Phylogenetic studies on uncultured Frankia populations in nodules of Datisca cannabina

1994 ◽  
Vol 40 (4) ◽  
pp. 313-318 ◽  
Author(s):  
M. Sajjad Mirza ◽  
Dittmar Hahn ◽  
Svetlana V. Dobritsa ◽  
Antoon D. L. Akkermans
Keyword(s):  
16S Rrna ◽  
Root Nodules ◽  
Alnus Glutinosa ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Phylogenetic Studies ◽  
Close Relationship ◽  
16S Rrna Sequence Analysis ◽  
Relationship Of ◽  
The 16S Rrna Gene

Part of the 16S rRNA gene was amplified directly from uncultured endophyte populations within the root nodules of Datisca cannabina and three strains isolated from nodules of Alnus glutinosa (AgKG′84/4), Coriaria nepalensis (Cn3), and D. cannabina (Dc2). Sequence comparison based on 930 nucleotides indicated that the endophyte of D. cannabina nodules belongs to the genus Frankia and is highly related to the endophyte of C. nepalensis root nodules. The relatedness of the endophytes of C. nepalensis and D. cannabina nodules was also reflected by closely related nifH sequences amplified from the nodules. 16S rRNA sequence analysis of the noninfective strains obtained from both D. cannabina (Dc2) and C. nepalensis (Cn3) nodules also revealed the close relationship of these strains to the genus Frankia.Key words: nitrogen fixation, Frankia, 16S rRNA, nifH.

scholarly journals Micromonospora pisi sp. nov., isolated from root nodules of Pisum sativum

2010 ◽  
Vol 60 (2) ◽  
pp. 331-337 ◽  
Author(s):  
Lorena C. Garcia ◽  
Eustoquio Martínez-Molina ◽  
Martha E. Trujillo
Keyword(s):  
Pisum Sativum ◽  
Gene Sequence ◽  
Root Nodules ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Close Relationship ◽  
Relationship Of ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain GUI 15T, isolated from the root nodules of a Pisum sativum plant was characterized taxonomically by using a polyphasic approach. The 16S rRNA gene sequence of strain GUI 15T showed highest similarity to Micromonospora pattaloongensis TJ2-2T (98.7 %) and Polymorphospora rubra TT 97-42T (98.5 %). Phylogenetic analysis based on the gyrase B gene also supported the close relationship of these three strains, but indicated that strain GUI 15T should be assigned to the genus Micromonospora. Chemotaxonomic results confirmed the position of the isolate in the genus Micromonospora, but revealed differences at the species level. The novel strain could be distinguished from recognized Micromonospora species by using a combination of physiological and biochemical tests. Based on these observations, strain GUI 15T is considered to represent a novel species of the genus Micromonospora, for which the name Micromonospora pisi sp. nov. is proposed. The type strain is GUI 15T (=DSM 45175T=LMG 24546T).

scholarly journals Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand

2007 ◽  
Vol 57 (5) ◽  
pp. 954-958 ◽  
Author(s):  
Soon-Wo Kwon ◽  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Youn-Kyung Baek ◽  
Seung-Joo Go
Keyword(s):  
16S Rrna ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Aerobic Bacterium ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Curved Rods ◽  
Taxonomic Approach ◽  
Seashore Sand ◽  
Sequence Similarities

A Gram-negative, aerobic bacterium, designated strain HO3-R19T, which was isolated from seashore sand in Pohang city, Korea, was characterized on the basis of a polyphasic taxonomic approach. Phylogenetic analyses of 16S rRNA gene sequences revealed that strain HO3-R19T represents a new lineage within the Gammaproteobacteria; sequence similarities between strain HO3-R19T and members of other related genera were less than 93.5 %. Strain HO3-R19T was also distinguished from related genera based on differences in several phenotypic characteristics. Cells were straight or slightly curved rods and formed white colonies on R2A agar. The major isoprenoid quinone was ubiquinone 8 (Q-8), and predominant cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and iso-C17 : 1 ω9c. The DNA G+C content of strain HO3-R19T was 65.0 mol%. Based on physiological, biochemical and chemotaxonomic traits together with results of comparative 16S rRNA sequence analysis, strain HO3-R19T is considered to represent a novel species in a new genus, for which the name Arenimonas donghaensis gen. nov., sp. nov. is proposed. The type strain of Arenimonas donghaensis is HO3-R19T (=KACC 11381T=DSM 18148T).

scholarly journals Mesorhizobium robiniae sp. nov., isolated from root nodules of Robinia pseudoacacia

2010 ◽  
Vol 60 (11) ◽  
pp. 2552-2556 ◽  
Author(s):  
Ping Fa Zhou ◽  
Wei Min Chen ◽  
Ge Hong Wei
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Root Nodules ◽  
Phylogenetic Analyses ◽  
Robinia Pseudoacacia ◽  
Rrna Gene ◽  
Gene Sequences ◽  
Type Strains ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Previously, five rhizobial strains isolated from root nodules of Robinia pseudoacacia were assigned to the same genospecies on the basis of identical 16S rRNA gene sequences and phylogenetic analyses of the nodA, nodC and nifH genes, in which the five isolates formed a well-supported group that excluded other sequences found in public databases. In this study, the 16S rRNA gene sequence similarities between the isolates and Mesorhizobium mediterraneum UPM-Ca36T and Mesorhizobium temperatum SDW018T were 99.5 and 99.6 %, respectively. The five isolates were also different from defined Mesorhizobium species using ERIC fingerprint profiles and they formed a novel Mesorhizobium lineage in phylogenetic analyses of recA and atpD gene sequences. DNA–DNA relatedness values between the representative strain, CCNWYC 115T, and type strains of defined Mesorhizobium species were found to be lower than 47.5 %. These results indicated that the isolates represented a novel genomic species. Therefore, a novel species, Mesorhizobium robiniae sp. nov., is proposed, with type strain CCNWYC 115T (=ACCC 14543T =HAMBI 3082T). Strain CCNWYC 115T can form effective nodules only on its original host.

scholarly journals Lysinibacillus Agricola sp. nov.Isolated from Soil

2021 ◽  
Author(s):  
Jia-Rui Lu ◽  
Guohong Liu
Keyword(s):  
16S Rrna ◽  
Dna Hybridization ◽  
Reference Strain ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Phenotypic Characters ◽  
Gram Staining ◽  
Farmland Soil ◽  
The 16S Rrna Gene

Abstract A Gram-staining-positive, rod-shaped cells, designed strain FJAT-51161T, was isolated from farmland soil collected from Fujian Province, China. Growth was observed at 25 - 40 °C (optimum 30 °C), pH 7.0-9.0 (optimum 7.0), and NaCl tolerance in the range of 0-7 % (w/v), respectively. Phylogenetic analysis based on the 16S rRNA gene sequences indicated that the strain FJAT-51161T belonged to the genus Lysinibacillus, and had the closest relationship with Lysinibacillus xylanilyticus XDB9T (with 99.0 % 16S rRNA sequence similarity). The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values based on the genome sequence analysis between strain FJAT-51161T and the closest reference strain were 38.0 % for dDDH and 88.7 % for ANI, respectively, lower than the prokaryotic species defined values. Further analysis showed that strain FJAT-51161T shared the fatty acid profiles such as iso-C15:0 (46.7%), iso-C16:0 (15.8%), C16:1 ω7c alcohol (14.0%), anteiso-C15:0 (6.9%) with other members of the genus Lysinibacillus. The peptidoglycan was L-Lys–D-Asp (type A4α). The main quinone was MK-7 and MK-6. The major polar lipids were diphosphatidylglycerol (DPG) and phosphatidylethanolamine (PE). The DNA G+C content is 36.6 mol%. Based on the phenotypic characters and taxono-genomics study, strain FJAT-51161T is considered to represent a novel Lysinibacillus species, for which the name Lysinibacillus agricola sp. nov. is proposed. The type strain is FJAT-51161T (= GDMCC1.2350T = KCTC XXXXXXT).

scholarly journals Comparative study on the diversity of endophytic actinobacteria communities from Ficus deltoidea using metagenomic and culturedependent approaches

2018 ◽  
Vol 19 (4) ◽  
pp. 1514-1520 ◽  
Author(s):  
ISRA JANATININGRUM ◽  
DEDY DURYADI SOLIHIN ◽  
ANJA MERYANDINI ◽  
YULIN LESTARI
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Comparative Study ◽  
Herbal Remedies ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Ficus Deltoidea ◽  
Close Relationship ◽  
The 16S Rrna Gene ◽  
Culture Dependent

Janatiningrum I, Solihin DD, Meryandini A, Lestari Y. 2018. Comparative study on the diversity of endophytic actinobacteriacommunities from Ficus deltoidea using metagenomic and culture-dependent approaches. Biodiversitas 19: 1514-1520. Actinobacteriaendophytes of medicinal plants may play an essential role in producing a variety of critical bioactive compounds. However, the possiblecontribution of such actinobacteria to the pharmacological properties of traditional herbal remedies remains mostly unknown. Forexample, the diversity and attributes of actinobacteria endophytes in Ficus deltoidea, a small tree species that has long been used to treatdiseases such as cancer, diabetes, and cardiovascular illnesses, have not been explored. Here, the actinobacteria endophyte communitystructure in F. deltoidea was investigated using both culture-dependent and metagenomics approaches. Based on morphologicalcharacteristics and 16S rRNA gene analysis, the dominant culturable actinobacteria isolates exhibited a close relationship withStreptomyces. The metagenomic technique using PCR-DGGE analysis of the 16S rRNA gene showed the presence of 11 OTUs in F.deltoidea tissue. Whereas the dominant culturable actinobacteria endophytes in F. deltoidea was Streptomyces, the metagenomicapproach showed non-Streptomyces, particularly Rhodococccus and Verrucosispora, to be also important. Thus, results from bothculture-dependent and metagenomic approaches provided useful indicators on the diversity and community structure of actinobacteriaendophytes in F. deltoidea.

Genome-based reclassification of Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii as later heterotypic synonyms of Caldicellulosiruptor acetigenus

2021 ◽  
Vol 71 (8) ◽  
Author(s):  
Neeli Habib ◽  
Manik Prabhu Narsing Rao ◽  
Min Xiao ◽  
Sohail Ahmad Jan ◽  
Wen-Jun Li
Keyword(s):  
16S Rrna ◽  
Type Species ◽  
Bacterial Species ◽  
Amino Acid Identity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
Relationship Of

The present study was carried out to re-clarify the taxonomic relationship of Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii . The 16S rRNA sequence similarities between these species of the genus Caldicellulosiruptor were above the threshold values (98.65%) for bacterial species delineation. Similarly, the digital DNA–DNA hybridization and average nucleotide and amino acid identity values were greater than the thresholds for bacterial species delineation. In phylogenetic (based on 16S rRNA gene sequences) and phylogenomic trees Caldicellulosiruptor acetigenus , Caldicellulosiruptor lactoaceticus and Caldicellulosiruptor kristjanssonii clade together. The results of our analysis indicated that these three taxa are conspecific. Therefore, Caldicellulosiruptor lactoaceticus Mladenovska et al. 1997 and Caldicellulosiruptor kristjanssonii Bredholt et al. 1999 should be reclassified as later heterotypic synonyms of Caldicellulosiruptor acetigenus (Nielsen et al. 1994) Onyenwoke et al. 2006.

scholarly journals Description of a new member of the family Erysipelotrichaceae: Dakotella fusiforme gen. nov., sp. nov., isolated from healthy human feces

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10071
Author(s):  
Sudeep Ghimire ◽  
Supapit Wongkuna ◽  
Joy Scaria
Keyword(s):  
16S Rrna ◽  
Optimal Growth ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
Healthy Human ◽  
Acid Product ◽  
The Family ◽  
Fatty Acid Product ◽  
Rrna Phylogeny ◽  
The 16S Rrna Gene

A Gram-positive, non-motile, rod-shaped facultative anaerobic bacterial strain SG502T was isolated from healthy human fecal samples in Brookings, SD, USA. The comparison of the 16S rRNA gene placed the strain within the family Erysipelotrichaceae. Within this family, Clostridium innocuum ATCC 14501T, Longicatena caecimuris strain PG-426-CC-2, Eubacterium dolichum DSM 3991T and E. tortuosum DSM 3987T(=ATCC 25548T) were its closest taxa with 95.28%, 94.17%, 93.25%, and 92.75% 16S rRNA sequence identities respectively. The strain SG502T placed itself close to C. innocuum in the 16S rRNA phylogeny. The members of genus Clostridium within family Erysipelotrichaceae was proposed to be reassigned to genus Erysipelatoclostridium to resolve the misclassification of genus Clostridium. Therefore, C. innocuum was also classified into this genus temporarily with the need to reclassify it in the future because of its difference in genomic properties. Similarly, genome sequencing of the strain and comparison with its 16S phylogenetic members and proposed members of the genus Erysipelatoclostridium, SG502T warranted a separate genus even though its 16S rRNA similarity was >95% when comapred to C. innocuum. The strain was 71.8% similar at ANI, 19.8% [17.4–22.2%] at dDDH and 69.65% similar at AAI to its closest neighbor C. innocuum. The genome size was nearly 2,683,792 bp with 32.88 mol% G+C content, which is about half the size of C. innocuum genome and the G+C content revealed 10 mol% difference. Phenotypically, the optimal growth temperature and pH for the strain SG502T were 37 °C and 7.0 respectively. Acetate was the major short-chain fatty acid product of the strain when grown in BHI-M medium. The major cellular fatty acids produced were C18:1ω9c, C18:0and C16:0. Thus, based on the polyphasic analysis, for the type strain SG502T (=DSM 107282T= CCOS 1889T), the name Dakotella fusiforme gen. nov., sp. nov., is proposed.

scholarly journals Characterization by 16S rRNA Sequence Analysis of Pseudomonads Causing Blotch Disease of Cultivated Agaricus bisporus

2001 ◽  
Vol 67 (9) ◽  
pp. 4316-4323 ◽  
Author(s):  
S. A. C. Godfrey ◽  
S. A. Harrow ◽  
J. W. Marshall ◽  
J. D. Klena
Keyword(s):  
16S Rrna ◽  
Agaricus Bisporus ◽  
Biochemical Analysis ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis ◽  
Brown Blotch ◽  
Repetitive Extragenic Palindromic Pcr

ABSTRACT Bacterial blotch of Agaricus bisporus has typically been identified as being caused by either Pseudomonas tolaasii (brown blotch) or Pseudomonas gingeri(ginger blotch). To address the relatedness of pseudomonads able to induce blotch, a pilot study was initiated in which pseudomonads were selectively isolated from mushroom farms throughout New Zealand. Thirty-three pseudomonad isolates were identified as being capable of causing different degrees of discoloration (separable into nine categories) of A. bisporus tissue in a bioassay. These isolates were also identified as unique using repetitive extragenic palindromic PCR and biochemical analysis. Relationships between these 33 blotch-causing organisms (BCO) and a further 22 selected pseudomonad species were inferred by phylogenetic analyses of near-full-length 16S rRNA gene nucleotide sequences. The 33 BCO isolates were observed to be distributed throughout thePseudomonas fluorescens intrageneric cluster. These results show that in addition to known BCO (P. tolaasii, P. gingeri, and Pseudomonas reactans), a number of diverse pseudomonad species also have the ability to cause blotch diseases with various discolorations. Furthermore, observation of ginger blotch discoloration of A. bisporus being independently caused by many different pseudomonad species impacts on the homogeneity and classification of the previously described P. gingeri.

scholarly journals 16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene

1998 ◽  
Vol 36 (6) ◽  
pp. 1761-1764 ◽  
Author(s):  
U. Reischl ◽  
K. Feldmann ◽  
L. Naumann ◽  
B. J. M. Gaugler ◽  
B. Ninet ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Fragment Length Polymorphism ◽  
Direct Sequencing ◽  
Rrna Gene ◽  
Polymorphism Analysis ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
The 16S Rrna Gene

Direct sequencing of the 16S rRNA gene (16S rDNA) ofMycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.

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