Phylogenetic basis for a taxonomic dissection of the genus Clostridium

The 16S rDNA-based phylogenetic analysis of the genus Clostridium has been completed by determination of the phylogenetic position of the type strains of 15 species and two non-validated species. These strains are members of phylogenetic clusters I, III, IV, V, IX, XIVa and XVIII as defined previously by Collins et al. [Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Members of the genus Clostridium span a large evolutionary distance and the genus is not a phylogenetically coherent taxon but is intermixed with members of different genera, exhibiting a combination of Clostridium- and non-Clostridium-type properties. Anaerobacter polyendosporus, Syntrophococcus sucromutans and Acetivibrio multivorans also cluster within the radiation of Clostridium species. Although several taxa have been described for former Clostridium species with distinct phenotypic properties, the majority of Clostridium species, which are not members of the core cluster I, can at present not be reclassified as long as taxon-specific, phenotypic properties are not available.     

Production of a single cyclic type of fructooligosaccharide structure by inulin‐degrading Paenibacillus sp. LX16 newly isolated from Jerusalem artichoke root

A novel inulin‐degrading bacterium was isolated from a soil sample collected on Jerusalem artichoke roots. It is a Gram‐positive, aerobic, motile and central endospore‐forming straight rod, and exhibits phenotypic properties being consistent with its classification in the genus Paenibacillus. The predominant cellular fatty acids were anteiso‐C15:0, C16:0 and anteiso‐C17:0. This strain represents a novel species of the genus Paenibacillus on the basis of phenotypic data together with phylogenetic analysis, and it is here designated as LX16 and deposited in China centre for type collection, China (= CCTCC 2015256). Strain LX16 could produce a cyclofructooligosaccharide fructanotransferase catalysing the formation of one type of fructooligosaccharide (FOS) from inulin. The FOS was identified as a cyclofructooligosaccharide with a degree of polymerization of 6. Such homology in inulin degradation products may be beneficial for the functional FOS production.     

The classification of streptococci and human streptococcal diseases

The modern nomenclature, phenotypic, medical, ecological and phylogenetic classification of streptococci and different classification of streptococcal human diseases are presented. All phylogenetic groups of streptococci have been shown to contain species causing diseases in man. The most medically significant groups are the phylogenetic groups Pyogenes and Mitis. Directions of the improvement of the classification of streptococci and streptococcal human diseases on the basis of modern concepts on the taxonomy of streptococci, the biological properties and ecology of the infective agents, as well as the genesis and clinical picture of diseases induced by them, have been determined.     

<Emphasis Type="Italic">Ancylobacter abiegnus</Emphasis> sp. nov., an oligotrophic member of the xylotrophic mycobacterial community

A new species of the genus Ancylobacter, exemplified by strain Z-0056, was isolated from dystrophic humified waters formed by xylotrophic fungi grown on decaying spruce wood. The cells of strain Z-0056 (0.65–0.9 μm) are coccoid, gram-negative, with fimbriae, and nonmotile. The strain is pleomorphic and reproduces by nonuniform division. Strain Z-0056 is an aerobic organoheterotroph and a mesophilic and moderately acidophilic oligotrophic microorganism. As an inhabitant of dystrophic ultrafresh waters, strain Z-0056 is sensitive to NaCl. The bacterium utilizes organic acids (acetate, pyruvate, oxalate, gluconate, malate, succinate, and citrate), as well as xylose and xylan. The microorganism grows in a pH range of 4.0–8.0, with an optimum at pH 5.5. The temperature range for growth is 15–25°C, with an optimum at 20°C. According to its ecophysiological properties, strain Z-0056 belongs to the group of ombrophilic dissipotrophs. The DNA G+C base content is 66.8 mol %. According to phylogenetic analysis, strain Z-0056 belongs to the genus Ancylobacter. Strain Z-0056 showed the highest similarity (98.3%) with the type strain of the species A. oerskovii. The phenotypic and phylogenetic properties of strain Z-0056 support classification of this microorganism within the genus Ancylobacter as the novel species Ancylobacter abiegnus sp. nov.     

Characterization of the Candiru antigenic complex (Bunyaviridae: Phlebovirus), a highly diverse and reassorting group of viruses affecting humans in tropical America

The genus Phlebovirus of the family Bunyaviridae consists of approximately 70 named viruses, currently assigned to nine serocomplexes (species) based on antigenic similarities. Sixteen other named viruses that show little serologic relationship to the nine recognized groups are also classified as tentative species in the genus. In an effort to develop a more precise classification system for phleboviruses, we are attempting to sequence most of the named viruses in the genus with the goal of clarifying their phylogenetic relationships. In this report, we describe the serologic and phylogenetic relationships of 13 viruses that were found to be members of the Candiru serocomplex; 6 of them cause disease in humans. Analysis of full genome sequences revealed branching inconsistencies that suggest five reassortment events, all involving the M segment, and thus appear to be natural reassortants. This high rate of reassortment illustrates the inaccuracy of a classification system based solely on antigenic relationships.     

First reliable record of a fossil species of Anthomyiidae (Diptera), with comments on the definition of recent and fossil clades in phylogenetic classification

All previous records of fossil Anthomyiidae are shown to be unsubstantiated. A female anthomyiid of a new genus and species is hereby described from a piece of Dominican amber (Upper Eocene-Oligocene). Character analysis suggests that the fossil, Coenosopsites poinari gen. & sp. nov. , belongs to a Neotropical clade with two recent genera, Phaonantho Albuquerque and Coenosopsia Malloch. Evidence for a sister-group relationship between Coenosopsites poinari and the genus Coenosopsia is provided. Clades are the only acceptable units of phylogenetic classification. Combining fossil and recent clades in phylogenetic classification requires them to be temporally delimited. Proper application of phylogenetic definitions is essential for this purpose. It is proposed that the units of phylogenetic classification should be taxa for recent clades and plesia for fossil clades. A taxon is defined as node-based with reference to its recent species, while a plesion is defined as apomorphy-based. The term lineage is proposed for a recent clade defined as stem-based with reference to its recent sister group. Individual recent species represent clades that can be incorporated into phylogenetic classification as minimal taxon units. Individual fossil species may not represent clades and thus do not count as proper units of phylogenetic classification. However, the names of fossil species are readily construed also to signify plesia with the fossil species as their only known component. As such, they are proper units of phylogenetic classification.     

HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees

MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn     

Phylogenetic analysis of Alysiella and related genera of Neisseriaceae: proposal of Alysiella crassa comb. nov., Conchiformibium steedae gen. nov., comb. nov., Conchiformibium kuhniae sp. nov. and Bergeriella denitrificans gen. nov., comb. nov

A phylogenetic analysis based on 16S rRNA gene sequences reveals that Alysiella filiformis belongs to the family Neisseriaceae. The genus Simonsiella is phylogenetically separated by the genera Kingella and Neisseria. The species Simonsiella crassa and A. filiformis show a close phylogenetic relationship, with the 16S rDNA sequence similarity and the DNA-DNA hybridization representing 98.7% and 35%, respectively. Therefore, S. crassa should be transferred from the genus Simonsiella to the genus Alysiella as Alysiella crassa comb. nov. Simonsiella steedae and Simonsiella sp. of cat origin show strong genetic affinities and are distantly related with the type species of Simonsiella, S. mulleri. Thus, a new genus, Conchiformibium is proposed; Conchiformibium steedae comb. nov. and Conchiformibium kuhniae sp. nov. are accommodated in this new genus. On the basis of the phylogenetic, phenotypic and chemotaxonomic distinction from the genus Neisseria, N. denitrificans should be reclassified, for which a new genus and new combination Bergeriella denitrificans are proposed.     

Phylogenetic analysis of correlation structure in stalk-eyed flies (Diasemopsis,Diopsidae)

Morphological divergence among species may be constrained by the pattern of genetic variances and covariances among traits within species. Assessing the existence of such a relationship in nature requires information on the stability of intraspecific correlation and covariance structure and the correspondence of this structure to the pattern of evolutionary divergence within a lineage. Here, we investigate these issues for nine morphological traits and 15 species of stalk-eyed flies in the genus Diasemopsis. Within-species matrices for these traits were generated from phenotypic data for all the Diasemopsis species and from genetic data for a single Diasemopsis species, D. dubia. The among-species pattern of divergence was assessed by calculating the evolutionary correlations for all pairwise combinations of the morphological traits along the phylogeny of these species. Comparisons of intraspecific matrices reveal significant similarity among all species in the phenotypic correlations matrices but not the covariance matrices. In addition, the differences in correlation structure that do exist among species are not related to their phylogenetic placement or change in the means of the traits. Comparisons of the phenotypic and phylogenetic matrices suggest a strong relationship between the pattern of evolutionary change among species and both the intraspecific correlation structure and the stability of this structure among species. The phenotypic and the phylogenetic matrices are significantly similar, and pairs of traits whose intraspecific correlations are more stable across taxa exhibit stronger coevolution on the phylogeny. These results suggest either the existence of strong constraints on the pattern of evolutionary change or a consistent pattern of correlated selection shaping both the phenotypic and phylogenetic matrices. The genetic correlation structure for D. dubia, however, does not correspond with patterns found in the phenotypic and phylogenetic data. Possible reasons for this disagreement are discussed.     

Bacterial phylogenetic clusters revealed by genome structure.

Current bacterial taxonomy is mostly based on phenotypic criteria, which may yield misleading interpretations in classification and identification. As a result, bacteria not closely related may be grouped together as a genus or species. For pathogenic bacteria, incorrect classification or misidentification could be disastrous. There is therefore an urgent need for appropriate methodologies to classify bacteria according to phylogeny and corresponding new approaches that permit their rapid and accurate identification. For this purpose, we have devised a strategy enabling us to resolve phylogenetic clusters of bacteria by comparing their genome structures. These structures were revealed by cleaving genomic DNA with the endonuclease I-CeuI, which cuts within the 23S ribosomal DNA (rDNA) sequences, and by mapping the resulting large DNA fragments with pulsed-field gel electrophoresis. We tested this experimental system on two representative bacterial genera: Salmonella and Pasteurella. Among Salmonella spp., I-CeuI mapping revealed virtually indistinguishable genome structures, demonstrating a high degree of structural conservation. Consistent with this, 16S rDNA sequences are also highly conserved among the Salmonella spp. In marked contrast, the Pasteurella strains have very different genome structures among and even within individual species. The divergence of Pasteurella was also reflected in 16S rDNA sequences and far exceeded that seen between Escherichia and Salmonella. Based on this diversity, the Pasteurella haemolytica strains we analyzed could be divided into 14 phylogenetic groups and the Pasteurella multocida strains could be divided into 9 groups. If criteria for defining bacterial species or genera similar to those used for Salmonella and Escherichia coli were applied, the striking phylogenetic diversity would allow bacteria in the currently recognized species of P. multocida and P. haemolytica to be divided into different species, genera, or even higher ranks. On the other hand, strains of Pasteurella ureae and Pasteurella pneumotropica are very similar to those of P. multocida in both genome structure and 16S rDNA sequence and should be regarded as strains within this species. We conclude that large-scale genome structure can be a sensitive indicator of phylogenetic relationships and that, therefore, I-CeuI-based genomic mapping is an efficient tool for probing the phylogenetic status of bacteria.     

Gordonia namibiensis sp. nov., a novel nitrile metabolising actinomycete recovered from an African sand

A polyphasic approach was used to establish the taxonomic position of two actinomycetes isolated from a Namibian soil and shown to utilise nitrile compounds as growth substrates. The organisms, strains NAM-BN063AT and NAM-BN063B, had chemical and morphological properties consistent with their assignment to the genus Gordonia. Direct 165 rRNA sequencing studies confirmed the taxonomic position of the strains following the generation of phylogenetic trees using four different algorithms. The strains consistently formed a distinct phylogenetic line within the evolutionary radiation occupied by gordoniae and were most closely related to Gordonia rubropertincta DSM 43197T. DNA:DNA relatedness studies indicated that the two organisms belonged to a genomic species that was readily distinguished from G. rubropertincta. The unique phenotypic profile of the strains sharply separated them from representatives of all of the validly described species of Gordonia. The combination of genotypic and phenotypic data indicates that the two strains should be classified in the genus Gordonia as a new species. The name proposed for this taxon is Gordonia namibiensis, the type strain is NAM-BN063AT (= DSM 44568T = NCIMB 13780T).     

Isolation and characterization of xanthan-degrading Enterobacter sp. nov. LB37 for reducing the viscosity of xanthan in petroleum industry

A Gram-negative, straight rod and facultative anaerobic bacterium was isolated from soil sample. It exhibits the phenotypic characteristics consistent with its classification in the genus Enterobacter. The isolate ferment glucose to acid and gas. Arginine dihydrolase, ornithin decarboxylase and gelatinase but not deoxyribonuclease was produced by this isolate. There was no hydrogen sulfide production. On the basis of the phenotypic data, together with phylogenetic analysis based on 16S rDNA gene sequences, this strain should represent a novel species of the genus Enterobacter and was designated as LB37. The strain LB37 could degrade xanthan molecules resulting in the rapid decrease of the viscosity of xanthan solution used in oil drilling process. Endoxanthanase activity was also detected in the culture supernatant. To our knowledge, it is the first report on the microbes being involved in the xanthan degradation for oil industry. The isolate LB37 would be useful for potential application in enhanced oil recovery and oil drilling field.     

Cellulose-degrading potentials and phylogenetic classification of carboxymethyl-cellulose decomposing bacteria isolated from soil

In a previous study, culturable carboxymethyl-cellulose (CMC) decomposing soil bacteria isolated from different sampling positions across an agricultural encatchment have been classified into 31 pattern groups by digestion of amplified 16S rDNA using a single restriction enzyme (Ulrich and Wirth: Microb. Ecol. 37, 238-247, 1999). In order to reveal relationships between phylogenetic diversity and phenotypic functions, a further differentiation of two selected site-specific pattern groups (I and H) was performed, resulting in a sub-classification of four and three ARDRA groups, respectively. Based on sequencing a representative isolate of each ARDRA group, the isolates were assigned to the genus Streptomyces. The ARDRA groups were dispersed across various clades of the genus with a direct affiliation to species known for cellulolytic activity in one group, only. The isolates differed in potentials to degrade colloidal, native or highly crystalline cellulose derivatives. Out of 39 isolates, 11 were capable of degrading all substrates, 17 were restricted to degrade CMC only, and 11 were active decomposers of exclusively both CMC and colloidal cellulose. In most cases, the genetic classification of the isolates corresponded with groupings based on cellulose degrading capabilities. Thus, isolates of four ARDRA groups were restricted to the degradation of CMC, while two further isolates which efficiently degraded all cellulose derivatives formed two separate ARDRA groups. The major ARDRA group, however; displayed a high variability of degradation capabilities. The study of additional phenotypic features revealed a broad potential to decompose a set of various carbon substrates, which matched the phylogenetic classification in several cases.     

Microtetraspora malaysiensis sp. nov., isolated from Malaysian primary dipterocarp forest soil

The taxonomic position of three actinomycete strains isolated from Malaysian soil was established by using a polyphasic approach. The isolates formed chains composed of four spores on the tip of sporophores branching from the aerial mycelium, and their chemotaxonomic properties were common to those of members of the family Streptosporangiaceae. These phenotypic properties as well as a phylogenetic analysis based on 16S rRNA gene sequences indicated that they should be classified in the genus Microtetraspora. The three isolates showed a unique pattern of cultural, physiological and biochemical properties that distinguished them from previously described species of the genus Microtetraspora. The isolates showed more than 72% DNA relatedness to each other, but only 58% or less relatedness to any previously described species. On the basis of the data presented, a new species of the genus Microtetraspora, Microtetraspora malaysiensis, is proposed. The type strain of the new species is strain H47-7(T) (=JCM 11278(T)=DSM 44579(T)).     

Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov., mesophilic actinomycetes isolated from arid Australian soils

The status of two mesophilic filamentous actinomycetes isolated from an arid Australian soil sample was determined using a polyphasic taxonomic approach. The isolates had chemical and morphological properties consistent with their classification in the genus Amycolatopsis, assignments that were supported by analysis of 16S rRNA gene sequence data. Isolate SF26^T formed a distinct phyletic line and hence was sharply separated from its nearest phylogenetic neighbour, Amycolatopsis sacchari DSM 44468^T. In contrast, isolate SF27^T formed a subclade in the Amycolatopsis tree with Amycolatopsis vancoresmycina DSM 44592^T but was separated readily from the latter by DNA:DNA pairing data. The two isolates were distinguished from one another and from their respective nearest phylogenetic neighbours using a range of phenotypic properties. These data indicate that the two isolates should be recognized as new species in the genus Amycolatopsis. The names proposed for these new taxa are Amycolatopsis bartoniae sp. nov. and Amycolatopsis bullii sp. nov. with isolates SF26^T (=NCIMB 14706^T = NRRL B-2846^T) and SF27^T (=NCIMB 14707^T = NRRL B-24847^T) as the respective type strains.     

Claims and limits of phylogenetic systematics1

Within the methodology of phylogenetic systematics four hierarchic levels are distinguished: the “Central Claim” (to reconstruct phylogeny), methodoloical postulate (to conclude analysis with a purely dichotomous cladogram if ever possible), method (search for sister-group relationships by character analysis), and “Taxonomic Principle” (establishment of a classification reflecting merely the recognized genealoy). Certain limits of applicability and reliability of traditional phylogenetic systematics are specified: genealogy can only be analysed among taxa with perceptible evolutionary novelties; reticulated genealogy is not yet regarded; events other than cladogenetic ones cannot be recognised. Phylogenetic systematics is an independent method which has not been absorbed by any type of “pattern” or “transformed” cladism. Phylogenetic systematics relies on the theory of evolution, which does not lead into circularity, since phylogenetic systematics does not claim to prove or to explain evolution whatsoever.     

Taxonomic studies in the Microbotryomycetidae: <Emphasis Type="Italic">Leucosporidium golubevii</Emphasis> sp. nov., <Emphasis Type="Italic">Leucosporidiella</Emphasis> gen. nov. and the new orders Leucosporidiales and Sporidiobolales

The subclass Microbotryomycetidae (Basidiomycota, Urediniomycetes) comprises a remarkably diverse assemblage of fungi. This group includes phytoparasites, mycoparasites and probably also saprobes that show a wide range of ecological preferences. In order to study the phylogenetic relationships within the Microbotryomycetidae, and to develop a more natural classification system, mitosporic and meiosporic taxa were investigated using an integrated approach. Sequence data of 26S rDNA D1/D2 domains were analyzed using several procedures, including the Bayesian Markov chain Monte Carlo method of phylogenetic inference. Ultrastructural markers such as the type of septal pore and presence / absence of colacosomes were investigated and micromorphological and nutritional properties were compared. In this study the current concept of the genus Leucosporidium and its apparent polyphyletic nature were addressed, as well as the relationships of this genus with the Microbotryales and Mastigobasidium. The classification of the anamorphic species closely related to Leucosporidium, and the concepts of the order Sporidiales and family Sporidiobolaceae were also reviewed.     

Evolutionary history of the burnet moth genus Zygaena Fabricius, 1775 (Lepidoptera: Zygaenidae) inferred from nuclear and mitochondrial sequence data: phylogeny, host–plant association, wing pattern evolution and historical biogeography

Burnet moths of the genus Zygaena are a striking group of primarily diurnal Lepidoptera displaying an exceptional phenotypic plasticity. Previous attempts to elucidate the phylogenetic history of the group had been confounded by a perplexing pattern of characters or insufficient taxon sampling. In the present study, we infer a phylogeny of the genus Zygaena by analysing 5.4 kb of their nuclear and mitochondrial DNA. Eighty‐four of the 98 currently recognized species in this genus are considered, including representatives of all described species groups. RNA coding sequences are aligned with reference to zygaenoid moth specific secondary structure models of corresponding molecules. We conduct phylogenetic analyses within a Bayesian framework applying partition specific substitution parameters; covariation of paired sites in RNA gene sequences is accommodated by using doublet substitution models. The molecular data reveal that a considerable number of currently recognized species groups in Zygaena are not monophyletic. The traditional subgeneric classification proves to be artificial as well; Agrumenia and Zygaena (sensu stricto) are polyphyletic. Only the subgenus Mesembrynus can be confirmed as a monophyletic species cluster. Optimization of larval host–plant associations and forewing patterns on sampled trees of the Bayesian analyses suggest convergent evolution of similar wing pattern types in distantly related species clusters and a shift from cyanogenic to acyanogenic host‐plants. The phylogenetic results challenge the classic assumption that early species diversification in Zygaena took place in the Irano–Turkestanian region. Rather, the molecular data point to the western Mediterranean area as the geographical origin of the group and imply a subsequent colonization of the Middle East and Central Asia. We discuss the apparently convergent evolution of similar wing patterns in context with the chemical defence system of burnet moths and suggest a species group concept for the genus Zygaena that accounts for the recent findings. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society, 2007, 92 , 501–520.