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 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 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 Cultivation-Dependant Assessment, Diversity, and Ecology of Haloalkaliphilic Bacteria in Arid Saline Systems of Southern Tunisia

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Darine El Hidri ◽  
Amel Guesmi ◽  
Afef Najjari ◽  
Hanen Cherif ◽  
Besma Ettoumi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Internal Transcribed Spacers ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Ecological Niches ◽  
Desert Plant ◽  
Gram Positive ◽  
Southern Tunisia ◽  
Haloalkaliphilic Bacteria

Haloalkaliphiles are polyextremophiles adapted to grow at high salt concentrations and alkaline pH values. In this work, we isolated 122 haloalkaliphilic bacteria upon enrichments of 23 samples from 5 distinct saline systems of southern Tunisia, growing optimally in media with 10% salt and at pH 10. The collection was classified into 44 groups based on the amplification of the 16S–23S rRNA internal transcribed spacers (ITS-PCR). Phylogenetic analysis and sequencing of the 16S rRNA genes allowed the identification of 13 genera and 20 distinct species. Three gram-positive isolates showing between 95 and 96% of 16S rRNA sequence homology with Bacillus saliphilus could represent new species or genus. Beside the difference in bacterial diversity between the studied sites, several species ecological niches correlations were demonstrated such asOceanobacillusin salt crust,Nesterenkoniain sand, andSalinicoccusin the rhizosphere of the desert plantSalicornia. The collection was further evaluated for the production of extracellular enzymes. Activity tests showed that gram-positive bacteria were mostly active, particularly for protease, lipase, DNase, and amylase production. Our overall results demonstrate the huge phenotypic and phylogenetic diversity of haloalkaliphiles in saline systems of southern Tunisia which represent a valuable source of new lineages and metabolites.

scholarly journals Phenotypic and Phylogenetic Characterization of Ruminal Tannin-Tolerant Bacteria

1998 ◽  
Vol 64 (10) ◽  
pp. 3824-3830 ◽  
Author(s):  
Karen E. Nelson ◽  
Michael L. Thonney ◽  
Tina K. Woolston ◽  
Stephen H. Zinder ◽  
Alice N. Pell
Keyword(s):  
16S Rrna ◽  
Cervus Elaphus ◽  
Ovis Aries ◽  
The Other ◽  
Rrna Genes ◽  
Capra Hircus ◽  
Gram Positive ◽  
Phylogenetic Characterization ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The 16S rRNA sequences and selected phenotypic characteristics were determined for six recently isolated bacteria that can tolerate high levels of hydrolyzable and condensed tannins. Bacteria were isolated from the ruminal contents of animals in different geographic locations, including Sardinian sheep (Ovis aries), Honduran and Colombian goats (Capra hircus), white-tail deer (Odocoileus virginianus) from upstate New York, and Rocky Mountain elk (Cervus elaphus nelsoni) from Oregon. Nearly complete sequences of the small-subunit rRNA genes, which were obtained by PCR amplification, cloning, and sequencing, were used for phylogenetic characterization. Comparisons of the 16S rRNA of the six isolates showed that four of the isolates were members of the genusStreptococcus and were most closely related to ruminal strains of Streptococcus bovis and the recently described organism Streptococcus gallolyticus. One of the other isolates, a gram-positive rod, clustered with the clostridia in the low-G+C-content group of gram-positive bacteria. The sixth isolate, a gram-negative rod, was a member of the familyEnterobacteriaceae in the gamma subdivision of the classProteobacteria. None of the 16S rRNA sequences of the tannin-tolerant bacteria examined was identical to the sequence of any previously described microorganism or to the sequence of any of the other organisms examined in this study. Three phylogenetically distinct groups of ruminal bacteria were isolated from four species of ruminants in Europe, North America, and South America. The presence of tannin-tolerant bacteria is not restricted by climate, geography, or host animal, although attempts to isolate tannin-tolerant bacteria from cows on low-tannin diets failed.

scholarly journals Diversity and Dynamics of a North Atlantic Coastal Vibrio Community

2004 ◽  
Vol 70 (7) ◽  
pp. 4103-4110 ◽  
Author(s):  
Janelle R. Thompson ◽  
Mark A. Randa ◽  
Luisa A. Marcelino ◽  
Aoy Tomita-Mitchell ◽  
Eelin Lim ◽  
...  
Keyword(s):  
16S Rrna ◽  
North Atlantic ◽  
Nutrient Status ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Temperature Trends ◽  
Unknown Significance ◽  
Temperature Ranges ◽  
Atlantic Coastal

ABSTRACT Vibrios are ubiquitous marine bacteria that have long served as models for heterotrophic processes and have received renewed attention because of the discovery of increasing numbers of facultatively pathogenic strains. Because the occurrence of specific vibrios has frequently been linked to the temperature, salinity, and nutrient status of water, we hypothesized that seasonal changes in coastal water bodies lead to distinct vibrio communities and sought to characterize their level of differentiation. A novel technique was used to quantify shifts in 16S rRNA gene abundance in samples from Barnegat Bay, N.J., collected over a 15-month period. Quantitative PCR (QPCR) with primers specific for the genus Vibrio was combined with separation and quantification of amplicons by constant denaturant capillary electrophoresis (CDCE). Vibrio populations identified by QPCR-CDCE varied between summer and winter samples, suggesting distinct warm-water and year-round populations. Identification of the CDCE populations by cloning and sequencing of 16S rRNA genes from two summer and two winter samples confirmed this distinction. It further showed that CDCE populations corresponded in most cases to ∼98% rRNA similarity groups and suggested that the abundance of these follows temperature trends. Phylogenetic comparison yielded closely related cultured and often pathogenic representatives for most sequences, and the temperature ranges of these isolates confirmed the trends seen in the environmental samples. Overall, this suggests that temperature is a good predictor of the occurrence of closely related vibrios but that considerable microdiversity of unknown significance coexists within this trend.

scholarly journals Prevalence of Corynebacterial 16S rRNA Sequences in Patients with Bacterial and “Nonbacterial” Prostatitis

1999 ◽  
Vol 37 (6) ◽  
pp. 1863-1870 ◽  
Author(s):  
Michael A. Tanner ◽  
Daniel Shoskes ◽  
Asha Shahed ◽  
Norman R. Pace
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Chronic Prostatitis ◽  
Bacterial Species ◽  
Rrna Genes ◽  
Prostatic Fluid ◽  
Identification Of Bacteria ◽  
Rrna Sequences ◽  
Prostate Fluid ◽  
16S Rrna Sequences

The etiology of chronic prostatitis syndromes in men is controversial, particularly when positive cultures for established uropathogens are lacking. Although identification of bacteria in prostatic fluid has relied on cultivation and microscopy, most microorganisms in the environment, including some human pathogens, are resistant to cultivation. We report here on an rRNA-based molecular phylogenetic approach to the identification of bacteria in prostate fluid from prostatitis patients. Positive bacterial signals were seen for 65% of patients with chronic prostatitis overall. Seven of 11 patients with bacterial signals but none of 6 patients without bacterial signals were cured with antibiotic-based therapy. Results indicate the occurrence in the prostate fluid of a wide spectrum of bacterial species representing several genera. Most rRNA genes were closely related to those of species belonging to the generaCorynebacterium, Staphylococcus,Peptostreptococcus, Streptococcus, andEscherichia. Unexpectedly, a wide diversity ofCorynebacterium species was found in high proportion compared to the proportions of other bacterial species found. A subset of these 16S rRNA sequences represent those of undescribed species on the basis of their positions in phylogenetic trees. These uncharacterized organisms were not detected in control samples, suggesting that the organisms have a role in the disease or are the consequence of the disease. These studies show that microorganisms associated with prostatitis generally occur as complex microbial communities that differ between patients. The results also indicate that microbial communities distinct from those associated with prostatitis may occur at low levels in normal prostatic fluid.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

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