Diversity of halophilic bacteria isolated from Rambla Salada, Murcia (Spain)

2014 ◽  
Vol 60 (12) ◽  
pp. 839-846 ◽  
Author(s):  
Rocío Luque ◽  
Victoria Béjar ◽  
Emilia Quesada ◽  
Inmaculada Llamas
Keyword(s):  
Bacterial Community ◽  
Halophilic Bacteria ◽  
Operational Taxonomic Units ◽  
Sequence Identity ◽  
Abundant Genus ◽  
Phenotypic Tests ◽  
Sampling Season ◽  
V3 Region ◽  
Rrna Sequences ◽  
16S Rrna Sequences

In this study we analyzed the diversity of the halophilic bacteria community from Rambla Salada during the years 2006 and 2007. We collected a total of 364 strains, which were then identified by means of phenotypic tests and by the hypervariable V1–V3 region of the 16S rRNA sequences (around 500 bp). The ribosomal data showed that the isolates belonged to Proteobacteria (72.5%), Firmicutes (25.8%), Actinobacteria (1.4%), and Bacteroidetes (0.3%) phyla, with Gammaproteobacteria the predominant class. Halomonas was the most abundant genus (41.2% isolates) followed by Marinobacter (12.9% isolates) and Bacillus (12.6% isolates). In addition, 9 strains showed <97% sequence identity with validly described species and may well represent new taxa. The diversity of the bacterial community analyzed with the DOTUR package determined 139 operational taxonomic units at 3% genetic distance level. Rarefaction curves and diversity indexes demonstrated that our collection of isolates adequately represented all the bacterial community at Rambla Salada that can be grown under the conditions used in this work. We found that the sampling season influenced the composition of the bacterial community, and bacterial diversity was higher in 2007; this fact could be related to lower salinity at this sampling time.

scholarly journals Correction to: Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ju-Hyeong Park ◽  
Angela R. Lemons ◽  
Jerry Roseman ◽  
Brett J. Green ◽  
Jean M. Cox-Ganser
Keyword(s):  
Public Schools ◽  
Environmental Factors ◽  
Bacterial Community ◽  
16S Rrna ◽  
Large City ◽  
Floor Dust ◽  
Community Assemblages ◽  
Rrna Sequences ◽  
16S Rrna Sequences

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals Extent and Variation of Phage-Borne Bacterial 16S rRNA Gene Sequences in Wastewater Environments

2011 ◽  
Vol 77 (15) ◽  
pp. 5529-5532 ◽  
Author(s):  
Antonio Del Casale ◽  
Paul V. Flanagan ◽  
Michael J. Larkin ◽  
Christopher C. R. Allen ◽  
Leonid A. Kulakov
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Total Bacterial Community ◽  
Rrna Sequences ◽  
16S Rrna Sequences ◽  
Bacterial 16S Rrna Gene

ABSTRACTPhage metagenomes isolated from wastewater over a 12-month period were analyzed. The results suggested that various strains ofProteobacteria,Bacteroidetes, and other phyla are likely to participate in transduction. The patterns of 16S rRNA sequences found in phage metagenomes did not follow changes in the total bacterial community.

scholarly journals Unusually High Archaeal Diversity in a Crystallizer Pond, Pomorie Salterns, Bulgaria, Revealed by Phylogenetic Analysis

Archaea ◽  
2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Margarita Kambourova ◽  
Iva Tomova ◽  
Ivanka Boyadzhieva ◽  
Nadja Radchenkova ◽  
Evgenia Vasileva-Tonkova
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Community Composition ◽  
Archaeal Community ◽  
Hypersaline Environment ◽  
Archaeal Diversity ◽  
Operational Taxonomic Units ◽  
Crystallizer Pond ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Recent studies on archaeal diversity in few salterns have revealed heterogeneity between sites and unique structures of separate places that hinder drawing of generalized conclusions. Investigations on the archaeal community composition in P18, the biggest crystallizer pond in Pomorie salterns (PS) (34% salinity), demonstrated unusually high number of presented taxa in hypersaline environment. Archaeal clones were grouped in 26 different operational taxonomic units (OTUs) assigned to 15 different genera from two orders, Halobacteriales and Haloferacales. All retrieved sequences were related to culturable halophiles or unculturable clones from saline (mostly hypersaline) niches. New sequences represented 53.9% of archaeal OTUs. Some of them formed separate branches with 90% similarity to the closest neighbor. Present results significantly differed from the previous investigations in regard to the number of presented genera, the domination of some genera not reported before in such extreme niche, and the identification of previously undiscovered 16S rRNA sequences.

scholarly journals 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community

1990 ◽  
Vol 75 (2-3) ◽  
pp. 105-115 ◽  
Author(s):  
David M. Ward ◽  
Roland Weller ◽  
Mary M. Bateson
Keyword(s):  
16S Rrna ◽  
Rrna Sequences ◽  
16S Rrna Sequences

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 Occurrence of diazotrophic bacteria in Araucaria angustifolia

2007 ◽  
Vol 64 (3) ◽  
pp. 303-304 ◽  
Author(s):  
Rafaela de Fátima Neroni ◽  
Elke Jurandy Bran Nogueira Cardoso
Keyword(s):  
16S Rrna ◽  
Acetylene Reduction ◽  
Araucaria Angustifolia ◽  
Diazotrophic Bacteria ◽  
Araucaria Forest ◽  
Solid Media ◽  
Reduction Assay ◽  
Semi Solid ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Araucaria angustifolia is an environmentally threatened tree and the whole biota of the Araucaria Forest should be investigated with the aim of its preservation. Diazotrophic bacteria are extremely important for the maintenance of ecosystems, but they have never been studied in Araucaria Forests. In this study, diazotrophic bacteria were isolated from Araucaria roots and soil, when grown in semi-specific, semi-solid media. The diazotrophic character of some recovered isolates could be confirmed using the acetylene reduction assay. According to their 16S rRNA sequences, most of these isolates belong to the genus Burkholderia.

scholarly journals Identification of Streptococci to Species Level by Sequencing the Gene Encoding the Manganese-Dependent Superoxide Dismutase

1998 ◽  
Vol 36 (1) ◽  
pp. 41-47 ◽  
Author(s):  
Claire Poyart ◽  
Gilles Quesne ◽  
Stephane Coulon ◽  
Patrick Berche ◽  
Patrick Trieu-Cuot
Keyword(s):  
Superoxide Dismutase ◽  
Pcr Assay ◽  
Degenerate Primers ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Type Strains ◽  
Internal Fragment ◽  
Rrna Sequences ◽  
16S Rrna Sequences

We have used a PCR assay based on the use of degenerate primers in order to characterize an internal fragment (sodAint ) representing approximately 85% of the genes encoding the manganese-dependent superoxide dismutase in various streptococcal type strains (S. acidominimus,S. agalactiae, S. alactolyticus, S. anginosus, S. bovis, S. constellatus,S. canis, S. cricetus, S. downei,S. dysgalactiae, S. equi subsp.equi, S. equi subsp. zooepidemicus,S. equinus, S. gordonii, S. iniae,S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis,S. pneumoniae, S. porcinus, S. pyogenes, S. salivarius, S. sanguis,S. sobrinus, S. suis, S. thermophilus, and S. vestibularis). Phylogenetic analysis of these sodAint fragments yields an evolutionary tree having a topology similar to that of the tree constructed with the 16S rRNA sequences. We have shown that clinical isolates could be identified by determining the positions of theirsodAint fragments on the phylogenetic tree of the sodAint fragments of the type species. We propose this method for the characterization of strains that cannot be assigned to a species on the basis of their conventional phenotypic reactions.

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