scholarly journals Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator Thlaspi goesingense

2004 ◽  
Vol 70 (5) ◽  
pp. 2667-2677 ◽  
Author(s):  
Rughia Idris ◽  
Radoslava Trifonova ◽  
Markus Puschenreiter ◽  
Walter W. Wenzel ◽  
Angela Sessitsch
Keyword(s):  
16S Rrna ◽  
Acc Deaminase ◽  
Rhizosphere Bacteria ◽  
Rrna Gene ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Plant Microbe Interaction ◽  
Gram Positive Bacteria ◽  
High Concentrations ◽  
Methylobacterium Mesophilicum

ABSTRACT Thlaspi goesingense is able to hyperaccumulate extremely high concentrations of Ni when grown in ultramafic soils. Recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. In this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing T. goesingense were characterized in detail by using both cultivation and cultivation-independent techniques. Bacteria were identified by 16S rRNA sequence analysis, and isolates were further characterized regarding characteristics that may be relevant for a beneficial plant-microbe interaction—Ni tolerance, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and siderophore production. In the rhizosphere a high percentage of bacteria belonging to the Holophaga/Acidobacterium division and α-Proteobacteria were found. In addition, high-G+C gram-positive bacteria, Verrucomicrobia, and microbes of the Cytophaga/Flexibacter/Bacteroides division colonized the rhizosphere. The community structure of shoot-associated bacteria was highly different. The majority of clones affiliated with the Proteobacteria, but also bacteria belonging to the Cytophaga/Flexibacter/Bacteroides division, the Holophaga/Acidobacterium division, and the low-G+C gram-positive bacteria, were frequently found. A high number of highly related Sphingomonas 16S rRNA gene sequences were detected, which were also obtained by the cultivation of endophytes. Rhizosphere isolates belonged mainly to the genera Methylobacterium, Rhodococcus, and Okibacterium, whereas the majority of endophytes showed high levels of similarity to Methylobacterium mesophilicum. Additionally, Sphingomonas spp. were abundant. Isolates were resistant to Ni concentrations between 5 and 12 mM; however, endophytes generally tolerated higher Ni levels than rhizosphere bacteria. Almost all bacteria were able to produce siderophores. Various strains, particularly endophytes, were able to grow on ACC as the sole nitrogen source.

The “Nostocoida limicola” story: resolving the phylogeny of this morphotype responsible for bulking in activated sludge

2002 ◽  
Vol 46 (1-2) ◽  
pp. 105-110 ◽  
Author(s):  
R.J. Seviour ◽  
J.-R. Liu ◽  
E.M. Seviour ◽  
C.A. McKenzie ◽  
L.L. Blackall ◽  
...  
Keyword(s):  
16S Rrna ◽  
Activated Sludge ◽  
Pure Culture ◽  
Sequence Analyses ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Culture Studies ◽  
Gram Positive Bacteria ◽  
Morphological Variants

On the basis of 16S rRNA sequence analyses of several isolates of “Nostocoida limicola” from activated sludge plants in Australia and other countries, it is clear that “N. limicola” I, II and III are not three morphological variants of a single bacterium but at least three phylogenetically different bacteria. Data show that “N. limicola” I are members of at least two genera in the low mol% G+C Gram-positive bacteria, while some isolates of “N.limicola” II belong to the high mol% G+C Gram positive bacteria, and “N.limicola” III is a member of the Planctomycetales. Design and application of 16S rRNA targeted probes for each to biomass samples suggests that their phylogeny is more diverse than pure culture studies would suggest.

scholarly journals Paenibacillus lutrae sp. nov., A Chitinolytic Species Isolated from A River Otter in Castril Natural Park, Granada, Spain

2019 ◽  
Vol 7 (12) ◽  
pp. 637
Author(s):  
Miguel Rodríguez ◽  
José Carlos Reina ◽  
Victoria Béjar ◽  
Inmaculada Llamas
Keyword(s):  
16S Rrna ◽  
Novel Species ◽  
Sequence Similarity ◽  
Acc Deaminase ◽  
Rrna Gene ◽  
River Otter ◽  
16S Rrna Sequence ◽  
Phenotypic Data ◽  
Natural Park ◽  
Phylogenomic Analyses

A highly chitinolytic facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive, rod-shaped bacterial strain N10T was isolated from the feces of a river otter in the Castril Natural Park (Granada, Spain). It is a slightly halophilic, motile, catalase-, oxidase-, ACC deaminase- and C4 and C8 lipase-positive strain. It is aerobic, respiratory and has a fermentative metabolism using oxygen as an electron acceptor, produces acids from glucose and can fix nitrogen. Phylogenetic analysis of the 16S rRNA gene sequence, multilocus sequence analysis (MLSA) of 16S rRNA, gyrB, recA and rpoB, as well as phylogenomic analyses indicate that strain N10T is a novel species of the genus Paenibacillus, with the highest 16S rRNA sequence similarity (95.4%) to P. chitinolyticus LMG 18047T and <95% similarity to other species of the genus Paenibacillus. Digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANIb) were 21.1% and <75%, respectively. Its major cellular fatty acids were anteiso-C15:0, C16:0, and iso-C15:0. G + C content ranged between 45%–50%. Using 16S rRNA phylogenetic and in silico phylogenomic analyses, together with chemotaxonomic and phenotypic data, we demonstrate that type strain N10T (= CECT 9541T =LMG 30535T) is a novel species of genus Paenibacillus and the name Paenibacillus lutrae sp. nov. is proposed.

scholarly journals Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria

2009 ◽  
Vol 58 (8) ◽  
pp. 1030-1036 ◽  
Author(s):  
Patrick C. Y. Woo ◽  
Jade L. L. Teng ◽  
Jeff K. L. Wu ◽  
Fion P. S. Leung ◽  
Herman Tse ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gram Positive ◽  
Gram Positive Bacteria ◽  
Rrna Gene Sequencing

This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40 % of medically important Gram-positive cocci (GPC), and 21 and 34 % of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34 % of medically important GPC and 14 and 25 % of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0–2 and 2–13 % of staphylococci, and 0 and 0–10 % of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36–56 and 11–14 % of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included.

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 Screenning and determination of polyhydroxyalkanoate production by Bacillus sp. strains

2020 ◽  
Vol 3 (3) ◽  
pp. 165-172
Author(s):  
Da Nguyen Thi ◽  
Linh Nguyen Trong ◽  
Trang Nguyen Thu ◽  
Hai Tran Manh ◽  
Huyen La Thi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacillus Megaterium ◽  
Basal Medium ◽  
Bacillus Sp ◽  
Reserve Material ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Gram Positive Bacteria ◽  
Gene Coding

Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by microbes as reserve material when they were cultured in a limitation of nutrients and excess C source mediums. PHAs can be synthesized by various bacteria including gram positive and gram-negative bacteria. Among the PHA-producing gram-positive bacteria, Bacillus sp. produce and accumulate various monomer compositions of PHAs. In this study, about 83,3% of strains (05/06 strains) can accumulate PHAs production. Bacillus sp. DV01 accumulated a amount of PHA 23,9% of CWD after 96h when cultured in modified basal medium containing 1% (w/v) glucose. Bacillus sp.&nbsp; DV01 was identified by sequecing the gene coding for 16S rRNA. BLAST results showed the obtained 16S rRNA sequence of this strain revealed 100% with the Bacillus megaterium and so-called Bacillus megaterium DV01.

scholarly journals An experimental intraradicular biofilm model in the pig for evaluating irrigation techniques

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Toshinori Tanaka ◽  
Yoshio Yahata ◽  
Keisuke Handa ◽  
Suresh V. Venkataiah ◽  
Mary M. Njuguna ◽  
...  
Keyword(s):  
16S Rrna ◽  
Root Canal ◽  
Apical Periodontitis ◽  
Exposure Model ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Bacterial Phyla ◽  
Biofilm Model ◽  
Biofilm Removal

Abstract Background We established an in vivo intraradicular biofilm model of apical periodontitis in pigs in which we compared the efficacy of different irrigant activation techniques for biofilm removal. Methods Twenty roots from the deciduous mandibular second premolar of 5 male pigs were used. After pulpectomy, canals were left open for 2 weeks and then sealed for 4 weeks to enable the development of an intracanal biofilm. The intraradicular biofilms was evaluated using SEM and bacterial 16S rRNA gene-sequencing. To investigate the efficacy of biofilm removal, root canal irrigations were performed using conventional needle, passive ultrasonic, subsonic, or laser-activated irrigation. Real-time PCR was conducted to quantitate the remaining biofilm components. Statistical analysis was performed using ANOVA followed by a Tukey kramer post-hoc test with α = 0.05. Results The pulp exposure model was effective in inducing apical periodontitis and SEM analysis revealed a multi-layer biofilm formation inside the root canal. 16S rRNA sequence analysis identified Firmicutes, Bacteroidetes, and Fusobacteria as the predominant bacterial phyla components, which is similar to the microbiome profile seen in humans. None of the tested irrigation techniques completely eradicated the biofilm components from the root canal, but the subsonic and laser-activated irrigation methods produced the lowest bacterial counts (p < 0.05). Conclusions An experimental intraradicular biofilm model has been successfully established in pigs. Within the limitations of the study, subsonic or laser-activated irrigation demonstrated the best biofilm removal results in the pig system.

Aggregatimonas Sangjinii Gen. Nov., Sp. Nov., A Novel Silver Nanoparticle Synthesizing Bacterium Belonging to the Family Flavobacteriaceaee

2021 ◽  
Author(s):  
Dawoon Chung ◽  
Jaoon Young Hwan Kim ◽  
Kyung Woo Kim ◽  
Yong Min Kwon
Keyword(s):  
16S Rrna ◽  
Genome Sequence ◽  
Sequence Similarity ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
The Family ◽  
The Media

Abstract A gram-negative, orange-pigmented, non-flagellated, gliding, rod-shaped, and aerobic bacterium, designated strain F202Z8T, was isolated from a rusty iron plate found in the intertidal region of Taean, South Korea. Notably, this strain synthesized silver nanoparticles (AgNPs), and 17 putative genes responsible for the synthesis of AgNPs were found in its genome. The complete genome sequence of strain F202Z8T is 4,723,614 bp, with 43.26% G + C content. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain F202Z8T forms a distinct lineage with closely related genera Maribacter, Pelagihabitans, Pseudozobellia, Zobellia, Pricia, and Costertonia belonging to the family Flavobacteriaceae. The 16S rRNA sequence similarity was < 94.5%. The digital DNA–DNA hybridization and average nucleotide identity values calculated from the whole genome-sequence comparison between strain F202Z8T and other members of the family Flavobacteriaceae were in the ranges of 12.7–16.9% and 70.3–74.4%, respectively. Growth was observed at 15–33°C (optimally at 30°C), at pH 6.5–7.5 (optimally at pH 7.0), and with the addition of 2.5–4.5% (w/v) NaCl to the media (optimally at 4.0%). The predominant cellular fatty acids were iso-C15: 0, iso-C15 :1 G, and iso-C17 :0 3-OH; the major respiratory quinone was MK-6. Polar lipids included phosphatidylethanolamine, five unidentified lipids, and two unidentified aminolipids. Our polyphasic taxonomic results suggested that this strain represents a novel species of a novel genus in the family Flavobacteriaceae, for which the name Aggregatimonas sangjinii gen. nov., sp. nov. is proposed. The type strain of Aggregatimonas sangjinii is F202Z8T (= KCCM 43411T = LMG 31494T).

Sulfitobacter maritimus sp. nov., isolated from coastal sediment

2021 ◽  
Vol 71 (2) ◽  
Author(s):  
Feng-Bai Lian ◽  
Yong-Qin Li ◽  
Jing Zhang ◽  
Shan Jiang ◽  
Zong-Jun Du
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
The Novel ◽  
16S Rrna Sequence ◽  
Respiratory Quinone ◽  
Content Type ◽  
A Genome ◽  
Bacterium Strain

A facultatively anaerobic bacterium, strain S0837T, was isolated from the marine sediment of Jingzi Wharf, Weihai, China. Cells of the novel strain were Gram-stain-negative, non-flagellated, non-gliding, non-pigmented and rod-shaped. Cells were around 0.3–0.5×1.0–1.4 µm in size and often appeared singly. Optimum growth occurred at 33 °C, with 2 % (w/v) NaCl and at pH 7.0–7.5. On the basis of the results of 16S rRNA gene sequences, stain S0837T had the closest relative with Sulfitobacter delicatus KCTC 32183T (98.0 %). Genome sequencing revealed a genome size of 3 785 026 bp, a G+C content of 59.8 mol% and several genes related with sulphur oxidation. The strain shared 98.0 % 16S rRNA sequence similarities with closely related type species and shared ANI value below 95–96 %, dDDH value of showed relatedness of 27.4, 25.2 and 25.2 % respectively with the closely related type species. Strain S0837T had ubiquinone-10 as the sole respiratory quinone, and possessed summed feature 8 (C18 : 1  ω7c/C18 : 1  ω6c) as the major fatty acid. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and phosphatidylethanolamine. According to the results of the phenotypic, chemotaxonomic characterization, phylogenetic properties and genome analysis, strain S0837T should represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter maritimus sp. nov. is proposed. The type strain is S0837T (=MCCC 1K04635T=KCTC 72860T).

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