Small-Subunit rRNA Genes and In Situ Hybridization with Oligonucleotides Specific for the Bacterial Symbionts in the Larvae of the Bryozoan Bugula neritina and Proposal of “Candidatus Endobugula sertula”

ABSTRACT A phylogenetic analysis of the sequences of 60 clones of archaeal small-subunit rRNA genes amplified from the termiteReticulitermes speratus revealed that most of them (56 clones) clustered in the genus Methanobrevibacter. Three clones were classified in the order Thermoplasmales. TheMethanobrevibacter-related symbionts were detected by in situ hybridization analysis.

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

Applied and Environmental Microbiology ◽

10.1128/aem.01232-12 ◽

2012 ◽

Vol 78 (20) ◽

pp. 7467-7475 ◽

Cited By ~ 33

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.

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Abundant and Diverse Fungal Microbiota in the Murine Intestine

Applied and Environmental Microbiology ◽

10.1128/aem.72.1.793-801.2006 ◽

2006 ◽

Vol 72 (1) ◽

pp. 793-801 ◽

Cited By ~ 113

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.

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α-Proteobacterial Symbionts of Marine Bryozoans in the Genus Watersipora

Applied and Environmental Microbiology ◽

10.1128/aem.00604-06 ◽

2006 ◽

Vol 73 (1) ◽

pp. 303-311 ◽

Cited By ~ 33

Author(s):

Christine M. Anderson ◽

Margo G. Haygood

Keyword(s):

Phylogenetic Analysis ◽

In Situ Hybridization ◽

16S Rrna ◽

Fluorescence In Situ Hybridization ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Symbionts ◽

California Coast ◽

Specific Fluorescence

ABSTRACT Bacterial symbionts that resembled mollicutes were discovered in the marine bryozoan Watersipora arcuata in the 1980s. In this study, we used PCR and sequencing of 16S rRNA genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of “W. subtorquata” and “W. arcuata” from several locations along the California coast are actually closely related α-Proteobacteria, not mollicutes. We propose the names “Candidatus Endowatersipora palomitas” and “Candidatus Endowatersipora rubus” for the symbionts of “W. subtorquata” and “W. arcuata,” respectively.

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Protocol for Rapid Fluorescence In Situ Hybridization of Bacteria in Cryosections of Microarthropods

Applied and Environmental Microbiology ◽

10.1128/aem.69.5.2875-2878.2003 ◽

2003 ◽

Vol 69 (5) ◽

pp. 2875-2878 ◽

Cited By ~ 19

Author(s):

Torsten Thimm ◽

Christoph C. Tebbe

Keyword(s):

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Bacterial Colonization ◽

Small Subunit ◽

Folsomia Candida ◽

Small Subunit Rrna ◽

Paraffin Embedding

ABSTRACT A protocol was developed to detect bacteria inhabiting microarthropods by means of small-subunit rRNA-targeted fluorescence in situ hybridization and microscopy. The protocol is based on cryosections of whole specimens. In contrast to more commonly applied paraffin-embedding techniques, the protocol is quicker and reduces the number of manipulations which might damage the microscopic material. The method allowed the study of the bacterial colonization of Folsomia candida (Collembola) and the detection of bacteria in both the gut and tissue.

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Phylogenetic Diversity Analysis of Subterranean Hot Springs in Iceland

Applied and Environmental Microbiology ◽

10.1128/aem.67.9.4242-4248.2001 ◽

2001 ◽

Vol 67 (9) ◽

pp. 4242-4248 ◽

Cited By ~ 83

Author(s):

Viggó Thór Marteinsson ◽

Sigurbjörg Hauksdóttir ◽

Cédric F. V. Hobel ◽

Hrefna Kristmannsdóttir ◽

Gudmundur Oli Hreggvidsson ◽

...

Keyword(s):

Hot Springs ◽

Tap Water ◽

Small Subunit ◽

Geothermal Water ◽

Rrna Genes ◽

Small Subunit Rrna ◽

Operational Taxonomic Units ◽

Pcr Products ◽

Geothermal Wells

ABSTRACT Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130°C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-μm-pore-size filter. Cells were observed in wells RG-39 (91.4°C) and MG-18 (71.8°C) and in hot tap water (76°C), but no cells were detected in wells SN-4, SN-5 (95 to 117°C), and RV-5 (130°C). Archaea and Bacteria were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the Archaea andBacteria domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85°C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with Desulfurococcales relatives. Two strains belonging to Desulfurococcus mobilis and to theThermus/Deinococcus group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles.

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Faculty Opinions recommendation of In situ accessibility of small-subunit rRNA of members of the domains Bacteria, Archaea, and Eucarya to Cy3-labeled oligonucleotide probes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1012830.187355 ◽

2003 ◽

Author(s):

Gerard Muyzer

Keyword(s):

Small Subunit ◽

Oligonucleotide Probes ◽

Small Subunit Rrna

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

Applied and Environmental Microbiology ◽

10.1128/aem.00378-06 ◽

2006 ◽

Vol 72 (10) ◽

pp. 6707-6715 ◽

Cited By ~ 38

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.

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