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PubMed2002

On the size distribution of live genera.

This article deals with the theoretical size (number of species) distribution of live genera, arising from a simple model of macroevolution in which speciations and extinctions are assumed to occur independently and at random, and in which new genera are formed by the random splitting of existing genera. Mathematically, the distribution is that of the state of a homogeneous birth-and-death process after an exponentially distributed time. An ordinary differential equation for the generating function of the distribution is derived and solved and a recurrence relation for computing the probabilities in the distribution presented. Some properties of the distribution, including asymptotic behaviour, are examined and the distribution of the time since establishment of a genus of a given size derived. Fitting the distribution to empirical taxon size distributions by maximum likelihood is discussed and two examples are presented.

Animals↗
PubMed2000

New larval mites (Acari: Prostigmata: Erythraeidae, Microtrombidiidae, Trombidiidae) from Turkey, Peru and Poland.

The following species are described as new: Erythraeus (E.) sifi n. sp., E. (Z.) didonae n. sp., Bursaustium gaspari n. sp. from Turkey, Charletonia alvedae n. sp., Balaustium medardii n. sp., Yucothrombium ilzae n. sp. from Peru and Allothrombium wolmari n. sp. from Poland. Three new genera are created: Rudaemannia n. gen., Bursaustium n. gen. and Yucothrombium n. gen. Erythraeus kresnensis, Charletonia cardinalis, Podothrombium proti, Allothrombium fuliginosum and A. triticium are new to the fauna of Turkey; Hauptmannia wratislaviensis is new to the fauna of Scotland. New localities in Poland are given for H. stanislavae and H. silesiacus and in Turkey for Rudaemannia rudeansis. Charletonia tamarae is synonymous to C. bucephalia; Hauptmannia victicola is synonymons to R. rudaensis.

Animals↗
PubMed2002

Emendation of the genus Sphingomonas Yabuuchi et al. 1990 and junior objective synonymy of the species of three genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastomonas ursincola.

The 16S rDNA sequence similarities between the type strains of Sphingomonas paucimobilis and 32 other Sphingomonas species range from 90.2 to 99.6%. It might be possible to divide the genus into several new genera according to a dendrogram drawn from 16S rDNA sequence similarity. However, the phenotypic and biochemical information needed to define clusters of strains representing distinct genera within this group of organisms was not previously available. Although the cellular lipids of type strains of all 28 Sphingomonas species tested contained glucuronosyl-(1 --> 1)-ceramide together with 2-hydroxymyristic acid, other molecular species of sphingoglycolipids were distributed randomly. Sphingomonas natatoria and Sphingomonas ursincola, bacteriochlorophyll a-containing, gram-negative facultative phototrophs, belong to the cluster of the genus Sphingomonas. Other phototrophic Porphyrobacter and Erythrobacter species in the Sphingomonadaceae were classified into a cluster different from the genus Sphingomonas, as reported previously. None of the physiological and biochemical characteristics considered, including cellular lipids and fatty acid composition, provided evidence for the division of the current genus Sphingomonas. It is therefore concluded that the genus Sphingomonas should remain undivided at this time. The species of three recently proposed genera, Sphingobium, Novosphingobium and Sphingopyxis, in conjunction with Blastobacter ursincola, are junior objective synonyms of species of the genus Sphingomonas.

Alphaproteobacteria↗
PubMed2002

Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family.

In this paper minimal standards for the description of new genera and cultivable species in the family Flavobacteriaceae are proposed in accordance with Recommendation 30b of the Bacteriological Code (1990 Revision). In addition to specified phenotypic characteristics, the description of new species should be based on DNA-DNA hybridization data, and the placement of new taxa should be consistent with phylogenetic data derived from 16S rRNA sequencing. An emended description of the family is also proposed as several new taxa have been described since 1996. These proposals have been endorsed by the members of the Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes.

Animals↗
PubMed2006

[Potamotrygon marinae n. sp., a new species of freshwater stingrays from French Guiana (Myliobatiformes, Potamotrygonidae)].

Six specimens of freshwater stingrays from the French Guiana belonging to the genus Potamotrygon [S.W. Garman, On the pelvis and external sexual organs of selachians, with special reference to the new genera Potamotrygon and Disceus, Proc. Bost. Soc. nat. Hist. 19 (1877) 197-215], do not present characters that are typically shown by species to which they have been attributed. Five belong to a new species here named Potamotrygon marinae n. sp. This species is differentiated from the others by the feebly development of the prepelvic process, the development of the postorbital process as an enlarged blade, the unsegmented angular cartilage, the dorsal surface coloration composed of wide circular patches themselves formed by smaller pale patches, the almost dark coloration of the ventral surface tessellated with pale patches, and the small sized spiny tubercles situated in the middorsal region, before the caudal sting.

Animals↗
PubMed2000

Phylogeny and biogeography of serolid isopods (Crustacea, Isopoda, Serolidae) and the use of ribosomal expansion segments in molecular systematics.

In this study, a molecular phylogenetic hypothesis for 16 species of serolid isopods (Crustacea, Isopoda, Serolidae) from Antarctic waters, the deep sea, South America, and Australia is presented. The genes used are a 500-bp fragment of the mitochondrial LSU rRNA gene and a 700-bp fragment located in the variable region V4 of the nuclear SSU rRNA gene. The species composition and monophyly of morphologically defined genera of which several members were available are confirmed by the molecular data (Ceratoserolis, Spinoserolis, and Cuspidoserolis). The molecular data also support the redefinition of Frontoserolis s.l. and Serolella and the erection of the new genera Septemserolis and Paraserolis, as proposed by W]agele. The relationship among several genera is resolved differently in the molecular hypothesis than in the two existing morphological hypotheses, however. The molecular phylogeny may have important consequences for understanding the biogeography of the Serolidae, indicating that all Antarctic species in this study form a monophyletic group which has probably derived from species with closest extant relatives in South America. All 3 species included in this study living today in deep waters (>2000 m) of the Southern Ocean are most closely related to species living on the Antarctic shelf, so that parallel colonization of the deep sea by way of polar submergence can be reconstructed. In this study, a V4 expansion segment is reported which exceeds the longest crustacean sequences known until now by more than 270 bp. Although the V4 expansion segment has proven useful for phylogenetic purposes in this study, there is circumstantial evidence that its mechanism of evolution may depend not only on inheritance of single-site substitutions, making its routine use in phylogenetic studies potentially dangerous.

Animals↗
PubMed2004

Evolution of ciliary patterns in the Oligotrichida (Ciliophora, Spirotricha) and its taxonomic implications.

Although the somatic ciliature of the Oligotrichida typically comprises only a girdle and ventral kinety, a considerable diversity of ciliary patterns occurs. The four main girdle kinety patterns are identically found in tailed and tail-less species. The contractile tail has a complicated and unique ultrastructure and is potentially useful for the cell's movement and/or stabilization during feeding. Accordingly, I assume that this structure has evolved only once, namely, in the Tontoniidae nov. fam., and that the different girdle kinety patterns developed convergently in the tailed and tail-less taxa. Further distinct features suggest the establishment of the families Cyrtostrombidiidae nov. fam. (with cyrtos-like pharyngeal fibres and lack of ventral membranelles and endoral) and Pelagostrombidiidae nov. fam. (with neoformation organelle). An attempt is made to reconstruct the evolution of the kinety patterns based on morphologic, ontogenetic, and ultrastructural data. Some genera of tail-less Oligotrichida base on differences in the ciliary pattern; Omegastrombidium nov. gen. is erected for a further girdle kinety pattern. Likewise, the tailed genus Tontonia is split, resulting in two new genera, viz., Pseudotontonia nov. gen. and Spirotontonia nov. gen. Furthermore, the genus Spirostrombidium is split due to the different origin of the parallel course of girdle and ventral kinety, and Parallelostrombidium nov. gen. is established. However, the genus Thigmostrombidium is rejected because its enlarged thigmotactic membranelles are interpreted as an adaptation to the benthic lifestyle, which occurred several times within different girdle kinety patterns.

Journal Article↗
PubMed1995

Identification, classification, and clinical relevance of catalase-negative, gram-positive cocci, excluding the streptococci and enterococci.

Several new genera and species of gram-positive, catalase-negative cocci that can cause infections in humans have been described. Although these bacteria were isolated in the clinical laboratory, they were considered nonpathogenic culture contaminants and were not thought to be the cause of any diseases. Isolation of pure cultures of these bacteria from normally sterile sites has led to the conclusion that these bacteria can be an infrequent cause of infection. This review describes the new bacteria and the procedures useful for clinical laboratories to aid in their identification. The clinical relevance and our experience with the various genera and species are reviewed and discussed.

Animals↗
PubMed2001

Proposal of the genera Anaerococcus gen. nov., Peptoniphilus gen. nov. and Gallicola gen. nov. for members of the genus Peptostreptococcus.

Members of genus Peptostreptococcus have previously been found to be distantly related to the type species, Peptostreptococcus anaerobius, on the basis of 16S rDNA sequence similarities. They were divided into three major phylogenetic groups, and their peptidoglycan structure and biochemical traits differed between groups. The reclassification of the species of these three groups into three new genera, Peptoniphilus gen. nov., Anaerococcus gen. nov. and Gallicola gen. nov., is proposed. The genus Peptoniphilus gen. nov. includes the following butyrate-producing, non-saccharolytic species that use peptone and amino acids as major energy sources: Peptoniphilus asaccharolyticus comb. nov. (type species), Peptoniphilus lacrimaris comb. nov., Peptoniphilus harei comb. nov., Peptoniphilus indolicus comb. nov. and Peptoniphilus ivorii comb. nov. The genus Anaerococcus gen. nov. contains the saccharolytic, butyrate-producing species Anaerococcus prevotii comb. nov. (type species), Anaerococcus tetradius comb. nov., Anaerococcus lactolyticus comb. nov., Anaerococcus hydrogenalis comb. nov., Anaerococcus vaginalis comb. nov. and Anaerococcus octavius sp. nov. The genus Gallicola gen. nov. contains a single species, Gallicola barnesae comb. nov.

Animals↗
PubMed2002

Recent taxonomic changes and terminology update of clinically significant anaerobic gram-negative bacteria (excluding spirochetes).

Because of access to 16S rDNA sequencing, changes in the taxonomy and nomenclature of anaerobic gram-negative bacteria have occurred lately. New genera and species have been described, and existing taxa have been reclassified. The present article compiles a list of clinically relevant anaerobes and provides synonyms as well as the old nomenclature used for these bacteria. Although names and classifications of anaerobic bacteria are changing quickly, it is important to keep track of new bacterial names to work toward better description and recognition of bacterium-disease associations.

Bacteroides↗
PubMed2004

Generic delimitation and phylogenetic relationships within the subtribe Chironiinae (Chironieae: Gentianaceae), with special reference to Centaurium: evidence from nrDNA and cpDNA sequences.

To better understand the evolutionary history of the genus Centaurium and its relationship to other genera of the subtribe Chironiinae (Gentianaceae: Chironieae), molecular analyses were performed using 80 nuclear ribosomal ITS and 76 chloroplast trnLF (both the trnL UAA intron and the trnL-F spacer) sequences. In addition, morphological, palynological, and phytochemical characters were included to a combined data matrix to detect possible non-molecular synapomorphies. Phylogenetic reconstructions support the monophyly of the Chironiinae and an age estimate of ca. 22 million years for the subtribe. Conversely, both molecular data sets reveal a polyphyletic Centaurium, with four well-supported main clades hereafter treated as separate genera. The primarily Mediterranean Centaurium s.s. is closely related to southern African endemics Chironia and Orphium, and to the Chilean species Centaurium cachanlahuen. The resurrected Mexican and Central American genus Gyrandra is closely related to Sabatia (from eastern North America). Lastly, the monospecific genus Exaculum (Mediterranean) forms a monophyletic group together with the two new genera: Schenkia (Mediterranean and Australian species) and Zeltnera (all other indigenous American centauries). Several biogeographical patterns can be inferred for this group, supporting a Mediterranean origin followed by dispersals to (1) North America, Central America, and South America, (2) southern Africa (including the Cape region), and (3) Australia and Pacific Islands.

Base Sequence↗
PubMed1989

Application of chemotaxonomic techniques to the taxonomy of anaerobic bacteria.

The use of chemical characters in bacterial classification and identification has proved to be an essential component of modern systematics. Several clinically important anaerobic genera, such as Bacteroides, Clostridium, Eubacterium, Fusobacterium and Peptostreptococcus, are known to be heterogeneous of the basis of chemotaxonomic and genetic data and are in need of further examination. Recent work on bacteriodes has led to the genus being redefined and restricted to species within the former Bacteroides fragilis group, and a number of new genera have been proposed. It is important that suitable phenotypic characters are identified so that newly-defined genospecies can be differentiated in diagnostic laboratories.

Bacteria, Anaerobic↗
PubMed2004

New feather mite taxa of the Rhytidelasma Gaud, 1966 generic group (Astigmata: Pterolichidae) from the red-flanked lorikeet Charmosyna placentis placentis (Psittacidae).

Two new genera and species related to Rhytidelasma Gaud, 1966 and Lorilichus Atyeo & Gaud, 1991 are described from the plumage of the red-flanked Lorikeet Charmosyna placentis placentis (Temminck) (Psittacidae). These are Ceratolichus mirabilis n. g., n. sp. and Charmosylichus anamphiestos n. g., n. sp. In addition, an improved diagnosis of Lorilichus is proposed and two new species of this genus are described from the red-flanked lorikeet, L. longiphallos n. sp. and L. paralobiger n. sp.

Animals↗
PubMed2005

Chemolithotrophic haloalkaliphiles from soda lakes.

This paper summarizes recent data on the occurrence and properties of lithotrophic prokaryotes found in extremely alkaline, saline (soda) lakes. Among the chemolithotrophs found in these lakes the obligately autotrophic sulfur-oxidizing bacteria were the dominant, most diverse group, best adapted to haloalkaline conditions. The culturable forms are represented by three new genera, Thioalkalimicrobium, Thioalkalivibrio and Thioalkalispira in the Gammaproteobacteria. Among them, the genus Thioalkalivibrio was most metabolically diverse, including denitrifying, thiocyanate-oxidizing and facultatively alkaliphilic species. Culturable methane-oxidizing populations in the soda lakes belong to the type I methanotroph group in the Gammaproteobacteria, mostly in the genus Methylomicrobium. The nitrifying bacteria in hyposaline soda lakes were represented by a new species Nitrobacter alkalicus (Alphaproteobacteria), and by an alkaliphilic subspecies of Nitrosomonas halophila (Betaproteobacteria). Both belonged to the low salt-tolerant alkaliphiles. The facultatively autotrophic haloalkaliphilic isolates able to grow with hydrogen as electron donor were identified as representatives of the alpha-3 subclass of the Proteobacteria (aerobic) and of the Natronolimnicola - Alkalispirillum group in the gammaproteobacteria (nitrate-reducing). While all chemolithotrophic isolates from soda lakes belong to the alkaliphiles with a pH optimum for growth around 10, only the sulfur-oxidizing group included species able to grow under hypersaline conditions. This indicates that carbon and nitrogen cycles in the hypersaline alkaline lakes might not be closed.

Fresh Water↗
PubMed1985

The classification and differentiation of the anaerobic gram-negative rods.

Within the family Bacteroidaceae differentiation of the genera Leptotrichia, Fusobacterium and Bacteroides still depends largely on the accumulation of certain fermentation products. The application of newer techniques, both genetical and chemical is leading to a reappraisal of the current classification. So far attention has focussed on the genus Bacteroides and has been concerned with the status of B. fragilis and related organisms and the description of a number of new species within the B. ruminicola/oralis group. The differentiation of pigment-producing strains, all known originally as B. melaninogenicus, has led to the establishment of at least 9 species. The transfer of certain Bacteroides species to new genera is also being considered.

Animals↗
PubMed2006

Diversity of culturable halophilic sulfur-oxidizing bacteria in hypersaline habitats.

Unexpectedly high culturable diversity of moderately and extremely halophilic obligately chemolithoautotrophic sulfur-oxidizing bacteria (SOB) was discovered in the sediments of various hypersaline habitats, including chloride-sulfate lakes in Mongolia, Russia and Ukraine, a sea saltern in Slovenia and a deep-sea salt brine from the Mediterranean. Six different groups of halophilic SOB, including four new genera, all belonging to the Gammaproteobacteria, were found. Two groups of moderately halophilic strictly aerobic SOB dominated at 2 M NaCl, including representatives of the genus Halothiobacillus (in fully aerobic conditions) and Thiomicrospira (in micro-oxic conditions). Under denitrifying conditions at 2 M NaCl, a group of moderately halophilic and facultatively anaerobic SOB was selected, capable of complete denitrification of nitrate. The group represents a new genus with closest relatives among as yet undescribed marine thiodenitrifying isolates. With thiocyanate as a substrate, an enrichment culture at 2 M NaCl yielded a pure culture of moderately halophilic SOB capable of aerobic growth with thiocyanate and thiosulfate at up to 4 M NaCl. Furthermore, this bacterium also grew anaerobically using nitrite as electron acceptor. It formed a new lineage distantly related to the genus Thiomicrospira. Enrichments at 4 M NaCl resulted in the domination of two different, previously unknown, groups of extremely halophilic SOB. Under oxic conditions, they were represented by strictly aerobic spiral-shaped bacteria, related to the Ectothiorhodospiraceae, while under denitrifying conditions a group of facultatively anaerobic nitrate-reducing bacteria with long rod-shaped cells was selected, distantly related to the genus Acidithiobacillus.

Aerobiosis↗
PubMed1998

Phylogeny of the family Moraxellaceae by 16S rDNA sequence analysis, with special emphasis on differentiation of Moraxella species.

Thirty-three strains previously classified into 11 species in the bacterial family Moraxellaceae were subjected to phylogenetic analysis based on 16S rRNA sequences. The family Moraxellaceae formed a distinct clade consisting of four phylogenetic groups as judged from branch lengths, bootstrap values and signature nucleotides. Group I contained the classical moraxellae and strains of the coccal moraxellae, previously known as Branhamella, with 16S rRNA similarity of > or = 95%. A further division of group I into five tentative clusters is discussed. Group II consisted of two strains representing Moraxella atlantae and Moraxella osloensis. These strains were only distantly related to each other (93.4%) and also to the other members of the Moraxellaceae (< or = 93%). Therefore, reasons for reclassification of these species into separate and new genera are discussed. Group III harboured strains of the genus Psychrobacter and strain 752/52 of [Moraxella] phenylpyruvica. This strain of [M.] phenylpyruvica formed an early branch from the group III line of descent. Interestingly, a distant relationship was found between Psychrobacter phenylpyruvicus strain ATCC 23333T (formerly classified as [M.] phenylpyruvica) and [M.] phenylpyruvica strain 752/52, exhibiting less than 96% nucleotide similarity between their 16S rRNA sequences. The establishment of a new genus for [M.] phenylpyruvica strain 752/52 is therefore suggested. Group IV contained only two strains of the genus Acinetobacter. Strategies for the development of diagnostic probes and distinctive sequences for 16S rRNA-based species-specific assays within group I are suggested. Although these findings add to the classificatory placements within the Moraxellaceae, analysis of a more comprehensive selection of strains is still needed to obtain a complete classification system within this family.

DNA Primers↗
PubMed2002

Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. no.

The phylogenetic relationships of Oceanospirillum strains were analysed by using the nucleotide sequences of 16S rRNA and gyrB genes. Results from sequence analysis demonstrated that the Oceanospirillum core group consisted of four species, Oceanospirillum linum, Oceanospirillum maris, Oceanospirillum beijerinckii and Oceanospirillum multiglobuliferum, with enough distance to separate them as different species. However, four other Oceanospirillum species occupied taxonomic positions separate from the Oceanospirillum core group: Oceanospirillum jannaschii, Oceanospirillum japonicum and Oceanospirillum kriegii in the gamma-Proteobacteria and Oceanospirillum pusillum in the alpha-Proteobacteria. Oceanospirillum jannaschii clustered with Marinobacterium georgiense, Pseudomonas iners and Pseudomonas stanieri on the basis of phylogenetic analysis of 16S rRNA and gyrB genes. The other three species did not cluster with known genera. Also, the sequence similarity values of the gyrB genes between the three subspecies of Oceanospirillum maris and those between the two subspecies of Oceanospirillum beijerinckii were above 99%. The close relationships between the subspecies of Oceanospirillum maris and of Oceanospirillum beijerinckii were further supported by similar physiological properties and high DNA-DNA hybridization values, suggesting that these subspecies should not be regarded as valid. From these results, Oceanospirillum sensu stricto should be defined to consist of Oceanospirillum linum, Oceanospirillum maris, Oceanospirillum beijerinckii and Oceanospirillum multiglobuliferum. We propose to create the following new genera: Pseudospirillum gen. nov. for Oceanospirillum japonicum as Pseudospirillum japonicum comb. nov.; Oceanobacter gen. nov. for Oceanospirillum kriegii as Oceanobacter kriegii comb. nov.; and Terasakiella gen. nov. for Oceanospirillum pusillum as Terasakiella pusilla comb. nov. The transfer is proposed of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Furthermore, Pseudomonas iners should be reclassified as a strain of Marinobacterium georgiense. Finally, the subspecies of Oceanospirillum maris (O. maris subsp. maris, O. maris subsp. hiroshimense and O. maris subsp. williamsae) and Oceanospirillum beijerinckii (O. beijerinckii subsp. beijerinckii and O. beijerinckii subsp. pelagicum) should be combined as Oceanospirillum maris and Oceanospirillum beijerinckii, respectively.

Alphaproteobacteria↗