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1 School of Pharmacy, University of Manchester, Manchester M13 9PL, UK
2 School of Biological Sciences, University of Manchester, Manchester M13 9PL, UK
3 Molecular and Cellular Pathology, University of Dundee, Dundee DD1 7SY, UK
Correspondence
P. Gilbert
Peter.Gilbert{at}man.ac.uk
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ABSTRACT |
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5c (16·9 %) and 15 : 0 iso 2-OH (16·5 %). Phylogenetic analysis of the 16S rRNA gene showed that the strain was a member of the family ‘Flexibacteraceae’ of the Cytophaga–Flavobacterium–Bacteroides group. Phenotypic and genotypic analyses indicated that the strain could not be assigned to any recognized genus; therefore a novel genus and species, Adhaeribacter aquaticus gen. nov., sp. nov., is proposed, with MBRG1.5T (=DSM 16391T=NCIMB 14008T) as the type strain.
Published online ahead of print on 29 October 2004 as DOI 10.1099/ijs.0.63337-0.
The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain MBRG1.5T is AJ626894.
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). In potable water systems, biofilms form readily at all solid–liquid interfaces, including the inner surfaces of pipes and storage vessels (Kerr et al., 2003). Many bacterial species, including members of the Proteobacteria, the Actinobacteria, low-G+C Gram-positive bacteria and members of the Cytophaga–Flavobacterium–Bacteroides (CFB) group, co-exist within potable water biofilms (Schmeisser et al., 2003; Norton & Lechevallier, 2000). The ability of these taxonomically diverse organisms to attach to surfaces and co-develop within multispecies biofilms is essential for their survival and persistence within such flowing freshwater environments (Bott & Grant, 2001; Purevdorj et al., 2002; Stoodley et al., 2002).
In the last 20 years, evidence has emerged that biofilms in potable water systems may pose a significant hazard to public health (Burke et al., 1984). In particular, potable water biofilms have been linked to outbreaks of gastrointestinal illness (Williams & Braun-Howland, 2003; Zalmum et al., 1998) and outbreaks of legionellosis (Steinert et al., 2002). Other problems that are associated with potable water biofilms include microbially induced corrosion of pipe surfaces and unpleasant taste and odour (Kerr et al., 2003). In general, biofilms in potable water systems are problematic because they are composed of numerous species of bacteria. Collectively, these generate multispecies biofilm communities that possess properties (such as a decreased susceptibility to antimicrobial agents and the ability to corrode metal) that are not displayed by the individual species (Gilbert et al., 2002). As a consequence, there is increasing interest in studies on the microbial diversity of freshwater biofilms and the physiological properties of the component organisms.
A recent study on the influence of water velocity on the community diversity of potable water biofilms demonstrated that the taxonomic diversity of biofilms developed at high velocities was much lower than that of biofilms developed under conditions of minimal velocity (Rickard et al., 2004). Some strains that were isolated on R2A agar (Reasoner & Geldreich, 1985) at the high velocities possessed unusual morphological and biochemical characteristics. In particular, strain MBRG1.5T possessed a low partial 16S rRNA gene sequence identity (92·7 %) when compared with sequences from species with validly published names in the EMBL database (Rickard et al., 2004). In this study, strain MBRG1.5T is described using morphological and physiological characterization, fatty acid methyl ester analysis and full 16S rRNA-based phylogenetic classification. On the basis of these data and the significant lack of information available on the closest relatives, we propose a novel genus and species, Adhaeribacter aquaticus gen. nov., sp. nov., with MBRG1.5T (=DSM 16391T=NCIMB 14008T) as the type strain.
Phylogeny
Almost the entirety of the 16S rRNA gene of MBRG1.5T was amplified by using a PCR with the universal primers 27f (5'-AGAGTTTGATCCTGGCTCAG-3'; Escherichia coli positions 8–27) (Edwards et al., 1989) and 1492r (5'-TACGGTTACCTTGTTACGACTT-3'; positions 1492–1512) (Weisberg et al., 1991). The PCR was carried out as described by Glockner et al. (1996) except that the annealing temperature was 55 °C. Sequencing of the amplified product was carried out using the primers 27f, 1492r, 518f (5'-CCAGCAGCCGCGGTAAT-3'; positions 518–534) and 1070r (5'-AGCTGACGACAGCCAT-3'; positions 1070–1085) according to the method of Lane (1991). Similarity searches with the 16S rRNA gene sequence derived were done in the EMBL database using the program FASTA (http://www.ebi.ac.uk/fasta33/) (Pearson & Lipman, 1988). Comparisons against 16S rRNA gene sequences in the EMBL database showed that strain MBRG1.5T possessed the highest identities with an unspeciated ‘Taxeobacter’ strain (SAFR-033; 92·1 %) and an uncultured member of the Cytophagales (Cytophagales bacterium clone FBP292; 88·8 %). The two speciated organisms with the highest identities to strain MBRG1.5T were Flexibacter aggregans (88·8 %) and Hymenobacter actinosclerus (87·5 %). The sequence identities to other members of the CFB group ranged from 85 to 87 %. Such low similarity to species with validly published names is indicative that the organism under study is likely to be a member of a novel genus (Stackebrandt & Goebel, 1994). To examine the phylogenetic relationships between strain MBRG1.5T and validated and closely related strains, CLUSTAL X (version 1.81) (Thompson et al., 1997) was used to align 1350 unambiguously identified base pairs of partial 16S rRNA gene sequences from strain MBRG1.5T against sequences from related strains in the EMBL database. Neighbour-joining analysis was conducted with the correction of Jukes & Cantor (1969), using TREECON (version 1.3b) (Van de Peer & De Watcher, 1997). The stability of the groupings was estimated by using bootstrap analysis (1000 replications). Flavobacterium aquatile (M62797) was used as the outgroup (Fig. 1). The tree clearly showed that strain MBRG1.5T formed a separate and distinct lineage within the family ‘Flexibacteraceae’ of the CFB group. Furthermore, it is clear that strain MBRG1.5T is unrelated to members of the genera Hymenobacter, ‘Taxeobacter’ and Flexibacter. The robustness of the phylogenetic relationships and the low sequence similarities between strain MBRG1.5T and the other validated strains within the CFB group strongly suggest that the strain represents a novel genus in the family ‘Flexibacteraceae’.
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. Cells in exponential phase (2-day liquid R2A batch cultures) were rod-shaped (typically 2·8–4·1x0·9–1·7 µm), produced copious amounts of extracellular polymeric substance (Fig. 2) and possessed a capsule (also confirmed by the addition of the acidic dye nigrosin). In stationary-phase cultures (10-day liquid R2A cultures), cells were much more variable in size (1·9–6·7x0·8–1·9 µm) (Fig. 3). Mesosomes were observed in stationary-phase cells. Reproduction occurred by binary fission; the separating daughter cells were half the size of the parent cells. Negative staining showed that all cells from exponential phase and stationary phase were completely covered in a dense fibrillar matrix, probably composed of extracellular polysaccharide (Fig. 2). The fibrillar matrix appeared to fuse between cells where the fibrils overlapped, and thicker bundles of fibrillar material were conspicuous (Fig. 2). The individual fibres of the matrix were extremely thin and radiated out from the cells. The majority of the cells showed evidence of plasymolysis, as the inner membrane had clearly shrunk away from the outer membrane in some cells (Fig. 2a, cell ‘A’). In other cells, the inner membrane was seen to be blebbing and shrinking inwards (Fig. 2a, cell ‘B’) but the outer membrane could not be detected. Around every cell, an electron-dense ‘halo’ was present, appearing to be underneath the fibrillar matrix and outside the cell membranes (Fig. 2).
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. Other biochemical investigations included tests for oxidase, catalase, nitrate reduction, urease activity and indole production. Growth on various standard bacteriological media was assessed by using CM3 nutrient agar (Oxoid), water agar (Reichenbach, 1992) and marine agar (Oxoid). Growth at different temperatures (4, 20, 25, 28, 30, 37, 42, 45, 50 °C) was investigated on R2A agar plates. Tolerance towards NaCl, at 30 °C, was studied on R2A agar plates supplemented with 0·5, 1, 2·5, 4, 5, 10, 20 and 25 % (w/v) NaCl (pH 7·4). Carbon-source utilization tests were done by supplementing 50 ml aliquots of minimal medium (Cohen-Bazire et al., 1957) with different carbon sources and testing for growth in 100 ml conical flasks that were subjected to shaking (250 r.p.m.) at 30 °C. Growth was determined by following the OD650 over 7 days. On R2A agar, strain MBRG1.5T grew at 30 °C, generating pink, gelatinous, convex, entire colonies 4±1 mm in diameter. Colonies were not easily emulsified in distilled water. No growth was detected on CM3 nutrient agar but growth could be detected on water agar and marine agar. Incubation of agar plates at 30 °C resulted in the generation of visible colonies after 2–4 days. Similar colony types were observed on water agar and marine agar; gliding motility was not observed. Strain MBRG1.5T was able to grow on R2A agar at temperatures from 4 to 37 °C. The maximum growth rate was observed at 30 °C with shaking at 250 r.p.m. Under these conditions, the mean generation time in R2A broth was between 1·5 and 2·5 h. If the speed of shaking or the temperature was altered, the mean generation time increased. Strain MBRG1.5T grew in the absence of NaCl and in the presence of 0·5, 1·0 and 2·5 % (w/v) NaCl. No growth was observed in the presence of >4·0 % (w/v) NaCl. No growth was detected in cultures incubated under anaerobic conditions. Strain MBRG1.5T grew equally well in the presence or absence of light. Starch hydrolysis and nitrate reduction were not detected. Catalase was detected (weak activity) and the strain was oxidase-positive. Using minimal medium as a base, the requirement for, and utilization of, 26 simple sugars and organic acids and 14 amino acids were tested (Table 1). Additionally, the enzymic hydrolysis of eight substrates was tested using BBL Crystal test kits (Becton Dickinson) according to the manufacturer's instructions. The biochemical and physiological characteristics of strain MBRG1.5T were compared with those of members of the two genera that were most closely related to strain MBRG1.5T (according to 16S rRNA gene sequence analysis, described below). A high degree of dissimilarity was evident with respect to both Hymenobacter actinosclerus (12 different characteristics) and Flexibacter aggregans (nine different characteristics). Unfortunately, in the case of the comparison between strain MBRG1.5T and Flexibacter aggregans, many of the characteristics could not be compared because many current techniques and tests were not available to the original investigators (Lewin & Lounsbery, 1969) (Table 1). Three other species with validly published names (Cyclobacterium marinum, Hongiella mannitolivorans and Algoriphagus ratkowskyi) were also included as representative members of the CFB group and were compared with strain MBRG1.5T. Strain MBRG1.5T is clearly distinct from all these representative members of the CFB group (Table 1).
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Chemotaxonomy
Strain MBRG1.5T was subcultured onto R2A agar, incubated for 4 days at 30 °C and harvested by washing with distilled water. Cells (40 mg) were harvested from triplicate cultures. Lysis of cells (saponification), methylation of fatty acids and extraction of the methyl esters into the organic phase were achieved using the methods of Ghanem et al. (1991). Fatty acid methyl ester profiles were generated using a model 5898A Microbial Identification system (Microbial ID) consisting of a Hewlett Packard model 6890 gas chromatograph fitted with two 5 % phenylmethyl silicone capillary columns (0·2 mmx25 m), flame-ionization detectors, a Hewlett Packard model 7637A automatic sampler and a Hewlett Packard Vectra XM computer. Samples (2 µl) were injected onto the columns with a temperature gradient rising from 170 to 270 °C, an injection port temperature of 300 °C and ultra-high-purity hydrogen as the carrier gas. Fatty acids were identified and peaks integrated automatically using MIS Library Generation Software (Microbial ID). All of the cellular fatty acids (CFAs) extracted from strain MBRG1.5T were identified by using the MIDI system. The fatty acid 15 : 0 iso represented the highest proportion (22·5 %), this being followed by 16 : 15c (16·9 %) and 15 : 0 iso 2-OH (16·5 %) (Table 2). A comparison with Hymenobacter actinosclerus (the most closely related strain to undergo CFA analysis) demonstrated that the types and amounts of CFA from strain MBRG1.5T were completely different. A review of the literature concerning the amounts of CFA isolated from strains belonging to the CFB group also suggests that the CFA profile for strain MBRG1.5T is unique; such a significant difference in fingerprint pattern has not been observed before.
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and the G+C content was determined by the Deutsche Sammlung von Mikroorganismen und Zellkulturen (Braunschweig, Germany) by using the thermal denaturation method (Mandel & Marmur, 1968). The G+C content of the DNA of strain MBRG1.5T was established as 40·0 mol%. The G+C contents of the most closely related species, Hymenobacter actinosclerus and Flexibacter aggregans, are significantly different (62 and 35 mol%, respectively; Table 1
).
Taxonomic conclusions
Members of the CFB group are widely distributed in nature and have previously been isolated from soil, subsurface sediments, plants and water (Junge et al., 2004; Buczolits et al., 2002; Garbeva et al., 2001; Hiorns et al., 1997). In many environments they are present as community members of multispecies biofilms (Kindaichi et al., 2004; Battin et al., 2001). The widespread distribution of members of the CFB group can be explained by their ability to survive and grow at relatively low temperatures (Rickard et al., 2004), at low nutrient concentrations (Junge et al., 2004) and in chemically or physically adverse environments (Rickard et al., 2004; Eiler et al., 2003). The broad range of different environments in which bacteria belonging to this group can survive is a reflection of the variety of species- and genus-specific biochemical and physiological properties that they possess (Staley & Gosink, 1999). Unfortunately, this is a significant problem when comparing them by using a polyphasic approach and subsequently assigning genus and species identities. This is further compounded by the phylogenetic heterogeneity of the group as a whole, a lack of named genera, and the fact that much of the work that was carried out on the CFB group was done more than 30 years ago (Lewin, 1969; Lewin & Lounsbery, 1969).
It is evident from this polyphasic study of an unusual freshwater biofilm isolate that the Gram-negative rod-shaped organism described is distinct from all other currently described members of the CFB group. A phylogenetic comparison of the 16S rRNA gene sequence of strain MBRG1.5T with sequences from established species clearly shows that it is genetically distinct, although pairwise sequence comparisons strongly indicate that it is a member of the family ‘Flexibacteraceae’ (Garrity & Holt, 2001). A comparison of the cell morphology of strain MBRG1.5T with those of the most closely related species (Flexibacter aggregans, Flexibacter elegans, Hymenobacter actinosclerus and ‘Taxeobacter ocellatus’) further demonstrated the difference between strain MBRG1.5T and other members of the ‘Flexibacteraceae’. None of the currently identified members of the ‘Flexibacteraceae’ with validly published names have similar cellular characteristics and none have been reported to produce large quantities of extracellular fibrillar material, which is characteristic of strain MBRG1.5T. Additionally, whilst only scant information is available on the biochemical/CFA characteristics of members of the ‘Flexibacteraceae’, strain MBRG1.5T possesses many biochemical/CFA characteristics unique to all other members of the ‘Flexibacteraceae’ (Tables 1 and 2; also reviewed by Reichenbach, 1992). Thus, strain MBRG1.5T is a novel member of the ‘Flexibacteraceae’ and all available evidence suggests that it is a member of a novel genus.
The most noteworthy characteristic of strain MBRG1.5T was that the colonies were mucoid in appearance and the cells did not pellet tightly when centrifuged. These observations can be explained by the presence of a capsule (detected by light microscopy) and the presence of the extracellular fibrillar matrix (detected by negative staining). However, it is not clear whether these two components detected by the two different methods are in fact the same component. In addition, the electron-dense ‘halo’ could represent the capsule. Further electron microscopy using fixation and thin sectioning would resolve the structural identity of the various layers, detected by negative staining, outside the inner membrane. Strain MBRG1.5T was isolated from a biofilm exposed to high fluid velocity (0·26 m s–1) (Rickard et al., 2004) and it is well known that extracellular polymeric materials provide cohesiveness in biofilms and are considered to be essential for the formation and maintenance of biofilms in situ (see review by Flemming et al., 2000). It is therefore likely that the fibrillar matrix material seen by means of negative staining and transmission electron microscopy is the extracellular polymer that enables the cells to become established within the biofilm and to resist the high shear force.
Description of Adhaeribacter gen. nov.
Adhaeribacter (Ad.haer'i.bac.ter. L. v. adhaereo, adhaere to adhere to, to stick fast; N.L. masc. n. bacter from Gr. n. bakterion rod; N.L. masc. n. Adhaeribacter sticky rod).
Cells are Gram-negative rods that are non-motile. Obligate aerobe, chemo-organotrophic and oxidase- and catalase-positive. Changes in cell size occur during growth in batch culture. Cells produce copious amounts of extracellular fibrillar material. The predominant CFAs are 15 : 0 iso (22·5 %), followed by 16 : 15c (16·9 %) and 15 : 0 iso 2-OH (16·5 %). As determined by 16S rRNA gene sequence analysis, the genus Adhaeribacter is a member of the ‘Flexibacteraceae’ in the CFB phylum. The type species is Adhaeribacter aquaticus.
Description of Adhaeribacter aquaticus sp. nov.
Adhaeribacter aquaticus (a.qua'ti.cus. L. masc. adj. aquaticus living, growing, or found in or by water, aquatic).
Displays the following properties in addition to those given in the genus description. Colonies on R2A agar are circular, entire, pink and not easily emulsified. Cells are 2·8–4·1 µm in length and 0·9–1·7 µm in width. No gliding motility is observed. Weak hydrolysis of starch is observed. Tests for nitrate reduction, H2S production and indole production are negative. Temperature for growth is 4–37 °C. Growth occurs in the range 4–37 °C and the optimal temperature for growth is 30 °C. NaCl is not required for growth; up to 4·0 % (w/v) NaCl is tolerated. Acid and gas are not produced from D-glucose. Adonitol, arabinose, D-fructose, D-gluconate, D-glucose, inositol, N-acetyl D-glucosamine, pyruvate, D-ribose, sucrose and D-trehalose are assimilated. Citrate, fumarate, galactose, D-lactate, lactose, malonate, D-maltose, D-mannose, D-rhamnose, salicin, sorbitol, suberate and xylose are not utilized. Hydrolysis of 
-D-glucoside, 
-D-glucoside bisphosphate, N-acetylglucosamine phosphate, phosphorylcholine, -galactoside and -galactoside detectable. Susceptible to methicillin, imipenem, gentamicin, trimethoprim, cefoperazone, vancomycin, erythromycin, carbenicillin, ciprofloxacin, cefotaxime, fusidic acid, cefsulodin, piperacillin, penicillin G, tobramycin, amikacin and ticarcillin. The DNA G+C content is 40·0 mol%.
The type strain is MBRG1.5T (=DSM 16391T=NCIMB 14008T), isolated from a freshwater biofilm, developed in a model system, which was exposed to a fluid velocity of 0·26 m s–1 over a 3-month period.
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ACKNOWLEDGEMENTS |
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K. Suresh, S. Mayilraj, and T. Chakrabarti Effluviibacter roseus gen. nov., sp. nov., isolated from muddy water, belonging to the family 'Flexibacteraceae' Int J Syst Evol Microbiol, July 1, 2006; 56(Pt 7): 1703 - 1707. [Abstract] [Full Text] [PDF]
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S. C. K. Lau, M. M. Y. Tsoi, X. Li, I. Plakhotnikova, S. Dobretsov, M. Wu, P.-K. Wong, J. R. Pawlik, and P.-Y. Qian Description of Fabibacter halotolerans gen. nov., sp. nov. and Roseivirga spongicola sp. nov., and reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov. Int J Syst Evol Microbiol, May 1, 2006; 56(Pt 5): 1059 - 1065. [Abstract] [Full Text] [PDF]
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L. A. O'Sullivan, J. Rinna, G. Humphreys, A. J. Weightman, and J. C. Fry Culturable phylogenetic diversity of the phylum 'Bacteroidetes' from river epilithon and coastal water and description of novel members of the family Flavobacteriaceae: Epilithonimonas tenax gen. nov., sp. nov. and Persicivirga xylanidelens gen. nov., sp. nov. Int J Syst Evol Microbiol, January 1, 2006; 56(1): 169 - 180. [Abstract] [Full Text] [PDF]
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O. I. Nedashkovskaya, S. B. Kim, M. Suzuki, L. S. Shevchenko, M. S. Lee, K. H. Lee, M. S. Park, G. M. Frolova, H. W. Oh, K. S. Bae, et al. Pontibacter actiniarum gen. nov., sp. nov., a novel member of the phylum 'Bacteroidetes', and proposal of Reichenbachiella gen. nov. as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003 Int J Syst Evol Microbiol, November 1, 2005; 55(6): 2583 - 2588. [Abstract] [Full Text] [PDF]
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