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1 Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
2 Institut für Bakteriologie, Mykologie und Hygiene, Veterinärmedizinische Universität, A-1210 Wien, Austria
3 Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, D-10317 Berlin, Germany
4 Institut für Mikrobiologie und Genetik, Universität Wien, A-1030 Wien, Austria
5 DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen, Mascheroder Weg 1b, D-38124 Braunschweig, Germany
Correspondence
Peter Kämpfer
peter.kaempfer{at}agrar.uni-giessen.de
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ABSTRACT |
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-2 subclass of the Proteobacteria related to Ochrobactrum tritici (95·6 %), Ochrobactrum grignonense (95·0 %) and Ochrobactrum anthropi (94·6 %), and the phylogenetic distance from any validly described species within the genus Brucella was less than 95 %. Chemotaxonomic data (major ubiquinone – Q-10; major polyamines – spermidine and putrescine; major polar lipids – phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine; major fatty acids – C18 : 1
7c and C19 : 0 cyclo 8c) supported the affiliation of strain Iso 196T to the genus Ochrobactrum. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Iso 196T from the four validly published Ochrobactrum species. Iso 196T therefore represents a new species, for which the name Ochrobactrum gallinifaecis sp. nov. is proposed, with the type strain Iso 196T (=DSM 15295T =CIP 107753T).
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain Iso 196T is AJ519939.
Supplementary fatty acid and phylogenetic trees are available in IJSEM Online.
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TOPABSTRACTMAIN TEXTREFERENCES |
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). This policy has been introduced not only for economic reasons, but also to allow a higher throughput of high-quality descriptions that combine the publication of taxa as printed material, as required by Rule 25a of the Bacteriological Code (1990 Revision) (Lapage et al., 1992), with the option of online access to supplementary data. Although the Note format has been well received, the Editors of IJSEM agreed that the provision of an even more standardized format would facilitate the efforts of both authors and referees. On the other hand, it has been made very clear that any format should not be seen purely from an economic point of view, and that some degree of flexibility should be granted at the discretion of the Editors, depending on the availability of salient characters that cannot be defined as supplementary data. It is unlikely that a single format will be appropriate for the description of all prokaryotic taxa, as the information needed to describe, for example, a chemolithoautotrophic organism, differs significantly from the description of an actinobacterium. Thus, several formats may need to be developed to cover the taxon species of the domains Archaea and Bacteria.
The following format is written for a heterotrophic, Gram-negative member of the Proteobacteria, a category to which a large number of recent newly described taxa belong. The following points highlight the most important features of the standardized format, but the authors are also asked to follow the Instructions for Authors. It should be stressed that the description should meet all the requirements of the Minimal Standards, if available. Presentation of results must be accompanied with the confirmation that the analyses carried out conformed to tests recommended in the minimal standards. Authors should also consult the report on the re-evaluation of the species definition in bacteriology (Stackebrandt et al., 2002).
Introduction: this section can be omitted in most descriptions; refrain from history of the genus, only listing references of already described species, listing of species names and ecological role. In most cases, it is not important to state the reasons why strains of the new taxon have been isolated:
The genus Ochrobactrum was first described by Holmes et al. (1988), and at present the genus comprises the four species, Ochrobactrum anthropi (Holmes et al., 1988), Ochrobactrum intermedium (Velasco et al., 1998), Ochrobactrum tritici and Ochrobactrum grignonense (Lebuhn et al., 2000).
All sections describing isolation and determination of characteristics should allow repetition of the work. Recent surveys on individual subsections have indicated rather extensive coverage of molecular methods and phylogenetic analysis. In many cases, citations can replace detailed descriptions of the procedures. Variations of the rRNA gene sequence and phylogenetic analysis, and analysis of chemical constituents only necessary for genus affiliation, should be described in comparison with published data as concisely as possible. Phylogenetic analyses should be done at least with the neighbour-joining algorithm and maximum-parsimony algorithm with bootstrap values to provide evidence for the robustness of the analysis. Phylogenetic dendrograms should only be shown if the position of the novel species changes significantly the intrageneric structure of previously published dendrograms. Large datasets should go into the supplementary data system in IJSEM Online.
During the characterization of organisms isolated from chicken faeces, strain Iso 196T was recovered on MacConkey agar (Oxoid) at 37 °C, showing a beige-coloured colony on nutrient agar. Subcultivation was done on tryptone soy agar (TSA) at 28 °C for 48 h. On this agar, Iso 196T was able to grow at 10–37 °C, but not at 4 or 45 °C. Growth at 37 °C was also observed on nutrient agar and R2A agar, but not on SS agar (all from Oxoid).
Gram-staining was performed as described by Gerhardt et al. (1994). Cell morphology was observed under a Zeiss light microscope at x1000, with cells grown for 3 days at 28 °C on TSA. The 16S rRNA gene was analysed as described by Kämpfer et al. (2003). Phylogenetic analysis was performed using the software packages ARB (Strunk et al., 2000) and MEGA (Molecular Evolutionary Genetics Analysis) version 2.1 (Kumar et al., 2001) after multiple alignment of data by CLUSTALX (Thompson et al., 1997). Distances (distance options according to the Kimura two-parameter model) and clustering with the neighbour-joining and maximum-parsimony methods were determined by using bootstrap values based on 1000 replications (results are available as supplementary data in IJSEM Online). The 16S rRNA sequence of strain Iso 196T was a continuous stretch of 1415 bp. Sequence similarity calculations after a neighbour-joining analysis indicated that the closest relatives of strain Iso 196T were O. tritici (95·6 %), O. grignonense (95·0 %) and O. anthropi (94·6 %). Lower sequence similarities (<95·0 %) were found with all validly described species of the genus Brucella.
Results of chemotaxonomic analyses are given in the species description. The following analytical procedures were performed as described: respiratory quinones (Tindall, 1990; Altenburger et al., 1996); polyamines (Busse & Auling, 1988; Busse et al., 1997); polar lipids (Ventosa et al., 1993); fatty acids (Kämpfer & Kroppenstedt, 1996). The quinone system supports affiliation of Iso 196T to the -Proteobacteria, where the majority of species (including O. anthropi) have Q-10 as the major quinone (Lechner et al., 1995; Yokota et al., 1992). The polyamine pattern is in excellent agreement with the patterns reported previously for two strains, including the type strain, of O. anthropi (Lechner et al., 1995; Hamana & Takeuchi, 1998) and is distinct from the polyamine patterns of members of the genera Rhizobium, Mesorhizobium, Sinorhizobium, Aminobacter, Pseudaminobacter, Phyllobacterium and Mycoplana, which were shown to contain sym-homospermidine in at least minor amounts (Busse & Auling, 1988; Hamana & Takeuchi, 1998; Kämpfer et al., 1999). The polar lipid profile of Iso 196T (available as supplementary data in IJSEM Online) is similar to those reported for species of the related genera Aminobacter, Pseudaminobacter (Kämpfer et al., 1999), Sinorhizobium (Geiger et al., 1999) and Mesorhizobium (Choma & Komaniecka, 2002). The presence of the unknown aminolipid (AL) distinguishes Iso 196T and O. anthropi LMG 7991 from both Aminobacter and Pseudaminobacter, but it may correspond to the phosphorus-free ornithine lipid detected in species of the genera Mesorhizobium and Sinorhizobium. The fatty acid profile of strain Iso 196T (available as supplementary data in IJSEM Online) was composed of C19 : 0 cyclo 8c (47·2 %), C18 : 17c (28·8 %), C16 : 0 (8·9 %), C18 : 0 (3·7 %), summed feature 3=C16 : 17c/i-C15 : 0 2-OH (3·7 %), C18 : 1 2-OH (1·5 %), C17 : 0 cyclo (2·9 %) and 11-methyl-C18 : 17t (1·1 %). No significant differences in the fatty acid profiles were found for the other Ochrobactrum species, except that O. tritici produced significantly lower amounts of C19 : 0 cyclo 8c (data not shown).
Phenotypic (here physiological) and genotypic properties for species differentiation within a genus should only be shown in comparison to phylogenetically related species (if possible all species of the genus) in table format (or in the text, if possible) and the species description should refer to this table. Only discriminatory reactions (on the basis of comparable methods, which has to be proven) should be shown in the body of the table, while identical reactions should be given in the legend.
Results of the physiological characterization are given in the species description, with methods as described previously (Kämpfer et al., 1991). DNA–DNA hybridization experiments were performed with Iso 196T and type strains of all Ochrobactrum species using the method described by Ziemke et al. (1998), except that for nick translation, 2 µg DNA was labelled during a 3 h incubation at 15 °C. Strain Iso 196T showed relatively low DNA–DNA similarity to the type strains of O. anthropi CIP 14970T (34 %), O. intermedium LMG 3301T (14 %), O. tritici LMG 18957T (33·5 %) and O. grignonense DSM 13338T (18·8 %). Pooled standard deviations of all hybridization experiments were between 2·0 and 11·6 %.
Species description: if necessary give emended description of the genus.
Description of Ochrobactrum gallinifaecis sp. nov.
Ochrobactrum gallinifaecis (gal.li.ni.fae'cis. L. fem. n. gallina hen; L. n. faex faeces; N.L. gen. n. gallinifaecis of the faeces of a hen).
Cells are non-motile, non-spore-forming rods (approx. 2 µm in length). Gram-negative, oxidase-positive, showing an oxidative metabolism. Good growth occurs on R2A agar, TSA, nutrient agar and MacConkey agar at 25–30 °C; beige, translucent and shiny colonies with entire edges form within 24 h, with a diameter of approximately 2 mm. Quinone system of strain Iso 196T consists of Q-10 (89·9 %), Q-9 (9·7 %) and Q-8 (0·4 %). Polyamine pattern consists of the major compounds spermidine [11·9 µmol (g dry wt)-1] and putrescine [6·5 µmol (g dry wt)-1], and minor amounts of 1,3-diaminopropane [0·8 µmol (g dry wt)-1] and spermine [0·1 µmol (g dry wt)-1]. Predominant polar lipids are phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and phosphatidylcholine (PC). Additionally, moderate amounts of phosphatidylmonomethylethanolamine (PME), phosphatidyldimethylethanolamine (PDE), diphosphatidylglycerol (DPG) and an unidentified phosphorus-free aminolipid (AL); small amounts of two unknown phospholipids (PL1, PL2) and three unknown lipids (L1, L2, L3) are detected. Fatty acid profile was largely composed of C18 : 17c (28·8 %) and C19 : 0 cyclo 8c (47·2 %). In addition, C18 : 1 2-OH (1·5 %) was detected. Carbon source utilization and hydrolysis of chromogenic substates (including differentiating characters for all Ochrobactrum species) are indicated in Table 1.
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ACKNOWLEDGEMENTS |
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REFERENCES |
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Kämpfer, P. & Kroppenstedt, R. M. (1996). Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42, 989–1005.
Kämpfer, P., Steiof, M. & Dott, W. (1991). Microbiological characterisation of a fuel-oil contaminated site including numerical identification of heterotrophic water and soil bacteria. Microb Ecol 21, 227–251.
Kämpfer, P., Müller, C., Mau, M., Neef, A., Auling, G., Busse, H.-J., Osborn, A. M. & Stolz, A. (1999). Description of Pseudaminobacter gen. nov. with two new species, Pseudaminobacter salicylatoxidans sp. nov. and Pseudaminobacter defluvii sp. nov. Int J Syst Bacteriol 49, 887–897.
Kämpfer, P., Dreyer, U., Neef, A., Dott, W. & Busse, H.-J. (2003). Chryseobacterium defluvii sp. nov., isolated from wastewater. Int J Syst Evol Microbiol 53, 93–97.
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-D-galactopyranoside*, pNP-
, itaconate, mesaconate, phenylacetate*,