Molecular bacterial diversity and distribution in waste from a steel plant

2008 ◽  
Vol 54 (12) ◽  
pp. 996-1005 ◽  
Author(s):  
Dulcecleide B. Freitas ◽  
Mariana P. Reis ◽  
Leandro M. Freitas ◽  
Paulo S. Assis ◽  
Edmar Chartone-Souza ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
16S Rdna ◽  
Bacterial Communities ◽  
Sequence Similarity ◽  
Diversity Indices ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
Partial Length ◽  
16S Rdna Sequences ◽  
Novel Taxa

We characterized the bacterial diversity of newly produced steelmaking wastes (NPSW) and steelmaking wastes deposited (SWD) in a restricted land area, generated by the siderurgic industry, using the 16S rDNA clone library approach. A total of 212 partial-length sequences were analyzed, revealing 123 distinct operational taxonomic units (OTUs) determined by the DOTUR program to 97% sequence similarity. Phylogenetic analysis of bacterial 16S rDNA sequences from the NPSW and SWD libraries demonstrated that Gammaproteobacteria, Betaproteobacteria, Alphaproteobacteria, Actinobacteria, Planctomycetes, Firmicutes, and Bacteroidetes were represented in both libraries. Deltaproteobacteria, Acidobacteria, Chloroflexi, Deinococcus-thermus, Gemmatimonadetes, and candidate divisions OP10 and OD1 were only present in the SWD library, and Nitrospira was only present in the NPSW library. The abundance of sequences affiliated with Gammaproteobacteria was high in both libraries. Six previously unclassified OTUs may represent novel taxa. Based on diversity indices (Simpson, Shannon–Weaver, Chao1, and ACE), the SWD library had a higher diversity. LIBSHUFF comparisons of the composition of the 2 libraries showed that they were significantly different. These results indicate that the bacterial communities in steelmaking wastes present high phylogenetic diversity and complexity. A possible association between the functional diversity and the bacterial communities’ complexity requires further phenotypic investigation.

Human intestinal spirochetosis diagnosed with colonoscopy and analysis of partial 16S rDNA sequences of involved spirochetes

2001 ◽  
Vol 2 (1) ◽  
pp. 111-116 ◽  
Author(s):  
Wolfgang Kraatz ◽  
Ulf Thunberg ◽  
Bertil Pettersson ◽  
Claes Fellström
Keyword(s):  
16S Rdna ◽  
Type Strain ◽  
Sequence Similarity ◽  
Rdna Sequences ◽  
Intestinal Spirochetosis ◽  
16S Rdna Sequences ◽  
Pcr Products ◽  
Human Intestinal Spirochetosis ◽  
Type Strains ◽  
Rrna Sequences

AbstractDNA was extracted from colonic biopsies of 33 patients with and three without evidence of intestinal spirochetosis (IS) in the large bowel. The biopsies were subjected to PCR. A pair of primers, generating a 207 bp fragment, were designed to detect specifically the 16S rDNA gene ofBrachyspira. PCR products of the expected size were obtained from 33 samples with histologic evidence of IS. The PCR amplicons were used for sequencing. The sequences obtained were aligned to the corresponding 16S rRNA sequences of five type strains ofBrachyspira. The sequences of 23 PCR products were 99–100% identical with the correspond-ingB.aalborgitype strain sequence. Two cases showed 99–100% sequence similarity with the type strain ofB.pilosicoliP43/6/78. Six cases could not be referred to any of the known species ofBrachyspira. Two PCR products gave incomplete sequences.

scholarly journals Seasonal Diversity of Endophytic Bacteria Associated with Cinnamomum camphora (L.) Presl.

Diversity ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 112 ◽  
Author(s):  
Abubakr Abdelwhab Hamd Elmagzob ◽  
Muhammed Mustapha Ibrahim ◽  
Guo-Fang Zhang
Keyword(s):  
16S Rdna ◽  
High Throughput Sequencing ◽  
Shannon Index ◽  
Ribosomal Database Project ◽  
Cinnamomum Camphora ◽  
Operational Taxonomic Units ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Endophytic Bacterial Community ◽  
Seasonal Diversity

Investigations on the density, diversity, and distribution of endophytic bacterial community associated with leaves of Cinnamomum camphora (L.) Presl. were carried out during three seasons using 16s rDNA high-throughput sequencing technology. Samples were collected from five species in Nanping (A, B, C, D, and E) and one from Fuqin (F) in the Fujian province, China in the months of April, July, and October (represented by 1, 2 and 3), indicating spring, summer, and early winter, respectively. Results from 16s rDNA sequences revealed 10,844,124 effective sequences. The highest OTUs (Operational taxonomic units) was highest in the A1 sample (1086), while the lowest was in C2 (509). Our observations showed that samples taken in October had the highest diversity of endophytes as indicated by the Shannon index (B3 = 5.3337), Chao1 (E3 = 1233.10), abundance-based coverage estimator (ACE) (A3 = 1764.72), and the Simpson indices of diversity (C3 = 0.1655) irrespective of the species. The order of the endophytes richness in the samples was April > July > October. The Ribosomal Database Project (RDP) classifier showed that the obtained sequences belonged to nine major phyla: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Acidobacteria, Planctomycetes, Chloroflexi, and Fusobacteria. Proteobacteria accounted for the highest proportion in each sample, ranging from 35.15% to 89.72%. These sequences belonged mainly to 10 orders: Rhizobiales, Clostridiales, Peseudomonadales, Burkholderiales, Bacteroidales, Enterobacteriales, Rhodocyclales, Sphingomonadales, Lactobacillales, and Bacillales. Also, other taxa with possible taxonomic statuses, which were unclassified, were present.

scholarly journals Shewanella gaetbuli sp. nov., a slight halophile isolated from a tidal flat in Korea

2004 ◽  
Vol 54 (2) ◽  
pp. 487-491 ◽  
Author(s):  
Jung-Hoon Yoon ◽  
Kook Hee Kang ◽  
Tae-Kwang Oh ◽  
Yong-Ha Park
Keyword(s):  
16S Rdna ◽  
Tidal Flat ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Phenotypic Properties ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Isoprenoid Quinones ◽  
Type Strains

A Gram-negative, motile, non-spore-forming, rod-shaped strain, TF-27T (=KCCM 41648T=JCM 11814T), was isolated from a tidal flat in Korea. This organism grew well at 25–35 °C, with optimum growth at 30 °C. Strain TF-27T grew optimally in the presence of 2 % NaCl; it did not grow without NaCl or in the presence of >8 % NaCl. Strain TF-27T simultaneously contained both menaquinones and ubiquinones as isoprenoid quinones. The predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The major fatty acids in strain TF-27T were iso-C15 : 0 (20·6 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (21·1 %). The DNA G+C content of strain TF-27T was 42 mol%. Phylogenetic analyses based on 16S rDNA sequences showed that strain TF-27T falls within the radiation of the cluster that is encompassed by the genus Shewanella. Levels of 16S rDNA sequence similarity between strain TF-27T and the type strains of Shewanella species were 93·2–96·8 %. On the basis of phenotypic properties and phylogenetic data, strain TF-27T should be placed in the genus Shewanella as a novel species, for which the name Shewanella gaetbuli sp. nov. is proposed.

scholarly journals Herbaspirillum chlorophenolicum sp. nov., a 4-chlorophenol-degrading bacterium

2004 ◽  
Vol 54 (3) ◽  
pp. 851-855 ◽  
Author(s):  
Wan-Taek Im ◽  
Hee-Sung Bae ◽  
Akira Yokota ◽  
Sung Taik Lee
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Rdna Sequence ◽  
The Novel ◽  
Comamonas Testosteroni ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
Degrading Bacterium ◽  
16S Rdna Sequences ◽  
Type Strains

A 4-chlorophenol-degrading bacterial strain, formerly designated as a strain of Comamonas testosteroni, was reclassified as a member of the genus Herbaspirillum based on its phenotypic and chemotaxonomic characteristics, as well as phylogenetic analysis using 16S rDNA sequences. Phylogenetic inference based on 16S rDNA sequences showed that strain CPW301T clusters in a phylogenetic branch that contains Herbaspirillum species. 16S rDNA sequence similarity of strain CPW301T to species of the genus Herbaspirillum with validly published names is in the range 98·7–98·9 %. Despite the considerably high 16S rDNA sequence similarity, strain CPW301T could be distinguished clearly from type strains of Herbaspirillum species with validly published names by DNA–DNA relatedness values, which were <15·7 %. The genomic DNA G+C content of strain CPW301T is 61·3 mol%. The predominant ubiquinone is Q-8 and the major cellular fatty acids are C16 : 0 and cyclo-C17 : 0. The strain does not fix nitrogen and is not plant-associated. It is an aerobic rod with one unipolar flagellum. On the basis of these characteristics, a novel Herbaspirillum species, Herbaspirillum chlorophenolicum sp. nov., is proposed. The type strain of the novel species is strain CPW301T (=KCTC 12096T=IAM 15024T).

scholarly journals TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation

2017 ◽  
Author(s):  
Ali Z Ijaz ◽  
Thomas Jeffries ◽  
Christopher Quince ◽  
Kelly Hamonts ◽  
Brajesh Singh
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Marker Gene ◽  
Evolutionary Conservation ◽  
Rrna Gene ◽  
Similarity Metric ◽  
Rdna Sequences ◽  
Fine Grain ◽  
16S Rdna Sequences ◽  
Taxonomic Annotation

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both in-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects.

scholarly journals Collimonas fungivorans gen. nov., sp. nov., a chitinolytic soil bacterium with the ability to grow on living fungal hyphae

2004 ◽  
Vol 54 (3) ◽  
pp. 857-864 ◽  
Author(s):  
Wietse de Boer ◽  
Johan H. J. Leveau ◽  
George A. Kowalchuk ◽  
Paulien J. A. Klein Gunnewiek ◽  
Edwin C. A. Abeln ◽  
...  
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Biochemical Properties ◽  
Phylogenetic Position ◽  
Strictly Aerobic ◽  
Novel Genus ◽  
Physiological Characterization ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Wide Range

A polyphasic approach was used to describe the phylogenetic position of 22 chitinolytic bacterial isolates that were able to grow at the expense of intact, living hyphae of several soil fungi. These isolates, which were found in slightly acidic dune soils in the Netherlands, were strictly aerobic, Gram-negative rods. Cells grown in liquid cultures were flagellated and possessed pili. A wide range of sugars, alcohols, organic acids and amino acids could be metabolized, whereas several di- and trisaccharides could not be used as substrates. The major cellular fatty acids were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. DNA G+C contents were 57–62 mol%. Analysis of nearly full-length 16S rDNA sequences showed that the isolates were related closely to each other (>98·6 % sequence similarity) and could be assigned to the β-Proteobacteria, family ‘Oxalobacteraceae’, order ‘Burkholderiales’. The most closely related species belonged to the genera Herbaspirillum and Janthinobacterium, exhibiting 95·9–96·7 % (Herbaspirillum species) and 94·3–95·6 % (Janthinobacterium species) 16S rDNA sequence similarity to the isolates. Several physiological and biochemical properties indicated that the isolates could be distinguished clearly from both of these genera. Therefore, it is proposed that the isolates described in this study are representatives of a novel genus, Collimonas gen. nov. Genomic fingerprinting (BOX-PCR), detailed analysis of 16S rDNA patterns and physiological characterization (Biolog) of the isolates revealed the existence of four subclusters. The name Collimonas fungivorans gen. nov., sp. nov. has been given to one subcluster (four isolates) that appears to be in the centre of the novel genus; isolates in the other subclusters have been tentatively named Collimonas sp. The type strain of Collimonas fungivorans gen. nov., sp. nov. is Ter6T (=NCCB 100033T=LMG 21973T).

scholarly journals Characterization of a ‘Bacteroidetes’ symbiont in Encarsia wasps (Hymenoptera: Aphelinidae): proposal of ‘Candidatus Cardinium hertigii’

2004 ◽  
Vol 54 (3) ◽  
pp. 961-968 ◽  
Author(s):  
Einat Zchori-Fein ◽  
Steve J. Perlman ◽  
Suzanne E. Kelly ◽  
Nurit Katzir ◽  
Martha S. Hunter
Keyword(s):  
Electron Microscopy ◽  
16S Rdna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
16S Rdna Sequence ◽  
Rdna Sequences ◽  
16S Rdna Sequences

Previously, analysis of 16S rDNA sequences placed a newly discovered lineage of bacterial symbionts of arthropods in the ‘Bacteroidetes’. This symbiont lineage is associated with a number of diverse host reproductive manipulations, including induction of parthenogenesis in several Encarsia parasitoid wasps (Hymenoptera: Aphelinidae). In this study, electron microscopy and phylogenetic analysis of the 16S rRNA and gyrB genes of symbionts from Encarsia hispida and Encarsia pergandiella are used to describe and further characterize these bacteria. Phylogenetic analyses based on these two genes showed that the Encarsia symbionts are allied with the Cytophaga aurantiaca lineage within the ‘Bacteroidetes’, with their closest described relative being the acanthamoeba symbiont ‘Candidatus Amoebophilus asiaticus’. The Encarsia symbionts share 97 % 16S rDNA sequence similarity with Brevipalpus mite and Ixodes tick symbionts and 88 % sequence similarity with ‘Candidatus A. asiaticus’. Electron microscopy revealed that many of the bacteria found in the ovaries of the two Encarsia species contained a regular, brush-like array of microfilament-like structures that appear to be characteristic of the symbiont. Finally, the role of this bacterium in parthenogenesis induction in E. hispida was confirmed. Based on phylogenetic analyses and electron microscopy, classification of the symbionts from Encarsia as ‘Candidatus Cardinium hertigii’ is proposed.

scholarly journals Transfer of Bacillus ehimensis and Bacillus chitinolyticus to the genus Paenibacillus with emended descriptions of Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov.

2004 ◽  
Vol 54 (3) ◽  
pp. 929-933 ◽  
Author(s):  
Jung-Sook Lee ◽  
Yu-Ryang Pyun ◽  
Kyung Sook Bae
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rdna ◽  
Dna Hybridization ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Pcr Primers ◽  
Specific Pcr ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Paenibacillus Ehimensis

The taxonomic status of Bacillus ehimensis and Bacillus chitinolyticus was examined, based on their 16S rDNA sequences, DNA–DNA hybridization and other taxonomic characteristics. A phylogenetic analysis using 16S rDNA sequences revealed that the two species belong to the genus Paenibacillus. In particular, B. ehimensis KCTC 3748T and B. chitinolyticus KCTC 3791T were found to be phylogenetically closely related to Paenibacillus koreensis YC300T (98·3 % sequence similarity) and Paenibacillus chinjuensis WN9T (95·2 % sequence similarity), respectively. DNA–DNA hybridization values between B. ehimensis KCTC 3748T and P. koreensis YC300T were less than 26 %. An experiment using Paenibacillus-specific PCR primers, PAEN515F and 1377R, revealed that B. ehimensis and B. chitinolyticus had the same amplified 16S rDNA fragment as members of the genus Paenibacillus. Accordingly, it is proposed that B. ehimensis and B. chitinolyticus be transferred to the genus Paenibacillus as Paenibacillus ehimensis comb. nov. and Paenibacillus chitinolyticus comb. nov., respectively.

scholarly journals TaxaSE: Exploiting evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotation

2017 ◽  
Author(s):  
Ali Z Ijaz ◽  
Thomas Jeffries ◽  
Christopher Quince ◽  
Kelly Hamonts ◽  
Brajesh Singh
Keyword(s):  
16S Rdna ◽  
Sequence Similarity ◽  
Marker Gene ◽  
Evolutionary Conservation ◽  
Rrna Gene ◽  
Similarity Metric ◽  
Rdna Sequences ◽  
Fine Grain ◽  
16S Rdna Sequences ◽  
Taxonomic Annotation

Amplicon based taxonomic analysis, which determines the presence of microbial taxa in different environments on the basis of marker gene annotations, often uses percentage identity as the main metric to determine sequence similarity against databases. These data are then used to study the distribution of biodiversity as well as response of microbial communities to environmental conditions. However the 16S rRNA gene displays varying degrees of sequence conservation along its length and percentage identity does not fully utilize this information. Additionally, the prevalent usage of Operational Taxonomic Unit, or OTUs is not without its own issues and may lead to a reduction in annotation capability of the system. Hence a novel approach to taxonomic annotation is needed. Here we introduce a new taxonomic annotation pipeline, TaxaSE, which utilizes Shannon entropy to quantify evolutionary conservation within 16S rDNA sequences for enhanced taxonomic annotations. Furthermore, the system is capable of annotation of individual sequences in order to improve fine grain taxonomic annotations. We present both in-silico comparison of the new similarity metric with percentage identity, as well as comparison with the popular QIIME pipeline. The results demonstrate the new similarity metric achieves better performance especially at lower taxa levels. Furthermore, the pipeline is able to extract more fine grain taxonomic annotations compared to QIIME. These exhibit not only the effectiveness of the new pipeline but also highlight the need to shift away from both percentage identity and OTU based approaches for ecological projects.

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