scholarly journals Phytoplankton distribution patterns in the northwestern Sargasso Sea revealed by small subunit rRNA genes from plastids

2011 ◽  
Vol 6 (3) ◽  
pp. 481-492 ◽  
Author(s):  
Alexander H Treusch ◽  
Elif Demir-Hilton ◽  
Kevin L Vergin ◽  
Alexandra Z Worden ◽  
Craig A Carlson ◽  
...  
Keyword(s):  
Distribution Patterns ◽  
Small Subunit ◽  
Rrna Genes ◽  
Sargasso Sea ◽  
Small Subunit Rrna ◽  
Phytoplankton Distribution

scholarly journals Culture-Independent Analysis of Indomethacin-Induced Alterations in the Rat Gastrointestinal Microbiota

2006 ◽  
Vol 72 (10) ◽  
pp. 6707-6715 ◽  
Author(s):  
Andrew B. Dalby ◽  
Daniel N. Frank ◽  
Allison L. St. Amand ◽  
Alison M. Bendele ◽  
Norman R. Pace
Keyword(s):  
Small Intestine ◽  
Lymph Nodes ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Mesenteric Lymph Nodes ◽  
Gastrointestinal Microbiota ◽  
Mesenteric Lymph ◽  
Independent Analysis ◽  
Culture Independent

ABSTRACT Nonsteroidal anti-inflammatory drugs (NSAIDs) are commonly prescribed for a variety of inflammatory conditions; however, the benefits of this class of drugs are accompanied by deleterious side effects, most commonly gastric irritation and ulceration. NSAID-induced ulceration is thought to be exacerbated by intestinal microbiota, but previous studies have not identified specific microbes that contribute to these adverse effects. In this study, we conducted a culture-independent analysis of ∼1,400 bacterial small-subunit rRNA genes associated with the small intestines and mesenteric lymph nodes of rats treated with the NSAID indomethacin. This is the first molecular analysis of the microbiota of the rat small intestine. A comparison of clone libraries and species-specific quantitative PCR results from rats treated with indomethacin and untreated rats revealed that organisms closely related to Enterococcus faecalis were heavily enriched in the small intestine and mesenteric lymph nodes of the treated rats. These data suggest that treatment of NSAID-induced ulceration may be facilitated by addressing the microbiological imbalances.

scholarly journals Specificity of Associations between Bacteria and the Coral Pocillopora meandrina during Early Development

2012 ◽  
Vol 78 (20) ◽  
pp. 7467-7475 ◽  
Author(s):  
Amy Apprill ◽  
Heather Q. Marlow ◽  
Mark Q. Martindale ◽  
Michael S. Rappé
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Polymorphism Analysis ◽  
Roseobacter Clade ◽  
Small Subunit Rrna ◽  
Content Type ◽  
Sterile Seawater ◽  
Show Evidence ◽  
Coral Health

ABSTRACTRelationships between corals and specific bacterial associates are thought to play an important role in coral health. In this study, the specificity of bacteria associating with the coralPocillopora meandrinawas investigated by exposing coral embryos to various strains of cultured marine bacteria, sterile seawater, or raw seawater and examining the identity, density, and location of incorporated cells. The isolates utilized in this experiment included members of the Roseobacter and SAR11 clades of theAlphaproteobacteria, aPseudoalteromonasspecies of theGammaproteobacteria, and aSynechococcusspecies of theCyanobacteriaphylum. Based on terminal restriction fragment length polymorphism analysis of small-subunit rRNA genes, similarities in bacterial communities associated with 170-h-old planulae were observed regardless of treatment, suggesting that bacteria may have been externally associated from the outset of the experiment. Microscopic examination ofP. meandrinaplanulae by fluorescencein situhybridization with bacterial and Roseobacter clade-specific oligonucleotide probes revealed differences in the densities and locations of planulae-associated cells. Planulae exposed to either raw seawater or strains ofPseudoalteromonasand Roseobacter harbored the highest densities of internally associated cells, of which 20 to 100% belonged to the Roseobacter clade. Planulae exposed to sterile seawater or strains of the SAR11 clade andSynechococcusdid not show evidence of prominent bacterial associations. Additional analysis of the raw-seawater-exposed planulae via electron microscopy confirmed the presence of internally associated prokaryotic cells, as well as virus-like particles. These results suggest that the availability of specific microorganisms may be an important factor in the establishment of coral-bacterial relationships.

The Relationships among Microorganisms in Paddy Soil of Rice Varieties at Sanamchaikate, Chachoengsao

2017 ◽  
Vol 866 ◽  
pp. 144-147
Author(s):  
Duongruitai Nicomrat ◽  
Paisan Kanthang ◽  
Siriphatrc Chamutpong
Keyword(s):  
Paddy Soil ◽  
Small Subunit ◽  
Organic Fertilizers ◽  
Rrna Genes ◽  
Most Probable Number ◽  
Small Subunit Rrna ◽  
Rice Varieties ◽  
Probable Number ◽  
Jasmine Rice ◽  
Ph Range

The research was conducted to understand the diversity of microbial communities in the rice cultivars KDM 105 in the rice fields at Sanamchaikate, Chachoengsao Province. The culturing bacterial community in paddy soil before planting, during the planting and sowing of rice, and after rice collection as well as isolation of free nitrogen fixing bacteria under aerobic and anaerobic conditions were identified by molecular comparision of 16S small subunit rRNA genes as well as species diversity and their richness by Most Probable Number (MPN) method. Culturable bacterial isolates in the soil around the roots of rice varieties were determined for their physical appearances on the solid culture (Plate culturing method) and the microscopic observation under light microscope. It was found that bacteria in the paddy soil complemented with organic fertilizers and no pesticide application for over five years had a pH range from 5.2 to 5.5 cultivated jasmine rice, 8-9 log Units of free N2-fixing bacteria near the roots compared with those in other area having 4-5 log Units. Most of them were identified to be Pseudomonas sp. Microbacterium sp. Bacillus sp. Stenotrophomonas sp. and Burkholderia sp., by homology comparison of 16S rDNA gene at 98, 97, 99, 99.5, and 99%, respectively. This research revealed the recognizable complex and change in soil bacteria presented in paddy ecosystem. In any critical change of to the soil, the study of microbial diversity, compositions and their richness can be further useful for indicating proper soil management.

scholarly journals Microbial Composition of Near-Boiling Silica-Depositing Thermal Springs throughout Yellowstone National Park

2002 ◽  
Vol 68 (10) ◽  
pp. 5123-5135 ◽  
Author(s):  
Carrine E. Blank ◽  
Sherry L. Cady ◽  
Norman R. Pace
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Hydrogen Oxidation ◽  
Large Subunit ◽  
Microbial Community Composition ◽  
Pcr Amplification ◽  
Small Subunit ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Microbial Composition

ABSTRACT The extent of hyperthermophilic microbial diversity associated with siliceous sinter (geyserite) was characterized in seven near-boiling silica-depositing springs throughout Yellowstone National Park using environmental PCR amplification of small-subunit rRNA genes (SSU rDNA), large-subunit rDNA, and the internal transcribed spacer (ITS). We found that Thermocrinis ruber, a member of the order Aquificales, is ubiquitous, an indication that primary production in these springs is driven by hydrogen oxidation. Several other lineages with no known close relatives were identified that branch among the hyperthermophilic bacteria. Although they all branch deep in the bacterial tree, the precise phylogenetic placement of many of these lineages is unresolved at this time. While some springs contained a fair amount of phylogenetic diversity, others did not. Within the same spring, communities in the subaqueous environment were not appreciably different than those in the splash zone at the edge of the pool, although a greater number of phylotypes was found along the pool's edge. Also, microbial community composition appeared to have little correlation with the type of sinter morphology. The number of cell morphotypes identified by fluorescence in situ hybridization and scanning electron microscopy was greater than the number of phylotypes in SSU clone libraries. Despite little variation in Thermocrinis ruber SSU sequences, abundant variation was found in the hypervariable ITS region. The distribution of ITS sequence types appeared to be correlated with distinct morphotypes of Thermocrinis ruber in different pools. Therefore, species- or subspecies-level divergences are present but not detectable in highly conserved SSU sequences.

Vairimorpha imperfecta n.sp., a microsporidian exhibiting an abortive octosporous sporogony in Plutella xylostella L. (Lepidoptera: Yponomeutidae)

Parasitology ◽  
1999 ◽  
Vol 119 (3) ◽  
pp. 273-286 ◽  
Author(s):  
E. U. CANNING ◽  
A. CURRY ◽  
S. CHENEY ◽  
N. J. LAFRANCHI-TRISTEM ◽  
M. A. HAQUE
Keyword(s):  
Plutella Xylostella ◽  
Phylogenetic Analyses ◽  
Diamondback Moth ◽  
Small Subunit ◽  
Rrna Genes ◽  
Direct Control ◽  
Small Subunit Rrna ◽  
Polar Tube ◽  
Cell Cytoplasm ◽  
Host Cell Cytoplasm

The microsporidian genus Nosema is characterized by development in direct control with host cell cytoplasm, diplokaryotic nuclei throughout development and disporous sporogony. The genus Vairimorpha exhibits the same features plus an octoporous sporogony producing uninucleate spores in a sporophorous vesicle. A microsporidium from diamondback moth, Plutella xylostella, falls between Nosema and Vairimorpha in that it initiates but fails to complete the octosporous sequence in this host. The name Vairimorpha imperfecta n.sp. is proposed. Merogony is mainly by formation of buds from multinucleate meronts, the buds remaining attached in chains. Diplokaryotic spores measure 4·3×2·0 μm (fresh) and have 15·5 coils of the polar tube in 1 rank. The octosporous sporogony is aborted owing to irregular formation of nuclear spindles, incomplete cytoplasmic fission and bizarre deposition of electron-dense episporontal secretions. Phylogenetic analyses of the sequences of the small subunit rRNA genes of V. imperfecta and of several Nosema and Vairimorpha spp. place V. imperfecta in a clade with Nosema spp. from Lepidoptera rather than in the clade containing the more typical species of Vairimorpha. It is suggested that the ancestors of the Vairimorpha/Nosema complex of species exhibited both disporous and octosporous sporogonies, as does the type species of Vairimorpha, Vairimorpha necatrix. It would follow that true Nosema spp. have lost the ability to express an octosporous sequence and that V. imperfecta is in the process of losing it. It is proposed that the genera Nosema and Vairimorpha be placed in the same family Nosematidae Labbé 1899, rather than in separate families and orders as at present.

scholarly journals Abundant and Diverse Fungal Microbiota in the Murine Intestine

2006 ◽  
Vol 72 (1) ◽  
pp. 793-801 ◽  
Author(s):  
Alexandra J Scupham ◽  
Laura L. Presley ◽  
Bo Wei ◽  
Elizabeth Bent ◽  
Natasha Griffith ◽  
...  
Keyword(s):  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Small Subunit Rrna ◽  
Culture Independent ◽  
Specific Pathogen ◽  
Health And Disease ◽  
Oligonucleotide Fingerprinting ◽  
Rrna Sequences

ABSTRACT Enteric microbiota play a variety of roles in intestinal health and disease. While bacteria in the intestine have been broadly characterized, little is known about the abundance or diversity of enteric fungi. This study utilized a culture-independent method termed oligonucleotide fingerprinting of rRNA genes (OFRG) to describe the compositions of fungal and bacterial rRNA genes from small and large intestines (tissue and luminal contents) of restricted-flora and specific-pathogen-free mice. OFRG analysis identified rRNA genes from all four major fungal phyla: Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota. The largest assemblages of fungal rRNA sequences were related to the genera Acremonium, Monilinia, Fusarium, Cryptococcus/Filobasidium, Scleroderma, Catenomyces, Spizellomyces, Neocallimastix, Powellomyces, Entophlyctis, Mortierella, and Smittium and the order Mucorales. The majority of bacterial rRNA gene clones were affiliated with the taxa Bacteroidetes, Firmicutes, Acinetobacter, and Lactobacillus. Sequence-selective PCR analyses also detected several of these bacterial and fungal rRNA genes in the mouse chow. Fluorescence in situ hybridization analysis with a fungal small-subunit rRNA probe revealed morphologically diverse microorganisms resident in the mucus biofilm adjacent to the cecal and proximal colonic epithelium. Hybridizing organisms comprised about 2% of the DAPI (4′,6-diamidino-2-phenylindole, dihydrochloride)-positive organisms in the mucus biofilm, but their abundance in fecal material may be much lower. These data indicate that diverse fungal taxa are present in the intestinal microbial community. Their abundance suggests that they may play significant roles in enteric microbial functions.

scholarly journals Succession of Microbial Communities during Hot Composting as Detected by PCR–Single-Strand-Conformation Polymorphism-Based Genetic Profiles of Small-Subunit rRNA Genes

2000 ◽  
Vol 66 (3) ◽  
pp. 930-936 ◽  
Author(s):  
Sabine Peters ◽  
Stefanie Koschinsky ◽  
Frank Schwieger ◽  
Christoph C. Tebbe
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
Single Strand Conformation Polymorphism ◽  
Small Subunit ◽  
Ssu Rdna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Small Subunit Rrna ◽  
Genetic Profiles ◽  
Conformation Polymorphism

ABSTRACT A cultivation-independent technique for genetic profiling of PCR-amplified small-subunit rRNA genes (SSU rDNA) was chosen to characterize the diversity and succession of microbial communities during composting of an organic agricultural substrate. PCR amplifications were performed with DNA directly extracted from compost samples and with primers targeting either (i) the V4–V5 region of eubacterial 16S rRNA genes, (ii) the V3 region in the 16S rRNA genes of actinomycetes, or (iii) the V8–V9 region of fungal 18S rRNA genes. Homologous PCR products were converted to single-stranded DNA molecules by exonuclease digestion and were subsequently electrophoretically separated by their single-strand-conformation polymorphism (SSCP). Genetic profiles obtained by this technique showed a succession and increasing diversity of microbial populations with all primers. A total of 19 single products were isolated from the profiles by PCR reamplification and cloning. DNA sequencing of these molecular isolates showed similarities in the range of 92.3 to 100% to known gram-positive bacteria with a low or high G+C DNA content and to the SSU rDNA of γ-Proteobacteria. The amplified 18S rRNA gene sequences were related to the respective gene regions of Candida krusei and Candida tropicalis. Specific molecular isolates could be attributed to different composting stages. The diversity of cultivated bacteria isolated from samples taken at the end of the composting process was low. A total of 290 isolates were related to only 6 different species. Two or three of these species were also detectable in the SSCP community profiles. Our study indicates that community SSCP profiles can be highly useful for the monitoring of bacterial diversity and community successions in a biotechnologically relevant process.

Redescriptions of three trachelocercid ciliates (Protista, Ciliophora, Karyorelictea), with notes on their phylogeny based on small subunit rRNA gene sequences

2013 ◽  
Vol 63 (Pt_9) ◽  
pp. 3506-3514 ◽  
Author(s):  
Ying Yan ◽  
Yuan Xu ◽  
Zhenzhen Yi ◽  
Alan Warren
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Small Subunit ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Small Subunit Rrna ◽  
Small Subunit Rrna Gene ◽  
Ssu Rrna Gene Sequence ◽  
First Time

Three trachelocercid ciliates, Kovalevaia sulcata (Kovaleva, 1966) Foissner, 1997, Trachelocerca sagitta (Müller, 1786) Ehrenberg, 1840 and Trachelocerca ditis (Wright, 1982) Foissner, 1996, isolated from two coastal habitats at Qingdao, China, were investigated using live observation and silver impregnation methods. Data on their infraciliature and morphology are supplied. The small subunit rRNA (SSU rRNA) genes of K. sulcata and Trachelocerca sagitta were sequenced for the first time. Phylogenetic analyses based on SSU rRNA gene sequence data indicate that both organisms, and the previously sequenced Trachelocerca ditis, are located within the trachelocercid assemblage and that K. sulcata is sister to an unidentified taxon forming a clade that is basal to the core trachelocercids.

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