scholarly journals МОНГОЛ ОРНЫ ХӨРСНӨӨС ЯЛГАСАН АКТИНОМИЦЕТИЙН АНГИЛАЛЗҮЙН СУДАЛГААНЫ ДҮНГЭЭС

2016 ◽  
pp. 66-72
Author(s):  
Б Пагмадулам ◽  
Мониша Канна ◽  
Д Цэрэндулам ◽  
Ц Рэнцэнханд
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Characteristics ◽  
Genus Streptomyces ◽  
Streptomyces Ghanaensis ◽  
Preliminary Study ◽  
Type Strains

Soil samples were collected from Khentii and Tuv provinces in Mongolia. Two strains (N11, N22) were selected for polyphasic approach which including morphological, physiological and phylogenetic analysis. Phylogenetic analysis revealed that the strain N22 has highest the 16S rRNA similarity of 99.39% with Streptomyces ghanaensis NBRC 15414(T). The 16S rRNA genes sequence of 1418 nucleotides was generated for N11 and compared to the validly described species of genus Streptomyces as closest neighbors. Phylogenetic analysis revealed that the strain N11 has highest the 16S rRNA similarity of 98.51% with Streptomyces yerevanensis NBRC 12517(T). Also some phenotypic characteristics were different from type strains. Preliminary study shows that strain N11 might be new actinomycete species. However, need to determine the genetic distance between two microorganisms by using DNA-DNA hybridization methods.

Amplification of 16S rRNA genes of Anaplasma species in China for phylogenetic analysis

2005 ◽  
Vol 107 (1-2) ◽  
pp. 145-148 ◽  
Author(s):  
Zhijie Liu ◽  
Jianxun Luo ◽  
Qi Bai ◽  
Miling Ma ◽  
Guiguan Guan ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes

scholarly journals Responses of Active Ammonia Oxidizers and Nitrification Activity in Eutrophic Lake Sediments to Nitrogen and Temperature

2019 ◽  
Vol 85 (18) ◽  
Author(s):  
Ling Wu ◽  
Cheng Han ◽  
Guangwei Zhu ◽  
Wenhui Zhong
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Ammonia Oxidizing Bacteria ◽  
Ammonia Oxidizers ◽  
Nitrogen Input ◽  
Nitrification Activity ◽  
Ammonia Oxidizing Archaea ◽  
Nitrogen Inputs

ABSTRACTAmmonium concentrations and temperature drive the activities of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB), but their effects on these microbes in eutrophic freshwater sediments are unclear. In this study, surface sediments collected from areas of Taihu Lake (China) with different degrees of eutrophication were incubated under three levels of nitrogen input and temperature, and the autotrophic growth of ammonia oxidizers was assessed using13C-labeled DNA-based stable-isotope probing (SIP), while communities were characterized using MiSeq sequencing and phylogenetic analysis of 16S rRNA genes. Nitrification rates in sediment microcosms were positively correlated with nitrogen inputs, but there was no marked association with temperature. Incubation of SIP microcosms indicated that AOA and AOBamoAgenes were labeled by13C at 20°C and 30°C in the slightly eutrophic sediment, and AOBamoAgenes were labeled to a much greater extent than AOAamoAgenes in the moderately eutrophic sediment after 56 days. Phylogenetic analysis of13C-labeled 16S rRNA genes revealed that the active AOA were mainly affiliated with theNitrosopumiluscluster, with theNitrososphaeracluster dominating in the slightly eutrophic sediment at 30°C with low ammonium input (1 mM). Active AOB communities were more sensitive to nitrogen input and temperature than were AOA communities, and they were exclusively dominated by theNitrosomonascluster, which tended to be associated withNitrosomonadaceae-like lineages.Nitrosomonassp. strain Is79A3 tended to dominate the moderately eutrophic sediment at 10°C with greater ammonium input (2.86 mM). The relative abundance responses of the major active communities to nitrogen input and temperature gradients varied, indicating niche differentiation and differences in the physiological metabolism of ammonia oxidizers that are yet to be described.IMPORTANCEBoth archaea and bacteria contribute to ammonia oxidation, which plays a central role in the global cycling of nitrogen and is important for reducing eutrophication in freshwater environments. The abundance and activities of ammonia-oxidizing archaea and bacteria in eutrophic limnic sediments vary with different ammonium concentrations or with seasonal shifts, and how the two factors affect nitrification activity, microbial roles, and active groups in different eutrophic sediments is unclear. The significance of our research is in identifying the archaeal and bacterial responses to anthropogenic activity and climate change, which will greatly enhance our understanding of the physiological metabolic differences of ammonia oxidizers.

scholarly journals Census of the Viral Metagenome within an Activated Sludge Microbial Assemblage

2010 ◽  
Vol 76 (8) ◽  
pp. 2673-2677 ◽  
Author(s):  
Larissa C. Parsley ◽  
Erin J. Consuegra ◽  
Stephen J. Thomas ◽  
Jaysheel Bhavsar ◽  
Andrew M. Land ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Activated Sludge ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Isolates ◽  
Microbial Assemblage ◽  
Culture Independent ◽  
Culture Dependent

ABSTRACT The viral metagenome within an activated sludge microbial assemblage was sampled using culture-dependent and culture-independent methods and compared to the diversity of activated sludge bacterial taxa. A total of 70 unique cultured bacterial isolates, 24 cultured bacteriophages, 829 bacterial metagenomic clones of 16S rRNA genes, and 1,161 viral metagenomic clones were subjected to a phylogenetic analysis.

scholarly journals Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 249-253 ◽  
Author(s):  
Moriyuki Hamada ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
Ken-ichiro Suzuki ◽  
Masayuki Hayakawa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Type Strains

Two novel Gram-stain-positive bacteria, designated HR08-7T and HR08-43T, were isolated from a sea sediment sample from Rishiri Island, Hokkaido, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains HR08-7T and HR08-43T and the members of the genus Demequina formed a monophyletic cluster with similarity range of 95.5–99.0 %. The peptidoglycan type of strains HR08-7T and HR08-43T was A4β. The predominant menaquinone of both strains was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains HR08-7T and HR08-43T were 64.5 and 62.4 mol%, respectively. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences of strains HR08-7T and HR08-43T from the recognized Demequina species in phenotypic characteristics, indicate that the two strains merit classification as representatives of two novel species of the genus Demequina , for which the names Demequina flava sp. nov. and Demequina sediminicola sp. nov. are proposed; the type strains are HR08-7T ( = NBRC 105854T = DSM 24865T) and HR08-43T ( = NBRC 105855T = DSM 24867T), respectively.

Phylogenetic analysis of several Thermus strains from Rehai of Tengchong, Yunnan, China

2005 ◽  
Vol 51 (10) ◽  
pp. 881-886 ◽  
Author(s):  
Lianbing Lin ◽  
Jie Zhang ◽  
Yunlin Wei ◽  
Chaoyin Chen ◽  
Qian Peng
Keyword(s):  
Phylogenetic Analysis ◽  
Secondary Structure ◽  
16S Rrna ◽  
Hot Springs ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Structure Comparison ◽  
Rdna Sequences ◽  
16S Rdna Sequences ◽  
Rehai Geothermal Area

Several Thermus strains were isolated from 10 hot springs of the Rehai geothermal area in Tengchong, Yunnan province. The diversity of Thermus strains was examined by sequencing the 16S rRNA genes and comparing their sequences. Phylogenetic analysis showed that the 16S rDNA sequences from the Rehai geothermal isolates form four branches in the phylogenetic tree and had greater than 95.9% similarity in the phylogroup. Secondary structure comparison also indicated that the 16S rRNA from the Rehai geothermal isolates have unique secondary structure characteristics in helix 6, helix 9, and helix 10 (reference to Escherichia coli). This research is the first attempt to reveal the diversity of Thermus strains that are distributed in the Rehai geothermal area.Key words: Thermus, diversity, phylogenetic analysis, RNA secondary structure.

scholarly journals Description of Pelomonas aquatica sp. nov. and Pelomonas puraquae sp. nov., isolated from industrial and haemodialysis water

2007 ◽  
Vol 57 (11) ◽  
pp. 2629-2635 ◽  
Author(s):  
Margarita Gomila ◽  
Botho Bowien ◽  
Enevold Falsen ◽  
Edward R. B. Moore ◽  
Jorge Lalucat
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Type Strain ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Type Strains

Three Gram-negative, rod-shaped, non-spore-forming bacteria (strains CCUG 52769T, CCUG 52770 and CCUG 52771) isolated from haemodialysis water were characterized taxonomically, together with five strains isolated from industrial waters (CCUG 52428, CCUG 52507, CCUG 52575T, CCUG 52590 and CCUG 52631). Phylogenetic analysis based on 16S rRNA gene sequences indicated that these isolates belonged to the class Betaproteobacteria and were related to the genus Pelomonas, with 16S rRNA gene sequence similarities higher than 99 % with the only species of the genus, Pelomonas saccharophila and to Pseudomonas sp. DSM 2583. The type strains of Mitsuaria chitosanitabida and Roseateles depolymerans were their closest neighbours (97.9 and 97.3 % 16S rRNA gene sequence similarity, respectively). Phylogenetic analysis was also performed for the internally transcribed spacer region and for three genes [hoxG (hydrogenase), cbbL/cbbM (Rubisco) and nifH (nitrogenase)] relevant for the metabolism of the genus Pelomonas. DNA–DNA hybridization, major fatty acid composition and phenotypical analyses were carried out, which included the type strain of Pelomonas saccharophila obtained from different culture collections (ATCC 15946T, CCUG 32988T, DSM 654T, IAM 14368T and LMG 2256T), as well as M. chitosanitabida IAM 14711T and R. depolymerans CCUG 52219T. Results of DNA–DNA hybridization, physiological and biochemical tests supported the conclusion that strains CCUG 52769, CCUG 52770 and CCUG 52771 represent a homogeneous phylogenetic and genomic group, including strain DSM 2583, clearly differentiated from the industrial water isolates and from the Pelomonas saccharophila type strain. On the basis of phenotypic and genotypic characteristics, these strains belong to two novel species within the genus Pelomonas, for which the names Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are proposed. The type strains of Pelomonas puraquae sp. nov. and Pelomonas aquatica sp. nov. are CCUG 52769T (=CECT 7234T) and CCUG 52575T (=CECT 7233T), respectively.

Polyphasic analysis for elucidating the taxonomic position of selected unicellular marine cyanobacteria from Indian and Hong Kong coast

Phytotaxa ◽  
2017 ◽  
Vol 307 (4) ◽  
pp. 263
Author(s):  
T. BHUVANESHWARI ◽  
M. SHYLAJANACIYAR ◽  
P. ARUL PRAKASAM ◽  
K. EZHILMARAN ◽  
L. KARTHICK ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Evolutionary Relationship ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Internal Transcribed Spacer Region ◽  
Ultrastructural Studies ◽  
Marine Habitats

Cyanobacteria, the primordial oxygenic photosynthetic prokaryotes encompass a wide spectrum of morphologies and ecologies. The diversity of twelve marine unicellular cyanobacteria isolated from different marine habitats was analyzed morphologically. The evolutionary relationship among the investigated strains was examined by phylogenetic analysis of nearly complete 16S rRNA gene and 16-23S internal transcribed spacer region. Phylogenetic analysis of both 16S rRNA genes and internal spacer regions exhibited coherent clustering patterns. The genetic relatedness of the investigated strains was largely congruent with morphology-based taxonomic groupings. All the investigated strains possess both the types of tRNA (tRNAIle and tRNAAla) in their 16-23S internal spacer regions and significantly varied GC contents and spacer sequence lengths. Further, ultrastructural studies provide a more valuable insight into the cyanobacterial taxa studied. Our study helps to apply the polyphasic approach (use of morphology, ultra-structure, ecology, and molecular analysis of complete 16S rRNA genes and 16-23S internal spacer regions) to resolve taxonomic ambiguities and provide a fairly robust cyanobacterial classification system among the unicellular forms studied.

scholarly journals Streptococcus orisuis sp. nov., isolated from the pig oral cavity

2007 ◽  
Vol 57 (6) ◽  
pp. 1272-1275 ◽  
Author(s):  
Kazuko Takada ◽  
Masatomo Hirasawa
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Mutans Streptococci ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Oral Streptococci ◽  
The Novel ◽  
Bacterial Strains

Five bacterial strains, designated as NUM 1001T, NUM 1002, NUM 1003, NUM 1004 and NUM 1005, were isolated from the oral cavities of pigs. Colonies grown on mitis salivarius agar were similar in morphology to those of mutans streptococci. The novel isolates were analysed biochemically using the Rapid ID 32 Strep microsystem, subjected to DNA–DNA hybridization with oral streptococci and had their 16S rRNA genes sequenced. On the basis of the phylogenetic and phenotypic evidence obtained, the strains represent a novel species of the genus Streptococcus, for which the name Streptococcus orisuis sp. nov. is proposed. The type strain is NUM 1001T (=JCM 14035T=DSM 18307T).

Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 833-838 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiyo Shibata ◽  
Yuumi Ishida ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three novel Gram-stain-positive bacteria, designated IY07-20T, IY07-56T and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus Agromyces , with similarity range of 95.6–98.7 %. The isolates contained l-2,4-diaminobutylic acid, d-alanine, d-glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces . The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20T, IY07-56T and IY07-113 and the species of the genus Agromyces with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus Agromyces , for which the names Agromyces iriomotensis sp. nov. and Agromyces subtropica sp. nov. are proposed; the type strains are IY07-20T ( = NBRC 106452T = DSM 26155T) and IY07-56T ( = NBRC 106454T = DSM 26153T), respectively.

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