–0.9 mm wide and 1.5–1.9 mm long lyophilized cells of both sporulated and unsporulated (Supplementary Fig. S1a, available in IJSEM Online), motile cultures of strain JA192T was carried out using a Fourier- (polar flagella; Supplementary Fig. S2) and multiplied by transform infrared (FT-IR) spectrometer (Perkin Elmer) binary fission (Fig. 2a). Electron photomicrographs of equipped with a KBr beam splitter and a DTGS detector. ultrathin sections of vegetative cells demonstrated the Spectra were recorded between 4000 and 450 cm21 at a presence of a vesicular type of internal membrane structures resolution of 4 cm21 and the data were processed using (Fig. 2d). Since JA192T was the only strain of phototroph spectrum one software. that grew from the thoroughly
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