Phylogenetic Analysis of Members of the Genus Vibrios Based on gyrB Genes and 16S rRNA Genes

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.

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Census of the Viral Metagenome within an Activated Sludge Microbial Assemblage

Applied and Environmental Microbiology ◽

10.1128/aem.02520-09 ◽

2010 ◽

Vol 76 (8) ◽

pp. 2673-2677 ◽

Cited By ~ 37

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.

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

Canadian Journal of Microbiology ◽

10.1139/w05-087 ◽

2005 ◽

Vol 51 (10) ◽

pp. 881-886 ◽

Cited By ~ 9

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.

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

Phytotaxa ◽

10.11646/phytotaxa.307.4.4 ◽

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.

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МОНГОЛ ОРНЫ ХӨРСНӨӨС ЯЛГАСАН АКТИНОМИЦЕТИЙН АНГИЛАЛЗҮЙН СУДАЛГААНЫ ДҮНГЭЭС

Proceedings of the Mongolian Academy of Sciences ◽

10.5564/pmas.v56i3.692 ◽

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.

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α-Proteobacterial Symbionts of Marine Bryozoans in the Genus Watersipora

Applied and Environmental Microbiology ◽

10.1128/aem.00604-06 ◽

2006 ◽

Vol 73 (1) ◽

pp. 303-311 ◽

Cited By ~ 33

Author(s):

Christine M. Anderson ◽

Margo G. Haygood

Keyword(s):

Phylogenetic Analysis ◽

In Situ Hybridization ◽

16S Rrna ◽

Fluorescence In Situ Hybridization ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Symbionts ◽

California Coast ◽

Specific Fluorescence

ABSTRACT Bacterial symbionts that resembled mollicutes were discovered in the marine bryozoan Watersipora arcuata in the 1980s. In this study, we used PCR and sequencing of 16S rRNA genes, specific fluorescence in situ hybridization, and phylogenetic analysis to determine that the bacterial symbionts of “W. subtorquata” and “W. arcuata” from several locations along the California coast are actually closely related α-Proteobacteria, not mollicutes. We propose the names “Candidatus Endowatersipora palomitas” and “Candidatus Endowatersipora rubus” for the symbionts of “W. subtorquata” and “W. arcuata,” respectively.

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Phylogenetic Analysis of Four Vibrio Strains of Pathogenic Bacteria Based on Hemolysin Genes and 16S rRNA Genes

2009 3rd International Conference on Bioinformatics and Biomedical Engineering ◽

10.1109/icbbe.2009.5163190 ◽

2009 ◽

Author(s):

Xiuli Wang ◽

Ye Yuan ◽

Hongyue Wang ◽

Qunlan Zhou ◽

Jian Zhu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Pathogenic Bacteria ◽

16S Rrna Genes ◽

Rrna Genes

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Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

BMC Bioinformatics ◽

10.1186/s12859-016-0992-y ◽

2016 ◽

Vol 17 (1) ◽

Cited By ~ 171

Author(s):

Bo Yang ◽

Yong Wang ◽

Pei-Yuan Qian

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Hypervariable Regions

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Phylogenetic Analysis of 16S rRNA Genes and PCR Analysis of the nec1 Gene from Streptomyces spp. Causing Common Scab, Pitted Scab, and Netted Scab in Finland

Phytopathology ◽

10.1094/phyto.1999.89.6.462 ◽

1999 ◽

Vol 89 (6) ◽

pp. 462-469 ◽

Cited By ~ 64

Author(s):

Jan F. Kreuze ◽

Sini Suomalainen ◽

Lars Paulin ◽

Jari P. T. Valkonen

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

Common Scab ◽

Potato Scab ◽

16S Rrna Genes ◽

Rrna Genes ◽

Pcr Analysis ◽

Xylose Utilization ◽

Pitted Scab ◽

Netted Scab

The sequences of the 16S rRNA genes (nucleotides 29 to 1,521) from various Streptomyces strains pathogenic to potato were compared. These included 10 pathogenic Streptomyces strains isolated from potato scab lesions in Finland, the type strains of S. aureofaciens NRRL 2209T and S. lydicus ATCC 25470T, ‘S. griseus subsp. scabies’ ATCC 10246, and two S. griseus strains that were originally deposited to the collection as pathogens. The nucleotide sequence (>94.5% sequence identity [SI]) and length (1,469 to 1,481 nucleotides) of the analyzed region varied. Phylogenetic analysis of 16S rRNA genes placed Finnish strains into three species, supported by previously characterized morphological and physiological traits. Six Finnish strains, including two strains that deviated from the others in one trait (no spiral sporophores or D-xylose utilization), had identical 16S rRNA genes and were identified as S. scabies (99.9% SI to S. scabies ATCC 49173). Three Finnish strains were identified as S. turgidiscabies, a species previously described only in Japan (99.9% SI to S. turgidiscabies ATCC 700248). Finnish strain 317 and S. aureofaciens NRRL 2209 (99.8% SI) were placed in a distinct phylogenetic cluster together with Kitosatospora spp., which suggests that S. aureofaciens may belong to the recently revived genus Kitosatospora. In pathogenicity tests, S. scabies caused characteristic symptoms of common scab, S. turgidiscabies caused mainly pitted scab, and S. aureofaciens caused netted scab and necrotic lesions on stolons of potato cultivars Bintje and Matilda in the greenhouse. The nec1 gene and the intergenic region between nec1 and the 5′ transposase pseudogene ORFtnp were successfully amplified by polymerase chain reaction from S. scabies ATCC 49173 and the pathogenic Finnish strains of S. scabies, but not from a nonpathogenic strain of S. scabies, three pathogenic and two nonpathogenic strains of S. turgidiscabies, and S. aureofaciens.

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