scholarly journals Mesorhizobium waimense sp. nov. isolated from Sophora longicarinata root nodules and Mesorhizobium cantuariense sp. nov. isolated from Sophora microphylla root nodules

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3419-3426 ◽  
Author(s):  
Sofie E. De Meyer ◽  
Heng Wee Tan ◽  
Peter B. Heenan ◽  
Mitchell Andrews ◽  
Anne Willems
Keyword(s):  
Phylogenetic Trees ◽  
Root Nodules ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Fatty Acid Profiles ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Mesorhizobium Loti ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

In total 14 strains of Gram-stain-negative, rod-shaped bacteria were isolated from Sophora longicarinata and Sophora microphylla root nodules and authenticated as rhizobia on these hosts. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, and the strains from S. longicarinata were most closely related to Mesorhizobium amorphae ACCC 19665T (99.8–99.9 %), Mesorhizobium huakuii IAM 14158T (99.8–99.9 %), Mesorhizobium loti USDA 3471T (99.5–99.9 %) and Mesorhizobium septentrionale SDW 014T (99.6–99.8 %), whilst the strains from S. microphylla were most closely related to Mesorhizobium ciceri UPM-Ca7T (99.8–99.9 %), Mesorhizobium qingshengii CCBAU 33460T (99.7 %) and Mesorhizobium shangrilense CCBAU 65327T (99.6 %). Additionally, these strains formed two distinct groups in phylogenetic trees of the housekeeping genes glnII, recA and rpoB. Chemotaxonomic data, including fatty acid profiles, supported the assignment of the strains to the genus Mesorhizobium and allowed differentiation from the closest neighbours. Results of DNA–DNA hybridizations, MALDI-TOF MS analysis, ERIC-PCR, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from their closest neighbouring species. Therefore, the strains isolated from S. longicarinata and S. microphylla represent two novel species for which the names Mesorhizobium waimense sp. nov. (ICMP 19557T = LMG 28228T = HAMBI 3608T) and Mesorhizobium cantuariense sp. nov. (ICMP 19515T = LMG 28225T = HAMBI 3604T), are proposed respectively.

scholarly journals Burkholderia sprentiae sp. nov., isolated from Lebeckia ambigua root nodules

2013 ◽  
Vol 63 (Pt_11) ◽  
pp. 3950-3957 ◽  
Author(s):  
Sofie E. De Meyer ◽  
Margo Cnockaert ◽  
Julie K. Ardley ◽  
Garth Maker ◽  
Ron Yates ◽  
...  
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Similarity ◽  
Root Nodules ◽  
Distinct Group ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type

Seven Gram-stain-negative, rod-shaped bacteria were isolated from Lebeckia ambigua root nodules and authenticated on this host. Based on the 16S rRNA gene phylogeny, they were shown to belong to the genus Burkholderia , with the representative strain WSM5005T being most closely related to Burkholderia tuberum (98.08 % sequence similarity). Additionally, these strains formed a distinct group in phylogenetic trees based on the housekeeping genes gyrB and recA. Chemotaxonomic data including fatty acid profiles and analysis of respiratory quinones supported the assignment of the strains to the genus Burkholderia . Results of DNA–DNA hybridizations, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of our strains from the closest species of the genus Burkholderia with a validly published name. Therefore, these strains represent a novel species for which the name Burkholderia sprentiae sp. nov. (type strain WSM5005T = LMG 27175T = HAMBI 3357T) is proposed.

scholarly journals Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia

2006 ◽  
Vol 56 (10) ◽  
pp. 2381-2385 ◽  
Author(s):  
Martha E. Trujillo ◽  
Reiner M. Kroppenstedt ◽  
Peter Schumann ◽  
Lorena Carro ◽  
Eustoquio Martínez-Molina
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Root Nodules ◽  
Rrna Gene ◽  
The Novel ◽  
Biochemical Tests ◽  
Actinomycete Strain ◽  
Type Strains ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

An actinomycete strain, NAR01T, was isolated from root nodules of a Coriaria plant. The 16S rRNA gene sequence of strain NAR01T showed most similarity to the type strains of Micromonospora endolithica (98.94 %) and Micromonospora chersina (98.4 %). The chemotaxonomic results obtained confirmed the taxonomic position of the isolate within the genus Micromonospora, and revealed differences at the species level. Physiological and biochemical tests showed that strain NAR01T could be clearly distinguished from its closest phylogenetic neighbours, while DNA–DNA hybridization results indicated that the isolate represents a novel species. On the basis of these results, strain NAR01T (=DSM 44875T=LMG 23557T) is proposed as the type strain of the novel species Micromonospora coriariae sp. nov.

scholarly journals Halomonas vilamensis sp. nov., isolated from high-altitude Andean lakes

2011 ◽  
Vol 61 (5) ◽  
pp. 1211-1217 ◽  
Author(s):  
Rodolfo Javier Menes ◽  
Claudia Elizabeth Viera ◽  
María Eugenia Farías ◽  
Manfredo J. Seufferheld
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Limited Range ◽  
Hypersaline Lake ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
Phenotypic Differentiation ◽  
Physiological And Biochemical ◽  
The 16S Rrna Gene

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming bacterium (SV325T) was isolated from the sediment of a hypersaline lake located 4600 m above sea level (Laguna Vilama, Argentina). Strain SV325T formed cream to pink colonies, was motile and moderately halophilic, and tolerated NaCl concentrations of 1–25 % (w/v) with an optimum of 5–10 % (w/v). Growth occurred at 5–40 °C (optimum around 30 °C) and at pH 5.0–10.0 (optimum 7.0–8.0). The bacterium did not produce exopolysaccharides and stained positively for intracellular polyphosphate granules but not for poly-β-hydroxyalkanoates. It produced catalase and oxidase, reduced nitrate to nitrite, hydrolysed gelatin, did not produce acids from sugars and utilized a limited range of substrates as carbon and energy sources: acetate, caproate, fumarate, dl-β-hydroxybutyrate, malate, maleate, malonate and succinate. The predominant ubiquinones were Q-9 (92.5 %) and Q-8 (7.5 %), the major fatty acids were C19 : 0 cyclo ω8c, C16 : 0, C17 : 0 cyclo and C16 : 1ω7c/iso-C15:0 2-OH, and the DNA G+C content was 55.0 mol%. Phylogenetic analyses based on the 16S rRNA gene indicated that strain SV325T belongs to the genus Halomonas in the class Gammaproteobacteria. Physiological and biochemical tests allowed phenotypic differentiation of strain SV325T from closely related species with validly published names. We therefore propose a novel species, Halomonas vilamensis sp. nov., with type strain SV325T ( = DSM 21020T  = LMG 24332T).

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 Catellatospora sichuanensis sp. nov., a novel actinobacterium isolated from soil

2020 ◽  
Vol 70 (5) ◽  
pp. 3309-3315 ◽  
Author(s):  
Chaolan Liu ◽  
Yidong Guo ◽  
Li Li ◽  
Xiwei Wang ◽  
Jiafu Lin ◽  
...  
Keyword(s):  
Type Species ◽  
Phylogenetic Trees ◽  
Distinct Species ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Content Type ◽  
Link Type ◽  
Pr China ◽  
Physiological And Biochemical

A novel actinobacterium, designated strain H14505T, was isolated from a soil sample collected in Hong Yuan, Sichuan, southwest PR China. The temperature, pH and NaCl ranges for growth were determined to be 15–35 °C (optimum, 28 °C), 6.0–8.0 (optimum, pH 7.0) and 0–2 % (w/v; optimum without NaCl), respectively. The polar lipdis detected for strain H14505T were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, glycolipid and four unidentified lipids. The predominant menaquinones of strain H14505T were MK-9(H4) and MK-9(H6), and the prevalent fatty acids (>10 %) were C18 : 1 ω9c, C17 : 1 ω8c, summed feature 5 (anteiso-C18 : 0/ C18 : 2 ω6,9c) and C16 : 0. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences indicated that strain H14505T showed high similarity to Catellatospora vulcania NEAU-JM1T (99.0 %) and Catellatospora paridis NEAU-CL2T (99.0 %), and formed a monophyletic clade within the the genus Catellatospora in the phylogenetic trees. However, the average nucleotide indentity and DNA–DNA hybridization values between strain H14505T and closely related Catellatospora species showed that it belonged to a distinct species. Furthermore, the results of morphological, physiological and biochemical tests allowed further phenotypic differentiation of strain H14505T from its closest relatives. Thus, it is proposed that strain H14505T represents a novel species of the genus Catellatospora , for which the name Catellatospora sichuanensis sp. nov. is proposed. The type strain of Catellatospora sichuanensis is H14505T (=JCM 32394T=CICC 11042T).

scholarly journals Streptomyces qinglanensis sp. nov., isolated from mangrove sediment

2012 ◽  
Vol 62 (Pt_3) ◽  
pp. 596-600 ◽  
Author(s):  
Huo Hu ◽  
Hai-Peng Lin ◽  
Qingyi Xie ◽  
Lei Li ◽  
Xin-Qiang Xie ◽  
...  
Keyword(s):  
Aerial Mycelium ◽  
Diaminopimelic Acid ◽  
Mangrove Sediment ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Phenotypic Differentiation ◽  
Mangrove Soil ◽  
Type Strains ◽  
Physiological And Biochemical

A Streptomyces-like strain, 172205T, was obtained from mangrove soil collected at Qinglan Harbour, Wenchang, Hainan, China. The strain was characterized by white aerial mycelium and long spore chains. Comparison of 16S rRNA gene sequences indicated that the strain represents a novel member of the genus Streptomyces, exhibiting highest levels of similarity (<98.29 %) to the type strains of members of the genus Streptomyces. However, DNA–DNA relatedness and phenotypic data readily distinguished strain 172205T from phylogenetically related type strains. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C15 : 0 (10.31 %), anteiso-C15 : 0 (35.19 %), iso-C16 : 0 (20.24 %) and anteiso-C17 : 0 (10.05 %). The diagnostic phospholipid was phosphatidylethanolamine. The cell wall contained ll-diaminopimelic acid and meso-diaminopimelic acid and whole-cell hydrolysates contained ribose, galactose and glucose. The results of DNA–DNA hybridization, physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain 172205T from phylogenetically related type strains. Therefore, strain 172205T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces qinglanensis sp. nov. is proposed. The type strain is 172205T ( = CGMCC 4.6825T  = DSM 42035T).

scholarly journals Yersinia nurmii sp. nov.

2011 ◽  
Vol 61 (10) ◽  
pp. 2368-2372 ◽  
Author(s):  
Anna Murros-Kontiainen ◽  
Maria Fredriksson-Ahomaa ◽  
Hannu Korkeala ◽  
Per Johansson ◽  
Riitta Rahkila ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenetic Trees ◽  
Housekeeping Genes ◽  
Rrna Gene ◽  
Yersinia Ruckeri ◽  
Phenotypic Properties ◽  
Broiler Meat ◽  
Dna Reassociation ◽  
The 16S Rrna Gene

This study was set up to identify three Gram-negative, rod-shaped strains originating from broiler meat packaged under a modified atmosphere. A polyphasic taxonomic approach, including multilocus sequence analysis (MLSA) of five genes (16S rRNA, glnA, gyrB, recA and HSP60), DNA–DNA reassociation between the closest phylogenetic neighbours and determination of relevant phenotypic properties, was applied. Phylogenetic analysis of the 16S rRNA gene sequences grouped these strains together and within the genus Yersinia. MLSA of the 16S rRNA gene and four housekeeping genes showed that the strains formed a monophyletic group separate from other Yersinia species in all phylogenetic trees constructed. The strains had a phenotypic profile different from those of other representatives of the genus Yersinia, but most similar to that of Yersinia ruckeri. Typical virulence markers for pathogenic Yersinia were not detected. Based on phylogenetic, phenotypic and DNA–DNA reassociation data, a novel species, Yersinia nurmii sp. nov., is proposed for the isolated strains. The type strain is APN3a-cT ( = DSM 22296T  = LMG 25213T).

scholarly journals Citricoccus parietis sp. nov., isolated from a mould-colonized wall and emended description of Citricoccus alkalitolerans Li et al. 2005

2010 ◽  
Vol 60 (2) ◽  
pp. 271-274 ◽  
Author(s):  
Jenny Schäfer ◽  
Karin Martin ◽  
Peter Kämpfer
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Polar Lipid Profile ◽  
Phenotypic Differentiation ◽  
Emended Description ◽  
Diamino Acid ◽  
Physiological And Biochemical ◽  
Sequence Similarities

A Gram-positive, coccoid-shaped organism (strain 02-Je-010T), forming yellow-pigmented colonies was isolated from the wall of an indoor environment. On the basis of 16S rRNA gene sequence similarity studies, it was shown that strain 02-Je-010T belongs to the genus Citricoccus with sequence similarities of 98.9 % to Citricoccus alkalitolerans DSM 15665T and 98.6 % to Citricoccus muralis DSM 14442T. Cell-wall sugars were mannose and glucose. The diagnostic diamino acid of the peptidoglycan was lysine. The major menaquinones detected were MK-9(H2) and MK-8(H2). The polar lipid profile consisted of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol and moderate amounts of two unknown phospholipids and two unknown glycolipids. The fatty acid profile comprised major amounts of anteiso-C15 : 0, anteiso-C17 : 0 and iso-C15 : 0. All these data supported the affiliation of strain 02-Je-010T to the genus Citricoccus. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 02-Je-010T from the two recognized Citricoccus species. For these reasons, strain 02-Je-010T represents a novel species, for which the name Citricoccus parietis sp. nov. is proposed, with the type strain 02-Je-010T (=CCUG 57388T=CCM 7609T).

scholarly journals Halorubrum tibetense sp. nov., a novel haloalkaliphilic archaeon from Lake Zabuye in Tibet, China

2004 ◽  
Vol 54 (4) ◽  
pp. 1213-1216 ◽  
Author(s):  
Huapeng Fan ◽  
Yanfen Xue ◽  
Yanhe Ma ◽  
Antonio Ventosa ◽  
William D. Grant
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
The Tibetan Plateau ◽  
Phylogenetic Distance ◽  
Biochemical Tests ◽  
Phenotypic Differentiation ◽  
Gene Sequence Analysis ◽  
Derivatives Of ◽  
Physiological And Biochemical

A novel haloalkaliphilic archaeon, strain 8W8T, was isolated from Lake Zabuye, on the Tibetan Plateau, China. On the basis of 16S rRNA gene sequence analysis, strain 8W8T was shown to belong to the genus Halorubrum and was related to Halorubrum vacuolatum (96·7 % sequence similarity), Halorubrum saccharovorum (96·0 %), Halorubrum lacusprofundi (95·4 %) and Halorubrum sodomense (95·3 %). The phylogenetic distance from any species within the other genera of Halobacteriales was lower than 90 %. The major polar lipids of strain 8W8T were C20C20 and C20C25 derivatives of phosphatidylglycerol phosphate and phosphatidylglycerol phosphate methyl ester. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 8W8T from the eight Halorubrum species with validly published names. Therefore, strain 8W8T represents a novel species, for which the name Halorubrum tibetense sp. nov. is proposed, with the type strain 8W8T (=AS 1.3239T=JCM 11889T).

scholarly journals Methylocystis rosea sp. nov., a novel methanotrophic bacterium from Arctic wetland soil, Svalbard, Norway (78° N)

2006 ◽  
Vol 56 (3) ◽  
pp. 541-547 ◽  
Author(s):  
Ingvild Wartiainen ◽  
Anne Grethe Hestnes ◽  
Ian R. McDonald ◽  
Mette M. Svenning
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Major Fatty Acid ◽  
Wetland Soil ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Phenotypic Data ◽  
Phenotypic Differentiation ◽  
Type Strains ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, non-motile, non-spore-forming, pink-pigmented bacterium, SV97T, was isolated from a wetland soil near Ny-Ålesund, Svalbard Islands, Norway (78° N). On the basis of 16S rRNA gene sequence similarity, strain SV97T was shown to belong to the Alphaproteobacteria and was highly related to a number of non-characterized Methylocystis strains with GenBank accession nos AJ458507 and AJ458502 (100 %) and AF177299, AJ458510, AJ458467, AJ458471, AJ431384, AJ458475, AJ458484, AJ458501 and AJ458466 (99 %). The most closely related type strains were Methylocystis parvus OBBPT (97·2 %) and Methylocystis echinoides IMET 10491T (97 %). The closest related recognized species within the genus Methylosinus was Methylosinus sporium NCIMB 11126T (96·0 % similarity). Chemotaxonomic and phenotypic data (C18 : 1 ω8 as the major fatty acid, non-motile, no rosette formation) supported the affiliation of strain SV97T to the genus Methylocystis. The results of DNA–DNA hybridization and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain SV97T from the two recognized Methylocystis species. Strain SV97T therefore represents a novel species, for which the name Methylocystis rosea sp. nov. is proposed, with the type strain SV97T (=DSM 17261T=ATCC BAA-1196T).

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