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 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 Discontinuous Occurrence of the hsp70(dnaK) Gene among Archaea and Sequence Features of HSP70 Suggest a Novel Outlook on Phylogenies Inferred from This Protein

1999 ◽  
Vol 181 (2) ◽  
pp. 434-443 ◽  
Author(s):  
Simonetta Gribaldo ◽  
Valentina Lumia ◽  
Roberta Creti ◽  
Everly Conway de Macario ◽  
Annamaria Sanangelantoni ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Thermotoga Maritima ◽  
Amino Acid Sequences ◽  
Phylogenetic Position ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Thermomicrobium Roseum ◽  
Hyperthermophilic Bacteria ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Occurrence of the hsp70 (dnaK) gene was investigated in various members of the domain Archaeacomprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria Aquifex pyrophilus andThermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16S rRNA sequences. The gene was not detected in 8 of 10 archaea examined but was found in A. pyrophilus and T. maritima, from which it was cloned and sequenced. Comparative analyses of the HSP70 amino acid sequences encoded in these genes, and others in the databases, showed that (i) in accordance with the vicinities seen in rRNA-based trees, the proteins from A. pyrophilus and T. maritima form a thermophilic cluster with that from the green nonsulfur bacteriumThermomicrobium roseum and are unrelated to their counterparts from gram-positive bacteria, proteobacteria/mitochondria, chlamydiae/spirochetes, deinococci, and cyanobacteria/chloroplasts; (ii) the T. maritima HSP70 clusters with the homologues from the archaea Methanobacterium thermoautotrophicum andThermoplasma acidophilum, in contrast to the postulated unique kinship between archaea and gram-positive bacteria; and (iii) there are exceptions to the reported association between an insert in HSP70 and gram negativity, or vice versa, absence of insert and gram positivity. Notably, the HSP70 from T. maritima lacks the insert, although T. maritima is phylogenetically unrelated to the gram-positive bacteria. These results, along with the absence ofhsp70 (dnaK) in various archaea and its presence in others, suggest that (i) different taxa retained either one or the other of two hsp70 (dnaK) versions (with or without insert), regardless of phylogenetic position; and (ii) archaea are aboriginally devoid of hsp70(dnaK), and those that have it must have received it from phylogenetically diverse bacteria via lateral gene transfer events that did not involve replacement of an endogenous hsp70(dnaK) gene.

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 New Lineage of Filamentous, Spore-Forming, Gram-Positive Bacteria from Soil

2006 ◽  
Vol 72 (6) ◽  
pp. 4360-4369 ◽  
Author(s):  
Linda Cavaletti ◽  
Paolo Monciardini ◽  
Ruggiero Bamonte ◽  
Peter Schumann ◽  
Manfred Rohde ◽  
...  
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Liquid Media ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Positive Strain ◽  
Italian Soil ◽  
High Bootstrap ◽  
Rrna Sequences

ABSTRACT A novel bacterial strain that was isolated from an Italian soil and was designated SOSP1-21T forms branched mycelia in solid and liquid media and has a filamentous morphology similar to that of some genera belonging to the Actinobacteria. Electron microscopy showed that this organism has a grape-like appearance, resulting from interlacing of spores originating from sporophoric hyphae. Ten strains that are morphologically related to SOSP1-21T were recovered from soil. Phylogenetic analyses of 16S rRNA gene segments confirmed the relatedness of these strains to SOSP1-21T and indicated that the newly isolated strains form separate clades in a deeply branching lineage. The closest matches for the 16S rRNA sequences of all the strains (around 79% identity) were matches with representatives of the Chloroflexi, although the affiliation with this division was not supported by high bootstrap values. The strains are mesophilic aerobic heterotrophs and are also capable of growing under microaerophilic conditions. They all stain gram positive. Strain SOSP1-21T contains ornithine, alanine, glutamic acid, serine, and glycine as the peptidoglycan amino acids. In addition, an unusual level of C16:1 2OH (30%) was found in the cellular fatty acids. The G+C content of SOSP1-21T genomic DNA is 53.9%, and MK-9(H2) was the only menaquinone detected. All these data suggest that SOSP1-21T and the related strains may constitute a new division of filamentous, spore-forming, gram-positive bacteria. We propose the name Ktedobacter racemifer gen. nov., sp. nov. for strain SOSP1-21T.

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 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 Elucidation of Gram-Positive Bacterial Iron(III) Reduction for Kaolinite Clay Refinement

Molecules ◽  
2021 ◽  
Vol 26 (11) ◽  
pp. 3084
Author(s):  
Hao Jing ◽  
Zhao Liu ◽  
Seng How Kuan ◽  
Sylvia Chieng ◽  
Chun Loong Ho
Keyword(s):  
Iron Reduction ◽  
Growth Conditions ◽  
Cellular Interaction ◽  
Kaolin Clay ◽  
Media Composition ◽  
Gram Positive ◽  
Kaolinite Clay ◽  
Gram Positive Bacteria ◽  
Rich Media ◽  
The Media

Recently, microbial-based iron reduction has been considered as a viable alternative to typical chemical-based treatments. The iron reduction is an important process in kaolin refining, where iron-bearing impurities in kaolin clay affects the whiteness, refractory properties, and its commercial value. In recent years, Gram-negative bacteria has been in the center stage of iron reduction research, whereas little is known about the potential use of Gram-positive bacteria to refine kaolin clay. In this study, we investigated the ferric reducing capabilities of five microbes by manipulating the microbial growth conditions. Out of the five, we discovered that Bacillus cereus and Staphylococcus aureus outperformed the other microbes under nitrogen-rich media. Through the biochemical changes and the microbial behavior, we mapped the hypothetical pathway leading to the iron reduction cellular properties, and found that the iron reduction properties of these Gram-positive bacteria rely heavily on the media composition. The media composition results in increased basification of the media that is a prerequisite for the cellular reduction of ferric ions. Further, these changes impact the formation of biofilm, suggesting that the cellular interaction for the iron(III)oxide reduction is not solely reliant on the formation of biofilms. This article reveals the potential development of Gram-positive microbes in facilitating the microbial-based removal of metal contaminants from clays or ores. Further studies to elucidate the corresponding pathways would be crucial for the further development of the field.

Sign in / Sign up

Export Citation Format

Share Document