Agrobacterium leguminum sp. nov., isolated from nodules of Phaseolus vulgaris in Spain

Author(s):  
Antonio Castellano-Hinojosa ◽  
David Correa-Galeote ◽  
Martha-Helena Ramírez-Bahena ◽  
Germán Tortosa ◽  
Jesús González-López ◽  
...  

Two endophytic strains, coded MOVP5T and MOPV6, were isolated from nodules of Phaseolus vulgaris plants grown on agricultural soil in Southeastern Spain, and were characterized through a polyphasic taxonomy approach. Their 16S rRNA gene sequences showed 99.3 and 99.4 %, 98.9 and 99.6 %, and 99.0 and 98.7% similarity to ‘ A. deltaense ’ YIC 4121T, A. radiobacter LGM 140T, and A. pusense NRCPB10T, respectively. Multilocus sequence analysis based on sequences of recA and atpD genes suggested that these two strains could represent a new Agrobacterium species with less than 96.5 % similarity to their closest relatives. PCR amplification of the telA gene, involved in synthesis of protelomerase, confirmed the affiliation of strains MOPV5T and MOPV6 to the genus Agrobacterium . Whole genome average nucleotide identity and digital DNA–DNA hybridization average values were less than 95.1 and 66.7 %, respectively, with respect to its closest related species. Major fatty acids in strain MOPV5T were C18 : 1 ω7c/C18 : 1 ω6c in summed feature 8, C19 : 0 cyclo ω8c, C16 : 0 and C16 : 0 3-OH. Colonies were small to medium, pearl-white coloured on YMA at 28 °C and growth was observed at 10–42 °C, pH 5.0–10.0 and with 0.0–0.5 % (w/v) NaCl. The DNA G+C content was 59.9 mol%. These two strains differ from all other genomovars of Agrobacterium found so far, including those that have not yet given a Latin name. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strain MOPV5T as representing a novel species of Agrobacterium , for which the name Agrobacterium leguminum sp. nov. is proposed. The type strain is MOPV5T (=CECT 30096T=LMG 31779T).

2013 ◽  
Vol 63 (Pt_8) ◽  
pp. 2823-2828 ◽  
Author(s):  
Aysel Veyisoglu ◽  
Mustafa Camas ◽  
Demet Tatar ◽  
Kiymet Guven ◽  
Anil Sazak ◽  
...  

A reddish-orange-pigmented, Gram-stain-negative, aerobic, facultatively methylotrophic strain, N4211T, isolated from arid soil, collected from Abuja, Nigeria, was analysed by using a polyphasic approach. Phylogenetic analysis, based on 16S rRNA gene sequences, showed that strain N4211T belonged to the genus Methylobacterium . Strain N4211T was most closely related to Methylobacterium aquaticum GR16T (98.56 %), Methylobacterium platani PMB02T (97.95 %) and Methylobacterium variabile GR3T (97.2 %), and the phylogenetic similarities to all other species of the genus Methylobacterium with validly published names were less than 97.0 %. The major ubiquinones detected were Q-10. The major fatty acids were summed feature 7 (C18 : 1 cis11/t9/t6). The DNA G+C content was 67.3 mol%. DNA–DNA relatedness of strain N4211T and the most closely related strains M. aquaticum DSM 16371T and M. platani KCTC 12901T were 60.0 and 48.2 %, respectively. On the basis of phenotypic, phylogenetic and DNA–DNA hybridization data, strain N4211T is assigned to a novel species of the genus Methylobacterium for which the name Methylobacterium tarhaniae sp. nov. is proposed. The type strain is N4211T( = KCTC 23615T = DSM 25844T).


2013 ◽  
Vol 63 (Pt_2) ◽  
pp. 484-489 ◽  
Author(s):  
Hangsak Huy ◽  
Long Jin ◽  
Young-Ki Lee ◽  
Keun Chul Lee ◽  
Jung-Sook Lee ◽  
...  

A Gram-negative, non-motile, non-spore-forming and rod-shaped bacterial strain, CH15-1T, was isolated from a sediment sample taken from Daechung Reservoir, South Korea, during the late-blooming period of cyanobacteria. Strain CH15-1T grew optimally at pH 7.0 and 30 °C. A phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain CH15-1T belongs to the genus Arenimonas with the similarity range from 92.6–97.4 % and is closely related to Arenimonas oryziterrae YC6267T (97.4 %), Arenimonas composti TR7-09T (95.4 %), Arenimonas metalli CF5-1T (94.7 %), Arenimonas malthae CC-JY-1T (94.6 %) and Arenimonas donghaensis HO3-R19T (92.6 %). However, the DNA–DNA hybridization between strain CH15-1T and the closest strain, Arenimonas oryziterrae YC6267T, was 8.9–12.9 %. The DNA G+C content was 63.9 mol% compared to A. oryziterrae YC626T, 65.8 mol%. Strain CH15-1T included Q-8 as the major ubiquinone and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidylmonomethylethanolamine as the major polar lipids. The major fatty acids (>5 %) were iso-C15 : 0, iso-C16 : 0, iso-C14 : 0, iso-C11 : 0 3-OH, iso-C17 : 0 and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl). On the basis of phylogenetic, phenotypic and genetic data, strain CH15-1T was classified in the genus Arenimonas as a member of a novel species, for which the name Arenimonas daechungensis sp. nov. is proposed. The type strain is CH15-1T ( = KCTC 23553T = DSM 24763T).


2014 ◽  
Vol 64 (Pt_8) ◽  
pp. 2593-2598 ◽  
Author(s):  
Delong Kong ◽  
Yanwei Wang ◽  
Bingqiang Zhao ◽  
Yanting Li ◽  
Jinlong Song ◽  
...  

A novel aerobic, halotolerant bacterium, designated strain LAM612T, was isolated from saline-alkaline soil samples from Lingxian County, Shandong Province, China. Cells of strain LAM612T were Gram-reaction-positive, endospore-forming, motile and rod-shaped. The optimal temperature and pH for growth were 35 °C and pH 6.0, respectively. Strain LAM612T could grow in the presence of up to 10 % (w/v) NaCl. The genomic DNA G+C conten was 36.4 mol% as detected by the T m method. Comparative analysis of 16S rRNA gene sequences revealed that LAM612T was closely related to Lysinibacillus sinduriensis KACC 16611T (98.0 %), L. chungkukjangi KACC 16626T (97.5 %), L. massiliensis KCTC 13178T (97.4 %), L. xylanilyticus KACC 15113T (97.2 %), L. macroides DSM 54T (97.0 %) and L. manganicus DSM 26584T (96.5 %). The DNA–DNA hybridization values between strain LAM612T and its closest relatives ranged from 20.6 % to 41.9 %. The major fatty acids of strain LAM612T were iso-C15 : 0 (40.8 %), iso-C16 : 0 (15.2 %) and anteiso-C15 : 0 (10.8 %). The cell-wall peptidoglycan content was A4α (l-Lys–d-Asp). The predominant menaquinone was MK-7 and the main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, five unknown glycolipids and an unknown lipid. Based on the DNA–DNA hybridization results and phenotypic, phylogenetic and chemotaxonomic properties, strain LAM612T could be distinguished from the recognized species of the genus Lysinibacillus , and was suggested to represent a novel species of this genus, for which the name Lysinibacillus halotolerans sp. nov. is proposed. The type strain is LAM612T ( = ACCC 00718T = JCM 19611T).


2014 ◽  
Vol 64 (Pt_10) ◽  
pp. 3346-3352 ◽  
Author(s):  
Bo Liu ◽  
Guo-Hong Liu ◽  
Gui-Hing Hu ◽  
Mei-Chun Chen

A Gram-stain-positive, short rod-shaped and motile, mildly halotolerant, endospore-forming bacterium, FJAT-13985T, was isolated from the internal tissues of Mesona chinensis root. Strain FJAT-13985T grew at 20–45 °C (optimum 30 °C) and pH 5.7–9.0 (optimum pH 7.0) and in the presence of 0–2 % (w/v) NaCl [optimum 1 % (w/v)]. The strain was catalase-positive and oxidase-negative. The cell wall of strain FJAT-13985T contained meso-diaminopimelic acid and the predominant isoprenoid quinone was MK-7 (97.4 %). The major fatty acids of the strain were anteiso-C15 : 0 (23.3 %) and iso-C15 : 0 (40.8 %). The DNA G+C content was 41.64 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain FJAT-13985T is a member of the genus Bacillus and is most closely related to Bacillus drentensis DSM 15600T (98.4 %), Bacillus vireti DSM 15602T (98.2 %) and Bacillus novalis DSM 15603T (98.3 %). DNA–DNA hybridization indicated that relatedness between strain FJAT-13985T and its closest relative, B. drentensis DSM 15600T, was 36.63 %. The phenotypic, chemotaxonomic and genotypic properties clearly indicate that strain FJAT-13985T represents a novel species of the genus Bacillus , for which the name Bacillus mesonae sp. nov. is proposed. The type strain is FJAT-13985T ( = DSM 25968T = CGMCC1.12238T).


2020 ◽  
Vol 70 (3) ◽  
pp. 1793-1799 ◽  
Author(s):  
Wan-Kui Jiang ◽  
Qin-Qin Gao ◽  
Lu Zhang ◽  
Gao-Jie Sun ◽  
Ming-Liang Zhang ◽  
...  

A Gram-stain-positive, aerobic, non-motile and coccoid-shaped bacterium, designated XNB-1T, was isolated from farmland soil in Taian, Shandong province, China. Strain XNB-1T contained iso-C15 : 0 and iso-C16 : 0 as the predominant fatty acids. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn←Gly(1, 2)←d-Glu. The polar lipid profile of strain XNB-1T consisted of diphosphatidylglycerol, phosphatidylglycerol, an unidentified phosphoglycolipid and three unidentified phospholipids. The predominant menaquinone of strain XNB-1T was MK-8(H4) and the DNA G+C content was 70.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain XNB-1T belonged to the genus Ornithinicoccus , and shared the highest similarity with Ornithinicoccus hortensis HKI 0125T (96.0 %), followed by Ornithinicoccus halotolerans EGI 80423T (95.5 %). Genome-based analysis of average nucleotide identity of strain XNB-1T with O. hortensis HKI 0125T and O. halotolerans EGI 80423T yielded values of 73.1 and 73.3 %, respectively, while the digital DNA–DNA hybridization values were 19.5 and 19.9 %, respectively. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain XNB-1T is considered to represent a novel species of the genus Ornithinicoccus , for which the name Ornithinicoccus soli sp. nov. is proposed. The type strain is XNB-1T (=CCTCC AB 2019099T=KCTC 49259T).


Author(s):  
Shin Ae Lee ◽  
Tae-Wan Kim ◽  
Mee-Kyung Sang ◽  
Jaekyeong Song ◽  
Soon-Wo Kwon ◽  
...  

A Gram-stain-negative, aerobic, non-motile and rod-shaped bacterium, designated KIS59-12T, was isolated from a soil sample collected on Hodo island, Boryeong, Republic of Korea. The strain grew at 10–33 °C, pH 6.0–7.5 and with 0–4 % NaCl (w/v). Results of phylogenetic analysis based on 16S rRNA gene sequences showed that strain KIS59-12T was in the same clade as Arachidicoccus rhizosphaerae Vu-144T and Arachidicoccus ginsenosidivorans Gsoil809T with 97.5 and 97.2 % sequence similarity, respectively. Comparative genome analysis between strain KIS59-12T and A. rhizosphaerae Vu-144T showed that average nucleotide identity value was 69.4 % and the digital DNA–DNA hybridization value was 19.1 %. The major respiratory quinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine and an unknown polar lipid. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH, which supported the affiliation of strain KIS59-12T with the genus Arachidicoccus . The major polyamines were homospermidine and putrescine. The genomic DNA G+C content was 36.4 mol%. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain KIS59-12T represents a novel species of the genus Arachidicoccus , for which the name Arachidicoccus soli sp. nov. is proposed. The type strain of Arachidicoccus soli is KIS59-12T (=KACC 17340T=NBRC 113161T).


2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1133-1137 ◽  
Author(s):  
Yuan-Yuan Bao ◽  
Zhi Huang ◽  
Dong-Mei Mao ◽  
Xia-Fang Sheng ◽  
Lin-Yan He

A novel actinomycete, designated strain A31T, was isolated from the surface of weathered biotite in Susong, Anhui Province, China. The organism grew optimally at 30 °C, at pH 8.0 and with 1 % (w/v) NaCl. Strain A31T had A3α as the cell-wall peptidoglycan type and galactose, mannose and rhamnose as whole-cell sugars. Anteiso-C15 : 0 and anteiso-C17 : 0 were the major cellular fatty acids and MK-9(H2) was the predominant respiratory quinone. In addition, the total polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylmonomethylethanolamine and four glycolipids. The genomic DNA G+C content of strain A31T was 70.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain A31T was related most closely to Sinomonas albida LC13T (98.3 % similarity), Sinomonas atrocyanea DSM 20127T (98.2 %), Sinomonas soli CW 59T (98.1 %), Sinomonas flava CW 108T (97.8 %), ‘Sinomonas mesophila’ MPKL 26 (97.3 %), Sinomonas echigonensis LC10T (97.1 %) and ‘ Sinomonas notoginsengisoli ’ SYP-B575 (96.7 %). DNA–DNA hybridization studies with the new isolate showed relatedness values of 16.0–56.6 % with its six closest neighbours. Based on phenotypic, chemotaxonomic and phylogenetic analysis, strain A31T represents a novel species of the genus Sinomonas , for which the name Sinomonas susongensis sp. nov. is proposed. The type strain is A31T ( = DSM 28245T = CCTCC AB 2014068T).


Author(s):  
Magdalena Ksiezarek ◽  
Teresa Gonçalves Ribeiro ◽  
Joana Rocha ◽  
Filipa Grosso ◽  
Svetlana Ugarcina Perovic ◽  
...  

Two Gram-stain-positive strains, c9Ua_26_MT and c11Ua_112_MT, were isolated from voided urine samples from two healthy women. Comparative 16S rRNA gene sequences demonstrated that these novel strains were members of the genus Limosilactobacillus . Phylogenetic analysis based on pheS gene sequences and core genomes showed that each strain formed a separated branch and are closest to Limosilactobacillus vaginalis DSM 5837T. The average nucleotide identity (ANI) and Genome-to-Genome Distance Calculator (GGDC) values between c9Ua_26_MT and the closest relative DSM 5837T were 90.7 and 42.9 %, respectively. The ANI and GGDC values between c11Ua_112_MT and the closest relative DSM 5837T were 91.2 and 45.0 %, and those among the strains were 92.9% and 51,0 %, respectively. The major fatty acids were C12 : 0 (40.2 %), C16 : 0 (26.7 %) and C18 : 1 ω9c (17.7 %) for strain c9Ua_26_MT, and C18 : 1 ω9c (38.0 %), C16 : 0 (33.3 %) and C12 : 0 (17.6 %) for strain c11Ua_112_MT. The genomic DNA G+C content of strains c9Ua_26_MT and c11Ua_112_MT was 39.9 and 39.7 mol%, respectively. On the basis of the data presented here, strains c9Ua_26_MT and c11Ua_112_MT represent two novel species of the genus Limosilactobacillus , for which the names Limosilactobacillus urinaemulieris sp. nov. (c9Ua_26_MT=CECT 30144T=LMG 31899T) and Limosilactobacillus portuensis sp. nov. (c11Ua_112_MT=CECT 30145T=LMG 31898T) are proposed.


2019 ◽  
Vol 69 (4) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xiang-yue Zhou ◽  
Zeng-hong Gao ◽  
Mei-hong Chen ◽  
Mei-qi Jian ◽  
Li-hong Qiu

Cells of bacterial strains 4 G-K06T and 4MSK11T, isolated from soil samples collected from monsoon evergreen broad-leaved forest of the Dinghushan Mountain (112° 31′ E 23° 10′ N), Guangdong Province, PR China, were Gram-stain-negative, aerobic, non-spore-forming, non-motile and rod-shaped. Strain 4 G-K06T grew at 10–37 °C, pH 3.5–7.5 and 0–3.5 % (w/v) NaCl; while 4MSK11T grew at 4–42 °C, pH 3.5–7.5 and 0–2.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed strain 4 G-K06T formed a clade with Dyella flagellata 4 M-K16T, Dyella acidisoli 4M-Z03T, Dyella humi DHG40T and Dyella nitratireducens DHG59T, while strain 4MSK11T formed a clade with Dyella caseinilytica DHOB09T and Dyella mobilis DHON07T, both within the genus Dyella . The result of the partial atpD, gyrB and lepA gene sequence analysis supported the conclusion based on 16S rRNA gene sequence analysis, which showed that these two strains represent two novel species of Dyella . The average nucleotide identity and digital DNA–DNA hybridization value for the whole genomes were 75.0–79.0 and 20.3–22.6 % between strains 4 G-K06T, 4MSK11T and those described Dyella species with genome sequences; while the DNA–DNA hybridization rates between strains 4 G-K06T, 4MSK11T and closely related Dyella species (without genome sequence) were 29.5–41.8 %. The major cellular fatty acids of these two strains were iso-C15 : 0, iso-C16 : 0 and iso-C17 : 1 ω9c, while the major polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several unidentified phospholipids and aminophospholipids. The only ubiquinone of these two strains was ubiquinone-8. The DNA G+C contents of 4 G-K06T and 4MSK11T were 60.4 and 61.3 mol%, respectively. On the basis of the evidence presented here, strains 4 G-K06T and 4MSK11T represent two novel species of the genus Dyella , for which the names Dyella monticola sp. nov. (type strain 4 G-K06T=LMG 30268T=GDMCC 1.1188T) and Dyella psychrodurans sp. nov. (type strain 4MSK11T=KCTC 62280T=GDMCC 1.1185T) are proposed.


Author(s):  
Ji Young Jung ◽  
Hye Kyeong Kang ◽  
Hyun Mi Jin ◽  
Sang-Soo Han ◽  
Young Chul Kwon ◽  
...  

A Gram-positive, facultative anaerobic, catalase-negative, non-motile, non-spore-forming and rod-shaped lactic acid bacterium strain, denoted as NFFJ11T and isolated from total mixed fermentation feed in the Republic of Korea, was characterized through polyphasic approaches, including sequence analyses of the 16S rRNA gene and housekeeping genes (rpoA and pheS), determination of average nucleotide identity and in silico DNA–DNA hybridization, fatty acid methyl ester analysis, and phenotypic characterization. Phylogenetic analyses based on 16S rRNA, rpoA and pheS gene sequences revealed that strain NFFJ11T belonged to the genus Companilactobacillus . The 16S rRNA gene sequence of strain NFFJ11T exhibited high similarity to Companilactobacillus formosensis S215T (99.66 %), Companilactobacillus farciminis Rv4 naT (99.53 %), Companilactobacillus crustorum LMG 23699T (99.19 %), Companilactobacillus futsaii YM 0097T (99.06 %), Companilactobacillus zhachilii HBUAS52074T (98.86 %) and Companilactobacillus heilongiiangensis S4-3T (98.66 %). However, average nucleotide identity and in silico DNA–DNA hybridization values for these type strains were in the range of 79.90–92.93 % and 23.80–49.30 %, respectively, which offer evidence that strain NFFJ11T belongs to a novel species of the genus Companilactobacillus . The cell-wall peptidoglycan type was A4α (l-Lys–d-Asp) and the G+C content of the genomic DNA was 35.7 mol%. The main fatty acids of strain NFFJ11T were C18 : 1  ω9c (43.3 %), C16 : 0 (20.1 %) and summed feature 7 (18.3 %; comprising any combination of C19 : 1  ω7c, C19 : 1  ω6c and C19 : 0 cyclo ω10c). Through polyphasic taxonomic analysis, it was observed that strain NFFJ11T represents a novel species belonging to the genus Companilactobacillus , for which the name Companilactobacillus pabuli sp. nov. is proposed. The type strain is NFFJ11T (= KACC 21771T= JCM 34088T).


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