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1 Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
2 DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7b, D-38124 Braunschweig, Germany
3 Technical University of Braunschweig, Institute of Organic Chemistry, Braunschweig, Germany
Correspondence
Irene Wagner-Döbler
irene.wagner-doebler{at}helmholtz-hzi.de
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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-2 subgroup of the Proteobacteria and was most closely related to Stappia aggregata (97.7 % similarity), Stappia alba (98.0 %) and Stappia marina (98.0 %). Dark-grown cells of strain DFL-11T contained small amounts of bacteriochlorophyll a (bchl a) and a carotenoid. Cells of strain DFL-11T were rods, 0.5–0.7x0.9–3.0 µm in size and motile by means of a single, subpolarly inserted flagellum. The novel strain was strictly aerobic and utilized a wide range of organic carbon sources, including fatty acids, tricarboxylic acid cycle intermediates and sugars. Biotin and thiamine were required as growth factors. Growth was obtained at sea salt concentrations of between 1 and 10 % (w/v), at a pH between 6 and 9.2 and at a temperature of up to 33 °C (optimum, 26 °C). Nitrate was not reduced and indole was not produced from tryptophan. Strain DFL11T was resistant to potassium tellurite and transformed it to elemental tellurium. The major respiratory lipoquinone was ubiquinone 10 (Q10). The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and the glycolipid sulphoquinovosyldiacylglyceride. The fatty acids comprised 16 : 1
7c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 11-methyl 20 : 16t, 20 : 17c, 22 : 0, 22 : 1 and the hydroxy fatty acids 3-OH 14 : 0, 3-OH 16 : 0 (ester-linked), 3-OH 18 : 0, 3-OH 20 : 1 and 3-OH 20 : 0, all of which are amide-linked. The DNA G+C value was 56 mol%. Comparative analysis of -2 subgroup 16S rRNA gene sequences showed that the type species of the genus Stappia, Stappia stellulata, is only distantly related to S. aggregata (95.3 % sequence similarity). Based on the combination of the 16S rRNA gene sequence data, a detailed chemotaxonomic study and the biochemical and physiological properties of members of the genera Stappia, Pannonibacter and Roseibium, it is proposed that S. aggregata, S. alba, S. marina are transferred to a new genus, Labrenzia gen. nov., as Labrenzia aggregata comb. nov., Labrenzia alba comb. nov. and Labrenzia marina comb. nov. The type species of the new genus is Labrenzia alexandrii sp. nov., with strain DFL-11T (=DSM 17067T=NCIMB 14079T) as the type strain. The pufLM genes of the photosynthesis reaction centre were shown to be present in some, but not all, species of the new genus Labrenzia and they were identified for the first time in S. stellulata. In accordance with the new data collected in this study, emended descriptions are provided for the genera Pannonibacter, Roseibium and Stappia.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain DFL-11T is AJ582083.
An electron micrograph showing flagellar insertion in cells of strain DFL-11T and a table featuring a similarity matrix of 16S rRNA gene sequences for strain DFL-11T and related taxa are available as supplementary material in IJSEM Online.
Present address: Heimstättenweg 10, 38126 Braunschweig, Germany. 
Present address: Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Alte Fischerhütte 2, 16775 Stechlin-Neuglobsow, Germany.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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; Rathgeber et al., 2004; Wagner-Döbler & Biebl, 2006). The majority of them belong to the -3 and -4 subgroups of the Proteobacteria, including members of the typical marine genera Roseobacter (-3) and Erythrobacter (-4), although early reports also centred on members of the genus Methylobacterium (see Harashima et al., 1989 for a review). A smaller group of four more or less extremophilic genera were assigned to the -1 subgroup. Within the -2 group, aerobic anoxygenic phototrophs were, until recently, represented only by members of the genus Roseibium, strains of which were isolated from biological material from Shark Bay in West Australia (Shiba et al., 1991; Nishimura et al., 1994; Suzuki et al., 2000).
During our search for aerobic marine bacteria that contain the genes encoding the photosynthetic reaction centre, pufL and pufM, we obtained two groups of aerobic anoxygenic phototrophs that belonged to the -2 subgroup of the Proteobacteria according to their 16S rRNA gene sequences (Allgaier et al., 2003). One group was found to be closely related to members of the genera Ahrensia and Hoeflea and has already been described (Biebl et al., 2006). The other group, presently consisting of only one strain, was found to be related to the genera Roseibium and Stappia and is characterized in the present study.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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), a suitable carbon source and 0.1 g yeast extract or a vitamin solution (Biebl et al., 2005). The pH was adjusted to 7.5 using 0.5 M H2SO4. Cultures were incubated at 30 °C in the dark unless otherwise indicated. Growth was measured turbidometrically at 650 nm. The influence of light and oxygen was tested in soft agar tubes (1 % agar) using the mineral medium with either acetate or glucose as substrates. Incubation was under aerobic and anaerobic conditions in the dark as well as in the light. A purple sulfur bacterium, Rhodobacter veldkampii DSM 11550T, was used for comparison. The following strains were used for reference: Stappia stellulata DSM 5886T, Stappia aggregata DSM 13394T, Stappia marina DSM 17023T, Stappia alba DSM 18320T, Roseibium denhamense JCM 10543T, Roseibium hamelinense JCM 10544T and Pannonibacter phragmitetus DSM 14782T.
Electron microscopy.
Cells in the mid-exponential growth phase were adsorbed onto carbon-Formvar foils for 1 min. Cells were washed once with water, blotted and air-dried. They were shadow-cast at 15° elevation with platinum–carbon and analysed with an energy-filtered transmission electron microscope (CEM902; Zeiss) as described by Golyshina et al. (2000). Cells were also embedded and processed for sectioning as described by Yakimov et al. (1998).
Physiological and biochemical tests.
Tests that required liquid cultures were performed in 22.5 ml metal-capped test tubes containing 5 ml medium. Sigma sea salts were used for determination of the salt requirement in the complex medium in concentrations up to 10.5 % (w/v). The temperature range for growth was determined using a gradient shaking incubator (Toyo Kogaku Sangyo Co. Ltd.) that allowed the temperature to be adjusted between 15 and 45 °C at intervals of 3 °C. The pH range was tested at intervals of 0.5 units between pH 5.0 and 9.5 (initial pH). Growth was measured at an early stage of the growth phase before the pH was appreciably changed by growth. Carbon sources for substrate tests were supplied at a concentration of 1 g l–1. Requirement for vitamins was determined in mixtures of seven vitamins (Biebl et al., 2005) in which one was omitted. The precultures were grown in a medium without any growth factors. Degradation of polymers was tested on agar plates using the complex medium. Starch was added at a concentration of 2 g l–1, alginate at 7.5 g l–1 and Tween 80 (lipase test) and gelatin at 4 g l–1. Starch degradation was demonstrated with Lugol's solution, alginate degradation by clear zones around the colonies, degradation of Tween 80 by the formation of insoluble calcium salts and gelatin liquefaction was confirmed by precipitation of undigested gelatin with saturated ammonium sulfate solution. Nitrate reduction capacity was checked in the 22.5 ml tubes with 10 ml of mineral medium supplemented with 0.4 g NaNO3 and 0.5 g yeast extract l–1. Nitrogen formation was demonstrated using Durham tubes and formation of nitrite and consumption of nitrate were tested with Merckoquant test sticks (Merck). The presence of catalase and oxidase and indole formation were determined according to Gerhardt et al. (1981). The reaction to tellurite was tested either in complex medium or in the mineral medium using sodium acetate (1.37 g l–1) as a carbon source. Analytical grade K2TeO4 was added aseptically to the autoclaved media from a sterile stock solution. Due to its limited solubility in seawater medium, in particular in acetate medium, K2TeO4 was added only up to a final concentration of 1 g l–1. The media were then adjusted to pH 7.6 with sterile 1 M NaOH and dispensed aseptically into sterile metal-capped test tubes in aliquots of 5 ml. Cultures were incubated at 30 °C on a rotary shaker. Tellurium formation was recognized by black–brown to jet-black colouration of the culture.
Photosynthetic pigments.
Photosynthetic pigments were extracted from 30 ml culture grown in complex medium in the dark. Bacterial cells were harvested by centrifugation and pigments were extracted with acetone/methanol (7 : 2). The absorption spectrum was recorded in a Shimadzu UV-3000 double beam spectrophotometer. Bacteriochlorophyll a (bchl a) absorption was measured at 772 nm after 1 h of incubation at room temperature in absolute darkness. An extinction coefficient of 75 mmol cm–1 (Clayton, 1963) was used for the calculation of bchl a concentration.
Fatty acids, respiratory lipoquinones and polar lipids.
Lipoquinones and polar lipids were extracted and separated according to the methods described by Tindall (1990). The fatty acid content was determined by the method described by Labrenz et al. (1999). The unusual fatty acids 11-methyl 18 : 16t and 13-methyl 20 : 16t were characterized by performing several microderivatizations on the methyl ester extracts obtained by acidic methanolysis and GC/MS analysis. Hydrogenation with Pd/C furnished saturated methyl esters carrying a methyl group at positions 11 or 13, respectively (Francke et al., 1989). Double bond positions were determined by the formation of dimethyl disulfide adducts, showing double bonds at C-12 or C-14 (Scribe et al., 1988). Alternatively, formation of 3-pyridinemethanol was performed, but the resulting mass spectra proved to be disappointing. They did not allow for the unequivocal determination of the localization of the double bonds in the methyl-branched compounds (Harvey, 1982). The configuration of the double bonds of 11-methyl 18 : 16t and the bishomologue (E)-13-methyleicosa-14-enoic acid (13-methyl 20 : 16t) were determined by comparison of GC retention behaviour with published values of synthesized (E)- and (Z)-diastereomers of 11-methyl 18 : 16 (Carballeira et al., 1998). While the (E)-diastereomer elutes slightly after 18 : 0 on an apolar phase, the (Z)-diastereomer elutes before this acid. The 13-methyl 20 : 16 present in the strains eluted slightly after 20 : 0, indicating the (E)-configuration of the double bond.
16S rRNA gene sequences and phylogenetic inferences.
DNA extraction, amplification and sequencing of the 16S rRNA gene has been described (Allgaier et al., 2003). The sequence was manually aligned and compared with published sequences from the DSMZ 16S rRNA gene sequence database, including sequences available from the Ribosomal Data Project (Maidak et al., 2001) and EMBL. The manual alignment was constructed with the BioEdit program (Hall, 1999) and used for calculating the distance matrix with DNAdist. A phylogenetic dendrogram was inferred using the Neighbour-Joining method contained in the PHYLIP package (Felsenstein, 1993). Bootstrap analysis was based on 1000 resamplings.
Determination of the DNA G+C content and amplification of the pufLM genes.
The G+C content of the DNA was determined by HPLC (Mesbah et al., 1989). Amplification of the pufLM genes was performed as described by Allgaier et al. (2003).
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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Cells of strain DFL-11T were rods of 0.5–0.7x0.9–3.0 µm. Unequal ends in the longer cells were often observed (Fig. 1). Aggregates, often star-shaped, occurred frequently and have previously been found in many taxa within the Alphaproteobacteria. Cells were motile by means of a single, subpolarly inserted flagellum (Fig. 2 and see Supplementary Fig. S1 in IJSEM Online). Ultrathin-sections showed a typical Gram-negative cell wall (Fig. 2, inset). Colonies on Marine Agar 2216 appeared beige to slightly pink, almost transparent and smooth with an entire margin.
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Addition of 1 g l–1 sodium thiosulfate resulted in a higher yield of cell mass (22 % increase in a mineral medium with 1 g l–1 acetate and 15 % in a peptone-based medium) suggesting that oxidation of this sulfur compound provides additional energy for growth. In contrast to the majority of Gram-negative bacteria, strain DFL-11T is only moderately sensitive to the rare earth salt potassium tellurite. At concentrations of 0.05 g l–1 tellurite, 65 % growth inhibition was observed in peptone medium and 35 % growth inhibition in mineral medium; this increased to 75 % growth inhibition at 0.5 g l–1 tellurite in peptone medium (60 % growth inhibition in mineral medium). Elemental tellurium was formed in small amounts in mineral medium, but not in peptone medium. This mode of reaction to tellurite is similar to that described for Roseococcus thiosulfatophilus by Yurkov et al. (1996).
Photosynthetic pigments in strain DFL-11T
Using specific primers, it has been shown previously that strain DFL-11T contained the photosynthetic reaction centre genes pufL and pufM, suggesting that the complete photosynthetic apparatus might be present. However bchl a could initially not be detected (Allgaier et al., 2003). Meanwhile, using higher amounts of cell mass, bchl a was clearly demonstrated after extraction with acetone/methanol (7 : 2). The bchl a content per cell mass was low in peptone-based medium [0.3 nmol (mg protein)–1], but in the same range as found for other weakly pigmented aerobic bacteriochlorophyll-producing bacteria (Sato, 1978; Yurkov et al., 1993). The absorption spectrum of the acetone/methanol extract showed the typical infra-red peak of bchl a at 772 nm (Fig. 3). Absorption between 420 and 550 nm is due to a carotenoid, probably spheroidenone as inferred from comparison with the absorption spectrum of Dinoroseobacter shibae, where this carotenoid has been identified (Biebl et al., 2005). Due to the low bchl a content, it was not possible to obtain an adequate in vivo absorption spectrum with the existing methods used to reduce light scattering of the cells. However, infrared maxima were seen at about 800 and 865 nm.
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). The absence of pufLM genes can be interpreted as a complete lack of ability to synthesize the photosynthetic reaction centre, however their presence requires more cautious interpretation. Given the fact that the presence of bchl a has not been described for S. stellulata, we analysed acetone extracts of the cells photometrically and obtained a very tiny peak at the expected wavelength. This shows that the cells are able to produce bchl a, albeit at low concentrations. Thus, their photosynthetic reaction centre can be assumed to be functional. Previous studies have shown that several strains of Roseovarius tolerans isolated from different depths were variable with respect to the presence of bchl a; hence the genus name (Labrenz et al., 1999). However, PCR showed that the pufLM genes were present in all of these strains and some showed production of bchl a after several years of maintenance in culture (Labrenz et al., 1999; Allgaier et al., 2003). Similarly, in Hoeflea phototrophica, in spite of the presence of the pufLM genes, bchl a was initially not detected, but was later found in experiments at low nutrient levels and decreased salt concentrations (Biebl et al., 2006). Thus, the expression of the photosynthetic reaction centre genes seems to be highly dependent on environmental parameters in these aerobic bchl a-producing bacteria. It is presently unclear whether the low amounts of bchl a seen in strain DFL-11T under standard cultivation conditions are representative of the expression level in the natural marine environment. It has been shown in chemostat culture of this strain, in which normally only trace amounts of bchl were detected, that starvation periods in combination with illumination caused a drastic increase in bchl production after nutrient supply and darkness were resumed (Biebl & Wagner-Döbler, 2006). However, even under environmental stress, the bchl a level was still low in comparison with the levels found in species such as Roseobacter denitrificans, where bacteriochlorophyll is clearly visible during the extraction of lipid material (B. Tindall, unpublished data) and ‘Erythromicrobium hydrolyticum’ (Yurkov & van Gemerden, 1993). The metabolic significance of this low bchl content is an open question. However, slight energetic advantages (i.e. the ability to harvest light energy, even if not used for photoautotrophic growth) might play an important role under the selective pressure of the open ocean environment.
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and Fig. 4
), bchl a is present in S. marina and strain DFL-11T, but absent in S. aggregata and S. alba. Due to the high degree of similarity of these organisms with respect to fatty acids, polar lipids and morphological and physiological characteristics, together with 16S rRNA gene sequence similarity values which lie between 97.7 and 99.1 %, we do not think that it is warranted to create new genera based mainly/solely on the presence or absence (of trace amounts) of bchl a. We encountered a similar case with two species of the genus Hoeflea. H. phototrophica contained bchl a and Hoeflea marina did not, although their 16S rRNA gene sequence similarity was 98.4 % and they were virtually identical in their chemical composition (Biebl et al., 2006). The pufLM genes encoding the photosynthetic reaction centre proteins have been found on linear plasmids, leading to speculation that they may be transferred horizontally to related species (Pradella et al., 2004). The taxonomic significance of their presence should therefore be viewed in perspective with other traits. Additional studies of further strains and species may support or refute our current taxonomic hypothesis.
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Thin layer chromatograms of extracts from cells of strain DFL-11T showed the presence of phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylmonomethylethanolamine (PMME), sulphoquinovosyldiacylglyceride (SQDG) and an unidentified aminolipid (AL) (Fig. 5). A very similar pattern was found for the two Roseibium species, S. aggregata, S. marina and S. alba. In some of the strains, the presence of PE could not be unambiguously distinguished from possible slight tailing effects from the lipid which runs above it, PMME. PMME is known to arise as a result of methylation of PE, indicating that this latter lipid must be synthesized, even if it could not be unambiguously detected. Furthermore, it is not known whether growth conditions/growth phase may also affect the relative composition of PE and PMME. P. phragmitetus and S. stellulata could clearly be differentiated from the other strains studied since SQDG was not present, providing support for their classification as members of separate genera. The presence of the phospholipids PG, DPG, PC, PE and PMME is a feature typical of certain subgroups within the Alphaproteobacteria. The taxonomic significance of the polar lipid pattern, including the presence/absence of lipids (e.g. SQDG or additional amino lipids), must be interpreted together with the fatty acid patterns.
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and see Supplementary Table S1 in IJSEM Online). In all species tested, fatty acid 18 : 17c was the main component (49–60 %), which is true for virtually all members of the Alphaproteobacteria, a fact usually missed in the majority of species descriptions relating to members of this major evolutionary group. All strains contained 3-OH 14 : 0, an ester-linked fatty acid, probably located in the lipopolysaccharide (and not derived from the polar lipid fraction). This fatty acid has also been reported in members of the Agrobacterium/Rhizobium/Ensifer (formerly the genus Sinorhizobium)/Mesorhizobium group (Tighe et al., 2000; Quan et al., 2005). Additional 3-OH fatty acids included 3-OH 16 : 0, 3-OH 18 : 0, 3-OH 18 : 1 and 3-OH 20 : 0, all of which appeared to be amide-linked. The distribution of these 3-OH fatty acids was such that 3-OH 16 : 0 appeared to be present in strain DFL-11T, S. stellulata and P. phragmitetus. Strain DFL-11T was the only strain in which the 3-OH 16 : 0 fatty acid appeared to be ester-linked, like the 3-OH 14 : 0. Fatty acid 3-OH 18 : 0 was present in all strains examined (albeit in trace amounts in strain DFL-11T). Fatty acid 3-OH 18 : 1 was present in S. stellulata and P. phragmitetus (trace amounts). All strains contained 3-OH derivatives of a C-20 fatty acid. In most cases both the 3-OH 20 : 0 and 3-OH 20 : 1 derivatives were present, the exceptions being S. stellulata (only 3-OH 20 : 0) and P. phragmitetus (only 3-OH 20 : 1). In addition, the majority of strains contained a 20 : 17c fatty acid, although the level in P. phragmitetus was very low and it was below the level of detection in S. stellulata. It is interesting to note that 20 : 17c has also been reported in members of the genus Nesiotobacter (Donachie et al., 2006), but it is apparently absent in members of the genus Pseudovibrio (Fukunaga et al., 2006). These results, taken together with the polar lipid patterns, provided unambiguous evidence for the chemical heterogeneity within the genus Stappia as currently defined and indicated that chemotaxonomy is a valuable parameter in delineating taxa within this group of organisms.
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6t has been previously identified in bacteria (Kerger et al., 1986; Couderc, 1995; Carballeira et al., 1997; Rontani et al., 2005). The bishomologue (E)-13-methyleicosa-14-enoic acid (11-methyl 20 : 16t), which was present in S. aggregata (3 %) and Rib. denhamense (2 %), has, to the best of our knowledge, not been reported before from nature.
Taxonomic position of strain DFL-11T and reorganization of the genus Stappia
The taxonomic position of strain DFL-11T as revealed by neighbour-joining analysis of the 16S rRNA gene sequence alignment is shown in Fig. 6. High similarity was found to S. aggregata IAM 12614T, S. alba 5OM6T and S. marina mano 18T (97.7, 98.0 and 98.0 % sequence similarity, respectively) and somewhat lower similarity to Rib. denhamense Och 254T (96.1 %) and Rib. hamelinense Och 368T (97.1 %). A lower degree of relatedness was exhibited with the non-bchl-containing species from a soda lake, P. phragmitetus (Borsodi et al., 2003) (95.0 % similarity) and still less with S. stellulata (94.3 %). Strain DFL-11T is distinct from the recently described marine genera Nesiotobacter and Pseudovibrio (Shieh et al., 2004; Donachie et al., 2006). The adjacent -2 subgroup of Proteobacteria around the genus Mesorhizobium was clearly separated (about 90 % similarity). The 16S rRNA gene sequence data clearly support the separation of strain DFL-11T, S. alba, S. marina and S. aggregata from S. stellulata, the type species of the genus Stappia.
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. Differences exist with respect to flagellation, polar lipid distribution, occurrence of photosynthetic pigments, reduction of nitrate, indole production, requirement for NaCl and DNA G+C content. Members of the genus Roseibium are characterized by peritrichous flagellation, while in all other species tested one or several flagella are inserted at the cell poles. They are also different from all other tested species in their ability to produce indole from tryptophan. The DNA G+C content of the members of the genus Roseibium is in the upper range for the group, i.e. 58–63 mol%, surpassed only by members of the genus Pannonibacter (65 mol%). In contrast, the DNA G+C content of strain DFL-11T is the lowest among the investigated species (56 mol%). Strain DFL-11T also differs from members of the genus Roseibium (and all described Stappia species) since it is unable to reduce nitrate. The coxL genes have been identified in strain DFL-11T (G. King, personal communication) and in all Stappia species tested so far (King, 2003); it is not known if they are present in species of the genus Roseibium. Photosynthetic pigments are present in members of the genus Roseibium and have been demonstrated to be present in small amounts in two of the four described Stappia species. In S. marina, the presence of only the pufLM genes was detected.
The chemical composition of all the strains examined indicated that many of the features present were typical of members of the class Alphaproteobacteria [i.e. the presence of Q10 and the dominance of 18 : 17c (+11,12-cyclopropane 19 : 0)], whereas other features allowed finer differentiation, in particular the presence/absence of SQDG among the polar lipids as well as the distribution and nature of the linkage of the 3-OH fatty acids. In summary, one of the problems that we have encountered is the fact that, in the past, polar lipid composition has not always been taken into consideration when examining the chemotaxonomy of organisms within the Roseibium–Stappia group. In addition, analysis of the fatty acid content of the strains has not always been as comprehensive as in the studies undertaken here. In particular, the longer chain 3-OH fatty acids have not been reported (although were probably present in the samples). In the case of the fatty acids 3-OH 20 : 1 and 3-OH 20 : 0, the standard identification system offered by MIDI does not presently include them in the peak-naming table. The relevance of the manner in which the 3-OH fatty acids are linked to their parent molecules (i.e. ester- or amide-linked) is an additional feature that allows differentiation, although it is rarely used. Further studies are needed in order to determine the nature of the parent molecule which gives rise to the amide-linked 3-OH fatty acids. The results also indicate that a thorough study of the chemotaxonomy of novel taxa, either within or closely related to this group, is essential in any future taxonomic study and this approach is in line with recommendations made by two ad hoc subcommittees (Wayne et al., 1987; Murray et al., 1990).
Based on these traits, the close relationship of strain DFL-11T with S. aggregata as well as to S. alba and S. marina appears obvious. S. stellulata is only distantly related to S. aggregata (95.3 % gene sequence similarity), justifying the placement of the former group in a separate genus. S. stellulata is the type species (Stapp & Knösel, 1954) which must be retained in the genus and the circumscription emended, while the species S. aggregata, S. alba, S. marina and strain DFL-11T do not fit within that emended circumscription of the genus Stappia and must be placed in a different genus, for which the name Labrenzia gen. nov. is proposed. Accordingly strain DFL-11T represents a novel species of this genus, to be designated Labrenzia alexandrii sp. nov., and also serves as the type species.
The description of S. stellulata must be extended with respect to the presence of the pufLM and coxL genes, the ability to produce small amounts of bchl a, the lack of SQDG and the fatty acid composition. Members of the new genus Labrenzia are differentiated from those of the genus Roseibium by their flagellation, slightly lower DNA G+C content, the presence of coxL genes, their requirement for NaCl and their lack of indole production, as well as in the details of their chemotaxonomy. Bchl a may be present in small amounts. The description of the genus Pannonibacter must also be emended in order to cater for the presence of PC (not phosphatidylserine) and to incorporate details of the fatty acid composition.
We do not consider the presence or absence of trace amounts of bacteriochlorophyll or the presence/absence of the pufLM genes to be a primary taxonomic marker at the genus level in the organisms under study here, although we do not dispute their potential role in the biology of the organisms concerned.
Emended description of the genus Pannonibacter Borsodi et al. 2003
In addition to the criteria given by Borsodi et al. (2003), the genus circumscription is emended as follows. The polar lipid composition comprises PG, DPG, PMME, PC, an amino lipid and an unidentified lipid running close to the amino lipid and PMME. PE is not detected, but it is a precursor of PMME. Neither phosphatidylserine nor the glycolipid SQDG are present. The fatty acids comprise 16 : 17c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 20 : 17c, 22 : 0 and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 16 : 0, 3-0H 18 : 1, 3-OH 18 : 0 and 3-OH 20 : 1, all of which are amide-linked. The type species of the genus is Pannonibacter phragmitetus with the type strain C6/19T (=DSM 14782T=NCAIM B02025T).
Emended description of the genus Stappia Uchino et al. 1999
The description of the genus Stappia is as given by Uchino et al. (1998) with the following additions. The polar lipid composition comprises PG, DPG, PE, PMME, PC and amino lipid. The glycolipid SQDG is absent. The fatty acids comprise 16 : 17c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 20 : 17c, 22 : 0, 22 : 1 and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 16 : 0, 3-OH 18 : 1, 3-OH 18 : 0 and 3-OH 20 : 0, all of which are amide-linked. The fatty acid 3-OH 18 : 0 predominates over 3-OH 18 : 1. Stappia stellulata is the type species of the genus.
Emended description of Stappia stellulata (Rüger and Höfle 1992) Uchino et al. 1999
Has the following characteristics in addition to those described for the genus. The pufLM genes of the photosynthesis reaction centre and the coxL genes for oxidation of carbon monoxide are present. Acetone extracts of dark-grown cells show a small peak at 772 nm, indicating the presence of bchl a. The type strain is ATCC 15215T (=DSM 5886T=CIP 105977T=NBRC 15764T).
Emended description of the genus Roseibium Suzuki et al. 2000
In addition to the criteria given by Suzuki et al. (2000), the genus circumscription is emended as follows. The polar lipid composition comprises PG, DPG, PE, PMME, PC, the glycolipid SQDG and amino lipid. The fatty acids comprise 16 : 0, 18 : 17c, 18 : 0, 20 : 17c and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 18 : 0, 3-OH 20 : 0 and 3-OH 20 : 1, all of which are amide-linked. The level of 20 : 17c is usually in the range 7–11 %. The fatty acid 11-methyl 18 : 16t is produced by all species of the genus and 11-methyl 20 : 16t is produced by some strains. The genus currently comprises Roseibium denhamense and Roseibium hamelinense, the former being the type species.
Emended description of Roseibium denhamense Suzuki et al. 2000
The description is the same as that given by Suzuki et al. (2000) with the addition that the polar lipid composition is consistent with that of the emended genus circumscription. The fatty acids comprise 16 : 17c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 11-methyl 20 : 16t, cyclopropane 197, 20 : 17c, 11-methyl 20 : 16t, 22 : 1 and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 18 : 0, 3-OH 20 : 1 and 3-OH 20 : 0, all of which are amide-linked. The type strain is OCh 254T (=ATCC BAA-251T=CIP 107047T=JCM 10543T=NBRC 16782T).
Emended description of Roseibium hamelinense Suzuki et al. 2000
The description is the same as that given by Suzuki et al. (2000) with the addition that the polar lipid composition is consistent with that of the emended genus circumscription. The fatty acids comprise 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 11-methyl 20 : 16t, 20 : 17c and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 18 : 0, 3-OH 20 : 1 and 3-OH 20 : 0, all of which are amide-linked. The type strain is OCh 368T (ATCC BAA-252T=CIP 107048T=JCM 10544T=NBRC 16783T).
Description of Labrenzia gen. nov.
Labrenzia (Lab.ren'zi.a. N.L. fem. n. Labrenzia from the name Labrenz, honouring Dr Matthias Labrenz, a German marine microbiologist who described many interesting bacterial isolates from hypersaline Ekho Lake, Antarctica, including three new genera of aerobic anoxygenic phototrophs, using a polyphasic approach).
Cells are Gram-negative rods. Motile by means of one or several polarly inserted flagella. Colonies are white to cream, but may become pink if incubated in the dark under appropriate conditions. Ability to produce bchl a in small amounts may be present. NaCl is required for growth. Optimum salinity range is 1–10 %. Optimum pH is 7.0–8.5. May be able to reduce nitrate to nitrite or to N2. Growth is chemoheterotrophic and non-fermentative under aerobic or anaerobic conditions. Indole is not produced. The major respiratory lipoquinone is Q10. The polar lipid composition comprises PG, DPG, PE, PMME, PC, the glycolipid SQDG and an amino lipid. The fatty acids comprise 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 20 : 17c and the hydroxy fatty acids 3-OH 14 : 0, 3-OH 18 : 0 and 3-OH 20 : 0, all of which are amide-linked. The level of fatty acid 20 : 17c is usually in the range 5–10 %. DNA G+C content is 56–60 mol%. The type species is Labrenzia alexandrii.
Description of Labrenzia alexandrii sp. nov.
Labrenzia alexandrii (a.le.xan'dri.i. N.L. gen. n. alexandrii of Alexandrium, the genus name of the dinoflagellate Alexandrium lusitanicum, the source of isolation of the type strain).
Displays the following characteristics in addition to those given in the genus description. Gram-negative rods of 0.5–0.7x0.9–3.0 µm, motile by means of a single, subpolarly inserted flagellum. Cell ends often unequal. Star-shaped aggregates occur. Colonies on Marine Agar 2216 (Difco) are beige to slightly pink, almost transparent, smooth and with entire margin. Strictly aerobic, non-fermentative heterotroph. Growth occurs within a salinity range of 1 to 10 %, a temperature range of 15 to 34 °C (optimum 26 °C) and a pH between 6.0 and 9.2 (optimum 7.0 to 8.5). The type strain uses acetate, butyrate, succinate, fumarate, malate, citrate, glutamate, pyruvate, glucose and fructose, but not methanol, ethanol or glycerol. Biotin and thiamine are required as growth factors. Gelatin is hydrolysed, but not starch, alginate or Tween 80. Nitrate is not reduced. Indole is not produced from tryptophan. Dark-grown cells contain small amounts of bchl a and a carotenoid. Cells are weakly resistant to potassium tellurite. The chemical composition of the cells is consistent with that of the genus circumscription. In addition, cells contain 3-OH 16 : 0 (ester-linked) as well as the following fatty acids: 16 : 0, 18 : 19c, 20 : 0, cyclo 21 : 0, 3-OH 20 : 1 and 22 : 1. The DNA G+C content of the type strain is 56.1 %.
The type strain, DFL-11T (=DSM 17067T=NCIMB 14079T), was isolated from cultured cells of the marine dinoflagellate Alexandrium lusitanicum.
Description of Labrenzia aggregata comb. nov.
Basonym: Stappia aggregata (ex Ahrens 1968) Uchino et al. 1999.
The description is the same as that for Stappia aggregata (Uchino et al., 1998) with the addition that the polar lipid composition is consistent with that of the genus circumscription. The fatty acids comprise 16 : 17c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 20 : 17c, 20 : 0 (trace amounts) and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 18 : 0, 3-OH 20 : 1 and 3-OH 20 : 0, all of which are amide-linked. The level of fatty acid 20 : 17c is usually in the range 5–6 %.
The type strain is B1T (=ATCC 25650T=IAM 12614T=DSM 13394T=NBRC 16684T=LMG 122T=NCIMB 2208T).
Description of Labrenzia marina comb. nov.
Basonym: Stappia marina Kim et al. 2006.
The description is the same as that given by Kim et al. (2006) with the addition that the polar lipid composition is consistent with that of the genus circumscription. The fatty acids comprise 16 : 17c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 11-methyl 20 : 16t, cyclopropane 197, 20 : 17c, 11-methyl 20 : 16t and the hydroxy fatty acids 3-OH 14 : 0 (ester-linked), 3-OH 18 : 0, 3-OH 20 : 1 and 3-OH 20 : 0, all of which are amide-linked.
The type strain is mano 18T (=DSM 17023T=KCTC 12288T).
Description of Labrenzia alba comb. nov.
Basonym: Stappia alba Pujalte et al. 2006.
The description is the same as that given by Pujalte et al. (2005), with the additions that the respiratory lipoquinone and polar lipid compositions are consistent with that of the genus circumscription. The fatty acids comprise 16 : 17c, 16 : 0, 18 : 17c, 18 : 0, 11-methyl 18 : 16t, 11-methyl 20 : 16t, 20 : 17c, 20 : 0, 11-methyl 20 : 16t and the hydroxy fatty acids, 3-OH 14 : 0 (ester-linked), 3-OH 18 : 0 and 3-OH 20 : 0, all of which are amide-linked.
The type strain is 5OM6T (=DSM 18380T=CECT 5095T=CIP 108402T).
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONREFERENCES |
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