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 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 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 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 More partners, more ranges: generalist legumes spread more easily around the globe

2018 ◽  
Author(s):  
Tia L. Harrison ◽  
Anna K. Simonsen ◽  
John R. Stinchcombe ◽  
Megan E. Frederickson
Keyword(s):  
16S Rrna ◽  
Range Expansion ◽  
Global Analysis ◽  
The Other ◽  
Published Data ◽  
Legume Species ◽  
Unexplained Variation ◽  
Rrna Sequences ◽  
16S Rrna Sequences ◽  
New Habitats

AbstractHow does mutualism affect range expansion? On one hand, mutualists might thrive in new habitats thanks to the resources, stress tolerance, or defense provided by their partners. On the other, specialized mutualists might fail to find compatible partners beyond their range margins, limiting further spread. A recent global analysis of legume ranges found that non-symbiotic legumes have been successfully introduced to more ranges than legumes that form symbioses with rhizobia, but there is still abundant unexplained variation in introduction success within symbiotic legumes. Here, we test the hypothesis that generalist legumes have spread to more introduced ranges than specialist legumes. We used published data and rhizobial 16S rRNA sequences from GenBank to quantify the number of rhizobia partners that associate with each of 159 legume species, spanning the legume phylogeny and the globe. We found that generalist legumes occur in more introduced ranges than specialist legumes, suggesting that among mutualists, specialization hinders range expansions.

scholarly journals 16S rRNA Sequences and Differences in Bacteria Isolated from the Muztag Ata Glacier at Increasing Depths

2005 ◽  
Vol 71 (8) ◽  
pp. 4619-4627 ◽  
Author(s):  
Shurong Xiang ◽  
Tandong Yao ◽  
Lizhe An ◽  
Bingliang Xu ◽  
Junxia Wang
Keyword(s):  
16S Rrna ◽  
Ice Core ◽  
Growth Conditions ◽  
Small Subunit ◽  
Bacterial Isolates ◽  
Gram Positive ◽  
Mountain Glacier ◽  
Gram Positive Bacteria ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Small subunit 16S rRNA sequences, growth temperatures, and phylogenetic relationships have been established for 129 bacterial isolates recovered under aerobic growth conditions from different regions of a 22-m ice core from the Muztag Ata Mountain glacier on the Pamirs Plateau (China). Only 11% were psychrophiles (grew at 2°C or −2°C up to ∼20°C), although the majority (82%) were psychrotolerant (grew at 2°C or −2°C up to 37°C). The majority of the isolates had 16S rRNA sequences similar to previously determined sequences, ranging from 85% to 100% identical to database sequences. Based on their 16S rRNA sequences, 42.6% of the isolates were high-G+C (HGC) gram-positive bacteria, 23.3% wereγ -Proteobacteria, 14.7% were α-Proteobacteria, 14.7% were Flavobacteria, and 4.7% were low-G+C (LGC) gram-positive bacteria. There were clear differences in the depth distribution, with Proteobacteria, HGC/Cytophaga-Flavobacterium-Bacteroides (CFB), Proteobacteria, LGC/CFB/HGC, Cryobacterium psychrophilum, HGC/CFB, Proteobacteria/HGC/CFB, and HGC/CFB being the predominant isolates from ice that originated from 2.7 to 3.8, 6.2, 7.5, 8.3, 9.0, 9.7, 12.5, and 15.3 m below the surface, respectively. This layered distribution of bacterial isolates presumably reflects both differences in bacteria inhabiting the glacier's surface, differences in bacteria deposited serendipitously on the glacier's surface by wind and snowfall, and nutrient availability within the ice.

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 Screening and identification of actinomycetes having antimicrobial activity isolated from marine organisms and sediment samples in Ly Son island, Quang Ngai

2020 ◽  
Vol 18 (1) ◽  
pp. 187-196
Author(s):  
Tran Thi Thanh Hoa ◽  
Le Thi Hong Minh ◽  
Vu Thi Quyen ◽  
Nguyen Mai Anh ◽  
Doan Thi Mai Huong ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
16S Rrna ◽  
Marine Environment ◽  
Marine Organisms ◽  
Biologically Active ◽  
Gram Positive ◽  
Genus Streptomyces ◽  
Gram Negative ◽  
Rrna Sequences ◽  
16S Rrna Sequences

The discovery of bioactive compounds from marine microorganisms for drug development has been currently widely studied. In which marine actinomycetes are highlighted as a potential source in finding antibiotics as well as substances with biological activity in general. The objective of this study is to isolate and screen the actinomycetes strains with antibacterial activity from the marine environment. Sixty one actinomycetes were isolated from 80 samples of marine organisms and sediments collected from Ly Son Island, Quang Ngai. The strains were fermented in the A1 medium and the culture broths were extracted by ethyl acetate and vacuum rotary evaporation to produce crude extracts. Antimicrobial activity of the extracts were carried out on 7 strains of tested microorganisms, including three strains of Gram-negative bacteria (Escherichia coli ATCC25922, Pseudomonas aeruginosa ATCC27853, Salmonella enterica ATCC13076), three Gram-positive strains (Enterococcus faecalis ATCC29212, Staphylococus aureus ATCC25923, Bacillus cereus ATCC 13245), and yeast Candida albicans ATCC10231. The screening results showed that three strains with the highest antimicrobial activity (G330, G336 and G361) were capable of inhibiting 5 of the 7 tested microorganisms with Minimum Inhibitory Concentration (MIC) values ranging from 4 to 256 μg/mL, depending on each tested strain. Specifically, all three strains inhibited C. albicans ATCC10231 and three Gram-positive strains (E. faecalis ATCC29212, S. aureus ATCC25923, B. cereus ATCC 13245). In addition, G330 and G336 also showed the inhibitory activity to Gram negative strain S. enterica ATCC13076 with value of 256 µg/mL, G361 has a good inhibitory ability for E. coli ATCC25922 with MIC value of 8 µg/mL. The strains were identified by morphological and the 16S rRNA gene sequences. The results showed that 16S rRNA sequences of the strains had over 99% similarity to the 16S rRNA sequences on the GeneBank database, strains G336 and G361 belonged to the genus Salinispora, whereas strain G330 belonged to the genus Streptomyces. These results showed that marine environment has a great potential in solation of actinomycetes strains for the search for antibacterial substances as well as other biologically active compounds.

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.

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