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PubMed1998

Toward the phylogeny of the family Lacertidae: implications from mitochondrial DNA 12S and 16S gene sequences (Reptilia: Squamata).

A phylogeny of the family Lacertidae was derived from mtDNA gene sequence data. Seventeen species, representing 16 currently recognized genera and subgenera, were included in the analysis. A total of 954 bp was obtained and aligned from 12S and 16S partial gene sequences. A preferred tree was selected based on weighted parsimony and functional ingroup and outgroup analyses. Decay analysis, bootstrapping, and permutation tail probability were used to evaluate support for the recovered nodes. The genus Gallotia was resolved as the basal taxon and the sister group of all remaining lacertids. Takydromus branched off next. All African lacertids grouped together and formed a monophyletic clade with the Eurasian genera Eremias and Ophisops. The remaining Eurasian lacertids sequentially branched off near the base of the tree in a "comb-like" fashion. The basal position of Gallotia and the monophyly of African lacertids are consistent with previous hypotheses. The European-origin hypothesis of lacertids is favored, and the distribution of lacertids in Africa is likely a Miocene dispersal event. Most of the extant European lacertids probably arose after the Eocene. The classification of the family needs to be revised.

Animals↗
PubMed1998

Nearly identical 16S rRNA sequences recovered from lakes in North America and Europe indicate the existence of clades of globally distributed freshwater bacteria.

We compared bacterial 16S ribosomal RNA gene sequences recovered from Lake Loosdrecht, the Netherlands, to reported sequences from lakes in Alaska and New York State. In each of the three lake systems, which differ in pH and trophic state, some sequence types were found without related sequences (sequence identity < 90%) in the data sets from the other two systems. Two sequences in the Actinomycetes and Verrucomicrobia radiations were more closely related to sequences from the New York lakes data set than to any other sequence in the global databases. However, the most striking similarities were found in the subdivisions alpha and beta of the Proteobacteria. In these subdivisions three different clusters of highly related bacteria were identified (97-100% sequence identity) that were represented in all three lake regions. The clusters contained no members other than freshwater bacteria. One cluster falls within a monophyletic aquatic supergroup that apparently diverged early in evolution into an exclusive freshwater cluster and an exclusive marine cluster, the so-called SAR11 cluster. The detection of these three bacterial clades in lakes distinguished by geographic distance as well as physical and chemical diversity suggests that these organisms are dispersed globally and that they possess unique functional capabilities enabling successful competition in a wide range of freshwater environments.

Actinomycetales↗
PubMed1999

Networks and groups within the genus Neisseria: analysis of argF, recA, rho, and 16S rRNA sequences from human Neisseria species.

To understand the pattern of nucleotide sequence variation among bacteria that frequently exchange chromosomal genes, we analyzed sequences of the recA, argF, and rho genes, as well as part of the small-subunit (16S) rRNA gene, from about 50 isolates of human commensal Neisseria species and the pathogenic N. meningitidis and N. gonorrhoeae. Almost all isolates of these species could be assigned to five phylogenetic groups that are found for all genes examined and generally are supported by high bootstrap values. In contrast, the phylogenetic relationships among groups varied according to the gene analyzed with notable incongruences involving N. cinerea and N. lactamica. Further analysis using split decomposition showed that for each gene, including 16S rRNA, the patterns of sequence divergence within N. meningitidis and closely related species were inconsistent with a bifurcating treelike phylogeny and better represented by an interconnected network. These data indicate that the human commensal Neisseria species can be separated into discrete groups of related species but that the relationships both within and among these groups, including those reconstructed using 16S rRNA, have been distorted by interspecies recombination events.

Base Sequence↗
PubMed1999

Molecular systematics of the Malagasy babblers (Passeriformes: timaliidae) and warblers (Passeriformes: sylviidae), based on cytochrome b and 16S rRNA sequences.

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy "babblers" are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy "babblers" are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.

Africa↗
PubMed2001

[Cloning and sequencing of 16S rRNA gene of Phytoplasma CWB1 strain associated with cactus witches' broom].

A 1.5 kb DNA fragment was amplified in DNA samples extracted from Opuntia salmiana porm showed witches'-broom symptom. The result indicates the existence of phytoplasma associated with this disease and this phytoplasma was designated as CWB1. The amplified fragment was ligated to pGEM-T easy vector and then transformed into JM109 strain of E. coli. Cloned DNA fragments were verified by PCR, restriction endonuclease (EcoRI) digestion and sequence analysis. The result revealed that the 16S rRNA gene of CWB1 consists of 1489 bp and shared 99.7% homology with Faba bean phyllody which belongs to phytoplasma 16S rII-C subgroup. So we can classify this strain into phytoplasma 16S rII-C subgroup.

Cloning, Molecular↗
PubMed2001

PCR-SSCP comparison of 16S rDNA sequence diversity in soil DNA obtained using different isolation and purification methods.

This study compared different methods of direct DNA extraction and purification from a silt loam soil and investigated the relationship between DNA quantity and sequence diversity. Five extraction methods and four purification techniques were investigated. Quantities of DNA extracted were between 3.4+/-0.55 and 54.3+/-8.18 &mgr;g g(-1) (dry wt) of soil with OD(260)/OD(230) purity ratios between 0.80 and 1.15. Analysis of sequence diversity in all extracts was conducted using PCR-single strand conformation polymorphism (SSCP). Profiles generated using universal 16S rDNA primers (Com1/Com2) were found to be identical when used to amplify 16S rDNA extracted directly from soil. The genus Pseudomonas was targeted in order to reduce profile complexity, which was apparent when using universal 16S rDNA primers, and which hindered direct comparison of sequence diversity. A Pseudomonas culture library and non-cultured Pseudomonas 16S rDNA genes were used to provide a background count of Pseudomonas operational taxonomic units present in the soil. Cloning and sequencing of amplicons generated using a Pseudomonas-specific (Ps-for) and a universal 16S rDNA (Com2) primer, coupled with nested amplification (Com1/Com2 amplification from Ps-for/Ps-rev amplicons), used in conjunction with SSCP, revealed that environmental contaminants co-extracted with DNA, such as humic acid, significantly reduced primer specificity. SSCP was sensitive enough to reveal template bias in different primer sets. PCR-restriction fragment length-SSCP of Pseudomonas 16S rDNA amplified from soil-extracted DNA revealed distinct differences in sequence representation between extraction methods and showed that greater DNA yield is not synonymous with higher sequence diversity. We, therefore, suggest that DNA extractions from soil should be evaluated not only in terms of quantity and purity, but also in terms of the sequence diversity present. SSCP proved to be a valuable tool for the assessment of the methodologies commonly used in PCR-mediated microbial ecology studies.

Journal Article↗
PubMed2001

Molecular phylogenetic analysis of the dragonfly genera Libellula, Ladona, and Plathemis (Odonata: Libellulidae) based on mitochondrial cytochrome oxidase I and 16S rRNA sequence data.

Molecular phylogenetic relationships among members of the odonate genus Libellula (Odonata: Anisoptera: Libellulidae) were examined using 735 bp of mitochondrial COI and 416 bp of 16S ribosomal RNA gene sequences. Considerable debate exists over several relationships within Libellula, as well over the status of two putative genera often placed as subgenera within Libellula: Ladona and Plathemis. Parsimony and maximum-likelihood analyses of the separate and combined data sets indicate that Plathemis is basal and monophyletic and that Ladona is the sister clade to the remainder of Libellula sensu stricto (s.s.) (all species within the genus Libellula, excluding Plathemis and Ladona). Moreover, two European taxa, Libellula fulva and L. depressa, were found to occupy a sister group relationship within the Ladona clade. Relationships within Libellula s.s. are less well resolved. However, monophyletic lineages within the genus are largely consistent with morphologically based subgeneric classifications. Although tree topologies from each analysis differed in some details, the differences were in no case statistically significant. The analysis of the combined COI and 16S data yielded trees with overall stronger support than analyses of either gene alone. Several analyses failed to support the monophyly of Libellula sensu lato due to the inclusion of one or more outgroup species. However, statistical comparisons of topologies produced by unconstrained analyses and analyses in which the monophyly of Libellula was constrained indicate that any differences are nonsignificant. Based on morphological data, we therefore reject the paraphyly of Libellula and accept the outgroup status of Orthemis ferruginea and Pachydiplax longipennis.

Animals↗
PubMed2000

Comparison of the nucleotide sequences of 16S rRNA, 444 Ep-ank, and groESL heat shock operon genes in naturally occurring Ehrlichia equi and human granulocytic ehrlichiosis agent isolates from Northern California.

We examined 11 naturally occurring isolates of Ehrlichia equi in horses and two human granulocytic ehrlichiosis agent isolates in California for sequence diversity in three genes. Ehrlichia equi isolates were from Sierra (n = 6), Mendocino (n = 3), Sonoma (n = 1), and Marin (n = 1) counties, and human granulocytic ehrlichiosis (HGE) agent isolates were obtained from Humboldt county. PCR with specific primers for 16S rRNA, 444 Ep-ank and groESL heat shock operon genes successfully produced amplicons for all 13 clinical samples. The 444 Ep-ank gene of the HGE agent and E. equi isolates from northern California is different from the eastern U.S. isolates BDS and USG3. The translated amino acid sequence of the groESL heat shock operon gene fragment is identical among E. equi, the HGE agent, and E. phagocytophila, with the exception of the northern Californian equine CASOLJ isolate. Microheterogeneity was observed in the 16S rRNA gene sequences of HGE agent and E. equi isolates from northern California. These results suggest that E. equi and the HGE agent found in California are similar or identical but may differ from the isolates of equine and human origin found in the eastern United States.

Animals↗
PubMed2002

Worldwide distribution of Nitrosococcus oceani, a marine ammonia-oxidizing gamma-proteobacterium, detected by PCR and sequencing of 16S rRNA and amoA genes.

Diversity of cultured ammonia-oxidizing bacteria in the gamma-subdivision of the Proteobacteria was investigated by using strains isolated from various parts of the world ocean. All the strains were very similar to each other on the basis of the sequences of both the 16S rRNA and ammonia monooxygenase genes and could be characterized as a single species. Sequences were also cloned directly from environmental DNA from coastal Pacific and Atlantic sites, and these sequences represented the first Nitrosococcus oceani-like sequences obtained directly from the ocean. Most of the environmental sequences clustered tightly with those of the cultivated strains, but some sequences could represent new species of NITROSOCOCCUS: These findings imply that organisms similar to the cultivated N. oceani strains have a worldwide distribution.

Ammonia↗
PubMed1988

Partial nucleotide sequence of 16S ribosomal RNA isolated from armadillo-grown Mycobacterium leprae.

Ribosomal RNA (rRNA) was isolated from Mycobacterium leprae recovered from infected tissue of the Nine-banded Armadillo, and nucleotide sequences near the 3' end of the 16S species were determined by primer extension in the presence of dideoxynucleotides. Previously published data for bacterial 16S rRNAs show a pattern of conserved and non-conserved sequences that fit a common secondary structure. Our data for M. leprae fits this general pattern.

Animals↗
PubMed2005

Phylogeny of Proteobacteria and Bacteroidetes from oxic habitats of a tidal flat ecosystem.

Bacteria of the phyla Proteobacteria and Bacteroidetes are known to be the most prominent heterotrophic organisms in marine surface waters. In order to investigate the occurrence of these phyla in a coastal environment, the tidal flat ecosystem German Wadden Sea, we analyzed a clone library of PCR-amplified and sequenced 16S rRNA gene fragments and isolated 46 new strains affiliated with these phyla from the water column with various polymers and complex media as substrates. The phylogenetic affiliation of these strains was analyzed on the basis of sequenced 16S rRNA gene fragments. Subsequently, a comprehensive phylogenetic analysis of Proteobacteria and Bacteroidetes including available sequences from oxic habitats of earlier studies of this ecosystem was performed. Sequences of the earlier studies were derived from isolation approaches and from denaturing gradient gel electrophoresis (DGGE) analyses of environmental samples and high dilution steps of MPN (most probable number) cultures. The majority of the 265 sequences included in this analysis affiliated with alpha-Proteobacteria (45.3%), gamma-Proteobacteria (31.7%), and Bacteroidetes (16.2%). Almost 7% belong to the delta-Proteobacteria and several of these clones affiliated with the Myxococcales, a group comprising obligate aerobic organisms. Within the alpha- and gamma-Proteobacteria specific clusters were identified including isolates from high dilution steps of dilution cultures and/or clones from the clone library or DGGE gels, implying a high abundance of some of these organisms. Within the gamma-Proteobacteria a new cluster is proposed, which consists of marine surface-attached organisms. This SAMMIC (Surface Attached Marine MICrobes) cluster comprises only uncultured phylotypes and exhibits a global distribution. Overall, the analysis indicates that Proteobacteria and Bacteroidetes of the Wadden Sea have a surprisingly high diversity, presumably a result of the signature of this ecosystem as a melting pot at the land-sea interface and comprising a great habitat variety.

Bacteroidetes↗
PubMed2001

Phylogeny of the seal mycoplasmas Mycoplasma phocae corrig., Mycoplasma phocicerebrale corrig. and Mycoplasma phocirhinis corrig. based on sequence analysis of 16S rDNA.

The nucleotide sequences of the 16S rRNA genes from the type strains of three seal mycoplasmas, Mycoplasma phocicerebrale, Mycoplasma phocae and Mycoplasma phocirhinis (formerly Mycoplasma phocacerebrale, Mycoplasma phocidae and Mycoplasma phocarhinis, respectively), were determined by direct DNA cycle sequencing. Polymorphisms were found in all three 16S rRNA gene sequences, showing the existence of two different rRNA operons. In M. phocae, a length difference was found between the operons, caused by an insertion or a deletion of an adenosine in one of the operons. The sequence information was used to construct phylogenetic trees. All three species were found to belong to the hominis group, but to different clusters. M. phocicerebrale and M. phocae were found to be members of the Mycoplasma hominis cluster, within which M. phocicerebrale grouped in the Mycoplasma alkalescens subcluster. M. phocirhinis was found to be a member of the Mycoplasma bovigenitalium subcluster of the Mycoplasma bovis cluster. The 16S rRNA gene sequences of all hitherto validly described species within the M. hominis and M. bovis clusters have now been determined.

Animals↗
PubMed2006

[Identification of sarcosaphagous flies by analyses the sequence of 16S rDNA].

OBJECTIVE: To solve the difficulties of identification of Sarcosaphagous flies such as Lucilia sericata (Meigen) and Lucilia cuprina (Wiedemann) which could not be identified by analyzing the 278bp and 635 bp regions of the gene encoding for cytochrome oxidase subunit I and II (CO I and CO II) in mtDNA. METHODS: Specimens were collected from the corpses of rabbits on the grassland in Huhhot and Chengdu, the sequences of 551 bp region of 16S rDNA of their mtDNA were analyzed, the multiple-alignment program DNAMAN(version 4.0) and MEGA 2.1 sofeware were employed for sequence alignments neighbour-joining tree construction. RESULTS: Lucilia sericata (Meigen) and Lucilia cuprina (Wiedemann) were distinguished successfully by sequence analysis of The 551 bp region of the gene of 16S rDNA. CONCLUSION: The 551 bp region of the gene of 16S rDNA of sarcosaphagous flies can be used for identifying them on species level effectively. It is likely to be a successful compliment to identify the sarcosaphagous flies by sequence analysis of CO I and CO II in mtDNA.

Animals↗
PubMed1994

Phylogeny of hard- and soft-tick taxa (Acari: Ixodida) based on mitochondrial 16S rDNA sequences.

Ticks are parasitiform mites that are obligate hematophagous ectoparasites of amphibians, reptiles, birds, and mammals. A phylogeny for tick families, subfamilies, and genera has been described based on morphological characters, life histories, and host associations. To test the existing phylogeny, we sequenced approximately 460 bp from the 3' end of the mitochondrial 16S rRNA gene (rDNA) in 36 hard- and soft-tick species; a mesostigmatid mite, Dermanyssus gallinae, was used as an outgroup. Phylogenies derived using distance, maximum-parsimony, or maximum-likelihood methods were congruent. The existing phylogeny was largely supported with four exceptions. In hard ticks (Ixodidae), members of Haemaphysalinae were monophyletic with the primitive Amblyomminae and members of Hyalomminae grouped within the Rhipicephalinae. In soft ticks (Argasidae), the derived phylogeny failed to support a monophyletic relationship among members of Ornithodorinae and supported placement of Argasinae as basal to the Ixodidae, suggesting that hard ticks may have originated from an Argas-like ancestor. Because most Argas species are obligate bird octoparasites, this result supports earlier suggestions that hard ticks did not evolve until the late Cretaceous.

Animals↗
PubMed2004

Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence.

Phylogenetic analysis of archaea in the rumen ecosystem was analysed by PCR of 16S rDNA from the bovine rumen using archaea-specific primers. The libraries were constructed from rumen fluid (AF), rumen solid (AS), and rumen epithelium (AE) from a rumen-fistulated Korean cow (Hanwoo). The 45 AF clones could be divided into three groups and the largest group was affiliated with the Methanomicrobiaceae family (96% of clones). The AF clones contained a high proportion of unidentifiable clones (67%). The 39 AE clones could be divided into two groups and the largest group was also affiliated with the Methanomicrobiaceae family (95% of clones). The AE clones contained a low proportion of unidentifiable clones (5%). The 20 AS clones could be divided into two groups that were affiliated with either the Methanobacteriaceae family (55%) or the Methanomicrobiaceae family (45%). The AS clones contained a moderate proportion of unidentifiable clones (40%). The predominant family of whole rumen archaea was found to belong to the Methanomicrobiaceae (85%). Methanomicrobiaceae were predominant in the rumen epithelium and the rumen fluid while Methanobacteriaceae were predominant in the rumen solid. One clone from the rumen fluid and two clones from the rumen epithelium contained rDNA sequences of Non-Thermophilic-Crenarchaeota (NTC) and Thermophilic-Crenarchaeota (TC), respectively, which have not previously been described from the rumen.

Journal Article↗
PubMed2000

The PCR amplification of non-tuberculous mycobacterial 16S rRNA sequences from soil.

Non-tuberculous mycobacteria are free living saprophytic organisms commonly found in soil and water. Some are major causes of opportunistic infection, particularly in immuno-compromised patients, and may influence the efficacy of bacille Calmette-Guérin vaccinations. Many of these organisms are not amenable to culture, so information about their distribution is limited. PCR primers designed to amplify part of the mycobacterial 16S rRNA gene were applied to DNA extracted from cultured organisms and soil. The PCR products from soil contained sequences with similarity to slow growing mycobacteria similar to Mycobacterium lentiflavum, and to fast growing mycobacteria such as the xenobiotic degraders PYR-I and RJGII.

Genes, Bacterial↗