scholarly journals Rhizobium lusitanum sp. nov. a bacterium that nodulates Phaseolus vulgaris

2006 ◽  
Vol 56 (11) ◽  
pp. 2631-2637 ◽  
Author(s):  
Angel Valverde ◽  
José M. Igual ◽  
Alvaro Peix ◽  
Emilio Cervantes ◽  
Encarna Velázquez
Keyword(s):  
Phaseolus Vulgaris ◽  
Type Strain ◽  
Random Amplified Polymorphic Dna ◽  
Intergenic Spacer ◽  
Rrna Gene ◽  
Rhizobium Tropici ◽  
The Family ◽  
Dna Pattern ◽  
Macroptilium Atropurpureum ◽  
Type Strains

The species Phaseolus vulgaris is a promiscuous legume nodulated by several species of the family Rhizobiaceae. During a study of rhizobia nodulating this legume in Portugal, we isolated several strains that nodulate P. vulgaris effectively and also Macroptilium atropurpureum and Leucaena leucocephala, but they form ineffective nodules in Medicago sativa. According to phylogenetic analysis of the 16S rRNA gene sequence, the strains from this study belong to the genus Rhizobium, with Rhizobium rhizogenes and Rhizobium tropici as the closest related species, with 99.9 and 99.2 % similarity, respectively, between the type strains of these species and strain P1-7T. The nodD and nifH genes carried by strain P1-7T are phylogenetically related to those of other species nodulating Phaseolus. This strain does not carry virulence genes present in the type strain of R. rhizogenes, ATCC 11325T. Analysis of the recA and atpD genes confirms this phylogenetic arrangement, showing low similarity with respect to those of R. rhizogenes ATCC 11325T (91.9 and 94.1 % similarity, respectively) and R. tropici IIB CIAT 899T (90.6 % and 91.8 % similarity, respectively). The intergenic spacer (ITS) of the strains from this study is phylogenetically divergent from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, with 85.9 and 82.8 % similarity, respectively, with respect to strain P1-7T. The tRNA profile and two-primer random amplified polymorphic DNA pattern of strain P1-7T are also different from those of R. rhizogenes ATCC 11235T and R. tropici CIAT 899T. The strains isolated in this study can be also differentiated from R. rhizogenes and R. tropici by several phenotypic characteristics. The results of DNA–DNA hybridization showed means of 28 and 25 % similarity between strain P1-7T and R. rhizogenes ATCC 11235T and R. tropici CIAT 899T, respectively. All these data showed that the strains isolated in this study belong to a novel species of the genus Rhizobium, for which we propose the name Rhizobium lusitanum sp. nov.; the type strain is P1-7T (=LMG 22705T=CECT 7016T).

Taxonomic study of the genus Salinicola: transfer of Halomonas salaria and Chromohalobacter salarius to the genus Salinicola as Salinicola salarius comb. nov. and Salinicola halophilus nom. nov., respectively

2010 ◽  
Vol 60 (4) ◽  
pp. 963-971 ◽  
Author(s):  
Rafael R. de la Haba ◽  
Cristina Sánchez-Porro ◽  
M. Carmen Márquez ◽  
Antonio Ventosa
Keyword(s):  
16S Rrna ◽  
Type Strain ◽  
Phylogenetic Trees ◽  
23S Rrna ◽  
Rrna Gene ◽  
Gene Sequences ◽  
The Family ◽  
23S Rrna Gene ◽  
Single Genus ◽  
Type Strains

We have carried out a polyphasic taxonomic characterization of the type strains of the species with the recently validated name Salinicola socius, together with two species that were phylogenetically closely related, Halomonas salaria and Chromohalobacter salarius. 16S rRNA gene sequence analyses showed that they constituted a coherent cluster, with sequence similarities between 98.7 and 97.7 %. We have determined the almost complete 23S rRNA gene sequences of these three type strains, and the percentage of similarity between them was 99.2–97.6 %. Phylogenetic trees based on the 16S rRNA and 23S rRNA gene sequences, obtained by using three different algorithms, were consistent and showed that these three species constituted a cluster separated from the other species of the genera of the family Halomonadaceae, supporting their placement in a single genus. All three species have ubiquinone 9 as the major respiratory quinone, and showed similar fatty acid and polar lipid profiles. The level of DNA–DNA hybridization between Salinicola socius DSM 19940T, Halomonas salaria DSM 18044T and Chromohalobacter salarius CECT 5903T was 41–21 %, indicating that they are different species of the genus Salinicola. A comparative phenotypic study of these strains following the proposed minimal standards for describing new taxa of the family Halomonadaceae has been carried out. The phenotypic data are consistent with the placement of these three species in a single genus and support their differentiation at the species level. On the basis of these data we have emended the description of the species Salinicola socius and we propose to transfer the species Halomonas salaria and Chromohalobacter salarius to the genus Salinicola, as Salinicola salarius comb. nov. (type strain M27T =KCTC 12664T =DSM 18044T) and Salinicola halophilus nom. nov. (type strain CG4.1T =CECT 5903T =LMG 23626T), respectively.

scholarly journals Planifilum fimeticola gen. nov., sp. nov. and Planifilum fulgidum sp. nov., novel members of the family ‘Thermoactinomycetaceae’ isolated from compost

2005 ◽  
Vol 55 (5) ◽  
pp. 2101-2104 ◽  
Author(s):  
Kouta Hatayama ◽  
Hirofumi Shoun ◽  
Yasuichi Ueda ◽  
Akira Nakamura
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
Cellular Fatty Acid ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
16S Rrna Gene Sequences ◽  
The Family ◽  
Type Strains

Four thermophilic, Gram-positive strains, designated H0165T, 500275T, C0170 and 700375, were isolated from a composting process in Japan. The isolates grew aerobically at about 65 °C on a solid medium with formation of substrate mycelia; spores were produced singly along the mycelia. These morphological characters resembled those of some type strains of species belonging to the family ‘Thermoactinomycetaceae’, except that aerial mycelia were not formed. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest related species to the isolates were members of the family ‘Thermoactinomycetaceae’, but that the isolates formed an independent phylogenetic lineage. Some chemotaxonomic characters of the isolates, such as DNA G+C contents of 58·7–60·3 mol%, MK-7 as the major menaquinone and cellular fatty acid profiles, differed from those of members of the family ‘Thermoactinomycetaceae’. DNA–DNA hybridization showed that the isolates could be divided into two genomic groups, strain H0165T and the other three strains. These results indicated that the four isolates should be classified into two species of a novel genus in the family ‘Thermoactinomycetaceae’, for which the names Planifilum fimeticola gen. nov., sp. nov. (type strain H0165T=ATCC BAA-969T=JCM 12507T) and Planifilum fulgidum sp. nov. (type strain 500275T=ATCC BAA-970T=JCM 12508T) are proposed.

scholarly journals Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae

2007 ◽  
Vol 57 (2) ◽  
pp. 265-269 ◽  
Author(s):  
Shams Tabrez Khan ◽  
Yasuyoshi Nakagawa ◽  
Shigeaki Harayama
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Rrna Gene ◽  
Okinawa Island ◽  
Phenotypic Differences ◽  
Phylogenetic Studies ◽  
The Family ◽  
The City ◽  
Type Strains

Two Gram-negative, chemoheterotrophic, non-motile strains, Mok-1-36T and MAOS-86T, were isolated from marine-sediment samples collected from the coasts of Okinawa island and the city of Odawara in Japan, respectively. Phylogenetic studies based on 16S rRNA gene sequences indicated that Mok-1-36T and MAOS-86T were members of the family Flavobacteriaceae, clustering with members of the genera Ulvibacter and Vitellibacter, respectively. Strains Mok-1-36T and MAOS-86T shared pairwise 16S rRNA gene sequence similarities of 93.5 and 89.1 % with the type strains of Ulvibacter litoralis and Vitellibacter vladivostokensis, respectively. Phylogenetic distinctiveness and phenotypic differences from their phylogenetic neighbours indicated that these strains represent two novel species and genera within the family Flavobacteriaceae, for which the names Sediminibacter furfurosus gen. nov., sp. nov. (MAOS-86T) and Gilvibacter sediminis gen. nov., sp. nov. (Mok-1-36T) are proposed. The type strain of Sediminibacter furfurosus is MAOS-86T (=NBRC 101622T=CIP 109285T) and the type strain of Gilvibacter sediminis is Mok-1-36T (=NBRC 101626T=CIP 109286T).

scholarly journals Alistipes indistinctus sp. nov. and Odoribacter laneus sp. nov., common members of the human intestinal microbiota isolated from faeces

2010 ◽  
Vol 60 (6) ◽  
pp. 1296-1302 ◽  
Author(s):  
Fumiko Nagai ◽  
Masami Morotomi ◽  
Yohei Watanabe ◽  
Hiroshi Sakon ◽  
Ryuichiro Tanaka
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The Family ◽  
End Products ◽  
Type Strains

Two anaerobic, non-spore-forming, non-motile, Gram-negative-staining bacteria, strains YIT 12060T and YIT 12061T, were isolated from human faeces. Cells of strain YIT 12060T were coccoid to rod-shaped with round ends, positive for catalase, negative for indole and oxidase production, produced succinic and acetic acids as end products of glucose metabolism in peptone/yeast extract/glucose medium and had a DNA G+C content of 55.2 mol%. The main respiratory quinones were MK-10 (40 %) and MK-11 (57 %). Fatty acid analysis demonstrated the presence of a high concentration of iso-C15 : 0 (56 %). Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to species of the genus Alistipes, with 90.9–92.6 % gene sequence similarities to type strains of this species. Phylogenetic analysis and biochemical data supported the affiliation of strain YIT 12060T to the genus Alistipes of the family ‘Rikenellaceae’. Strain YIT 12060T therefore represents a novel species of the genus Alistipes for which the name Alistipes indistinctus sp. nov. is proposed; the type strain is YIT 12060T (=DSM 22520T=JCM 16068T). Cells of the other isolate, strain YIT 12061T, were pleomorphic rods that were asaccharolytic, catalase- and oxidase-negative, positive for gelatin hydrolysis and indole production, produced small amounts of succinic, acetic and iso-valeric acids as end products of metabolism in peptone/yeast extract medium and had a DNA G+C content of approximately 42.4 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family ‘Porphyromonadaceae’ and related to the type strains of Odoribacter splanchnicus (89.6 %) and Odoribacter denticanis (86.2 %); similarity values with strains of recognized species within the family ‘Porphyromonadaceae’ were less than 84 %. Biochemical data supported the affiliation of strain YIT 12061T to the genus Odoribacter. Strain YIT 12061T therefore represents a novel species for which the name Odoribacter laneus sp. nov. is proposed; the type strain is YIT 12061T (=DSM 22474T=JCM 16069T).

Halovivax ruber sp. nov., an extremely halophilic archaeon isolated from Lake Xilinhot, Inner Mongolia, China

2007 ◽  
Vol 57 (5) ◽  
pp. 1024-1027 ◽  
Author(s):  
A. M. Castillo ◽  
M. C. Gutiérrez ◽  
M. Kamekura ◽  
Y. Xue ◽  
Y. Ma ◽  
...  
Keyword(s):  
Inner Mongolia ◽  
Type Strain ◽  
Lipid Analysis ◽  
Rrna Gene ◽  
Halophilic Archaeon ◽  
Physiological Characterization ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Extremely Halophilic Archaeon ◽  
Type Strains

A Gram-negative, pleomorphic, extremely halophilic archaeon, designated strain XH-70T, was isolated from the saline Lake Xilinhot, in Inner Mongolia, China. It formed small (0.9–1.5 mm), red-pigmented, elevated colonies on agar medium. The strain required at least 2.5 M NaCl and 5 mM Mg2+ for growth. The 16S rRNA gene sequence analysis indicated that strain XH-70T belongs to the family Halobacteriaceae, showing 99.5 % similarity to the type strain of Halovivax asiaticus and 94.7 and 94.6 % similarity, respectively, to the type strains of Natronococcus amylolyticus and Natronococcus occultus. Polar lipid analysis supported the placement of strain XH-70T in the genus Halovivax. DNA–DNA hybridization studies (32 % with Halovivax asiaticus CGMCC 1.4248T), as well as biochemical and physiological characterization, allowed strain XH-70T to be differentiated from Halovivax asiaticus. A novel species, Halovivax ruber sp. nov., is therefore proposed to accommodate this strain. The type strain is XH-70T (=CGMCC 1.6204T=DSM 18193T=JCM 13892T).

scholarly journals Paenibacillus ginsengarvi sp. nov., isolated from soil from ginseng cultivation

2007 ◽  
Vol 57 (8) ◽  
pp. 1810-1814 ◽  
Author(s):  
Min-Ho Yoon ◽  
Leonid N. Ten ◽  
Wan-Taek Im
Keyword(s):  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
The Family ◽  
Ginseng Cultivation ◽  
Type Strains

A Gram-positive, aerobic, non-motile, rod-shaped, spore-forming bacterium, designated Gsoil 139T, was isolated from soil from a ginseng field in Pocheon Province, South Korea, and was characterized using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil 139T belongs to the family Paenibacillaceae. The greatest sequence similarity was found with respect to the type strains of Paenibacillus hodogayensis (95.6 %) and Paenibacillus koleovorans (93.8 %). The strain showed less than 93.8 % sequence similarity with respect to other species of the genus Paenibacillus. The G+C content of the genomic DNA was 48.1 mol%. In addition, the presence of MK-7 as the major menaquinone and C15 : 0 anteiso as a major fatty acid (27.9 %) justifies its affiliation to the genus Paenibacillus. On the basis of its phenotypic characteristics and phylogenetic distinctiveness, strain Gsoil 139T represents a novel species within the genus Paenibacillus, for which the name Paenibacillus ginsengarvi sp. nov. is proposed. The type strain is Gsoil 139T (=KCTC 13059T =DSM 18677T).

scholarly journals Fontibacter flavus gen. nov., sp. nov., a member of the family ‘Cyclobacteriaceae’, isolated from a hot spring

2010 ◽  
Vol 60 (9) ◽  
pp. 2066-2070 ◽  
Author(s):  
Peter Kämpfer ◽  
Chiu-Chung Young ◽  
Wen-Ming Chen ◽  
P. D. Rekha ◽  
Kerstin Fallschissel ◽  
...  
Keyword(s):  
Type Strain ◽  
Hot Spring ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Novel ◽  
Polar Lipid Profile ◽  
Bright Orange ◽  
The Family ◽  
Southern Taiwan ◽  
Type Strains

The taxonomic position of a bright orange-pigmented bacterial strain, designated CC-GZM-130T, isolated from a water sample of the Guan-zing-ling hot spring, southern Taiwan, was studied. The strain was able to grow on nutrient agar at 25–40 °C and in the presence of 1–3 % (w/v) NaCl. Comparative analyses of the 16S rRNA gene sequence showed that the isolate was grouped in the vicinity of the genus Aquiflexum with the highest sequence similarity of 92.1 % to the type strain of Aquiflexum balticum, followed by sequence similarities of 92.0, 91.6 and 91.5 % to the type strains of Algoriphagus ornithinivorans, Algoriphagus hitonicola and Belliella baltica, respectively. The polyamine pattern showed that the major compound was sym-homospermidine. The quinone system was menaquinone MK-7. The polar lipid profile was composed predominantly of phosphatidylethanolamine, three polar lipids and one aminolipid. Minor amounts of other lipids were also detectable. The main characteristics of the fatty acid profiles of strain CC-GZM-130T, B. baltica and Aquiflexum balticum were similar, with iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH as the major fatty acids, but some qualitative and quantitative differences were observed. The DNA G+C content of the novel strain was 53.2 mol%. The isolate clearly differed genotypically and phenotypically from representatives of the most closely related genera. On the basis of these differences, a novel species in a new genus, Fontibacter flavus gen. nov., sp. nov., is proposed with CC-GZM-130T (=CCUG 57694T=CCM 7650T) as the type strain of the type species.

scholarly journals Nocardia goodfellowii sp. nov. and Nocardia thraciensis sp. nov., isolated from soil

2012 ◽  
Vol 62 (Pt_6) ◽  
pp. 1228-1234 ◽  
Author(s):  
Anil Sazak ◽  
Nevzat Sahin ◽  
Mustafa Camas
Keyword(s):  
Type Strain ◽  
Type Species ◽  
Rrna Gene ◽  
Phenotypic Data ◽  
Content Type ◽  
Link Type ◽  
Soil Actinomycetes ◽  
Gene Sequence Analysis ◽  
The Family ◽  
Type Strains

The taxonomic position of two soil actinomycetes, strains A2012T and A2019T, isolated from Turkish soils, was determined using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that the strains belonged to the family Nocardiaceae . Strains A2012T and A2019T were most closely related to Nocardia caishijiensis DSM 44831T (98.9 %) and Nocardia mexicana CIP 108295T (98.6 %), respectively; similarity to other type strains of the genus Nocardia ranged from 96.9 to 97.9 %. However, DNA–DNA relatedness and phenotypic data demonstrated that strains A2012T and A2019T could be clearly distinguished from members of the most closely related Nocardia species. It is evident from the genotypic and phenotypic data that the two isolates represent two novel species of the genus Nocardia . It is proposed, therefore, that strains A2012T and A2019T be classified in the genus Nocardia as representatives of Nocardia goodfellowii sp. nov. (type strain A2012T = DSM 45516T = NRRL B-24833T = KCTC 19986T) and Nocardia thraciensis sp. nov. (type strain A2019T = DSM 45517T = NRRL B-24834T = KCTC 19985T), respectively.

scholarly journals Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov.

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3636-3643 ◽  
Author(s):  
H. Christensen ◽  
W. Nicklas ◽  
M. Bisgaard
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
New Genus ◽  
Gene Sequence ◽  
Published Data ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Type Strains

Eleven strains from hamster of Bisgaard taxa 23 and 24, also referred to as Krause’s groups 2 and 1, respectively, were investigated by a polyphasic approach including data published previously. Strains showed small, regular and circular colonies with smooth and shiny appearance, typical of members of the family Pasteurellaceae . The strains formed two monophyletic groups based on 16S rRNA gene sequence comparison to other members of the family Pasteurellaceae . Partial rpoB sequencing as well as published data on DNA–DNA hybridization showed high genotypic relationships within both groups. Menaquinone 7 (MK7) was found in strains of both groups as well as an unknown ubiquinone with shorter chain length than previously reported for any other member of the family Pasteurellaceae . A new genus with one species, Mesocricetibacter intestinalis gen. nov., sp. nov., is proposed to accommodate members of taxon 24 of Bisgaard whereas members of taxon 23 of Bisgaard are proposed to represent Cricetibacter osteomyelitidis gen. nov., sp. nov. Major fatty acids of type strains of type species of both genera are C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0. The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae . The type strain of Mesocricetibacter intestinalis is HIM 933/7T ( = Kunstyr 246/85T = CCUG 28030T = DSM 28403T) while the type strain of Cricetibacter osteomyelitidis is HIM943/7T ( = Kunstyr 507/85T = CCUG 36451T = DSM 28404T).

scholarly journals Reclassification of Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus as Archangium disciforme comb. nov., Archangium minus comb. nov. and Archangium violaceum comb. nov., unification of the families Archangiaceae and Cystobacteraceae, and emended descriptions of the families Myxococcaceae and Archangiaceae

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4032-4042 ◽  
Author(s):  
Elke Lang ◽  
Peter Schumann ◽  
Brian J. Tindall ◽  
Kathrin I. Mohr ◽  
Cathrin Spröer
Keyword(s):  
Type Strain ◽  
Rrna Gene ◽  
Monophyletic Cluster ◽  
The Family ◽  
Group A ◽  
Respective Type ◽  
Fatty Acid Patterns ◽  
Close Relatedness ◽  
Type Strains ◽  
The 16S Rrna Gene

The species Archangium gephyra, Angiococcus disciformis, Cystobacter minus and Cystobacter violaceus are currently classified in three different genera of the order Myxococcales. The 16S rRNA gene sequences of the respective type strains show a similarity higher than 98.4 % and form a tight phylogenetic group. A dendrogram calculating the similarity of MALDI-TOF spectra confirmed the close relatedness of the four species that grouped in a monophyletic cluster in the neighbourhood of other species of the genus Cystobacter. The type strains shared similar fatty acid patterns of high complexity with iso-C15 : 0, C16 : 1ω5c and iso-C14 : 0 3-OH as the major components. The vegetative cells of these species are uniformly long needle-shaped rods, and the myxospores are short rods, ovoid or irregularly spherical thus differing from the myxospores of species related to Cystobacter fuscus, the type species of this genus. Some enzymic and hydrolysing reactions of the type strains are described. As a result of the high relatedness and similarity of the four species, it is proposed to place them into one genus, and due to phylogenetic and morphological distinctness, the species should be classified in a genus distinct from the genus Cystobacter as Archangium gephyra (type strain M18T = DSM 2261T = ATCC 25201T = NBRC 100087T), Archangium disciforme comb. nov. (type strain CMU 1T = DSM 52716T = ATCC 33172T), Archangium minus comb. nov. (proposed neotype strain Cb m2 = DSM 14751 = JCM 12627) and Archangium violaceum comb. nov. (type strain Cb vi61T = DSM 14727T = CIP 109131T = JCM 12629T). Since the family Archangiaceae Jahn 1924 AL has priority over the family Cystobacteraceae McCurdy 1970 AL, it is proposed to assign the genera Archangium, Anaeromyxobacter, Cystobacter, Hyalangium, Melittangium and Stigmatella to the family Archangiaceae. Emended descriptions of the families Myxococcaceae and Archangiaceae are also provided.

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