scholarly journals Characterization of rumen ciliate community composition in domestic sheep, deer, and cattle, feeding on varying diets, by means of PCR-DGGE and clone libraries

2011 ◽  
Vol 75 (3) ◽  
pp. 468-481 ◽  
Author(s):  
Sandra Kittelmann ◽  
Peter H. Janssen
Keyword(s):  
Community Composition ◽  
Domestic Sheep ◽  
Clone Libraries ◽  
Ciliate Community ◽  
Cattle Feeding

Description of Diploplastron dehorityi sp. nov. (Entodiniomorphida, Ophryoscolecidae), a new rumen ciliate from Brazilian sheep (Ovis aries)

Zootaxa ◽  
2017 ◽  
Vol 4258 (6) ◽  
pp. 581 ◽  
Author(s):  
FRANCIANE CEDROLA ◽  
ROBERTO JÚNIO PEDROSO DIAS ◽  
ISABEL MARTINELE ◽  
MARTA D’AGOSTO
Keyword(s):  
New Species ◽  
Body Shape ◽  
The Body ◽  
Ovis Aries ◽  
Domestic Sheep ◽  
Diagnostic Features ◽  
Ciliate Community ◽  
The Right ◽  
A New Species

To date the genus Diploplastron comprised only one species of ophryoscolecid ciliate, Diploplastron affine, which is characterized by having two retractable ciliary zones in the anterior end of the body, two slender and juxtaposed skeletal plates on the right side, a rod shape macronucleus, and two contractile vacuoles. During study on the characterization of rumen ciliate community composition in Brazilian domestic sheep, we observed ciliates with atypical morphology but with diagnostic features of genus Diploplastron. This study describes Diploplastron dehorityi, a new species of ophryoscolecid ciliate, that differs from D. affine, primarily, in the morphology of skeletal plates, morphology of nuclear apparatus and body shape. In addition to the similarities between the new species and congener species, D. dehorityi has some morphological similarities to species of genus Eremoplastron.

scholarly journals Molecular Characterization of Subject-Specific Oral Microflora during Initial Colonization of Enamel

2006 ◽  
Vol 72 (4) ◽  
pp. 2837-2848 ◽  
Author(s):  
Patricia I. Diaz ◽  
Natalia I. Chalmers ◽  
Alexander H. Rickard ◽  
Colin Kong ◽  
Craig L. Milburn ◽  
...  
Keyword(s):  
Community Composition ◽  
Bacterial Species ◽  
Microbial Community Composition ◽  
Microbial Colonization ◽  
Rrna Gene ◽  
Dependent Manner ◽  
Clone Libraries ◽  
Tooth Surfaces ◽  
Biofilm Development

ABSTRACT The initial microbial colonization of tooth surfaces is a repeatable and selective process, with certain bacterial species predominating in the nascent biofilm. Characterization of the initial microflora is the first step in understanding interactions among community members that shape ensuing biofilm development. Using molecular methods and a retrievable enamel chip model, we characterized the microbial diversity of early dental biofilms in three subjects. A total of 531 16S rRNA gene sequences were analyzed, and 97 distinct phylotypes were identified. Microbial community composition was shown to be statistically different among subjects. In all subjects, however, 4-h and 8-h communities were dominated by Streptococcus spp. belonging to the Streptococcus oralis/Streptococcus mitis group. Other frequently observed genera (comprising at least 5% of clone sequences in at least one of the six clone libraries) were Actinomyces, Gemella, Granulicatella, Neisseria, Prevotella, Rothia, and Veillonella. Fluorescence in situ hybridization (FISH) confirmed that the proportion of Streptococcus sp. sequences in the clone libraries coincided with the proportion of streptococcus probe-positive organisms on the chip. FISH also revealed that, in the undisturbed plaque, not only Streptococcus spp. but also the rarer Prevotella spp. were usually seen in small multigeneric clusters of cells. This study shows that the initial dental plaque community of each subject is unique in terms of diversity and composition. Repetitive and distinctive community composition within subjects suggests that the spatiotemporal interactions and ecological shifts that accompany biofilm maturation also occur in a subject-dependent manner.

Spectral fluorometric characterization of phytoplankton community composition using the Algae Online Analyser®

2010 ◽  
Vol 44 (8) ◽  
pp. 2461-2472 ◽  
Author(s):  
Tammi L. Richardson ◽  
Evelyn Lawrenz ◽  
James L. Pinckney ◽  
Rodney C. Guajardo ◽  
Elyse A. Walker ◽  
...  
Keyword(s):  
Community Composition ◽  
Phytoplankton Community ◽  
Phytoplankton Community Composition

scholarly journals Characterization of Microbial Community Structure in Gulf of Mexico Gas Hydrates: Comparative Analysis of DNA- and RNA-Derived Clone Libraries

2005 ◽  
Vol 71 (6) ◽  
pp. 3235-3247 ◽  
Author(s):  
Heath J. Mills ◽  
Robert J. Martinez ◽  
Sandra Story ◽  
Patricia A. Sobecky
Keyword(s):  
Phylogenetic Analysis ◽  
Microbial Community ◽  
Gulf Of Mexico ◽  
Gas Hydrate ◽  
Phylogenetic Analyses ◽  
Active Fraction ◽  
Clone Libraries ◽  
Dna And Rna ◽  
Rna And Dna

ABSTRACT The characterization of microbial assemblages within solid gas hydrate, especially those that may be physiologically active under in situ hydrate conditions, is essential to gain a better understanding of the effects and contributions of microbial activities in Gulf of Mexico (GoM) hydrate ecosystems. In this study, the composition of the Bacteria and Archaea communities was determined by 16S rRNA phylogenetic analyses of clone libraries derived from RNA and DNA extracted from sediment-entrained hydrate (SEH) and interior hydrate (IH). The hydrate was recovered from an exposed mound located in the northern GoM continental slope with a hydrate chipper designed for use on the manned-submersible Johnson Sea Link (water depth, 550 m). Previous geochemical analyses indicated that there was increased metabolic activity in the SEH compared to the IH layer (B. N. Orcutt, A. Boetius, S. K. Lugo, I. R. Macdonald, V. A. Samarkin, and S. Joye, Chem. Geol. 205:239-251). Phylogenetic analysis of RNA- and DNA-derived clones indicated that there was greater diversity in the SEH libraries than in the IH libraries. A majority of the clones obtained from the metabolically active fraction of the microbial community were most closely related to putative sulfate-reducing bacteria and anaerobic methane-oxidizing archaea. Several novel bacterial and archaeal phylotypes for which there were no previously identified closely related cultured isolates were detected in the RNA- and DNA-derived clone libraries. This study was the first phylogenetic analysis of the metabolically active fraction of the microbial community extant in the distinct SEH and IH layers of GoM gas hydrate.

scholarly journals Comparative Analysis of Eukaryotic Marine Microbial Assemblages from 18S rRNA Gene and Gene Transcript Clone Libraries by Using Different Methods of Extraction

2012 ◽  
Vol 78 (11) ◽  
pp. 3958-3965 ◽  
Author(s):  
Amy Koid ◽  
William C. Nelson ◽  
Amy Mraz ◽  
Karla B. Heidelberg
Keyword(s):  
Community Composition ◽  
18S Rrna ◽  
Northwest Pacific ◽  
Rrna Gene ◽  
Gene Transcript ◽  
Acid Extraction ◽  
Phylogenetic Groups ◽  
Northwest Pacific Ocean ◽  
Clone Libraries ◽  
Sequencing Platform

ABSTRACTEukaryotic marine microbes play pivotal roles in biogeochemical nutrient cycling and ecosystem function, but studies that focus on the protistan biogeography and genetic diversity lag-behind studies of other microbes. 18S rRNA PCR amplification and clone library sequencing are commonly used to assess diversity that is culture independent. However, molecular methods are not without potential biases and artifacts. In this study, we compare the community composition of clone libraries generated from the same water sample collected at the San Pedro Ocean Time Series (SPOTs) station in the northwest Pacific Ocean. Community composition was assessed using different cell lysis methods (chemical and mechanical) and the extraction of different nucleic acids (DNA and RNA reverse transcribed to cDNA) to build Sanger ABI clone libraries. We describe specific biases for ecologically important phylogenetic groups resulting from differences in nucleic acid extraction methods that will inform future designs of eukaryotic diversity studies, regardless of the target sequencing platform planned.

scholarly journals Diversity pattern of nitrogen fixing microbes in nodules of <i>Trifolium arvense</i> (L.) at different initial stages of ecosystem development

2012 ◽  
Vol 9 (9) ◽  
pp. 13135-13160
Author(s):  
S. Schulz ◽  
M. Engel ◽  
D. Fischer ◽  
F. Buegger ◽  
M. Elmer ◽  
...  
Keyword(s):  
Community Composition ◽  
Nifh Gene ◽  
Ecosystem Development ◽  
Nitrogen Fixing ◽  
Clone Libraries ◽  
Carbon And Nitrogen ◽  
Soil Age ◽  
Trifolium Arvense ◽  
Nitrogen Contents ◽  
The Impact

Abstract. Legumes can be considered as pioneer plants during ecosystem development, as they form a symbiosis with different nitrogen fixing rhizobia species, which enable the plants to grow on soils with low available nitrogen content. In this study we compared the abundance and diversity of nitrogen fixing microbes based on the functional marker gene nifH, which codes for a subunit of the Fe-protein of the dinitrogenase reductase, in nodules of different size classes of Trifolium arvense (L.). Additionally, carbon and nitrogen contents of the bulk soil and plant material were measured. Plants were harvested from different sites, reflecting 2 (2a) and 5 (5a) yr of ecosystem development, of an opencast lignite mining area in the south of Cottbus, Lower Lusatia (Germany) where the artificial catchment "Chicken Creek" was constructed to study the development of terrestrial ecosystems. Plants from the 5a site revealed higher amounts of carbon and nitrogen, although nifH gene abundances in the nodules and carbon and nitrogen contents between the two soils did not differ significantly. Analysis of the nifH clone libraries showed a significant effect of the nodule size on the community composition of nitrogen fixing microbes. Medium sized nodules (2–5 mm) contained a uniform community composed of Rhizobium leguminosarum bv. trifolii, whereas the small nodules (< 2 mm) consisted of a diverse community including clones with non-Rhizobium nifH gene sequences. Regarding the impact of the soil age on the community composition a clear distinction between the small and the medium nodules can be made. While clone libraries from the medium nodules were pretty similar at both soil ages, soil age had a significant effect on the community compositions of the small nodules, where the proportion of R. leguminosarum bv. trifolii increased with soil age.

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