Molecular Profiling of Bacterial Communities via 16S rRNA Gene Based Approaches - Focus T-RFLP

2012 ◽  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Molecular Profiling ◽  
Rrna Gene

Molecular Profiling of Bacterial Communities via 16S rRNA Gene Based Approaches – Focus T-RFLP

2010 ◽  
pp. 4113-4125 ◽  
Author(s):  
S. Païssé ◽  
M. S. Goñi-Urriza ◽  
A. Fahy ◽  
R. Duran
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Molecular Profiling ◽  
Rrna Gene

Molecular characterization of the bacterial communities present in sheep's milk and cheese produced in South Brazilian Region via 16S rRNA gene metabarcoding sequencing

LWT ◽  
2021 ◽  
Vol 147 ◽  
pp. 111579
Author(s):  
Creciana M. Endres ◽  
Ícaro Maia S. Castro ◽  
Laura D. Trevisol ◽  
Juliana M. Severo ◽  
Michele B. Mann ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Bacterial Communities ◽  
Rrna Gene

scholarly journals Sponge-Associated Bacteria Are Strictly Maintained in Two Closely Related but Geographically Distant Sponge Hosts

2011 ◽  
Vol 77 (20) ◽  
pp. 7207-7216 ◽  
Author(s):  
Naomi F. Montalvo ◽  
Russell T. Hill
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Sponge Species ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Associated Bacteria ◽  
Content Type ◽  
Key Species ◽  
Sponge Associated Bacteria

ABSTRACTThe giant barrel spongesXestospongiamutaandXestospongiatestudinariaare ubiquitous in tropical reefs of the Atlantic and Pacific Oceans, respectively. They are key species in their respective environments and are hosts to diverse assemblages of bacteria. These two closely related sponges from different oceans provide a unique opportunity to examine the evolution of sponge-associated bacterial communities. Mitochondrial cytochrome oxidase subunit I gene sequences fromX.mutaandX.testudinariashowed little divergence between the two species. A detailed analysis of the bacterial communities associated with these sponges, comprising over 900 full-length 16S rRNA gene sequences, revealed remarkable similarity in the bacterial communities of the two species. Both sponge-associated communities include sequences found only in the twoXestospongiaspecies, as well as sequences found also in other sponge species and are dominated by three bacterial groups,Chloroflexi,Acidobacteria, andActinobacteria. While these groups consistently dominate the bacterial communities revealed by 16S rRNA gene-based analysis of sponge-associated bacteria, the depth of sequencing undertaken in this study revealed clades of bacteria specifically associated with each of the twoXestospongiaspecies, and also with the genusXestospongia, that have not been found associated with other sponge species or other ecosystems. This study, comparing the bacterial communities associated with closely related but geographically distant sponge hosts, gives new insight into the intimate relationships between marine sponges and some of their bacterial symbionts.

scholarly journals Diversity and Structure of the Endophytic Bacterial Communities Associated With Three Terrestrial Orchid Species as Revealed by 16S rRNA Gene Metabarcoding

2020 ◽  
Vol 11 ◽  
Author(s):  
Pasquale Alibrandi ◽  
Sylvia Schnell ◽  
Silvia Perotto ◽  
Massimiliano Cardinale
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Host Plant ◽  
Bacterial Communities ◽  
Reproductive Organs ◽  
Distribution Model ◽  
Rrna Gene ◽  
Orchid Species ◽  
Core Microbiota

The endophytic microbiota can establish mutualistic or commensalistic interactions within the host plant tissues. We investigated the bacterial endophytic microbiota in three species of Mediterranean orchids (Neottia ovata, Serapias vomeracea, and Spiranthes spiralis) by metabarcoding of the 16S rRNA gene. We examined whether the different orchid species and organs, both underground and aboveground, influenced the endophytic bacterial communities. A total of 1,930 operational taxonomic units (OTUs) were obtained, mainly Proteobacteria and Actinobacteria, whose distribution model indicated that the plant organ was the main determinant of the bacterial community structure. The co-occurrence network was not modular, suggesting a relative homogeneity of the microbiota between both plant species and organs. Moreover, the decrease in species richness and diversity in the aerial vegetative organs may indicate a filtering effect by the host plant. We identified four hub OTUs, three of them already reported as plant-associated taxa (Pseudoxanthomonas, Rhizobium, and Mitsuaria), whereas Thermus was an unusual member of the plant microbiota. Core microbiota analysis revealed a selective and systemic ascent of bacterial communities from the vegetative to the reproductive organs. The core microbiota was also maintained in the S. spiralis seeds, suggesting a potential vertical transfer of the microbiota. Surprisingly, some S. spiralis seed samples displayed a very rich endophytic microbiota, with a large number of OTUs shared with the roots, a situation that may lead to a putative restoring process of the root-associated microbiota in the progeny. Our results indicate that the bacterial community has adapted to colonize the orchid organs selectively and systemically, suggesting an active involvement in the orchid holobiont.

Two-dimensional single strand conformation polymorphism (SSCP) of 16S rRNA gene fragments reveals highly dissimilar bacterial communities in an acidic fen

2008 ◽  
Vol 44 (5-6) ◽  
pp. 495-500 ◽  
Author(s):  
Achim Schmalenberger ◽  
Christoph C. Tebbe ◽  
Michael A. Kertesz ◽  
Harold L. Drake ◽  
Kirsten Küsel
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Rrna Gene ◽  
Two Dimensional ◽  
Conformation Polymorphism

scholarly journals Functional profiling of bacterial communities in Lake Tuz using 16S rRNA gene sequences

2020 ◽  
Vol 35 (1) ◽  
pp. 1-10
Author(s):  
Habeebat Adekilekun Oyewusi ◽  
Roswanira Abdul Wahab ◽  
Mohamed Faraj Edbeib ◽  
Mohd Azrul Naim Mohamad ◽  
Azzmer Azzar Abdul Hamid ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Functional Profiling

scholarly journals The Bacterial Communities of Full-Scale Biologically Active, Granular Activated Carbon Filters Are Stable and Diverse and Potentially Contain Novel Ammonia-Oxidizing Microorganisms

2015 ◽  
Vol 81 (19) ◽  
pp. 6864-6872 ◽  
Author(s):  
Timothy M. LaPara ◽  
Katheryn Hope Wilkinson ◽  
Jacqueline M. Strait ◽  
Raymond M. Hozalski ◽  
Michael J. Sadowksy ◽  
...  
Keyword(s):  
Activated Carbon ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Communities ◽  
Granular Activated Carbon ◽  
Full Scale ◽  
Biologically Active ◽  
Rrna Gene ◽  
Ammonia Oxidizing Bacteria ◽  
Content Type

ABSTRACTThe bacterial community composition of the full-scale biologically active, granular activated carbon (BAC) filters operated at the St. Paul Regional Water Services (SPRWS) was investigated using Illumina MiSeq analysis of PCR-amplified 16S rRNA gene fragments. These bacterial communities were consistently diverse (Shannon index, >4.4; richness estimates, >1,500 unique operational taxonomic units [OTUs]) throughout the duration of the 12-month study period. In addition, only modest shifts in the quantities of individual bacterial populations were observed; of the 15 most prominent OTUs, the most highly variable population (aVariovoraxsp.) modulated less than 13-fold over time and less than 8-fold from filter to filter. The most prominent population in the profiles was aNitrospirasp., representing 13 to 21% of the community. Interestingly, very few of the known ammonia-oxidizing bacteria (AOB; <0.07%) and no ammonia-oxidizingArchaeawere detected in the profiles. Quantitative PCR ofamoAgenes, however, suggested that AOB were prominent in the bacterial communities (amoA/16S rRNA gene ratio, 1 to 10%). We conclude, therefore, that the BAC filters at the SPRWS potentially contained significant numbers of unidentified and novel ammonia-oxidizing microorganisms that possessamoAgenes similar to those of previously described AOB.

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