scholarly journals Pseudomonas palmensis sp. nov., a Novel Bacterium Isolated From Nicotiana glauca Microbiome: Draft Genome Analysis and Biological Potential for Agriculture

2021 ◽  
Vol 12 ◽  
Author(s):  
Enrique Gutierrez-Albanchez ◽  
Ana García-Villaraco ◽  
José A. Lucas ◽  
Ignacio Horche ◽  
Beatriz Ramos-Solano ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Iron Nutrition ◽  
Rrna Gene ◽  
Nicotiana Glauca ◽  
Phenotypic Analysis ◽  
Nutrient Mobilization ◽  
Biological Potential

A novel Pseudomonas, designated strain BBB001T, an aerobic, rod-shaped bacterium, was isolated from the rhizosphere of Nicotiana glauca in Las Palmas Gran Canaria, Spain. Genomic analysis revealed that it could not be assigned to any known species of Pseudomonas, so the name Pseudomonas palmensis sp. nov. was proposed. A 16S rRNA gene phylogenetic analysis suggested affiliation to the Pseudomonas brassicae group, being P. brassicae MAFF212427 T the closest related type strain. Upon genomic comparisons of both strains, all values were below thresholds established for differentiation: average nucleotide identity (ANI, 88.29%), average amino acid identity (AAI, 84.53%), digital DNA-DNA hybridization (dDDH, 35.4%), and TETRA values (0.98). When comparing complete genomes, a total of 96 genes present exclusively in BBB001T were identified, 80 of which appear associated with specific subsystems. Phenotypic analysis has shown its ability to assimilate glucose, potassium gluconate, capric acid malate, trisodium citrate, and phenylacetic acid; it was oxidase positive. It is able to produce auxins and siderophores in vitro; its metabolic profile based on BIOLOG Eco has shown a high catabolic capacity. The major fatty acids accounting for 81.17% of the total fatty acids were as follows: C16:0 (33.29%), summed feature 3 (22.80%) comprising C16:1 ω7c and C16:1 ω6c, summed feature 8 (13.66%) comprising C18:1 ω7c, and C18:1ω6c and C17:0 cyclo (11.42%). The ability of this strain to improve plant fitness was tested on tomato and olive trees, demonstrating a great potential for agriculture as it is able to trigger herbaceous and woody species. First, it was able to improve iron nutrition and growth on iron-starved tomatoes, demonstrating its nutrient mobilization capacity; this effect is related to its unique genes related to iron metabolism. Second, it increased olive and oil yield up to 30% on intensive olive orchards under water-limiting conditions, demonstrating its capacity to improve adaptation to adverse conditions. Results from genomic analysis together with differences in phenotypic features and chemotaxonomic analysis support the proposal of strain BBB001T (=LMG 31775T = NCTC 14418T) as the type strain of a novel species for which the name P. palmensis sp. nov is proposed.

scholarly journals Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3333-3338 ◽  
Author(s):  
Wei Fang ◽  
Yong Li ◽  
Han Xue ◽  
Guozhong Tian ◽  
Laifa Wang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Populus Euramericana ◽  
The Family ◽  
Distinct Branch ◽  
The 16S Rrna Gene ◽  
Sequence Similarities

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100 % similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2 %) and Xenophilus arseniciresistens YW8T (95.0 %), and less than 95.0 % sequence similarities with members of other species. Their major fatty acids were C16 : 0, C17 : 0 cyclo, C18 : 1ω7c and C16 : 1ω7c/C16 : 1ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0 mol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T ( = CFCC 12099T = KCTC 42091T).

Mucilaginibacter soyangensis sp. nov., isolated from a lake

2014 ◽  
Vol 64 (Pt_2) ◽  
pp. 413-419 ◽  
Author(s):  
Yochan Joung ◽  
Haneul Kim ◽  
Heeyoung Kang ◽  
Beom-Il Lee ◽  
Tae-Seok Ahn ◽  
...  
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
Type Strain ◽  
Type Species ◽  
Novel Species ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Content Type ◽  
Link Type ◽  
Yellow Orange

A non-motile, yellow–orange-pigmented bacterial strain, designated HME6664T, was isolated from Lake Soyang, Republic of Korea. The major fatty acids of strain HME6664T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 44.7 %) and iso-C15 : 0 (20.2 %). The DNA G+C content was 40.8 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME6664T formed a lineage within the genus Mucilaginibacter . Strain HME6664T was closely related to Mucilaginibacter ximonensis (96.7 %), Mucilaginibacter dorajii (96.5 %) and Mucilaginibacter lappiensis (96.3 %). On the basis of the evidence presented in this study, strain HME6664T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter soyangensis sp. nov., is proposed. The type strain is HME6664T ( = KCTC 23261T = CECT 7824T).

Description of Sulfitobacter sediminilitoris sp. nov., isolated from a tidal flat

2020 ◽  
Vol 367 (9) ◽  
Author(s):  
Sooyeon Park ◽  
Siyu Chen ◽  
Jung-Sook Lee ◽  
Wonyong Kim ◽  
Jung-Hoon Yoon
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Tidal Flat ◽  
Type Strain ◽  
Sequence Similarity ◽  
Genomic Analysis ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Properties ◽  
Type Strains

ABSTRACT A Gram-stain-negative bacterial strain, JBTF-M27T, was isolated from a tidal flat from Yellow Sea, Republic of Korea. Neighbor-joining phylogenetic tree of 16S rRNA gene sequences showed that strain JBTF-M27T fell within the clade comprising the type strains of Sulfitobacter species. Strain JBTF-M27T exhibited the highest 16S rRNA gene sequence similarity (98.8%) to the type strain of S. porphyrae. Genomic ANI and dDDH values of strain JBTF-M27T between the type strains of Sulfitobacter species were less than 76.1 and 19.2%, respectively. Mean DNA-DNA relatedness value between strain JBTF-M27T and the type strain of S. porphyrae was 21%. DNA G + C content of strain JBTF-M27T from genome sequence was 57.8% (genomic analysis). Strain JBTF-M27T contained Q-10 as the predominant ubiquinone and C18:1ω7c as the major fatty acid. The major polar lipids of strain JBTF-M27T were phosphatidylcholine, phosphatidylglycerol and one unidentified aminolipid. Distinguished phenotypic properties, along with the phylogenetic and genetic distinctiveness, revealed that strain JBTF-M27T is separated from recognized Sulfitobacter species. On the basis of the data presented, strain JBTF-M27T ( = KACC 21648T = NBRC 114356T) is considered to represent a novel species of the genus Sulfitobacter, for which the name Sulfitobacter sediminilitoris sp. nov. is proposed.

scholarly journals Chryseobacterium flavum sp. nov., isolated from polluted soil

2007 ◽  
Vol 57 (8) ◽  
pp. 1765-1769 ◽  
Author(s):  
Yu Zhou ◽  
Jing Dong ◽  
Xu Wang ◽  
Xing Huang ◽  
Ke-Yun Zhang ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Novel Species ◽  
Polluted Soil ◽  
Rrna Gene ◽  
Taxonomic Study ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Gram Negative ◽  
Genotypic Characteristics

A Gram-negative, non-motile, rod-shaped bacterial strain, designated CW-E 2T, was isolated from a polluted soil sample collected from Jiangsu Province, China. A taxonomic study of the isolate, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was carried out. The predominant menaquinone was MK-6 and the major fatty acids were i-C15 : 0, i-C17 : 0 3-OH, i-C17 : 1 ω9c and summed feature 4. The G+C content of the DNA was 37.2 mol%. Based on phenotypic and genotypic characteristics, strain CW-E 2T represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium flavum sp. nov. is proposed. The type strain is CW-E 2T (=KCTC 12877T=CCTCC AB 206147T).

scholarly journals Marinithermofilum abyssi gen. nov., sp. nov. and Desmospora profundinema sp. nov., isolated from a deep-sea sediment, and emended description of the genus Desmospora Yassin et al. 2009

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2622-2629 ◽  
Author(s):  
Yi Zhang ◽  
Jie Li ◽  
Xinpeng Tian ◽  
Si Zhang
Keyword(s):  
Fatty Acids ◽  
Deep Sea ◽  
Type Strain ◽  
Novel Species ◽  
Polar Lipids ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Deep Sea Sediment ◽  
The Family ◽  
Diamino Acid

Two novel filamentous bacteria, strains SCSIO 11157T and SCSIO 11154T, were isolated from a deep-sea sediment sample. Strain SCSIO 11157T grew optimally at 55–60 °C, while strain SCSIO 11154T grew optimally at 40 °C. Both strains produced aerial and substrate mycelia. Phylogenetic analysis of the 16S rRNA gene sequences of strains SCSIO 11157T and SCSIO 11154T showed that the isolates were affiliated to the family Thermoactinomycetaceae. The two isolates contained ll-diaminopimelic acid as the cell-wall diamino acid, and did not have diagnostic sugars. The major polar lipids of strain SCSIO 11157T were diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol, and the major polar lipids of SCSIO 11154T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant menaquinone of both strains was MK-7. The major cellular fatty acids of strain SCSIO 11157T were iso-C15 : 0, C18 : 1ω9c and iso-C17 : 0, and strain SCSIO 11154T contained iso-C15 : 0 and iso-C17 : 0 as major fatty acids. The DNA G+C contents of strains SCSIO 11157T and SCSIO 11154T were 54.2 and 51.8 mol %, respectively. On the basis of its phenotypic and phylogenetic properties, strain SCSIO 11157T represents a novel species in the new genus, for which we propose the name Marinithermofilum abyssi gen. nov., sp. nov. The type strain of Marinithermofilum abyssi is SCSIO 11157T ( = CGMCC 1.15179T = NBRC 109939T). Strain SCSIO 11154T represents a novel species of the genus Desmospora, for which we propose the name Desmospora profundinema sp. nov. The type strain is SCSIO 11154T ( = DSM 45903T = NBRC 109626T).

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals Rheinheimera texasensis sp. nov., a halointolerant freshwater oligotroph

2007 ◽  
Vol 57 (10) ◽  
pp. 2376-2380 ◽  
Author(s):  
Mubina M. Merchant ◽  
Allana K. Welsh ◽  
Robert J. C. McLean
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Gram Negative ◽  
Physiological And Biochemical

A Gram-negative, rod-shaped, motile, non-spore-forming bacterium, designated strain A62-14BT, was isolated from a constant-temperature, spring-fed, freshwater lake. On the basis of the complete 16S rRNA gene sequence, strain A62-14BT was shown to belong to the class Gammaproteobacteria, being most closely related to Rheinheimera sp. HTB082 (96.2 % sequence similarity), Rheinheimera baltica (95.01 %), Rheinheimera pacifica (96.35 %), Rheinheimera perlucida and Alishewanella fetalis (95.9 %). The major fatty acids (C16 : 1 ω7c, 38.56 %; C16 : 0, 19.04 %; C12 : 0 3-OH, 12.83 %; C18 : 1 ω7c, 7.70 %) and the motility of strain A62-14BT support its affiliation to the genus Rheinheimera. The salt intolerance of strain A62-14BT, together with the results of other physiological and biochemical tests, allowed the differentiation of this strain from the three species of the genus Rheinheimera with validly published names. Therefore strain A62-14BT represents a novel species of the genus Rheinheimera, for which the name Rheinheimera texasensis sp. nov. is proposed. The type strain is A62-14BT (=ATCC BAA-1235T=DSM 17496T). The description of the genus Rheinheimera is emended to reflect the halointolerance and freshwater origin of strain A62-14BT.

scholarly journals Bacillus axarquiensis sp. nov. and Bacillus malacitensis sp. nov., isolated from river-mouth sediments in southern Spain

2005 ◽  
Vol 55 (3) ◽  
pp. 1279-1285 ◽  
Author(s):  
Cristina Ruiz-García ◽  
Emilia Quesada ◽  
Fernando Martínez-Checa ◽  
Inmaculada Llamas ◽  
Maria C. Urdaci ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Sequence Similarity ◽  
Saturated Fatty Acids ◽  
River Mouth ◽  
Southern Spain ◽  
Rrna Gene ◽  
16S Rrna Gene Analysis ◽  
Bacillus Mojavensis ◽  
Phenotypic Tests

Two Gram-positive, rod-shaped, endospore-forming bacteria (strains CR-119T and CR-95T) were isolated from brackish sediments in the mouth of the river Vélez in Málaga, southern Spain, and subjected to a polyphasic taxonomic study. Phenotypic tests showed that these strains were related to other Bacillus species at a similarity level of less than 87·6 %. Both strains are halotolerant, aerobic, chemoheterotrophic, motile with peritrichous flagella and biosurfactant producers. Their endospores are oval, subterminal and non-deforming structures. The predominant menaquinone in both strains is MK-7. The fatty-acid profiles of both strains contain large quantities of branched and saturated fatty acids. The major fatty acids (%) are 15 : 0 anteiso (32·4), 15 : 0 iso (16·8), 17 : 0 iso (13·4), 16 : 0 (11·5) and 17 : 0 anteiso (10·2) in strain CR-119T and 15 : 0 anteiso (37·5), 17 : 0 iso (16·0) and 17 : 0 anteiso (15·8) in strain CR-95T. The G+C contents of strains CR-119T and CR-95T are 41·0 and 42·5 mol%, respectively. RAPD analysis confirmed the low degree of similarity between the two strains and also amongst other Bacillus species. 16S rRNA gene analysis of strain CR-119T showed the highest sequence similarity to be 97·4 %, with Bacillus mojavensis and Bacillus subtilis subsp. spizizenii. In the case of strain CR-95T, the maximum similarity value was 99·5 %, with B. mojavensis. DNA–DNA hybridization of strains CR-119T and CR-95T with the above species produced values lower than 46·9 %. Therefore, on the basis of phenotypic characteristics, phylogenetic data and genomic distinctiveness, we conclude that these Bacillus strains merit classification as novel species, for which we propose the names Bacillus axarquiensis sp. nov. (type strain CR-119T=CECT 5688T=LMG 22476T) and Bacillus malacitensis sp. nov. (type strain CR-95T=CECT 5687T=LMG 22477T).

scholarly journals Shewanella electrodiphila sp. nov., a psychrotolerant bacterium isolated from Mid-Atlantic Ridge deep-sea sediments

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 2882-2889 ◽  
Author(s):  
Jinwei Zhang ◽  
J. Grant Burgess
Keyword(s):  
Fatty Acids ◽  
Type Strain ◽  
Anaerobic Respiration ◽  
Anaerobic Growth ◽  
Rrna Gene ◽  
Carbon Cloth ◽  
Gene Sequence Analysis ◽  
Mid Atlantic Ridge ◽  
Psychrotolerant Bacterium ◽  
Type Strains

Strains MAR441T and MAR445 were isolated from Mid-Atlantic Ridge sediments from a depth of 2734 m, and were found to belong to the genus Shewanella. The strains were rod-shaped, pigmented, non-motile and capable of anaerobic growth either by fermentation of carbohydrates or by anaerobic respiration. The strains utilized a variety of electron acceptors, including nitrate and ferric compounds, and could utilize peptone when grown anaerobically in a two-chambered microbial fuel cell, which used carbon cloth electrodes and delivered a stable power output of ∼150–200 mW m− 2. The major fatty acids were typical of the genus Shewanella, with major components C13 : 0, iso-C13 : 0, iso-C15 : 0, C16 : 0, C16 : 1ω7c, C18 : 1ω7c and C20 : 5ω3 fatty acids. The DNA G+C content of strains MAR441T and MAR445 was 42.4 mol%. 16S rRNA gene sequence analysis indicated that strains MAR441T and MAR445 were most closely related to Shewanella olleyana (sequence similarities 97.9  % to the type strain). DNA–DNA hybridization demonstrated only 15.6–37.2  % relatedness between strain MAR441T and the type strains of related species of the genus Shewanella. Phenotypic characteristics confirmed that these isolates constituted a novel species of the genus Shewanella, for which the name Shewanella electrodiphila sp. nov. is proposed; the type strain is MAR441T ( = ATCC BAA-2408T = DSM 24955T).

Proposal of Solimonas aquatica sp. nov., reclassification of Sinobacter flavus Zhou et al. 2008 as Solimonas flava comb. nov. and Singularimonas variicoloris Friedrich and Lipski 2008 as Solimonas variicoloris comb. nov. and emended descriptions of the genus Solimonas and its type species Solimonas soli

2011 ◽  
Vol 61 (9) ◽  
pp. 2284-2291 ◽  
Author(s):  
Shih-Yi Sheu ◽  
Nian-Tsz Cho ◽  
A. B. Arun ◽  
Wen-Ming Chen
Keyword(s):  
Fatty Acids ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Type Species ◽  
Phylogenetic Trees ◽  
Polar Lipids ◽  
Experimental Comparison ◽  
Rrna Gene ◽  
The Novel

A bacterial strain designated NAA16T was isolated from a freshwater spring in Taiwan and was characterized using a polyphasic taxonomic approach. Strain NAA16T was aerobic, Gram-staining-negative, rod-shaped, non-spore-forming and motile by means of a single polar flagellum. Growth occurred at 20–40 °C (optimum, 25 °C), at pH 7.0–8.0 (optimum, pH 7.5) and with up to 1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that the closest relatives of strain NAA16T were Singularimonas variicoloris MN28T, Sinobacter flavus CW-KD 4T and Solimonas soli DCY12T, with respective sequence similarities of 96.7, 96.6 and 96.2 %. Phylogenetic trees reconstructed from 16S rRNA gene or rpoB sequences (encoding the β-subunit of the RNA polymerase) revealed that the novel strain NAA16T and these three closest relatives formed an independent phylogenetic clade within the Gammaproteobacteria. Strain NAA16T contained C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as predominant fatty acids and possessed phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids. The major isoprenoid quinone was Q-8. The DNA G+C content of strain NAA16T was 66.2 mol%. The taxonomic relationship of strain NAA16T, Singularimonas variicoloris DSM 15731T, Sinobacter flavus DSM 18980T and Solimonas soli LMG 24014T was clarified by means of a direct experimental comparison. Based on phenotypic, chemotaxonomic and phylogenetic data, the descriptions of the genus Solimonas and its type species Solimonas soli are emended. Members of the genus are Gram-negative, oxidase- and catalase-positive, aerobic or facultatively anaerobic and chemo-organotrophic. Chemotaxonomically, members of the genus Solimonas possess Q-8 as the major respiratory quinone, C16 : 0 and C18 : 1ω7c as predominant fatty acids and phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an uncharacterized aminophospholipid as dominant polar lipids; the DNA G+C content is 64.9–68.4 mol%. Phylogenetic evidence, supported by chemotaxonomic and phenotypic data, allowed us to assign strain NAA16T to the genus Solimonas within the novel species Solimonas aquatica sp. nov. (type strain NAA16T  = BCRC 17835T  = LMG 24500T). The reclassification of Sinobacter flavus as Solimonas flava comb. nov. (type strain CW-KD 4T  = DSM 18980T  = KCTC 12881T  = CCTCC AB 206145T) and Singularimonas variicoloris as Solimonas variicoloris comb. nov. (type strain MN28T  = DSM 15731T  = LMG 22844T) is also proposed.

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