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At least 163 records · Page 9Linked to original sources
PubMed1999

Psychrophilic sulfate-reducing bacteria isolated from permanently cold arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov.

Five psychrophilic, Gram-negative, sulfate-reducing bacteria were isolated from marine sediments off the coast of Svalbard. All isolates grew at the in situ temperature of -1.7 degrees C. In batch cultures, strain PSv29T had the highest growth rate at 7 degrees C, strains ASv26T and LSv54T had the highest growth rate at 10 degrees C, and strains LSv21T and LSv514T had the highest growth rate at 18 degrees C. The new isolates used the most common fermentation products in marine sediments, such as acetate, propionate, butyrate, lactate and hydrogen, but only strain ASv26T was able to oxidize fatty acids completely to CO2. The new strains had growth optima at neutral pH and marine salt concentration, except for LSv54T which grew fastest with 1% NaCl. Sulfite and thiosulfate were used as electron acceptors by strains ASv26T, PSv29T and LSv54T, and all strains except PSv29T grew with Fe3+ (ferric citrate) as electron acceptor. Chemotaxonomy based on cellular fatty acid patterns and menaquinones showed good agreement with the phylogeny based on 16S rRNA sequences. All strains belonged to the delta subclass of Proteobacteria but had at least 9% evolutionary distance from known sulfate reducers. Due to the phylogenetic and phenotypic differences between the new isolates and their closest relatives, establishment of the new genera Desulfotalea gen. nov., Desulfofaba gen. nov. and Desulfofrigus gen. nov. is proposed, with strain ASv26T as the type strain of the type species Desulfofrigus oceanense sp. nov., LSv21T as the type strain of Desulfofrigus fragile sp. nov., PSv29T as the type strain of the type species Desulfofaba gelida sp. nov., LSv54T as the type strain of the type species Desulfotalea psychrophila sp. nov. and LSv514T as the type strain of Desulfotalea arctica sp. nov.

Arctic Regions↗
PubMed1999

A re-evaluation of the taxonomy of the genus Anaerovibrio, with the reclassification of Anaerovibrio glycerini as Anaerosinus glycerini gen. nov., comb. nov., and Anaerovibrio burkinabensis as Anaeroarcus burkinensis [corrig.] gen. nov., comb. nov.

Chemotaxonomic, electron microscopic and 16S rRNA gene sequence analyses of the three described species of the genus Anaerovibrio demonstrated only remote similarities to each other. The 16S rRNA gene sequence similarities between Anaerovibrio lipolytica, Anaerovibrio glycerini and Anaerovibrio burkinabensis and the derived phylogenetic relationships of the three species studied fell below genus level. All three species clustered within the Sporomusa-Pectinatus-Selenomonas phyletic group. Each species showed a distinct phospholipid pattern and whole-cell fatty acid distribution. Several isoprenologues of the lipoquinone 'lipid F' were found to differ in their quantitative distribution in the Anaerovibrio species. On the basis of these results, the new genera Anaerosinus gen. nov. and Anaeroarcus gen. nov. are proposed. The type species of Anaerosinus is Anaerosinus glycerini comb. nov., and the type species of Anaeroarcus is Anaeroarcus burkinensis [corrig.] comb. nov. The genus Anaerovibrio is consequently restricted to a single species, namely Anaerovibrio lipolyticus [corrig.]

Bacterial Typing Techniques↗
PubMed2001

Simplified technique for identification of the aerobic spore-forming bacteria by phenotype.

The use of modern research approaches of genetics, biochemistry and molecular biology has led to progress in bacterial taxonomy. Systematic study of the aerobic spore-forming bacteria has resulted in the realignment of the genus Bacillus into several new genera. In the meantime, the identification process has become more difficult for the non-specialist in Bacillus taxonomy. This paper presents a key for the simplified phenotypic identification of the mesophilic, aerobic, spore-forming bacteria belonging to the genera Bacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Geobacillus and Virgibacillus. A total of 81 species were included and 115 morphological and physiological tests were analysed for their discriminative efficiency. This key is practical for rough but quick identification of aerobic spore-forming bacteria isolated from nature. Such preliminary identification will be helpful for the selection of reference strains and methods for more precise identification using the newest techniques. The reliability of the proposed identification key was tested on 100 cultures from the Ukrainian Collection of Microorganisms. The developed identification key is represented in interactive mode on a website (http://www/imv.kiev.ua/key/).

Bacillaceae↗
PubMed2002

Transfer of Bifidobacterium inopinatum and Bifidobacterium denticolens to Scardovia inopinata gen. nov., comb. nov., and Parascardovia denticolens gen. nov., comb. nov., respectively.

Bifidobacterium inopinatum Crociani et al. 1996 and Bifidobacterium denticolens Crociani et al. 1996 have distinct phenotypic characteristics and low G+C contents compared with other bifidobacteria. In the 16S rRNA phylogenetic tree, these two species grouped in an independent subcluster. In our previous work, partial heat-shock protein 60 (HSP60) gene-sequence analysis also indicated that these two species had distinct taxonomic positions. In this work, the complete HSP60 genes of five representative bacterial strains were sequenced by using an inverse PCR method. The complete sequence similarities turned out to be at the same level as those of the partial genes, thus confirming the result based on partial sequence analysis. On the basis of all the evidence mentioned above, it is proposed that these two species should be transferred to two new genera as Scardovia inopinata gen. nov., comb. nov., and Parascardovia denticolens gen. nov., comb. nov.

Bacterial Typing Techniques↗
PubMed1997

Phylogenetic diversity of a bacterial community determined from Siberian tundra soil DNA.

Genomic DNA was isolated from the active layer of tundra soil collected from the Kolyma lowland, Northeast Eurasia, near the Arctic Ocean coast. The SSU (small subunit) rRNA genes were amplified with eubacterial primers from the bulk genomic community DNA and cloned into plasmid vectors. Forty-three SSU rDNA clones were obtained, and all of them had different RFLP patterns. Phylogenetic analysis based on partial sequences (about 300 bp) established with the maximum likelihood method revealed the presence of three major and several minor groups that fell into 11 of the established lines of bacteria, and one sequence that could not be assigned to any of the described groups. Most of the clones belonged to the alpha (20.9%) and delta (25.6%) subdivisions of the Proteobacteria, with lesser proportions in the beta (9.3%) and gamma (4.7%) subdivisions, groups typically isolated from soil by culture methods. Fewer than 12% of the clones belonged to Gram-positive bacteria, and 16% of the clones were related to Fibrobacter. The majority of the clones (70%) had sequences that were 5-15% different from those in the current databases, and 7% of the clones had sequences that differed by more than 20% from those in the database. The results suggest that these tundra-derived clones are very diverse in phylogeny, and that many probably reflect new genera or families. Hence, most of the tundra soil bacterial community has never been isolated and thus the physiology and function of its dominant members appears to be unknown.

Arctic Regions↗
PubMed1993

Classification and typing methods of black-pigmented gram-negative anaerobes.

Until recently, black-pigmented Gram-negative anaerobes were classified as 'black-pigmented Bacteroides'. At present, 11 distinct species are recognized in this group. Because of major differences with Bacteroides fragilis, the type species of the genus Bacteroides, new genera have been proposed: Porphyromonas for three asaccharolytic species, and Prevotella for the saccharolytic species. Typing methods have been developed for some species of black-pigmented Gram-negative anaerobes. These include biotyping and serotyping, but relatively few types can be distinguished with these methods. Recently, DNA restriction endonuclease analysis has been used for typing of P. gingivalis, Pr. intermedia and P. endodontalis strains. Great heterogeneity was observed within all three species. This typing method can be useful for epidemiological studies.

Bacterial Typing Techniques↗
PubMed2006

New taxonomic concepts for the important forest pathogen Cryphonectria parasitica and related fungi.

Species of Cryphonectria include some of the world's most important and devastating tree pathogens. Largely through the application of DNA sequence phylogenies, the taxonomy of these fungi has undergone major changes in recent years. Cryphonectria, including the chestnut blight pathogen Cryphonectria parasitica, has been restricted to species that have semi-immersed stromata, orange and pulvinate conidiomata, and one-septate ascospores. Other species of Cryphonectria with different morphological characteristics have been transferred to new genera that are strongly supported by phylogenetic data. This review represents a summary of the taxonomic changes to species of Cryphonectria sensu lato, and we discuss the impact that these changes might have on the understanding of their ecology, pathology and worldwide distribution.

Ascomycota↗
PubMed1994

Changes in Bacteria Recoverable from Subsurface Volcanic Rock Samples during Storage at 4 degrees C.

The abundance of viable microorganisms recovered from deep subsurface volcanic rock samples increased after rock perturbation and storage for 1 week at 4 degrees C, while the diversity and evenness of recoverable heterotrophic bacterial communities generally decreased. One sample of each morphologically distinct colony type, recovered both before and after storage of U12n rock samples, was purified and characterized by fatty acid methyl ester (MIDI) and API rapid NFT strips. As determined by MIDI cluster analysis, the composition of the recoverable microbial communities changed with storage of rock samples; some groups of organisms were recovered only before, only after, or at both sample times. In general, the isolates recovered only after storage of rock samples had a greater ability to utilize the carbohydrates included in API test strips and had faster generation times than isolates recovered only on initial plating. The nutritional versatility and faster growth rates of organisms recovered in higher proportions after sample storage provide evidence that some microbial community changes may be due to the proliferation of a few bacterial types. However, because some new genera are recovered only after storage, the possibility also exists that dormant bacterial types are resuscitated during sample perturbation and storage.

Journal Article↗
PubMed2003

Phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core.

The examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. We developed a method for aseptically sampling a sediment-containing portion of a Greenland ice core that had remained at -9 degrees C for over 100,000 years. Epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. Anaerobic enrichment cultures inoculated with melted ice were grown and maintained at -2 degrees C. Genomic DNA extracted from these enrichments was used for the PCR amplification of 16S rRNA genes with bacterial and archaeal primers and the preparation of clone libraries. Approximately 60 bacterial inserts were screened by restriction endonuclease analysis and grouped into 27 unique restriction fragment length polymorphism types, and 24 representative sequences were compared phylogenetically. Diverse sequences representing major phylogenetic groups including alpha, beta, and gamma Proteobacteria as well as relatives of the Thermus, Bacteroides, Eubacterium, and Clostridium groups were found. Sixteen clone sequences were closely related to those from known organisms, with four possibly representing new species. Seven sequences may reflect new genera and were most closely related to sequences obtained only by PCR amplification. One sequence was over 12% distant from its closest relative and may represent a novel order or family. These results show that phylogenetically diverse microorganisms have remained viable within the Greenland ice core for at least 100,000 years.

Anaerobiosis↗
PubMed1995

Genomic organization of GB viruses A and B: two new members of the Flaviviridae associated with GB agent hepatitis.

The genomes of two positive-strand RNA viruses have recently been cloned from the serum of a GB agent-infected tamarin by using representational difference analysis. The two agent, GB viruses A and B (GBV-A and GBV-B, respectively), have genomes of 9,493 and 9,143 nucleotides, respectively, and single large open reading frames that encode potential polyprotein precursors of 2,972 and 2,864 amino acids, respectively. The genomes of these agents are organized much like those of other pestiviruses and flaviviruses, with genes predicted to encode structural and nonstructural proteins located at the 5' and 3' ends, respectively. Amino acid sequence alignments and subsequent phylogenetic analysis of the RNA-dependent RNA polymerases (RdRps) of GBV-A and GBV-B show that they possess conserved sequence motifs associated with supergroup II RNA polymerases of positive-strand RNA viruses. On the basis of similar analyses, the GBV-A- and GBV-B-encoded helicases show significant identity with the supergroup II helicases of positive-strand RNA viruses. Within the supergroup II RNA polymerases and helicases, GBV-A and GBV-B are most closely related to the hepatitis C virus group. Across their entire open reading frames, the GB agents exhibit 27% amino sequence identity to each other, approximately 28% identity to hepatitis C virus type 1, and approximately 20% identity to either bovine viral diarrhea virus or yellow fever virus. The degree of sequence divergence between GBV-A and GBV-B and other Flaviviridae members demonstrates that the GB agents are representatives of two new genera within the Flaviviridae family.

Amino Acid Sequence↗
PubMed2004

Ancient coevolution of baculoviruses and their insect hosts.

If the relationships between baculoviruses and their insect hosts are subject to coevolution, this should lead to long-term evolutionary effects such as the specialization of these pathogens for their hosts. To test this hypothesis, a phylogeny of the Baculoviridae, including 39 viruses from hosts of the orders Lepidoptera, Diptera, and Hymenoptera, was reconstructed based on sequences from the genes lef-8 and ac22. The tree showed a clear division of the baculoviruses according to the order of their hosts. This division highlighted the need to reconsider the classification of the baculoviruses to include one or possibly two new genera. Furthermore, the specialization of distinct virus lineages to particular insect orders suggests ancient coevolutionary interactions between baculoviruses and their hosts.

Animals↗
PubMed1996

Methanotrophic bacteria.

Methane-utilizing bacteria (methanotrophs) are a diverse group of gram-negative bacteria that are related to other members of the Proteobacteria. These bacteria are classified into three groups based on the pathways used for assimilation of formaldehyde, the major source of cell carbon, and other physiological and morphological features. The type I and type X methanotrophs are found within the gamma subdivision of the Proteobacteria and employ the ribulose monophosphate pathway for formaldehyde assimilation, whereas type II methanotrophs, which employ the serine pathway for formaldehyde assimilation, form a coherent cluster within the beta subdivision of the Proteobacteria. Methanotrophic bacteria are ubiquitous. The growth of type II bacteria appears to be favored in environments that contain relatively high levels of methane, low levels of dissolved oxygen, and limiting concentrations of combined nitrogen and/or copper. Type I methanotrophs appear to be dominant in environments in which methane is limiting and combined nitrogen and copper levels are relatively high. These bacteria serve as biofilters for the oxidation of methane produced in anaerobic environments, and when oxygen is present in soils, atmospheric methane is oxidized. Their activities in nature are greatly influenced by agricultural practices and other human activities. Recent evidence indicates that naturally occurring, uncultured methanotrophs represent new genera. Methanotrophs that are capable of oxidizing methane at atmospheric levels exhibit methane oxidation kinetics different from those of methanotrophs available in pure cultures. A limited number of methanotrophs have the genetic capacity to synthesize a soluble methane monooxygenase which catalyzes the rapid oxidation of environmental pollutants including trichloroethylene.

Base Sequence↗
PubMed1999

Isolation and characterization of thermophilic bacteria capable of degrading dehydroabietic acid.

Using a semi-continuous enrichment method, we isolated two thermophilic bacterial strains, which could completely degrade abietane resin acids, including dehydroabietic acid (DhA). Strain DhA-73, isolated from a laboratory-scale bioreactor treating bleached kraft mill effluent at 55 degrees C, grew on DhA as sole carbon source; while DhA-71, isolated from municipal compost, required dilute tryptic soy broth for growth on DhA. DhA-71 grew on DhA from 30 degrees C to 60 degrees C with maximum growth at 50 degrees C; while, DhA-73 grew on DhA from 37 degrees C to 60 degrees C with maximum growth at 55 degrees C. At 55 degrees C, the doubling times for DhA-71 and DhA-73 were 3.3 and 3.7 h, respectively. DhA-71 and DhA-73 had growth yields of 0.26 and 0.19 g of protein per g of DhA, respectively. During growth on DhA, both strains converted DhA to CO2, biomass, and dissolved organic carbon. Analyses of the 16S-rDNA sequences of these two strains suggest that they belong to two new genera in the Rubrivivax subgroup of the beta subclass of the Proteobacteria. Strains DhA-71 and DhA-73 are the first two bacteria isolated and characterized that are capable of biodegradation of resin acids at high temperatures. This study provided direct evidence for biodegradation of resin acids and feasibility for biotreatment of pulp mill effluent at elevated temperatures.

Abietanes↗
PubMed1983

A new genus and species of adapid primate from the middle Eocene of Alsace, and a new genus for 'Adapis' ruetimeyeri Stehlin, 1912.

A new primate genus and species, represented by isolated teeth, is described from the middle Eocene Alsatian site of Bouxwiller. This new form is closely related to Egerkingen 'Adapis' ruetimeyeri, for which a new genus is proposed because of the important distinctions from type Adapis present in its dentition. Nonetheless, both new genera are closely related to Adapis and Leptadapis.

Animals↗
PubMed2005

A review of the development of two types of human skeletal muscle infections from microsporidia associated with pathology in invertebrates and cold-blooded vertebrates.

Traditionally, the Microsporidia were primarily studied in insects and fish. There were only a few human cases of microsporidiosis reported until the advent of AIDS, when the number of human microsporidian infections dramatically increased and the importance of these new pathogens to medicine became evident. Over a dozen different kinds of microsporidia infecting humans have been reported. While some of these infections were identified in new genera (Enterocytozoon, Vittaforma), there were also infections identified from established genera such as Pleistophora and Encephalitozoon. The genus Pleistophora, originally erected for a species described from fish muscle, and the genus Encephalitozoon, originally described from disseminated infection in rabbits, suggested a link between human infections and animals. In the 1980's, three Pleistophora sp. infections were described from human skeletal muscle without life cycles presented. Subsequently, the genus Trachipleistophora was established for a human-infecting microsporidium with developmental differences from species of the genus Pleistophora. Thus, the existence of a true Pleistophora sp. or spp. in humans was put into question. We have demonstrated the life-cycle stages of the original Pleistophora sp. infection from human muscle, confirming the existence of a true Pleistophora species in humans, P. ronneafiei Cali et Takvorian, 2003, the first demonstrated in a mammalian host. Another human infection, caused by a parasite from invertebrates, was Brachiola algerae Lowman, Takvorian et Cali, 2000. The developmental stages of this human muscle-infecting microsporidium demonstrate morphologically what we have also confirmed by molecular means, that B. algerae, the mosquito parasite, is the causative agent of this human skeletal muscle infection. B. algerae had previously been demonstrated in humans but only in surface infections, skin and eye. The diagnostic features of B. algerae and P. ronneafiei infections in human skeletal muscle are presented. While Encephalitozoon cuniculi has been known as both an animal (mammal) and human parasite, the idea of human microsporidial infections derived from cold-blooded vertebrates and invertebrates has only been suggested by microsporidian phylogeny based on small subunit ribosomal DNA sequences but has not been appreciated. The morphological data presented here demonstrate these relationships. Additionally, water, as a link that connects microsporidial spores in the environment to potential host organisms, is diagrammatically presented.

Animals↗
PubMed2003

Bakkeius moragai n. gen. et n. sp. and Pojmanskia riosae n. gen. et n. sp. (Trematoda: Digenea: Brachylaimoidea) in birds from the Area de Conservación Guanacaste, Costa Rica.

We describe 2 new species of leucochloridiid-like brachylaimoid digeneans parasitizing a variety of birds in the Area de Conservación Guanacaste, Costa Rica, each of which we assign to a new genus. According to Pojmanska's (Pojmanska, T. 2002a. Superfamily Brachylaimoidea Joyeux & Foley, 1930. In Keys to the Trematoda, D. I. Gibson, A. Jones, and R. A. Bray [eds.]. CAB International and The Natural History Museum, London, U.K., p. 31-36.) key for the Brachylaimoidea, we are unable to place either species in any family. One species most closely resembles members of Leucochloridium by having well-developed suckers, lacking an esophagus, and having cecal shoulders, gonads at the posterior end, and the genital pore at posterior end of body but differs by having symmetrical testes, a posttesticular ovary, and a terminal genital pore; thus, we propose the genus Bakkeius for it. The second new genus resembles members of Michajlovia by having ventral genital pores but differs by having extracecal uterine loops in the forebody, a cirrus sac containing the pars prostatica and seminal vesicle, and gland cells surrounding the genital pore; thus, we propose Pojmanskia for it. These new genera must currently be treated as incertae sedis according to Pojmanska (op. cit.); however, we feel that future phylogenetic analyses will require emendation of the family diagnosis for Leucochloridiidae to include those taxa with terminal and ventral genital pores and with preovarian testes.

Animals↗
PubMedDate not supplied

[A new approach to modeling the diversity dynamics of Phanerozoic marine biota].

Modeling of fossil diversity dynamics is usually done with the help of the models borrowed from the population dynamics theory. However there are principal differences between organisms and taxa, reproduction and divergence, mortality and extinction that make this approach doubtful. Another model is presented here, in which absolute origination rate does not depend on diversity, the ability of new genera to sustain unpredictable environmental changes increases three times abruptly at Cambrian/Ordovician, Permian/Triassic and Cretaceous/Tertiary boundaries. In this model the diversity increases due to accumulation of long-lived genera. The computer simulation showed that the model agrees with empirical data by 15 major criteria. The laws of community evolution apparently can explain the general pattern of punctuated equilibrium in the evolution of marine biota.

Fossils↗
PubMed2002

[Phenogenetic characterization of a group of giant Phi KZ-like bacteriophages of Pseudomonas aeruginosa].

A comparative study was made of a group of Pseudomonas aeruginosa virulent giant DNA bacteriophages similar to phage phi KZ in several genetic and phenotypic properties (particle size, particle morphology, genome size, appearance of negative colonies, high productivity, broad spectrum of lytic activity, ability to overcome the suppressing effect of plasmids, absence of several DNA restriction sites, capability of general transduction, pseudolysogeny). We have recently sequenced the phage phi KZ genome (288,334 bp) [J. Mol. Biol., 2002, vol. 317, pp. 1-19]. By DNA homology, the phages were assigned to three species (represented by phage phi KZ, Lin68, and EL, respectively) and two new genera (phi KZ and EL). Restriction enzyme analysis revealed the mosaic genome structure in four phages of the phi KZ species (phi KZ, Lin21, NN, and PTB80) and two phages of the EL species (EL and RU). Comparisons with respect to phage particle size, number of structural proteins, and the N-terminal sequences of the major capsid protein confirmed the phylogenetic relatedness of the phages belonging to the phi KZ genus. The origin and evolution of the phi KZ-like phages are discussed. Analysis of protein sequences encoded by the phage phi KZ genome made it possible to assume wide migration of the phi KZ-like phages (wandering phages) among various prokaryotes and possibly eukaryotes. Since the phage phi KZ genome codes for potentially toxic proteins, caution must be exercised in the employment of large bacteriophages in phage therapy.

Biological Evolution↗