scholarly journals Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

2004 ◽  
Vol 186 (9) ◽  
pp. 2629-2635 ◽  
Author(s):  
Silvia G. Acinas ◽  
Luisa A. Marcelino ◽  
Vanja Klepac-Ceraj ◽  
Martin F. Polz
Keyword(s):  
16S Rrna ◽  
Thermophilic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Genomes ◽  
16S Rrna Sequence ◽  
Thermoanaerobacter Tengcongensis ◽  
Copy Numbers ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16S rRNA-based methods. Furthermore, the occurrence of widespread horizontal gene transfer (HGT) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. For this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16S rRNA sequences were evaluated. Bacterial genomes display up to 15 operons and operon numbers up to 7 are commonly found, but ∼40% of the organisms analyzed have either one or two operons. Among the Archaea, a single operon appears to dominate and the highest number of operons is five. About 40% of sequences among 380 operons in 76 bacterial genomes with multiple operons were identical to at least one other 16S rRNA sequence in the same genome, and in 38% of the genomes all 16S rRNAs were invariant. For Archaea, the number of identical operons was only 25%, but only five genomes with 21 operons are currently available. These considerations suggest an upper bound of roughly threefold overestimation of bacterial diversity resulting from cloning and sequencing of 16S rRNA genes from the environment; however, the inclusion of genomes with a single rrn operon may lower this correction factor to ∼2.5. Divergence among operons appears to be small overall for both Bacteria and Archaea, with the vast majority of 16S rRNA sequences showing <1% nucleotide differences. Only five genomes with operons with a higher level of nucleotide divergence were detected, and Thermoanaerobacter tengcongensis exhibited the highest level of divergence (11.6%) noted to date. Overall, four of the five extreme cases of operon differences occurred among thermophilic bacteria, suggesting a much higher incidence of HGT in these bacteria than in other groups.

scholarly journals Relationships of Bradyrhizobia from the LegumesApios americana and Desmodium glutinosum

1999 ◽  
Vol 65 (11) ◽  
pp. 4914-4920 ◽  
Author(s):  
Matthew A. Parker
Keyword(s):  
16S Rrna ◽  
Root Nodule ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Enzyme Electrophoresis ◽  
Nodule Bacteria ◽  
Root Nodule Bacteria ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Multilocus enzyme electrophoresis, partial 23S rRNA sequences, and nearly full-length 16S rRNA sequences all indicated high genetic similarity among root-nodule bacteria associated with Apios americana, Desmodium glutinosum, andAmphicarpaea bracteata, three common herbaceous legumes whose native geographic ranges in eastern North America overlap extensively. A total of 19 distinct multilocus genotypes (electrophoretic types [ETs]) were found among the 35 A. americana and 33 D. glutinosum isolates analyzed. Twelve of these ETs (representing 78% of all isolates) were either identical to ETs previously observed in A. bracteatapopulations, or differed at only one locus. Within both 23S and 16S rRNA genes, several isolates from A. americana and D. glutinosum were either identical to A. bracteataisolates or showed only single nucleotide differences. Growth rates and nitrogenase activities of A. bracteata plants inoculated with isolates from D. glutinosum were equivalent to levels found with native A. bracteata bacterial isolates, but none of the three A. americana isolates tested had high symbiotic effectiveness on A. bracteata. Phylogenetic analysis of both 23S and 16S rRNA sequences indicated that bothA. americana and D. glutinosum harbored rare bacterial genotypes similar to Bradyrhizobium japonicumUSDA 110. However, the predominant root nodule bacteria on both legumes were closely related to Bradyrhizobium elkanii.

scholarly journals Effect of Freezing on PCR Amplification of 16S rRNA Genes from Microbes Associated with Black Band Disease of Corals

2009 ◽  
Vol 75 (8) ◽  
pp. 2581-2584 ◽  
Author(s):  
Raju Sekar ◽  
Longin T. Kaczmarsky ◽  
Laurie L. Richardson
Keyword(s):  
16S Rrna ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Black Band Disease ◽  
Black Band ◽  
Sulfur Oxidizing ◽  
Polymicrobial Disease ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Molecular analysis of black band disease of corals revealed that samples frozen immediately after collection yielded more proteobacterial 16S rRNA sequences, while unfrozen samples produced more cyanobacterial and sulfur-oxidizing bacterial sequences. These results suggest the need to use multiple approaches for preparation of samples to characterize this complex polymicrobial disease.

scholarly journals Effect of Temperature and Light on Growth of and Photosynthesis by Synechococcus Isolates Typical of Those Predominating in the Octopus Spring Microbial Mat Community of Yellowstone National Park

2006 ◽  
Vol 72 (1) ◽  
pp. 544-550 ◽  
Author(s):  
Jessica P. Allewalt ◽  
Mary M. Bateson ◽  
Niels Peter Revsbech ◽  
Kimberly Slack ◽  
David M. Ward
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Effect Of Temperature ◽  
Ecological Niches ◽  
Genotype Distribution ◽  
Unicellular Cyanobacterium ◽  
Temperature Ranges ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Previous molecular analysis of the Octopus Spring cyanobacterial mat revealed numerous genetically distinct 16S rRNA sequences from predominant Synechococcus populations distantly related to the readily cultivated unicellular cyanobacterium Synechococcus lividus. Patterns in genotype distribution relative to temperature and light conditions suggested that the organisms contributing these 16S rRNA sequences may fill distinct ecological niches. To test this hypothesis, Synechococcus isolates were cultivated using a dilution and filtration approach and then shown to be genetically relevant to natural mat populations by comparisons of similarities of 16S rRNA genes and 16S-23S internal transcribed spacer (ITS) regions. Most isolates were identical or nearly identical at both loci to predominant mat genotypes; others showed 1- to 2-nucleotide differences at the 16S rRNA locus and even greater difference in ITS sequences. Isolates with predominant mat genotypes had distinct temperature ranges and optima for growth that were consistent with their distributions in the mat. Isolates with genotypes not previously detected or known to be predominant in the mat exhibited temperature ranges and optima that were not representative of predominant mat populations and also grew more slowly. Temperature effects on photosynthesis did not reflect temperature relations for growth. However, the isolate with the highest temperature optimum and upper limit was capable of performing photosynthesis at a higher temperature than other isolates. Growth rate and photosynthetic responses provided evidence for light acclimation but evidence of, at best, only subtle light adaptation.

scholarly journals Archaeal Diversity and the Prevalence of Crenarchaeota in Salt Marsh Sediments

2009 ◽  
Vol 75 (12) ◽  
pp. 4211-4215 ◽  
Author(s):  
Katelyn A. Nelson ◽  
Nicole S. Moin ◽  
Anne E. Bernhard
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Archaeal Diversity ◽  
Group I ◽  
Marsh Sediments ◽  
Salt Marsh Sediments ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Crenarchaeal 16S rRNA sequences constituted over 70% of the archaeal clones recovered from three salt marsh sites dominated by different grasses. Group I.1a Crenarchaeota dominated at two sites, while group I.3b Crenarchaeota sequences were most abundant at a third site. Abundances of 16S rRNA genes related to “Candidatus Nitrosopumilus maritimus” differed by site and sampling date.

scholarly journals Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

1999 ◽  
Vol 65 (8) ◽  
pp. 3287-3292 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Chih-Ching Chien ◽  
Bruce J. Paster ◽  
Rebecca L. Ericson ◽  
Roger P. Orcutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
Single Species ◽  
Rapid Identification ◽  
Sequence Information ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
16S Rrna Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The “altered Schaedler flora” (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified asLactobacillus acidophilus (strain ASF 360),Lactobacillus salivarius (strain ASF 361), andBacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus andLactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in theCytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipesphylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes,Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster,Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.

scholarly journals In-depth analysis of Bacillus anthracis 16S rRNA genes and transcripts reveals intra- and intergenomic diversity and facilitates anthrax detection

2021 ◽  
Author(s):  
Peter Braun ◽  
Fee Zimmermann ◽  
Mathias C Walter ◽  
Sonja Mantel ◽  
Karin Aistleitner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Species ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Close Relative ◽  
Rrna Gene ◽  
Copy Numbers ◽  
Depth Analysis

Analysis of 16S ribosomal RNA (rRNA) genes provides a central means of taxonomic classification of bacterial species. Based on presumed sequence identity among species of the Bacillus cereus sensu lato group, the 16S rRNA genes of B. anthracis have been considered unsuitable for diagnosis of the anthrax pathogen. With the recent identification of a single nucleotide polymorphism in some 16S rRNA gene copies, specific identification of B. anthracis becomes feasible. Here, we designed and evaluated a set of in situ-, in vitro- and in silico-assays to assess the yet unknown 16S-state of B. anthracis from different perspectives. Using a combination of digital PCR, fluorescence in situ hybridization, long-read genome sequencing and bioinformatics we were able to detect and quantify a unique 16S rRNA gene allele of B. anthracis (16S-BA-allele). This allele was found in all available B. anthracis genomes and may facilitate differentiation of the pathogen from any close relative. Bioinformatics analysis of 959 B. anthracis genome data-sets inferred that abundances and genomic arrangements of the 16S-BA-allele and the entire rRNA operon copy-numbers differ considerably between strains. Expression ratios of 16S-BA-alleles were proportional to the respective genomic allele copy-numbers. The findings and experimental tools presented here provide detailed insights into the intra- and intergenomic diversity of 16S rRNA genes and may pave the way for improved identification of B. anthracis and other pathogens with diverse rRNA operons.

scholarly journals Abundance of narG, nirS, nirK, and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

2006 ◽  
Vol 72 (9) ◽  
pp. 5957-5962 ◽  
Author(s):  
Ellen Kandeler ◽  
Kathrin Deiglmayr ◽  
Dagmar Tscherko ◽  
David Bru ◽  
Laurent Philippot
Keyword(s):  
16S Rrna ◽  
Primary Succession ◽  
Early Stage ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Glacier Foreland ◽  
Copy Numbers ◽  
Genes Encoding ◽  
Target Molecules ◽  
Denitrification Genes

ABSTRACT Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 � 105 to 8.9 � 105 copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 � 103 to 2.6 � 104, 7.4 � 102 to 1.4 � 103, 2.5 � 102 to 6.4 � 103, and 1.2 � 103 to 5.5 � 103, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.

scholarly journals Phylogenetic Relationships and Functional Genes: Distribution of a Gene (mnxG) Encoding a Putative Manganese-Oxidizing Enzyme in Bacillus Species

2008 ◽  
Vol 74 (23) ◽  
pp. 7265-7271 ◽  
Author(s):  
Lisa E. Mayhew ◽  
Elizabeth D. Swanner ◽  
Andy P. Martin ◽  
Alexis S. Templeton
Keyword(s):  
16S Rrna ◽  
Gene Loss ◽  
Sequence Similarity ◽  
Bacillus Species ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Vertical Inheritance ◽  
Mn Oxide ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Several Bacillus and Paenibacillus species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the mnxG gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in Bacillus species. Seven of eight Bacillus species were capable of Mn(II) oxidation; however, the mnxG gene was detected in only one isolate. Using sequences of known Bacillus species both with and without amplifiable mnxG genes and Henderson Mine isolates, the 16S rRNA and mnxG gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable mnxG gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable mnxG gene in the isolates. The data revealed a complex phylogenetic distribution of the mnxG gene in which vertical inheritance and gene loss influence the distribution of the gene among the Bacillus species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the mnxG gene within the Bacillus clade.

scholarly journals Combined Approach for Characterization of Uncultivated Magnetotactic Bacteria from Various Aquatic Environments

2005 ◽  
Vol 71 (5) ◽  
pp. 2723-2731 ◽  
Author(s):  
Christine B. Flies ◽  
Jörg Peplies ◽  
Dirk Schüler
Keyword(s):  
16S Rrna ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Restriction Analysis ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
Magnetotactic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
16S Rrna Sequence ◽  
16S Rna

ABSTRACT Both magnetic collection and “race track” purification techniques were highly effective for selective enrichment of magnetotactic bacteria (MTB) from complex communities, as suggested by amplified ribosomal DNA restriction analysis and denaturing gradient gel electrophoresis combined with sequence analysis of 16S rRNA genes. Using these purification methods, the occurrence and diversity of MTB in microcosms from various marine and freshwater environments were assayed by using a combined microscopic, molecular, and cultivation approach. Most microcosms were dominated by magnetotactic cocci. Consistently, the majority of retrieved 16S RNA sequences were affiliated with a distinct cluster in the Alphaproteobacteria. Within this lineage the levels of sequence divergence were <1 to 11%, indicating genus-level diversity between magnetotactic cocci from various microcosms, as well as between MTB from different stages of succession of the same microcosms. The community composition in microscosms underwent drastic succession during incubation, and significant heterogeneities were observed between microcosms from the same environmental sources. A novel magnetotactic rod (MHB-1) was detected in a sediment sample from a lake in northern Germany by fluorescence in situ hybridization. MHB-1 falls into the Nitrospira phylum, displaying 91% 16S rRNA sequence similarity to “Magnetobacterium bavaricum.” In extensive cultivation attempts, we failed to isolate MHB-1, as well as most other MTB present in our samples. However, although magnetotactic spirilla were not frequently observed in the enrichments, 10 novel isolates of the genus Magnetospirillum which had not routinely been isolated in pure culture before were obtained.

scholarly journals Improved microbial community characterization of 16S rRNA via metagenome hybridization capture enrichment

2020 ◽  
Author(s):  
Megan Sarah Beaudry ◽  
Jincheng Wang ◽  
Troy Kieran ◽  
Jesse Thomas ◽  
Natalia Juliana Bayona-Vasquez ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Metagenomic Sequencing ◽  
Sequencing Data ◽  
16S Rrna Sequence ◽  
Shotgun Metagenomics ◽  
Reference Databases ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Environmental microbial diversity is often investigated from a molecular perspective using 16S ribosomal RNA (rRNA) gene amplicons and shotgun metagenomics. While amplicon methods are fast, low-cost, and have curated reference databases, they can suffer from amplification bias and are limited in genomic scope. In contrast, shotgun metagenomic methods sample more genomic regions with fewer sequence acquisition biases. However, shotgun metagenomic sequencing is much more expensive (even with moderate sequencing depth) and computationally challenging. Here, we develop a set of 16S rRNA sequence capture baits that offer a potential middle ground with the advantages from both approaches for investigating microbial communities. These baits cover the diversity of all 16S rRNA sequences available in the Greengenes (v. 13.5) database, with no sequence having < 80% sequence similarity to at least one bait for all segments of 16S. The use of our baits provide comparable results to 16S amplicon libraries and shotgun metagenomic libraries when assigning taxonomic units from 16S sequences within the metagenomic reads. We demonstrate that 16S rRNA capture baits can be used on a range of microbial samples (i.e., mock communities and rodent fecal samples) to increase the proportion of 16S rRNA sequences (average >400-fold) and decrease analysis time to obtain consistent community assessments. Furthermore, our study reveals that bioinformatic methods used to analyze sequencing data may have a greater influence on estimates of community composition than library preparation method used, likely in part to the extent and curation of the reference databases considered.

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