scholarly journals Phylogenetic Diversity, Abundance, and Axial Distribution of Bacteria in the Intestinal Tract of Two Soil-Feeding Termites (Cubitermes spp.)

2003 ◽  
Vol 69 (10) ◽  
pp. 6007-6017 ◽  
Author(s):  
Dirk Schmitt-Wagner ◽  
Michael W. Friedrich ◽  
Bianca Wagner ◽  
Andreas Brune
Keyword(s):  
Intestinal Tract ◽  
Companion Paper ◽  
Rrna Gene ◽  
Molecular Fingerprinting ◽  
Axial Distribution ◽  
Phylogenetic Groups ◽  
Clone Libraries ◽  
Gram Positive Bacteria ◽  
Good Agreement

ABSTRACT The hindgut of soil-feeding termites is highly compartmentalized and characterized by pronounced axial dynamics of the intestinal pH and microbial processes such as hydrogen production, methanogenesis, and reductive acetogenesis. Nothing is known about the bacterial diversity and the abundance or axial distribution of the major phylogenetic groups in the different gut compartments. In this study, we showed that the variety of physicochemical conditions is reflected in the diversity of the microbial communities in the different gut compartments of two Cubitermes species (Termitidae: Termitinae). 16S rRNA gene clones from the highly alkaline first proctodeal segment (P1) of Cubitermes orthognathus represented almost exclusively gram-positive bacteria with low G+C content (LGC bacteria). In the posterior gut segments, their proportion decreased progressively, and the clone libraries comprised a variety of phyla, including the Cytophaga-Flexibacter-Bacteroides group, various subgroups of Proteobacteria, and the spirochetes. Phylogenetic analysis revealed that many of the clones clustered with sequences from the guts of other termites, and some even formed clusters containing only clones from C. orthognathus. The abundance and axial distribution of major phylogenetic groups in the gut of Cubitermes ugandensis were determined by fluorescence in situ hybridization with group-specific oligonucleotide probes. While the results were generally in good agreement with those of the clonal analysis, direct counts with probes specific for the Planctomycetales revealed a severe underestimation of representatives of this phylum in the clone libraries. Results obtained with newly designed FISH probes directed against two clusters of LGC clones from C. orthognathus indicated that the clones were restricted to specific gut regions. A molecular fingerprinting analysis published in a companion paper (D. Schmitt-Wagner, M. W. Friedrich, B. Wagner, and A. Brune, Appl. Environ. Microbiol. 69:6018-6024, 2003) corroborated the presence of compartment-specific bacterial communities in the gut of different Cubitermes species.

scholarly journals Nocturnal Production of Endospores in Natural Populations of Epulopiscium-Like Surgeonfish Symbionts

2005 ◽  
Vol 187 (21) ◽  
pp. 7460-7470 ◽  
Author(s):  
Joseph F. Flint ◽  
Dan Drzymalski ◽  
W. Linn Montgomery ◽  
Gordon Southam ◽  
Esther R. Angert
Keyword(s):  
Intestinal Tract ◽  
Dipicolinic Acid ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Rrna Gene ◽  
Gram Positive Bacteria ◽  
Close Relationship ◽  
Close Relatives ◽  
In Situ Hybridizations

ABSTRACT Prior studies have described a morphologically diverse group of intestinal microorganisms associated with surgeonfish. Despite their diversity of form, 16S rRNA gene surveys and fluorescent in situ hybridizations indicate that these bacteria are low-G+C gram-positive bacteria related to Epulopiscium spp. Many of these bacteria exhibit an unusual mode of reproduction, developing multiple offspring intracellularly. Previous reports have suggested that some Epulopiscium-like symbionts produce dormant or phase-bright intracellular offspring. Close relatives of Epulopiscium, such as Metabacterium polyspora and Clostridium lentocellum, are endospore-forming bacteria, which raises the possibility that the phase-bright offspring are endospores. Structural evidence and the presence of dipicolinic acid demonstrate that phase-bright offspring of Epulopiscium-like bacteria are true endospores. In addition, endospores are formed as part of the normal daily life cycle of these bacteria. In the populations studied, mature endospores were seen only at night and the majority of cells in a given population produced one or two endospores per mother cell. Phylogenetic analyses confirmed the close relationship between the endospore-forming surgeonfish symbionts characterized here and previously described Epulopiscium spp. The broad distribution of endospore formation among the Epulopiscium phylogenetic group raises the possibility that sporulation is a characteristic of the group. We speculate that spore formation in Epulopiscium-like symbionts may be important for dispersal and may also enhance survival in the changing conditions of the fish intestinal tract.

scholarly journals Change in Bacterial Community Structure during In Situ Biostimulation of Subsurface Sediment Cocontaminated with Uranium and Nitrate

2004 ◽  
Vol 70 (8) ◽  
pp. 4911-4920 ◽  
Author(s):  
Nadia N. North ◽  
Sherry L. Dollhopf ◽  
Lainie Petrie ◽  
Jonathan D. Istok ◽  
David L. Balkwill ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Quantitative Pcr ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Clone Libraries ◽  
Subsurface Sediments

ABSTRACT Previous studies have demonstrated that metal-reducing microorganisms can effectively promote the precipitation and removal of uranium from contaminated groundwater. Microbial communities were stimulated in the acidic subsurface by pH neutralization and addition of an electron donor to wells. In single-well push-pull tests at a number of treated sites, nitrate, Fe(III), and uranium were extensively reduced and electron donors (glucose, ethanol) were consumed. Examination of sediment chemistry in cores sampled immediately adjacent to treated wells 3.5 months after treatment revealed that sediment pH increased substantially (by 1 to 2 pH units) while nitrate was largely depleted. A large diversity of 16S rRNA gene sequences were retrieved from subsurface sediments, including species from the α, β, δ, and γ subdivisions of the class Proteobacteria, as well as low- and high-G+C gram-positive species. Following in situ biostimulation of microbial communities within contaminated sediments, sequences related to previously cultured metal-reducing δ-Proteobacteria increased from 5% to nearly 40% of the clone libraries. Quantitative PCR revealed that Geobacter-type 16S rRNA gene sequences increased in biostimulated sediments by 1 to 2 orders of magnitude at two of the four sites tested. Evidence from the quantitative PCR analysis corroborated information obtained from 16S rRNA gene clone libraries, indicating that members of the δ-Proteobacteria subdivision, including Anaeromyxobacter dehalogenans-related and Geobacter-related sequences, are important metal-reducing organisms in acidic subsurface sediments. This study provides the first cultivation-independent analysis of the change in metal-reducing microbial communities in subsurface sediments during an in situ bioremediation experiment.

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 Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Giampiero Batani ◽  
Kristina Bayer ◽  
Julia Böge ◽  
Ute Hentschel ◽  
Torsten Thomas
Keyword(s):  
Cell Sorting ◽  
New Method ◽  
Probe Design ◽  
Rrna Gene ◽  
Bacterial Cells ◽  
Phylogenetic Groups ◽  
Live Fish ◽  
Taxonomic Groups ◽  
Living Bacteria

AbstractDespite the development of several cultivation methods, the rate of discovery of microorganisms that are yet-to-be cultivated outpaces the rate of isolating and cultivating novel species in the laboratory. Furthermore, no current cultivation technique is capable of selectively isolating and cultivating specific bacterial taxa or phylogenetic groups independently of morphological or physiological properties. Here, we developed a new method to isolate living bacteria solely based on their 16S rRNA gene sequence. We showed that bacteria can survive a modified version of the standard fluorescence in situ hybridization (FISH) procedure, in which fixation is omitted and other factors, such as centrifugation and buffers, are optimized. We also demonstrated that labelled DNA probes can be introduced into living bacterial cells by means of chemical transformation and that specific hybridization occurs. This new method, which we call live-FISH, was then combined with fluorescence-activated cell sorting (FACS) to sort specific taxonomic groups of bacteria from a mock and natural bacterial communities and subsequently culture them. Live-FISH represents the first attempt to systematically optimize conditions known to affect cell viability during FISH and then to sort bacterial cells surviving the procedure. No sophisticated probe design is required, making live-FISH a straightforward method to be potentially used in combination with other single-cell techniques and for the isolation and cultivation of new microorganisms.

Molecular evidence of the existence of anaerobic ammonia oxidation bacteria in the gut of polychaete (Neanthes glandicincta)

2016 ◽  
Vol 1 (1) ◽  
pp. 19 ◽  
Author(s):  
Meng Li ◽  
Ji-Dong GU
Keyword(s):  
Ammonia Oxidation ◽  
Coastal Sediments ◽  
Anammox Bacteria ◽  
Molecular Evidence ◽  
Rrna Gene ◽  
Natural Environments ◽  
Axial Distribution ◽  
Anaerobic Ammonia Oxidation ◽  
Neanthes Glandicincta

Neanthes are one of the most important groups of polychaete in coastal sediments, which play an important role on the nutrient cycling in coastal sediments. Here we report on the existence of anammox bacteria in the gut of polychaete Neanthes glandicincta based on the analysis of 16S rRNA gene and fluorescence in situ hybridization (FISH). Three distinct clusters of anammox bacteria are found in different gut sections of N. glandicincta, and one of them is considered as a novel, gut specific anammox bacteria after comparing with the anammox bacteria recovered from surrounding pre-digested sediment. The uniform axial distribution of anammox bacteria in different gut sections of N. glandicincta is also found in present study. These results extend our knowledge of microbial ecology of anammox bacteria in the natural environments.

scholarly journals Intestinal Integrity and Akkermansia muciniphila, a Mucin-Degrading Member of the Intestinal Microbiota Present in Infants, Adults, and the Elderly

2007 ◽  
Vol 73 (23) ◽  
pp. 7767-7770 ◽  
Author(s):  
M. Carmen Collado ◽  
Muriel Derrien ◽  
Erika Isolauri ◽  
Willem M. de Vos ◽  
Seppo Salminen
Keyword(s):  
Early Life ◽  
Intestinal Tract ◽  
The Elderly ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Akkermansia Muciniphila ◽  
Intestinal Integrity ◽  
The 16S Rrna Gene ◽  
Human Intestinal Tract

ABSTRACT Fluorescence in situ hybridization and real-time PCR analysis targeting the 16S rRNA gene of Akkermansia muciniphila were performed to determine its presence in the human intestinal tract. These techniques revealed that an A. muciniphila-like bacterium is a common member of the human intestinal tract and that its colonization starts in early life and develops within a year to a level close to that observed in adults (108 cells/g) but decreases (P < 0.05) in the elderly.

scholarly journals Two Bacteria Phylotypes Are Predominant in the Suiyo Seamount Hydrothermal Plume

2004 ◽  
Vol 70 (2) ◽  
pp. 1190-1198 ◽  
Author(s):  
Michinari Sunamura ◽  
Yowsuke Higashi ◽  
Chiwaka Miyako ◽  
Jun-ichiro Ishibashi ◽  
Akihiko Maruyama
Keyword(s):  
Bottom Layer ◽  
Rrna Gene ◽  
Phylogenetic Groups ◽  
Dapi Staining ◽  
Hydrothermal Plume ◽  
Filtration System ◽  
Group Belonging ◽  
Complex Relationships ◽  
Almost All

ABSTRACT Microbial diversity and populations in a hydrothermal plume that was present inside the caldera of the Suiyo Seamount, a submarine volcano on the Izu-Bonin Arc, were investigated by performing a phylogenetic analysis of the 16S rRNA gene and by using fluorescence in situ hybridization (FISH). Corresponding to transmissivity, an indicator of turbidity, the vertical total cell count as determined by 4′,6′-diamidino-2-phenylindole (DAPI) staining varied from 5.6 × 104 to 1.1 × 105 cells ml−1, and the apparent plume layer was assessed to be at a depth of 1,050 to 1,200 m inside the caldera and to contain 1.0 × 105 to 1.1 × 105 cells ml−1. From microbial samples collected in the plume by an in situ filtration system, the following two major phylogenetic groups, which were closely related to sulfur-oxidizing microbes, were obtained: the SUP05 group belonging to the gamma subclass of the Proteobacteria (13 of 20 clones) and the SUP01 group belonging to the epsilon subclass of the Proteobacteria (5 of 20 clones). Specific oligonucleotide probes for these groups (SUP05-187 and SUP01-63) were designed and were used with various water samples obtained from the Suiyo Seamount. In the apparent plume layer, up to 66% of the total counts of microbial cells were estimated to be Bacteria cells that hybridized to EUB338, and few cells were identified by the archaeal probe ARCH915. Almost all Bacteria cells were hard to identify with the known group-specific probes, such as ALF19, GAM42a, and CF319, while 88 to 90% of the Bacteria cells hybridized with SUP05-187 and >98% of them were considered members of the SUP05 and SUP01 populations. In a low-temperature vent fluid emitted from a bivalve-colonized mound, the SUP05 cells accounted for >99% of the Bacteria cells, suggesting that a portion of the plume cells originated on the surface of the seafloor at a depth of about 1,380 m. From further analysis of cell morphology (i.e., cell size and cell elongation index) we inferred that the SUP05 cells were active in the plume layer at a depth of 1,050 to 1,200 m compared to the activity in a near-bottom layer, while many elongated cells were found between these layers. These findings suggest that the morphology and distribution of SUP05 cells have complex relationships with hydrothermal activities and water circulation. Although growth and production rates remain to be defined, we concluded that this Suiyo Seamount caldera has functioned as a natural continuous incubator for these two phylotypes of Bacteria in an aphotic deep-sea environment.

Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries

2002 ◽  
Vol 4 (11) ◽  
pp. 713-720 ◽  
Author(s):  
Andreas Schramm ◽  
Bernhard M. Fuchs ◽  
Jeppe L. Nielsen ◽  
Mauro Tonolla ◽  
David A. Stahl
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Fluorescence In Situ Hybridization ◽  
Rrna Gene ◽  
Clone Libraries

scholarly journals Molecular Characterisation of Bacterial Community Structure along the Intestinal Tract of Zebrafish (Danio rerio): A Pilot Study

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Chuan-Ching Lan ◽  
Donald R. Love
Keyword(s):  
Pilot Study ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Danio Rerio ◽  
Intestinal Tract ◽  
Restriction Analysis ◽  
Operational Taxonomic Unit ◽  
Rrna Gene ◽  
Clone Libraries

The bacterial composition along the intestinal tract of Danio rerio was investigated by cultivation-independent analysis of the 16S rRNA gene. Clone libraries were constructed for three compartments of the intestinal tract of individual fish. 566 individual clones were differentiated by amplified 16S rRNA gene restriction analysis (ARDRA), and clone representatives from each operational taxonomic unit (OTU) were sequenced. As reported in other studies, we found that Proteobacteria was the most prominent phylum among clone libraries from different fish. Data generated from this pilot study indicated some compositional differences in bacterial communities. Two dominant classes, Gammaproteobacteria and Bacilli, displayed different levels of abundance in different compartments; Gammaproteobacteria increased along the intestinal tract, while Bacilli decreased its abundance along the proximal-distal axis. Less obvious spatial patterns were observed for other classes. In general, bacterial diversity in the intestinal bulb was greater than that in the posterior intestine. Interindividual differences in bacterial diversity and composition were also noted in this study.

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