Microbial Ecology Group, Department of Biosciences, Technical University of Munich, Weihenstephaner Berg 3, D-85350 Freising-Weihenstephan, Germany1
Author for correspondence: Siegfried Scherer. Tel: +49 8161 713516. Fax: +49 8161 714512. e-mail: siegfried.scherer{at}lrz.tum.de
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ABSTRACT |
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Keywords: coryneform bacteria, actinomycetes, 16S rDNA sequence analysis, identification, taxonomy
Abbreviations: FT-IR; Fourier-transform infrared
The GenBank accession numbers for the 16S rDNA gene sequences reported in this paper are AY017065 to AY017067, AY017069 to AY017087, and AF426135 to AF426143 for Brevibacterium linens; AY017088 to AY017091, AY017093 to AY017104, AY017107 to AY017111, and AF426144 to AF426149 for Corynebacterium glutamicum; and AY017113 to AY017126, AY017128 to AY017138, and AF426150 to AF426153 for Rhodococcus erythropolis.
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INTRODUCTION |
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Knowledge on intraspecific diversity is also important for a correct allocation of isolates to a species contained in any identification database: the more diverse a species is, the more strains must be included in the database in order to represent this species adequately and, consequently, the more reliable is the identification obtained. Fourier-transform infrared (FT-IR) spectroscopy is on its way to becoming a valuable tool for the rapid identification of micro-organisms (e.g. Helm et al., 1991 ; Curk et al., 1994
; Naumann et al., 1994
; Holt et al., 1995
; Goodacre et al., 1998
; Kümmerle et al., 1998
). A validated comprehensive FT-IR spectral reference library has been established, by Oberreuter et al. (2002)
, which allows the rapid identification of coryneform bacteria and related taxa from the two suborders Micrococcineae and Corynebacterineae (Actinomycetales, Actinobacteria) (Stackebrandt et al., 1997
).
FT-IR spectroscopy has been used in combination with other techniques for qualitative studies on intraspecific diversity (Seltmann et al., 1994 , 1995
; Irmscher et al., 1999
; Stan-Lotter et al., 1999
), but, as far as we are aware, the method has not previously been applied to quantitative assessment of intraspecific diversity, i.e. to quantification of the degree of heterogeneity.
In the present paper, three actinomycete species were chosen which, to our knowledge, have not been previously subjected to any analysis of intraspecific diversity. During the investigation, it became clear that a significant number of strains from official collections were misclassified, in some cases even carrying incorrect genus names. On the basis of polyphasic taxonomical analyses, we propose reclassifications for these strains.
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METHODS |
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16S rDNA sequence analysis.
After 22 h growth on tryptone soya agar at 30 °C, the cells of single colonies were lysed and a PCR amplification of the almost complete 16S rDNA molecule was performed according to von Stetten et al. (1998) . Two universal 16S rDNA binding primers were used for the 30-cycle amplification PCR: 5'f (5'-AGAGTTTGATCCTGGCTCA-3'; position 826 in the Escherichia coli numbering system) (Brosius et al., 1978
) and 3'r (5'-CGGCTACCTTGTTACGAC-3'; position 15111493 in the E. coli numbering system). After PCR amplification, the DNA was purified using the QIAquick PCR purification kit (Qiagen) according to the instructions of the manufacturer, followed by a PEG precipitation of the purified product according to Facius et al. (1999)
. After purification, the samples were subjected to a cycle-sequencing PCR according to Facius et al. (1999)
, using the ThermoSequenase fluorescent labelled primer cycle sequencing kit with 7-deaza-dGTP (Amersham Pharmacia Biotech). DMSO (11%, v/v) and formamide (7%, v/v) were added to facilitate the cycle-sequencing PCR. Fluorescently labelled primers 5'f, 699R [5'-GGGTTG(AGT)GCTCGTT-3', E. coli numbering 11141100] and/or 927r (5'-CCGCTTGTGCGGGCCC-3', E. coli numbering 942927) were used for the cycle-sequencing PCR [primer 699R, Ludwig & Strunk (1999)
; primer 927r, Amann et al. (1995)
] in order to sequence both DNA strands. Considering the addition of formamide, the annealing temperatures for the different cycle sequencing primers used were as follows: 42 °C for 5'f, 37 °C for 699R and 50 °C for 927r; 25 cycles were carried out. Sequencing was performed on a LI-COR sequencer (MWG Biotech), typically yielding sequence lengths of approximately 700900 bases per run.
The sequences were aligned using the ARB alignment editor (Ludwig & Strunk, 1999 ) and trimmed to comprise positions 64716 in the E. coli numbering system. The ARB software environment was employed to calculate a matrix listing pair-wise similarity values between the strains of each species, using a separate consensus filter for each species (Ludwig et al., 1998
). Thereby, only those positions at which unambiguous sequence infomation was available for the complete set of reference organisms (600620 nt) were compared. We restricted our analysis to the highly variable part of the 16S rDNA gene in order to increase the resolving power for this molecule.
Identification of the strains for reclassification was accomplished by comparison of the partial sequences with database sequences from ARB, GenBank (Altschul et al., 1997 ) and the Ribosomal Database Project (Maidak et al., 2000
). Identification of a sequence in the ARB software environment was accomplished by addition of the aligned query sequence into a validated and optimized maximum-parsimony tree based on 16S rDNA sequences while keeping the tree topology constant (Ludwig et al., 1998
).
Statistical evaluation.
The matrices listing pair-wise spectral distance or similarity values for all strains of each species contain n±(n-1)/2 elements, where n is the number of strains, i.e. 351 values for 27 strains of Corynebacterium glutamicum, 406 values for 29 strains of Rhodococcus erythropolis, and 465 values for 31 strains of B. linens. Spectral distance and 16S rDNA similarity distributions (histograms) were created by a computer program which grouped the matrix values into classes and determined the relative frequency of occurrence in each class. Class widths of 0·25 distance units for spectral distances and 0·5 percentage points for 16S rDNA similarity values were chosen for visualization. Distance or similarity values coinciding with a class boundary were counted in the lower of the two possible classes. The frequency values were normalized to make the sum of all relative frequency values 100% and were plotted as histograms versus the corresponding class intervals. Distance versus similarity correlation graphs were created by plotting the pair-wise spectral distance versus the corresponding 16S rDNA sequence similarity for each combination of strains.
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RESULTS AND DISCUSSION |
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All 25 strains of C. glutamicum, including the strains which carry invalid species names given in single quotes, are grouped into the same cluster (E I) in the numerical analysis by Seiler (1983) . Most of these strains were also analysed by Kämpfer et al. (1993)
and Kämpfer & Kroppenstedt (1996)
. In the latter two publications, all of them are located in the same respective clusters of C. glutamicum except for strains ATCC 13655 and 14066, which were grouped differently into a small Brevibacterium/Corynebacterium cluster (Kämpfer et al., 1993
), in which, however, a strain denoted as C. glutamicum was also included. An FT-IR cluster analysis (Fig. 1
) depicting the spectral similarities between these strains as well as type strains from other Corynebacterium spp. clearly shows that all of these strains exhibit a relatively high level of spectral similarity. They are clearly separated from the type strains of other Corynebacterium species. Comparative 16S rDNA sequence analysis of the partial sequences with the programs RDP, ARB and GenBanks BLAST resulted in an overall allocation to the species C. glutamicum in all cases. The minimal similarity between the partial sequences of all strains and the type strains sequence was 97·5%. On the basis of this polyphasic approach, we propose reclassification of the strains ATCC 13744, ATCC 13747, ATCC 14017, ATCC 14066, ATCC 14399, ATCC 14915, ATCC 15283, ATCC 19165, ATCC 19240 and NCIB 9666 (Table 1
) as Corynebacterium glutamicum.
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All 23 strains of B. linens displayed an orange colony colour after 2 d incubation in light on tryptone soya agar. A drop of 20% KOH resulted in red colony pigmentation, a behaviour typical of, and probably specific to, B. linens (Grecz & Dack, 1961 ; Jones et al., 1973
). The strains which have been investigated by Seiler (1983)
, Kämpfer et al. (1993)
and Kämpfer & Kroppenstedt (1996)
were part of the same cluster in each case. The partial 16S rDNA sequences of all strains showed a level of similarity of at least 96·7% to the sequence of the type strain. In the cases of WS 2903, WS 2906 and WS 3459, sequence similarities to the closely related type strains of Brevibacterium casei or Brevibacterium iodinum were noted. However, since these two species are characterized by different colony morphology and pigmentation, the strains may be considered strains of the species B. linens. Therefore, we propose reclassification of AC 474 (Table 1
) as B. linens.
According to Stackebrandt & Goebel (1994) , a 16S rDNA similarity of more than 97% for complete sequences strongly points to species identity between the queried sequence and the type-strain sequence, although there are exceptions to this rule (e.g. Fox et al., 1992
; Lechner et al., 1998
). Some pair-wise similarity values are somewhat lower than the cut-off value of 97% sequence similarity, but we decided not to question species identity in these cases. Considering, in addition, that major sequence variations occur in the first part of the sequence (Chatellier et al., 1998
; Ludwig et al., 1998
), the complete sequences show greater percentage similarity to the sequence of the type strain than do the partial sequences. Moreover, it has been recommended that the threshold value be lowered in order to maintain flexibility in the phylogenetic definition of a species (Stackebrandt & Goebel, 1994
; Rosselló-Mora & Amann, 2001
).
Based on this approach as well as the polyphasic taxonomic data reported in the literature, we conclude that all strains included in this analysis indeed belong to one of the three species under investigation. This result is a prerequisite for assessing intraspecific variability, which is the main topic of this publication and is reported in the following section. Concerning species identification, it is important to note that for 86 out of 87 strains investigated, FT-IR spectroscopic analysis arrived at the same result as 16S rDNA sequence analysis. The only exception was B. linens WS 3541, whose IR spectrum was misidentified as that of Demetria terragena at the first hit while all other hits of the identification hit list consisted of B. linens strains. This demonstrates that FT-IR spectroscopy is a fast and reliable screening method for identifying unknown actinomycetes at the species level (compare Tindall et al., 2000 ). However, as has been stated previously, this method cannot be used for classification (Kümmerle et al., 1998
; Oberreuter et al., 2002
).
Intraspecific variability of different species
Reliable assessment of intraspecific variability depends on correct strain allocation to a particular species (see above). Furthermore, it is only possible if the strains under investigation are of independent origin. Table 1 lists the original depositor or source together with the isolation locus for each strain, as far as could be determined from the information available in the official collections. These data are not always precise enough to derive firm conclusions as to strain origins. It is probable, however, that most of the strains from C. glutamicum and R. erythropolis were isolated from East-Asian environmental sources, and that the B. linens strains came from Middle-European sources. We also assume that the majority of these strains represent different isolates, except for the five C. glutamicum strains ATCC 13059, ATCC 13060, ATCC 13286, ATCC 13287 and ATCC 21492, which appear to be mutants of the type strain (Table 1
).
The 27 strains of C. glutamicum exhibited a comparatively high degree of spectral similarity (Fig. 2a). The distribution of pair-wise FT-IR spectral distance values ranged from 0·07 to 1·51 (mean at 0·48), focusing around 0·3 and then declining relatively steeply towards higher spectral distance values. On the other hand, the degree of 16S rDNA sequence similarity between the strains of C. glutamicum was lower. The distribution of the pair-wise sequence similarity values ranged from 95·7 to 100% (mean at 98·5%). This means that even though each of the strains showed a sequence similarity of at least 97·5% to the type-strain sequence, pair-wise sequence comparison between the individual strains revealed similarities as low as 95·7%.
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The highest intraspecific diversity was noted for B. linens. Spectral distance values between the 31 strains analysed ranged from 0·19 to 2·94 with a mean value of 1·3 (Fig. 2c). The distance distribution closely resembles a Gaussian bell curve around the mean. For this species, a comparatively wide distribution of spectral distance values between the different strains was observed. The distribution of pair-wise 16S rDNA similarity values is likewise spread out rather far between 95·3 to 100%, with a maximum between 98·5 and 99·0% (mean at 98·0%). Much as for C. glutamicum, 16S rDNA sequence similarities as low as 95·3% were noted between different strains in pair-wise comparisons, although each of the strains showed a minimal sequence similarity of 96·6% to the type strain sequence.
Several publications report on the use of comparative 16S rDNA sequence analysis for assessment of intraspecific variability, but in-depth studies dealing with larger numbers of strains are comparatively rare. Sixteen strains of Xylella fastidiosa exhibited a 16S rDNA sequence similarity of 99·0100% over the complete sequence (Chen et al., 2000 ), much like R. erythropolis. Campylobacter hyointestinalis (Harrington & On, 1999
) and Streptococcus suis (Chatellier et al., 1998
) displayed a high levels of interstrain sequence variability (95·7100% and 93·9100% over the complete sequence, respectively) similar to those for C. glutamicum and especially B. linens. It appears to be a significant result of our study that the intraspecific heterogeneity of these three bacterial species is quite different. When a high variability is found within the members of a species, such species are termed polytypic when distinct subspecies can be defined. When no clear subspecies occur, the term polymorphic is more appropriate (Mallet, 2001
). B. linens appears to be a polymorphic species, according to both 16S rDNA and FT-IR spectroscopic variability. However, this conclusion needs to be supported by sequencing of other loci as well. Only such analyses will show whether 16S rDNA or FT-IR data are suitable markers for a polymorphic species structure. Generally, comparative analyses of the heterogeneity within bacterial species are still at an early stage (compare Rosselló-Mora & Amann, 2001
).
FT-IR spectral similarity and 16S rDNA similarity are not correlated
FT-IR spectroscopy as a physico-chemical, whole-cell fingerprint technique analyses microbial cells on a completely different basis from techniques focusing on a small conserved region of the genome such as the 16S rDNA gene. We wanted to determine if FT-IR spectroscopy reflects the diversity obtained by sequence comparison, at least to some degree; in other words, whether a correlation exists between the pair-wise IR spectral distance values and the pair-wise 16S rDNA similarity values. For this purpose, spectral distances were plotted against their corresponding 16S rDNA similarity values for each pair of strains (Fig. 3). This analysis shows that within C. glutamicum and B. linens (Fig. 3a
, c
) there are strain pairs which are spectrally very close but have a low 16S rDNA similarity (bottom left of each plot). Others display a highly similar 16S rDNA but have very different IR absorption spectra (top right of each plot). In the former cases, the 16S rDNA sequence analysis has a better resolution than FT-IR spectroscopy, whereas in the latter cases, different strains which cannot be distinguished by partial 16S rDNA analysis can be distinguished via FT-IR spectroscopy. The strains of R. erythropolis (Fig. 3b
) differed at only two nucleic acid positions, and therefore the entire observed spectral variability is plotted against sequence similarities of 99·9 and 100 percentage points. However, a considerable number of strain pairs can be distinguished by FT-IR spectroscopy.
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ACKNOWLEDGEMENTS |
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Received 24 October 2001;
accepted 14 January 2002.