scholarly journals New Degenerate Cytophaga-Flexibacter-Bacteroides-Specific 16S Ribosomal DNA-Targeted Oligonucleotide Probes Reveal High Bacterial Diversity in River Taff Epilithon

2002 ◽  
Vol 68 (1) ◽  
pp. 201-210 ◽  
Author(s):  
Louise A. O’Sullivan ◽  
Andrew J. Weightman ◽  
John C. Fry
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Small Subunit ◽  
Target Range ◽  
Probe Design ◽  
Ribosomal Database Project ◽  
Bacterial Populations ◽  
16S Ribosomal Dna ◽  
South Wales

ABSTRACT River microbial communities play an important role in global nutrient cycles, and aggregated bacteria such as those in epilithic biofilms may be major contributors. In this study the bacterial diversity of River Taff epilithon in South Wales was investigated. A 16S ribosomal DNA (rDNA) clone library was constructed and analyzed by partial sequencing of 76 of 347 clones and hybridization with taxon-specific probes. The epilithon was found to be very diverse, with an estimated 59.6% of the bacterial populations not accounted for by these clones. Members of the Cytophaga-Flexibacter-Bacteroides division (CFBs) were most abundant in the library, representing 25% of clones, followed by members of the α subdivision of the division Proteobacteria (α-Proteobacteria), γ-Proteobacteria, gram-positive bacteria, Cyanobacteria, β-Proteobacteria, δ-Proteobacteria, and the Prosthecobacter group. This study concentrated on the epilithic CFB populations, and a new set of degenerate 16S rDNA probes was developed to enhance their detection, namely, CFB560, CFB562, and CFB376. The commonly used probe CF319a/b may frequently lead to the underestimation of CFB populations in environmental studies, because it does not fully detect members of the division. CFB560 had exact matches to 95.6% of CFBs listed in the Ribosomal Database Project (release 8.0) small-subunit phylogenetic trees, compared to 60% for CF319a/b. The CFB probes detected 66 of 347 epilithon TAF clones, and 60 of these were partially sequenced. They affiliated with the RDP-designated groups Cytophaga, Sphingobacterium, Lewinella, and Cytophaga aurantiaca. CFB560 and CF319a/b detected 94% (62 of 66) and 48.5% (32 of 66) of clones, respectively, and therefore CFB560 is recommended for future use. Probe design in this study illustrated that multiple degenerate positions can greatly increase target range without adversely effecting specificity or experimental performance.

scholarly journals Characterization and Molecular Epidemiology of a Fungal Infection of Edible Crabs (Cancer pagurus) and Interaction of the Fungus with the Dinoflagellate Parasite Hematodinium

2012 ◽  
Vol 79 (3) ◽  
pp. 783-793 ◽  
Author(s):  
Amanda L. Smith ◽  
Kristina M. Hamilton ◽  
Lucy Hirschle ◽  
Emma C. Wootton ◽  
Claire L. Vogan ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Host Response ◽  
Small Subunit ◽  
Fungal Isolate ◽  
Content Type ◽  
Cancer Pagurus ◽  
South Wales ◽  
Disease Condition ◽  
Fungal Sepsis ◽  
Host Tissues

ABSTRACTThis study reports on an emerging fungal disease of the edible crab,Cancer pagurus. Juvenile (prerecruit) crabs were found to be subject to this disease condition during the months of May to September at two intertidal sites in South Wales, United Kingdom. Histopathology revealed that the fungi overwhelm the host response in the tissues, leading to progressive septicemia. The causative agent of this infection was isolated and grown in pure culture and was identified as a member of theOphiocordycepsclade by sequencing of the small subunit of the fungal ribosomal DNA (rDNA). Of the crabs naturally infected with the fungus, 94% had a coinfection with the parasitic dinoflagellateHematodiniumspecies. To determine if there was any interaction between the two disease-causing agents, apparently fungus-free crabs, both with and without naturalHematodiniuminfections, were challenged with the fungal isolate. The presence ofHematodiniumcaused a significant reduction in fungal multiplication in the hemocoel of the crabs in comparison to that inHematodinium-free individuals. Histopathology of coinfected crabs showed a systemic multiplication ofHematodiniumwithin host tissues, leading to a rapid death, whileHematodinium-free crabs experimentally infected with the fungal isolate died due to fungal sepsis (septicemia) with the same characteristic pathology as seen in natural infections.

Morphology and phylogeny of Pseudorobillarda eucalypti sp. nov., from Thailand

Phytotaxa ◽  
2014 ◽  
Vol 176 (1) ◽  
pp. 251 ◽  
Author(s):  
NARUMON TANGTHIRASUNUN ◽  
PHILIPPE SILAR ◽  
DARBHE JAYARAMA BHAT ◽  
EKACHAI CHUKEATIROTE ◽  
D.N. NALIN WIJAYAWARDENE ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Large Subunit ◽  
Elongation Factor ◽  
Morphological Characteristics ◽  
Distinct Species ◽  
Small Subunit ◽  
Family Status

Pseudorobillarda is a coelomycete genus of Dothideomycetes with appendaged conidia and 15 species epithets. In this study, we isolated four strains of Pseudorobillarda from dead leaves in Thailand. DNA sequence data generated from the large subunit (28S) ribosomal DNA (nuLSU) gene was used in phylogenetic studies. The phylogenetic trees generated indicate that Pseudorobillarda form a distinct lineage in Dothideomycetes that may eventually require separate family status. The Pseudorobillarda strains comprised two distinct species and this is also supported by morphological characteristics. In this paper we introduce a new species of Pseudorobillarda, P. eucalypti and compare it with other species of the genus. We also deposit data from the internal transcribed spacer (ITS), small subunit (18S) ribosomal DNA (nuSSU),the RNA polymerase II 2nd largest subunit genes (RPB2), Translation Elongation Factor 1-α (TEF1-α) and β-Tubulin (Bt) genes from each strain in GenBank for future studies.

scholarly journals 16S Ribosomal DNA Terminal Restriction Fragment Pattern Analysis of Bacterial Communities in Feces of Rats Fed Lactobacillus acidophilus NCFM

2001 ◽  
Vol 67 (4) ◽  
pp. 1935-1939 ◽  
Author(s):  
Christopher W. Kaplan ◽  
Johanna C. Astaire ◽  
Mary Ellen Sanders ◽  
Bandaru S. Reddy ◽  
Christopher L. Kitts
Keyword(s):  
Restriction Fragment ◽  
Ribosomal Dna ◽  
Lactobacillus Acidophilus ◽  
Bacterial Communities ◽  
Pattern Analysis ◽  
Bacterial Populations ◽  
Fragment Pattern ◽  
16S Ribosomal Dna ◽  
Restriction Fragment Pattern ◽  
Lactobacillus Acidophilus Ncfm

ABSTRACT 16S ribosomal DNA terminal restriction fragment patterns from rat fecal samples were analyzed to track the dynamics ofLactobacillus acidophilus NCFM and discern bacterial populations that changed during feeding with NCFM. Lactobacillus johnsonii and Ruminococcus flavefaciens were tentatively identified as such bacterial populations. The presence ofL. johnsonii was confirmed by isolation from feces.

scholarly journals Molecular Phylogenetic Exploration of Bacterial Diversity in a Bakreshwar (India) Hot Spring and Culture of Shewanella-Related Thermophiles

2003 ◽  
Vol 69 (7) ◽  
pp. 4332-4336 ◽  
Author(s):  
Dhritiman Ghosh ◽  
Bijay Bal ◽  
V. K. Kashyap ◽  
Subrata Pal
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Dna ◽  
Hot Spring ◽  
Culture Conditions ◽  
Gram Positive ◽  
Sediment Samples ◽  
Gram Positive Bacteria ◽  
16S Ribosomal Dna ◽  
Culture Independent ◽  
Molecular Phylogenetic

ABSTRACT The bacterial diversity of a hot spring in Bakreshwar, India, was investigated by a culture-independent approach. 16S ribosomal DNA clones derived from the sediment samples were found to be associated with gamma-Proteobacteria, cyanobacteria, and green nonsulfur and low-GC gram-positive bacteria. The first of the above phylotypes cobranches with Shewanella, a well-known iron reducer. This phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing microorganisms.

scholarly journals Phylogenetic Diversity of Archaea and Bacteria in the Anoxic Zone of a Meromictic Lake (Lake Pavin, France)

2007 ◽  
Vol 73 (6) ◽  
pp. 2016-2019 ◽  
Author(s):  
Anne-Catherine Lehours ◽  
Paul Evans ◽  
Corinne Bardot ◽  
Keith Joblin ◽  
Fonty Gérard
Keyword(s):  
Water Column ◽  
Bacterial Diversity ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Mountain Lake ◽  
Anoxic Zone ◽  
Bacterial Populations ◽  
Different Depths ◽  
Lake Pavin ◽  
Sediment Interface

ABSTRACT The compositions of archaeal and bacterial populations at different depths (60 m [mixolimnion-chemocline interface], 70 m [chemocline-subchemocline interface], 90 m, and 92 m [the water-sediment interface]) in the anoxic zone of the water column in Lake Pavin, a freshwater permanently stratified mountain lake in France, were determined. Phylogenetic trees were constructed from sequences to assess archaeal and bacterial diversity at the four sites.

scholarly journals High-Density Microarray of Small-Subunit Ribosomal DNA Probes

2002 ◽  
Vol 68 (5) ◽  
pp. 2535-2541 ◽  
Author(s):  
Kenneth H. Wilson ◽  
Wendy J. Wilson ◽  
Jennifer L. Radosevich ◽  
Todd Z. DeSantis ◽  
Vijay S. Viswanathan ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Bacterial Species ◽  
Small Subunit ◽  
Rrna Genes ◽  
Biological Research ◽  
Ribosomal Database Project ◽  
Small Subunit Rrna ◽  
Phylogenetic Groups ◽  
Chip Technology ◽  
Small Subunit Ribosomal Dna

ABSTRACT Ribosomal DNA sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven useful in many areas of biological research. Some of the most promising applications of this approach are presently limited by the rate at which sequences can be analyzed. As a step toward overcoming this limitation, we have investigated the use of photolithography chip technology to perform sequence analyses on amplified small-subunit rRNA genes. The GeneChip (Affymetrix Corporation) contained 31,179 20-mer oligonucleotides that were complementary to a subalignment of sequences in the Ribosomal Database Project (RDP) (B. L. Maidak et al., Nucleic Acids Res. 29:173-174, 2001). The chip and standard Affymetrix software were able to correctly match small-subunit ribosomal DNA amplicons with the corresponding sequences in the RDP database for 15 of 17 bacterial species grown in pure culture. When bacteria collected from an air sample were tested, the method compared favorably with cloning and sequencing amplicons in determining the presence of phylogenetic groups. However, the method could not resolve the individual sequences comprising a complex mixed sample. Given these results and the potential for future enhancement of this technology, it may become widely useful.

scholarly journals 16S Ribosomal DNA-Based Analysis of Bacterial Diversity in Purified Water Used in Pharmaceutical Manufacturing Processes by PCR and Denaturing Gradient Gel Electrophoresis

2002 ◽  
Vol 68 (2) ◽  
pp. 699-704 ◽  
Author(s):  
Mako Kawai ◽  
Eiichi Matsutera ◽  
Hisashi Kanda ◽  
Nobuyasu Yamaguchi ◽  
Katsuji Tani ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Ribosomal Dna ◽  
Gel Electrophoresis ◽  
Esterase Activity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Pharmaceutical Manufacturing ◽  
Manufacturing Processes ◽  
Culturable Bacteria ◽  
16S Ribosomal Dna ◽  
Gradient Gel Electrophoresis

ABSTRACT The bacterial community in partially purified water, which is prepared by ion exchange from tap water and is used in pharmaceutical manufacturing processes, was analyzed by denaturing gradient gel electrophoresis (DGGE). 16S ribosomal DNA fragments, including V6, -7, and -8 regions, were amplified with universal primers and analyzed by DGGE. The bacterial diversity in purified water determined by PCR-DGGE banding patterns was significantly lower than that of other aquatic environments. The bacterial populations with esterase activity sorted by flow cytometry and isolated on soybean casein digest (SCD) and R2A media were also analyzed by DGGE. The dominant bacterium in purified water possessed esterase activity but could not be detected on SCD or R2A media. DNA sequence analysis of the main bands on the DGGE gel revealed that culturable bacteria on these media were Bradyrhizobium sp., Xanthomonas sp., and Stenotrophomonas sp., while the dominant bacterium was not closely related to previously characterized bacteria. These data suggest the importance of culture-independent methods of quality control for pharmaceutical water.

Ottolenchus sinipersici n. sp. (Rhabditida: Tylenchidae) from the Persian Gulf mangrove forests, Iran

Nematology ◽  
2021 ◽  
pp. 1-15
Author(s):  
Manouchehr Hosseinvand ◽  
Ali Eskandari ◽  
Joaquín Abolafia ◽  
Akbar Karegar ◽  
Reza Ghaderi ◽  
...  
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Large Subunit ◽  
Small Subunit ◽  
The Body ◽  
Lsu Rdna ◽  
Mangrove Forests ◽  
Body Contour ◽  
Lateral Field

Summary A new species of Tylenchidae from the rhizosphere of mangrove trees in Hormozgan and Khuzestan provinces, Iran, is described based on morphological and molecular data. Ottolenchus sinipersici n. sp., is characterised by a slightly fusiform body 560-665 μm long, lateral field in the form of a narrow band with two faint incisures that are not visible in fatter females, indistinct transverse annuli under the light microscope, cephalic region continuous with the body contour, smooth and flattened dorsoventrally, longitudinal and narrow sigmoid amphidial slits, stylet delicate, 10.1-11.2 μm long, with small rounded to slightly posteriorly sloping knobs, well-developed median bulb, offset and pyriform pharyngeal basal bulb, vulva located at 66.9-69.6% of body length, offset spermatheca, short post-vulval uterine sac, spicules 18.5-20.5 μm long with highly curved blades, and a 113-135 μm long filiform tail with a hook-like or coiled terminus. In Bayesian inference phylogenetic trees based on the partial small subunit ribosomal DNA (SSU rDNA) and D2-D3 expansion segment of large subunit ribosomal DNA (D2-D3 LSU rDNA) genes, the new species clustered together with O. facultativus (KJ869310) in SSU, and forms a clade with three isolates of O. discrepans in LSU phylogeny. Ottolenchus fungivorus n. comb. (= Filenchus fungivorus) is proposed.

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