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PubMed1998

Phylogenetic and physiological diversity of sulphate-reducing bacteria isolated from a salt marsh sediment.

The phylogenetic and physiological diversity of sulphate-reducing bacteria inhabiting a salt marsh rhizosphere were investigated. Sulphate-reducing bacteria were isolated from a salt marsh rhizosphere using enrichment cultures with electron donors thought to be prevalent in the rhizosphere of Spartina alterniflora. The relationship between phylogeny and nutritional characteristics of 10 strains was investigated. None of the isolates had 16S rRNA sequences identical to other delta subclass sulphate-reducers, sharing 85.3 to 98.1% sequence similarity with 16S rRNA sequences of their respective closest relatives. Phylogenetic analysis placed two isolates, obtained with ethanol as an electron donor, within the Desulfovibrionaceae. Seven isolates, obtained with acetate, butyrate, propionate, or benzoate, were placed within the Desulfobacteriaceae. One isolate, obtained with butyrate, fell within the Desulfobulbus assemblage, which is currently considered part of the Desulfobacteriaceae family. However, due to the phylogenetic breadth and physiological traits of this group, we propose that it be considered a new family, the "Desulfobulbusaceae." The isolates utilised an array of electron donors similar to their closest relatives with a few exceptions. As a whole, the phylogenetic and physiological data indicate isolation of several sulphate-reducing bacteria which might be considered as new species and representative of new genera. Comparison of the Desulfobacteriaceae isolates' 16S rRNA sequences to environmental clones originating from the same study site revealed that none shared more than 86% sequence similarity. The results provide further insight into the diversity of sulphate-reducing bacteria inhabiting the salt marsh ecosystem, as well as supporting general trends in the phylogenetic coherence of physiological traits of delta Proteobacteria sulphate reducers.

Base Sequence↗
PubMedDate not supplied

The cyanobacteriales: a legitimate order based on the type strain Cyanobacterium stanieri?

As a logical consequence of the definition of a bacterium (Stanier and van Niel, 1962), R. Y. Stanier created the name "cyanobacteria" as a replacement for "blue-green algae". As such, cyanobacteria entered the 8th issue of Bergey's Manual of Determinative Bacteriology 1974 as members of the Procaryotae Murray 1968, this kingdom being composed of two divisions, Cyanobacteria and Bacteria. An even tighter integration of cyanobacteria with other bacteria was proposed by Gibbons and Murray (1978) for the next edition of Bergey's Manual. These authors suggested that the cyanobacteria be integrated as an order Cyanobacteriales in the class Photobacteria. However, this proposal was doomed to failure by constraints imposed under present rules of the Bacteriological Code (Lapage et al., 1976), one of which is that the type of an order is the genus upon whose name the higher taxon is based. A genus Cyanobacterium did not exist when Gibbons and Murray made their proposal, and a subsequent special request by the same authors for an exemption from this rule was not granted (Judicial Commission of the International Committee on Systematic Bacteriology, Holt, 1978). We present here a revised classification for unicellular cyanobacteria dividing in one plane wherein we propose, among other changes, the creation of two new genera. Cyanobium and Cyanobacterium. With the creation of the latter genus, the requirement for recognition of cyanobacteria as a legal order Cyanobacteriales under the Bacteriological Code should be fulfilled. We suggest that the type species of this genus by Cyanobacterium stanieri, in honor of the late Roger Y. Stanier.

Base Composition↗
PubMed2002

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study.

Animals↗
PubMed2000

Comparison of nutrient transport across the placenta of lizards differing in placental complexity.

We have reviewed published and new quantitative data on the net uptake of nutrients by embryos of oviparous and viviparous lizards that vary in chorioallantoic placental complexity to better understand the evolution of complex placentae. We assessed net nutrient uptake during embryonic development by measuring the total dry mass, or the mass of separate nutrients, in the egg at about the time of ovulation and in the neonate. There is no significant difference in the fresh egg to neonate dry mass ratio of oviparous and viviparous species that have simple placentae, indicating that there is little, if any, net uptake of nutrients by viviparous species with simple chorioallantoic placentae. In contrast, there is significant uptake of dry matter and individual nutrients across the placenta of species with complex chorioallantoic placentae. Species of the genus Niveoscincus have a range of placentae and nutrient uptakes, even among populations of one species, suggesting that further studies among populations of single species are required. Data are available for relatively few clades, and all the data for the three most complex chorioallantoic placental types are derived from a single genus. Thus, further research on new genera of lizards is required to overcome the potentially confounding effects of phylogeny in our analyses.

Allantois↗
PubMed1978

Ascaridoid nematodes of amphibians and reptiles: Gedoelstascaris n.g. and Ortleppascaris n.g.

Two new genera, Gedoelstascaris and Orleppascaris, are proposed for species of ascaridoid nematodes occurring in crocodilians and previously included in Dujardinascaris. Species included in Gedoelstascaris are vandenbrandeni Baylis, 1929 as type species and australiensis Baylis, 1931 (= salomonis Kreis, 1940). These species occur in Crocodylus spp. in Africa and Australia respectively and are characterised by lips with a rostral plate, without interlocking processes or dentigerous ridges, with well-developed interlabia, lobulated ventriculus, and excetory pore in front of the nerve ring. Species included in Ortleppascaris are: nigra Gedoelst, 1916 (= tasmani Ortlepp, 1932) as type species; alata Baylis, 1947: antipini Mozgovoy, 1950. These species occur in Crocodylus, Caiman and Alligator and are characterized by flat lips with alate margins, without anterior rostral plate, interlocking processes or dentigerous ridges, with weakly developed interlabia, by an irregular-shaped ventriculus, excretory pore behind or between the subventral lips, and by the presence of lateral alae or cuticular thickenings in the oesophageal region. The significance of this proposal is discussed in relation to the radiation and dispersal of ascaridoids of crocodilians.

Alligators and Crocodiles↗
PubMed1988

Microfossils from oolites and pisolites of the Upper Proterozoic Eleonore Bay Group, Central East Greenland.

Silicified oolites and pisolites from Bed 18 of the Upper Proterozoic (about 700-800 Ma) Limestone-Dolomite "Series" of the Eleonore Bay Group, central East Greenland, contain a diverse suite of organically preserved microfossils that is, for the most part. [Of the] assemblages previously described from Proterozoic cherts and shales. Three principal assemblages occur in these rocks: 1) a class bound assemblage found in detrital carbonate grains (now silicified) that served as nuclei for ooid and pisoid growth, as well as in uncoated mud and mat clasts that were carried into the zone of ooid and pisoid deposition; 2) an epilithic and interstitial assemblage consisting of microorganisms that occurred on top of and between grains; and 3) a euendolithic assemblage composed of microbes that actively bored into coated grains. The Upper Proterozoic euendolithic assemblage closely resembles a community of euendolithic cyanobacteria found today in shallow marine ooid sands of the Bahama Banks. Thirteen species are described, of which eight are new, five representing new genera: Eohyella dichotoma n. sp., Eohyella endoatracta n. sp., Eohyella rectoclada n. sp., Thylacocausticus globorum n. gen. and sp., Cunicularius halleri n. gen. and sp., Graviglomus incrustus n. gen. and sp., Perulagranum obovatum n. gen. and sp., and Parenchymodiscus endolithicus n. gen. and sp.

Calcium Carbonate↗
PubMed2004

Trypanosomatid biodiversity in Costa Rica: genotyping of parasites from Heteroptera using the spliced leader RNA gene.

The biodiversity of insect trypanosomes is largely unknown, resulting in significant gaps in the understanding of pathogen evolution. A culture-independent preliminary survey of trypanosomatid fauna was conducted for the parasites of Heteroptera (Hemiptera) from several localities in Costa Rica. Trypanosomatid infections were detected by light microscopy of smeared gut contents. Out of 257 insects representing 6 families, infections were found in 62 cases; cultures were obtained for 29 new isolates. Gut material from infected hosts was preserved in the field using an SDS-EDTA buffer solution for subsequent DNA extraction in the laboratory. PCR amplification of the trypanosomatid-specific spliced leader (SL) RNA gene repeats was successful for 60 field samples. Eighteen distinct SL RNA typing units were identified in a set of 28 samples analysed in detail. Cluster analysis indicated that these typing units were unique and thus could represent new species and, in some cases, new genera. This study reveals only a minor fraction of the trypanosomatid biodiversity, which is anticipated to be high.

Animals↗
PubMed2003

Coelomycetes in Dominican and Mexican amber.

Three species of fossil epiphyllous coelomycetes are described from Dominican and Mexican amber in the new genera, Asteromites gen. nov., Leptostromites gen. nov. and Leptothyrites gen. nov. Characters of the pycnidia and spores most closely resemble members of their extant respective genera, Leptostroma, Asteromella, and Leptothyrium, respectively. A. mexicanus sp. nov. occurs on a petal (possibly from a caesalpinoid legume such as Peltogyne) in Mexican amber. Leptostromites ellipticus sp. nov. occurs on a dicot leaf in Dominican amber, and Leptothyrites dominicanus sp. nov. on a monocot (grass?) leaf in Dominican amber.

Amber↗
PubMed2004

A natural classification of Lasiosphaeria based on nuclear LSU rDNA sequences.

The current circumscription of Lasiosphaeria includes taxa with a wide variety of ascomatal walls, ascomatal wall vestitures, and ascospore morphologies and a broad range of putative anamorphs. Despite the complexity of morphological characters in the genus, species within Lasiosphaeria can be arranged into four groups based on ascospore morphology. Taxa which possessed ascospores in each of the four groups were used in phylogenetic analyses of partial nuclear large subunit (LSU) rDNA sequences to test the monophyly of the genus and determine relationships among its species. Lasiosphaeria was found to be highly polyphyletic in that species segregated into seven well-supported monophyletic clades dispersed among several orders. Three new genera, Echinosphaeria, Hilberina, and Immersiella, are erected for three of these clades while the genus Lasiosphaeris is reintroduced for a fourth clade. These data support Ruzenia as a previously established genus and the transfer of Lasiosphaeria raciborskii to Chaetosphaeria. The circumscription of Lasiosphaeria has been considerably narrowed to better reflect a natural classification. These taxonomic changes are additionally supported by a combination of morphological characters which are discussed in relation to the phylogenetic trees.

Base Sequence↗
PubMed2004

New quill mites of the family Syringophilidae (Acari: Cheyletoidea).

Five new species and two new genera belonging to the family Syringophilidae (Acari: Cheyletoidea) are described from birds that died in the Antwerp Zoo during their quarantine: Charadriaulobia vanelli n. g., n. sp. from Vanellus chilensis (Charadriiformes: Charadriidae) in Brazil; Fritschisyringophilus lonchurae n. g., n. sp. from Lonchura punctulata (Passeriformes: Estrildidae) in India; Mironovia coturnae n. sp. from Coturnix coturnix (Galliformes: Phasianidae) in Europe; Syringophiloidus daberti n. sp. from Passerina ciris (Passeriformes: Emberizidae) in Mexico; and S. serini n. sp. from Serinus mozambicus (Passeriformes: Fringillidae) in Central Africa. Charadriaulobia n. g. differs from the closely related Aulobia Kethley, 1970, in both sexes, by the divergent epimeres I; in females, by the absence of protuberances on the hypostomal apex and by the situation of the bases of setae l4 distinctly anterior the bases of setae d4. Fritschisyringophilus n. g. differs from the closely related Syringophiloidus Kethley, 1972, in both sexes, by the presence of setae vs ' on legs II, the absence of setae dT on legs III and IV; in females, by the presence of median hypostomal protuberances and by short setae l1, l2 and l3. The relationships between the Syringophilidae and their hosts are briefly discussed. A list of all known syringophilid genera and their distribution on bird families is provided.

Animals↗
PubMed2003

Number of ancestral human species: a molecular perspective.

Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest migration out of Africa. These findings call into question the mitochondrial "African Eve" hypothesis based on a far more recent origin for H. sapiens and show that humans did not go through a bottleneck in their recent evolutionary history. Given the large offset in evolutionary rates of molecules and morphology seen in human evolution, Homo species are likely to be characterised by high levels of morphological variation and low levels of genetic variability. Thus, molecular data suggest the limits for intraspecific morphological variation used by many palaeoanthropologists have been set too low. The role of phenotypic plasticity has been greatly underestimated in human evolution. We call into question the use of mtDNA for studies of human evolution. This DNA is under strong selection, which violates the assumption of selective neutrality. This issue should be addressed by geneticists, including a reassessment of its use for molecular clocks. There is a need for greater cooperation between palaeoanthropologists and anthropological geneticists to better understand human evolution and to bring palaeoanthropology into the mainstream of evolutionary biology.

Animals↗
PubMed2003

Biodegradation of methyl tertiary butyl ether (MTBE) by a bacterial enrichment consortia and its monoculture isolates.

Methyl tertiary butyl ether (MTBE), an important gasoline additive, is a recalcitrant compound posing serious environmental health problems. In this study, MTBE-degrading bacteria were enriched from five environmental samples. Enrichments from Stewart Lake sediments and an MTBE contaminated soil displayed the highest rate of MTBE removal; 29.6 and 27.8% respectively, in 28 days. A total of 12 bacterial monocultures isolated from enrichment cultures were screened for MTBE degradation in liquid cultures. In a nutrient-limited medium containing MTBE as the sole source of carbon and energy, the highest rate of MTBE elimination was achieved with IsoSL1, which degraded 30.6 and 50.2% in 14 and 28 days, respectively. In a nutrient-rich medium containing ethanol and yeast extract, the bacterium (Iso2A) substantially removed MTBE (20.3 and 28.1% removal in 14 and 28 days, respectively). Based upon analysis of the 16s rRNA gene sequence and data base comparison, IsoSL1 and Iso2A were identified as a Streptomyces sp. and Sphingomonas sp., respectively. The Streptomyces sp. is a new genera of bacteria degrading MTBE and could be useful for MTBE bioremediation.

Biodegradation, Environmental↗
PubMed2000

Taxonomy of the caliciviruses.

The International Committee on Taxonomy of Viruses (ICTV) has recently approved several proposals submitted by the present Caliciviridae Study Group. These proposals include the division of the family into 4 new genera designated Lagovirus, Vesivirus, "Norwalk-like viruses (NLVs), and "Sapporo-like viruses (SLVs); the latter 2 genera were assigned temporary names until acceptable names can be determined by the scientific community. The genera have been further divided into the following species: Feline calicivirus and Vesicular exanthema of swine virus (genus Vesivirus), Rabbit hemorrhagic disease virus and European brown hare syndrome virus (genus Lagovirus), Norwalk virus (genus NLV), and Sapporo virus (genus SLV). In addition, the ICTV approved a proposal to remove the hepatitis E virus from the Caliciviridae into an "unassigned classification status.

Animals↗
PubMed1997

Phylogenetic analyses of DNA and allozyme data suggest that Gonioctena leaf beetles (Coleoptera; Chrysomelidae) experienced convergent evolution in their history of host-plant family shifts.

A phylogenetic analysis of the genus Gonioctena (Coleoptera, Chrysomelidae) based on allozyme data (17 loci) and mitochondrial DNA sequence data (three gene fragments, 1,391 sites) was performed to study the evolutionary history of host-plant shifts among these leaf beetles. This chrysomelid genus is characteristically associated with a high number of different plant families. The diverse molecular data gathered in this study are to a large extent congruent, and the analyses provide a well-supported phylogenetic hypothesis to address questions about the evolution of host-plant shifts in the genus Gonioctena. The most-parsimonious reconstruction of the ancestral host-plant associations, based on the estimated phylogeny, suggests that the Fabaceae was the ancestral host-plant family of the genus. Although most of the host-plant shifts (between different host species) in Gonioctena have occurred within the same plant family or within the same plant genus, at least eight shifts have occurred between hosts belonging to distantly related and chemically dissimilar plant families. In these cases, host shifts may have been simply directed toward plant species available in the environment. Yet, given that two Gonioctena lineages have independently colonized the same three new plant families (Salicaceae, Betulaceae, Rosaceae), including four of the same new genera (Salix, Alnus, Prunus, Sorbus), some constraints are likely to have limited the different possibilities of interfamilial host-plant shifts.

Animals↗
PubMed1996

Phylogenetic positions of Desulfofustis glycolicus gen. nov., sp. nov., and Syntrophobotulus glycolicus gen. nov., sp. nov., two new strict anaerobes growing with glycolic acid.

The glycolate-oxidizing, sulfate-reducing bacterium strain PerGlyS and the syntrophically glycolate-oxidizing bacterium strain FlGlyR were studied with respect to their phylogenetic relationships on the basis of in vitro amplification and direct sequencing of 16S rRNA-encoding DNA. Strain PerGlyS clustered with representatives of the delta subclass of the class Proteobacteria, close to "Desulforhopalus vacuolatus" but sufficiently distinct to preclude its assignment to this genus. These organisms, together with Desulfobulbus propionicus, represent a phylogenetic subgroup among members of the delta subclass of Proteobacteria. Strain FlGlyR was found to cluster with the gram-positive bacteria with low-G + C DNA, and Desulfitobacterium dehalogenans and Desulfotomaculum orientis are its closest relatives. Other species of the genus Desulfotomaculum are phylogenetically only moderately closely related to these organisms. These results necessitate the establishment of new genera and species for these two strains. Strain PerGlyS was designated the type strain of Desulfofustis glycolicus gen. nov., sp. nov., and strain FlGlyR was designated the type strain of Syntrophobotulus glycolicus gen. nov., sp. nov.

Bacteria, Anaerobic↗
PubMed1997

Reorganization of the genus Erythromicrobium: description of "Erythromicrobium sibiricum" as Sandaracinobacter sibiricus gen. nov., sp. nov., and of "Erythromicrobium ursincola" as Erythromonas ursincola gen. nov., sp. nov.

The results of investigations on the morphology, physiology, pigment composition, light-harvesting antenna and reaction center organization, and electron carriers of five Erythromicrobium representatives, and on phylogenetic relations among them, are summarized. On the basis of clear phenotypic differences and distinct phylogenetic positions shown by 16S ribosomal DNA analysis, the tentative species "Erythromicrobium sibiricum" and "Erythromicrobium ursincola" are formally described as the type species of two new genera: Sandaracinobacter sibiricus gen. nov., sp. nov., and Erythromonas ursincola gen. nov., sp. nov., respectively. The genus Erythromicrobium is at present composed of the type species, E. ramosum, and two species, "E. hydrolyticum" and "E. ezovicum," whose nomenclature is yet to be validated. All species studied group within the alpha-4 subclass of Proteobacteria.

Absorptiometry, Photon↗
PubMed1998

Proposal of Craurococcus roseus gen. nov., sp. nov. and Paracraurococcus ruber gen. nov., sp. nov., novel aerobic bacteriochlorophyll a-containing bacteria from soil.

Sequences of the 16S rRNA gene were determined for three strains of aerobic bacteriochlorophyll a-containing bacteria isolated from soil. The sequence of two strains (NS89(T) and NS102) were identical for approximately 1500 nucleotides. Phylogenetic analysis revealed that the three strains belonged to the alpha-1 subclass of the Proteobacteria, constituting one line of descent. The three strains are comparatively related to Roseoccus thiosulfatophilus, which is an aerobic bacteriochlorophyll a-containing bacterium. The 16S rRNA gene sequence similarity and the DNA-DNA relatedness allow the proposal of two new genera, Craurococcus gen. nov. and Paracraurococcus gen. nov. The type species are Craurococus roseus sp. nov. and Paracraurococcus ruber sp. nov., and their type strains are NS130(T) (=JCM 9933(T)) and NS89(T) (=JCM 9931(T)), respectively.

Bacteriochlorophylls↗
PubMed1999

The family Coriobacteriaceae: reclassification of Eubacterium exiguum (Poco et al. 1996) and Peptostreptococcus heliotrinreducens (Lanigan 1976) as Slackia exigua gen. nov., comb. nov. and Slackia heliotrinireducens gen. nov., comb. nov., and Eubacterium lentum (Prevot 1938) as Eggerthella lenta gen. nov., comb. nov.

16S rRNA gene sequences were determined for Eubacterium exiguum and Peptostreptococcus heliotrinreducens. These species were found to be closely related and, together with Eubacterium lentum, to constitute a branch of the Coriobacteriaceae. Two new genera are proposed on the basis of phenotypic characteristics and 16S rRNA gene sequence comparisons: Slackia to include the bile-sensitive species Eubacterium exiguum and P. heliotrinreducens, and Eggerthella to include the bile-resistant Eubacterium lentum. It is proposed that Eubacterium exiguum and Peptostreptococcus heliotrinreducens are transferred to the genus Slackia gen. nov. as Slackia exigua gen. nov., comb. nov. (type strain ATCC 700122T) and Slackia heliotrinireducens gen. nov., comb. nov. (type strain NTCC 11029T), respectively, and Eubacterium lentum is transferred to the genus Eggerthella gen. nov. as Eggerthella lenta gen. nov., comb. nov. with Eggerthella lenta as the type species.

Base Composition↗