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1.
J Mol Evol ; 92(2): 169-180, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38502221

ABSTRACT

The bacterial strain SECRCQ15T was isolated from seeds of Chenopodium quinoa in Spain. Phylogenetic, chemotaxonomic, and phenotypic analyses, as well as genome similarity indices, support the classification of the strain into a novel species of the genus Ferdinandcohnia, for which we propose the name Ferdinandcohnia quinoae sp. nov. To dig deep into the speciation features of the strain SECRCQ15T, we performed a comparative genomic analysis of the genome of this strain and those of the type strains of species from the genus Ferdinandcohnia. We found several genes related with plant growth-promoting mechanisms within the SECRCQ15T genome. We also found that singletons of F. quinoae SECRCQ15T are mainly related to the use of carbohydrates, which is a common trait of plant-associated bacteria. To further reveal speciation events in this strain, we revealed genes undergoing diversifying selection (e.g., genes encoding ribosomal proteins) and functions likely lost due to pseudogenization. Also, we found that this novel species contains 138 plant-associated gene-cluster functions that are unique within the genus Ferdinandcohnia. These features may explain both the ecological and taxonomical differentiation of this new taxon.


Subject(s)
Fatty Acids , Plants , Phylogeny , Plants/genetics , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Sequence Analysis, DNA
2.
Article in English | MEDLINE | ID: mdl-37093735

ABSTRACT

Strain CRRU44T was isolated from the stems of Rubus ulmifolius plants growing in Salamanca (Spain). The phylogenetic analysis of the 16S rRNA gene sequence places this strain within the family Rhizobiaceae showing that it is equidistant to the type species of several genera from this family with similarity values ranging from 91.0 to 96.3 %. Strain CRRU44T formed a divergent lineage which clustered with Endobacterium cereale RZME27T, Neorhizobium galegae HAMBI540T and Pseudorhizobium pelagicum R1-200B4T. The phylogenomic analysis showed that strain CRRU44T was equal to or more distant from the remaining genera of the family Rhizobiaceae than other genera among them. The calculated average nucleotide identity based on blast and average amino acid identity values with respect to the type species of all genera from the family Rhizobiaceae were lower than 78.5 and 76.5 %, respectively, which are the currently cut-off values proposed to differentiate genera within this family. All these results together with those from phenotypic and chemotaxonomic analyses support that strain CRRU44T represents a novel species of a novel genus within the family Rhizobiaceae, for which the name Ferranicluibacter rubi gen. nov., sp. nov. is proposed (type strain CRRU44T=CECT 30117T=LMG 31822T).


Subject(s)
Rhizobiaceae , Rubus , Rubus/genetics , Fatty Acids/chemistry , Sequence Analysis, DNA , Spain , Phylogeny , RNA, Ribosomal, 16S/genetics , Bacterial Typing Techniques , DNA, Bacterial/genetics , Base Composition
3.
Int J Mol Sci ; 23(9)2022 Apr 22.
Article in English | MEDLINE | ID: mdl-35563043

ABSTRACT

In recent years, many efforts have been made to identify micronutrients or nutritional strategies capable of preventing, or at least, attenuating, exercise-induced muscle damage and oxidative stress, and improving athlete performance. The reason is that most exercises induce various changes in mitochondria and cellular cytosol that lead to the generation of reactive species and free radicals whose accumulation can be harmful to human health. Among them, supplementation with phenolic compounds seems to be a promising approach since their chemical structure, composed of catechol, pyrogallol, and methoxy groups, gives them remarkable health-promoting properties, such as the ability to suppress inflammatory processes, counteract oxidative damage, boost the immune system, and thus, reduce muscle soreness and accelerate recovery. Phenolic compounds have also already been shown to be effective in improving temporal performance and reducing psychological stress and fatigue. Therefore, the aim of this review is to summarize and discuss the current knowledge on the effects of dietary phenolics on physical performance and recovery in athletes and sports practitioners. Overall, the reports show that phenolics exert important benefits on exercise-induced muscle damage as well as play a biological/physiological role in improving physical performance.


Subject(s)
Athletic Performance , Dietary Supplements , Athletes , Athletic Performance/physiology , Exercise/physiology , Humans , Myalgia
4.
Int J Mol Sci ; 23(6)2022 Mar 16.
Article in English | MEDLINE | ID: mdl-35328621

ABSTRACT

Plant-derived products and their extracted compounds have been used in folk medicine since early times. Zimbro or common juniper (Juniperus communis) is traditionally used to treat renal suppression, acute and chronic cystitis, bladder catarrh, albuminuria, leucorrhea, and amenorrhea. These uses are mainly attributed to its bioactive composition, which is very rich in phenolics, terpenoids, organic acids, alkaloids, and volatile compounds. In the last few years, several studies have analyzed the huge potential of this evergreen shrub, describing a wide range of activities with relevance in different biomedical discipline areas, namely antimicrobial potential against human pathogens and foodborne microorganisms, notorious antioxidant and anti-inflammatory activities, antidiabetic, antihypercholesterolemic and antihyperlipidemic effects, and neuroprotective action, as well as antiproliferative ability against cancer cells and the ability to activate inductive hepato-, renal- and gastroprotective mechanisms. Owing to these promising activities, extracts and bioactive compounds of juniper could be useful for the development of new pharmacological applications in the treatment of several acute and chronic human diseases.


Subject(s)
Juniperus , Anti-Inflammatory Agents/pharmacology , Anti-Inflammatory Agents/therapeutic use , Antioxidants/pharmacology , Antioxidants/therapeutic use , Female , Humans , Phenols/pharmacology , Plant Extracts/pharmacology , Plant Extracts/therapeutic use
5.
Int J Syst Evol Microbiol ; 70(9): 5172-5176, 2020 Sep.
Article in English | MEDLINE | ID: mdl-32915125

ABSTRACT

The original type strains of Agrobacterium radiobacter and Agrobacterium tumefaciens recorded in the eighth edition of Bergey's Manual of Determinative Bacteriology published in 1974 were NCIB 9042T and ATCC 4720T, respectively. However, in the list of the valid names of bacteria compiled in 1980, both strains were changed, A. radiobacter NCIB 9042T to ATCC 19358T and A. tumefaciens ATCC 4720T to ATCC 23308T. These changes were unjustified, particularly in the case of A. tumefaciens whose type strain was replaced by another strain from the same collection, although the original type strain ATCC 4720T was never lost and it is currently available in several culture collections. Therefore, we request that the type strain of A. tumefaciens be corrected from ATCC 23308T to ATCC 4720T.


Subject(s)
Agrobacterium tumefaciens/classification , Phylogeny , Terminology as Topic
6.
Int J Syst Evol Microbiol ; 70(10): 5512-5519, 2020 Oct.
Article in English | MEDLINE | ID: mdl-32910749

ABSTRACT

A bacterial strain designated as RZME10T was isolated from a Zea mays L. root collected in Spain. Results of analysis of the 16S rRNA gene sequence showed that this strain belongs to the genus Agrobacterium with Agrobacterium larrymoorei ATCC 51759T being the most closely related species with 99.9 % sequence similarity. The similarity values of the rpoB, recA, gyrB, atpD and glnII genes between strain RZME10T and A. larrymoorei ATCC 51759T were 93.5, 90.0, 88.7, 87.9 and 90.1 %, respectively. The estimated average nucleotide identity using blast and digital DNA-DNA hybridization values between these two strains were 80.4 and 30.2 %, respectively. The major fatty acids of strain RZME10T are those from summed feature 8 (C18 : 1 ω6c/C18 : 1 ω7c) and C16 : 0. Pathogenicity tests on tomato and carrot roots showed that strain RZME10T was not able to induce plant tumours. Based on the results of genomic, chemotaxonomic and phenotypic analyses, we propose that strain RZME10T represents a novel species named Agrobacterium cavarae sp. nov. (type strain RZME10T=CECT 9795T=LMG 31257T).


Subject(s)
Agrobacterium/classification , Phylogeny , Plant Roots/microbiology , Zea mays/microbiology , Agrobacterium/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genes, Bacterial , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spain
7.
Int J Syst Evol Microbiol ; 67(6): 1789-1792, 2017 Jun.
Article in English | MEDLINE | ID: mdl-28598309

ABSTRACT

The species Arthrobacter viscosus was isolated from soil from Guatemala and it was classified into the genus Arthrobacter on the basis of phenotypic traits. Nevertheless, the results of16S rRNA gene analysis indicated that this species is a member of the genus Rhizobium, with Rhizobium alamii GBV016T and Rhizobium mesosinicum CCBAU 25010T as the most closely related species with 99.64 and 99.48 % similarity, respectively. The similarity values for the recA gene are 92.2 and 94.4 % with respect to R. alamii GBV016T and R. mesosinicum CCBAU 25010T, respectively, and those for the atpD gene are 92.9 and 98.7 %, respectively. Results of DNA-DNA hybridization analysis yield averages of 46 and 41 % relatedness with respect to the type strains of R. alamii and R. mesosinicum, respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Rhizobium. Therefore, based on the data obtained in this study, we propose to classify strain LMG 16473T as representing a novel species named Rhizobiumviscosum comb. nov. (type strain LMG 16473T=CECT 908T).


Subject(s)
Arthrobacter/classification , Phylogeny , Rhizobium/classification , Soil Microbiology , Bacterial Typing Techniques , DNA, Bacterial/genetics , Genes, Bacterial , Guatemala , Nucleic Acid Hybridization , Sequence Analysis, DNA
8.
Int J Syst Evol Microbiol ; 67(7): 2312-2316, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28699855

ABSTRACT

A bacterial strain designated RTAE36T was isolated from wheat roots in northern Spain. Phylogenetic analyses based on 16S rRNA gene sequence placed the isolate into the genus Paenibacillus with its closest relative being Paenibacillus borealis DSM 13188T with 97.7 % sequence similarity. Cells of the isolate were facultatively anaerobic, Gram-stain-positive, motile and sporulating rods. Catalase and oxidase were positive. Gelatin, casein and starch were not hydrolysed. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected, and anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C16 : 0 were the major fatty acids. The polar lipids profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, one unidentified aminolipid, two unidentified phospholipids, three unidentified phosphoaminolipids, one unidentified glycolipid and one unidentified lipid. meso-Diaminopimelic acid was detected in the cell-wall peptidoglycan. Strains RTAE36T and P. borealis DSM 13188T had an mean DNA-DNA relatedness of 39 % and differed in several phenotypic and chemotaxonomic characteristics, confirming that strain RTAE36T should be considered as a representative of a novel species of the genus Paenibacillus, for which the name Paenibacillus tritici sp. nov. is proposed. The type strain is RTAE36T (=LMG 29502T=CECT 9125T).


Subject(s)
Phylogeny , Plant Roots/microbiology , Triticum/microbiology , Bacterial Typing Techniques , Base Composition , Cell Wall/chemistry , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Glycolipids/chemistry , Nucleic Acid Hybridization , Paenibacillus/classification , Paenibacillus/genetics , Paenibacillus/isolation & purification , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spain , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
9.
Int J Syst Evol Microbiol ; 67(7): 2236-2241, 2017 Jul.
Article in English | MEDLINE | ID: mdl-28671523

ABSTRACT

Two slow-growing strains, AMBPC1010T and AMBPC1011, were isolated from nodules of Cajanus cajan in the Dominican Republic. 16S rRNA gene analysis placed these strains within the genus Bradyrhizobium, being phylogenetically equidistant to several species of this genus. Analysis of the recA and atpD genes showed that the strains isolated belong to a cluster containing the strains Bradyrhizobium ottawaense OO99T, 'Bradyrhizobium americanum' CMVU44 and Bradyrhizobium daqingense CCBAU 15774T, and presented similarity values lower than 96 % for both genes with respect to the strains nodulating C. cajan. DNA-DNA hybridization analysis showed averages of 36, 40 and 39 % relatedness with respect to the representative strains of Bradyrhizobium ottawaense, 'Bradyrhizobium americanum' and Bradyrhizobium daqingense, respectively. Phenotypic characteristics also differed from those of the most closely related species of the genus Bradyrhizobium. Therefore, based on the data obtained in this study, we propose to classify the strains AMBPC1010T (=LMG 29967T=CECT 9227T) and AMBPC1011 into a novel species named Bradyrhizobium cajani sp. nov.


Subject(s)
Bradyrhizobium/classification , Cajanus/microbiology , Phylogeny , Root Nodules, Plant/microbiology , Bacterial Typing Techniques , Base Composition , Bradyrhizobium/genetics , Bradyrhizobium/isolation & purification , DNA, Bacterial/genetics , Dominican Republic , Genes, Bacterial , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis
10.
Int J Syst Evol Microbiol ; 66(12): 4936-4941, 2016 Dec.
Article in English | MEDLINE | ID: mdl-27565417

ABSTRACT

In this work we revise the taxonomic status of the Lotus-nodulating strains MAFF 303099T and R7A isolated in Japan and New Zealand, respectively. Their 16S rRNA gene sequences are identical and show 98.0, 99.7, 99.8 and 99.9 % similarity values with respect to Mesorhizobium loti NZP 2213T, M. jarvisii ATCC 33669T, M. huakuii USDA 4779T (=CCBAU 2609T) and M. erdmanii USDA 3471T, respectively. The analysis of recA and glnII gene sequeces showed that M. jarvisii ATCC 33669T and M. huakuii USDA 4779T (=CCBAU 2609T) are the most closely related strains to MAFF 303099T and R7A, with similarity values suggesting that these two strains belong to a different species for which MAFF 303099T is selected as the type strain. The DNA-DNA relatedness values between strain MAFF 303099T and its closest phylogenetic relatives ranged from 53 to 60 % in average. Strains MAFF 303099T and R7A presented slight differences in the proportions of C18 : 1ω7c 11-methyl and C19 : 0 cyclo ω8c fatty acids with respect to M. jarvisii ATCC 33669T and M. huakuii USDA 4779T, and also in several phenotypic characteristics. Therefore, we propose the reclassification of these two strains into a novel species named Mesorhizobium japonicum sp. nov., with the type strain being MAFF 303099T (=LMG 29417T=CECT 9101T).


Subject(s)
Lotus/microbiology , Mesorhizobium/classification , Phylogeny , Root Nodules, Plant/microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genes, Bacterial , Japan , Mesorhizobium/genetics , New Zealand , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis
11.
Int J Syst Evol Microbiol ; 65(7): 2337-2340, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25888545

ABSTRACT

The species Seliberia stellata was described in 1963 and the name validly published in 1980. Its type strain, INMI N-9(T), was deposited in the VKM collection by one of the authors reporting its 5S rRNA gene sequence. Based on the analysis of this sequence, the currently distributed strains VKM B-1340 and CECT 7960 are not the original type strain of Seliberia stellata. A 16S rRNA gene sequence analysis of strain CECT 7960 had previously shown that this strain belongs to the species Bradyrhizobium betae, and this result was confirmed in the present paper by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS analysis for both CECT 7960 and VKM B-1340. Therefore, we propose that the Judicial Commission consider the following. (1) That the organism currently deposited as VKM B-1340 and CECT 7960 be recognized as a member of the species Bradyrhizobium betae. (2) That the organism deposited as VKM B-1340 and CECT 7960 does not represent the type strain of the species Seliberia stellata. (3) To place the species name Seliberia stellataAristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names if a suitable replacement strain, or a neotype, cannot be found within two years of publication of this Request (Rule 18c). (4) To place the genus name SeliberiaAristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names (Recommendation 20d) if a suitable replacement type strain or a neotype for the type species of the genus SeliberiaAristovskaya and Parinkina 1963 (Approved Lists 1980) is not identified as indicated in point (3).


Subject(s)
Hyphomicrobiaceae/classification , Phylogeny , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 5S/genetics , Sequence Analysis, DNA , Terminology as Topic
12.
Int J Syst Evol Microbiol ; 65(Pt 6): 1703-1708, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25736411

ABSTRACT

The species Mesorhizobim loti was isolated from nodules of Lotus corniculatus and its type strain deposited in several collections. Some of these type strains, such as those deposited in the USDA and ATCC collections before 1990, are not coincident with the original strain, NZP 2213T, deposited in the NZP culture collection. The analysis of the 16S rRNA gene showed that strains USDA 3471T and ATCC 33669T formed independent branches from that occupied by Mesorhizobium loti NZP 2213T and related to those occupied by Mesorhizobium opportunistum WSM2075T and Mesorhizobium huakuii IFO 15243T, respectively, with 99.9 % similarity in both cases. However, the analysis of concatenated recA, atpD and glnII genes with similarities lower than 96, 98 and 94 %, respectively, between strains USDA 3471T and M. opportunistum WSM2075T and between strains ATCC 33669T and M. huakuii IFO 15243T, indicated that the strains USDA 3471T and ATCC 33669T represent different species of the genus Mesorhizobium. These results were confirmed by DNA-DNA hybridization experiments and phenotypic characterization. Therefore, the two strains were reclassified as representatives of the two species Mesorhizobium erdmanii sp. nov. (type strain USDA 3471T = CECT 8631T = LMG 17826t2T) and Mesorhizobium jarvisii sp. nov. (type strain ATCC 33669T = CECT 8632T = LMG 28313T).


Subject(s)
Lotus/microbiology , Mesorhizobium/classification , Phylogeny , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Genes, Bacterial , Mesorhizobium/genetics , Molecular Sequence Data , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Root Nodules, Plant/microbiology , Sequence Analysis, DNA , United States , United States Department of Agriculture
13.
Int J Syst Evol Microbiol ; 65(Pt 4): 1213-1219, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25609676

ABSTRACT

The species Rhizobium lupini was isolated from Lupinus nodules and included in the Approved Lists of Bacterial Names in 1980. Nevertheless, on the basis of the analysis of the type strain of this species available in DSMZ, DSM 30140(T), whose 16S rRNA gene was identical to that of the type strain of Bradyrhizobium japonicum , R. lupini was considered a later synonym of this species. In this study we confirmed that the strain DSM 30140(T) belongs to the species B. japonicum , but also that it cannot be the original strain of R. lupini because this species effectively nodulated Lupinus whereas strain DSM 30140(T) was able to nodulate soybean but not Lupinus. Since the original type strain of R. lupini was deposited into the USDA collection by L. W. Erdman under the accession number USDA 3051(T) we analysed the taxonomic status of this strain showing that although it belongs to the genus Bradyrhizobium instead of genus Rhizobium , it is phylogenetically distant from B. japonicum and closely related to Bradyrhizobium canariense . The type strains R. lupini USDA 3051(T) and B. canariense BTA-1(T) share 16S rRNA, recA and glnII gene sequences with similarities of 99.8%, 96.5% and 97.1%, respectively. They presented a DNA-DNA hybridization value of 36% and also differed in phenotypic characteristics and slightly in the proportions of some fatty acids. Therefore we propose the reclassification of the species Rhizobium lupini as Bradyrhizobium lupini comb. nov. The type strain is USDA 3051(T) ( = CECT 8630(T) = LMG 28514(T)).


Subject(s)
Bradyrhizobium/classification , Phylogeny , Rhizobium/classification , Bacterial Typing Techniques , DNA, Bacterial/genetics , Lupinus/microbiology , Molecular Sequence Data , Nucleic Acid Hybridization , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Symbiosis
14.
Antonie Van Leeuwenhoek ; 107(5): 1315-21, 2015 May.
Article in English | MEDLINE | ID: mdl-25772303

ABSTRACT

A bacterial strain designated A4STR04(T) was isolated from the inner root tissue of potatoes in Spain. Phylogenetic analysis based on the 16S rRNA gene sequence placed the isolate into the genus Fontibacillus, being most closely related to Fontibacillus panacisegetis KCTC 13564(T) with 99% identity. The isolate was observed to form Gram-positive, motile and sporulating rods. The catalase test was found to be negative and oxidase positive. Nitrate was found to be reduced to nitrite. ß-Galactosidase and caseinase were observed to be produced but the production of gelatinase, urease, arginine dehydrolase, ornithine and lysine decarboxylase was negative. Aesculin hydrolysis was found to be positive and acetoin production was negative. Growth was found to be supported by many carbohydrates and organic acids as carbon source. MK-7 was the only menaquinone detected and the major fatty acid (61.5%) was identified as anteiso-C(15:0), as occurs in the other species of genus Fontibacillus. The strain A4STR04(T) was found to display a complex lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, a glycolipid, two phospholipids, a lipid and two aminophospholipids. Mesodiaminopimelic acid was detected in the peptidoglycan. The G+C content was determined to be 50.5 mol% (Tm). Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain A4STR04(T) (=LMG 28458 (T) = CECT 8693(T)) should be classified as representing a novel species of genus Fontibacillus, for which the name Fontibacillus solani sp. nov. is proposed.


Subject(s)
Bacillales/classification , Bacillales/isolation & purification , Plant Roots/microbiology , Solanum tuberosum/microbiology , Bacillales/genetics , Bacillales/metabolism , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Fatty Acids/metabolism , Molecular Sequence Data , Phylogeny , Plant Roots/genetics , RNA, Ribosomal, 16S/genetics
15.
Int J Syst Evol Microbiol ; 64(Pt 1): 83-87, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24021729

ABSTRACT

A bacterial strain designated RLAHU4B(T) was isolated from root nodules of Lupinus albus in León (Spain). The 16S rRNA gene sequence of this strain showed similarities lower than 97 % with respect to species of the genus Cohnella. The strain was a Gram-variable, sporulating rod, motile by means of peritrichous flagella, and facultatively anaerobic. It was positive for oxidase, catalase and ß-galactosidase production but negative for urease, amylase and gelatinase. Strain RLAHU4B(T) grew in the presence of 5 % NaCl. MK-7 was the predominant menaquinone and meso-diaminopimelic acid was present in the peptidoglycan. anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0 and C16 : 0 were the major fatty acids. Major polar lipids of strain RLAHU4B(T) were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three unknown phospholipids, two unknown aminophospholipids and one unknown lipid. The DNA G+C content was 57.8 mol%. Strain RLAHU4B(T) presented phenotypic differences from all recognized species of the genus Cohnella. The phylogenetic, chemotaxonomic and phenotypic data indicated that strain RLAHU4B(T) belongs to a novel species of the genus Cohnella, for which the name Cohnella lupini sp. nov. is proposed, with strain RLAHU4B(T) ( = LMG 27416(T) = CECT 8236(T)) as the type strain.


Subject(s)
Bacillales/classification , Lupinus/microbiology , Phylogeny , Root Nodules, Plant/microbiology , Bacillales/genetics , Bacillales/isolation & purification , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Endophytes/classification , Endophytes/genetics , Endophytes/isolation & purification , Fatty Acids/chemistry , Molecular Sequence Data , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spain , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
16.
Int J Syst Evol Microbiol ; 64(Pt 9): 3028-3033, 2014 Sep.
Article in English | MEDLINE | ID: mdl-24928428

ABSTRACT

A bacterial strain designated RLAHU15(T) was isolated from root nodules of Lupinus albus in Spain. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus, with its closest relatives being Paenibacillus catalpae D75(T), Paenibacillus glycanilyticus DS-1(T), Paenibacillus endophyticus PECAE04(T) and Paenibacillus xinjiangensis B538(T) with 98.8 %, 98.9 %, 97.4 % and 97.4 % similarity, respectively. DNA-DNA hybridization studies showed values lower than 45 % between the strain RLAHU15(T) and any of these species. The isolate was a Gram-stain positive, motile and sporulating rod. Catalase activity was weak and oxidase activity was positive. Casein and starch were hydrolysed but gelatin was not. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 54.4 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RLAHU15(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lupini sp. nov. is proposed. The type strain is RLAHU15(T) ( = LMG 27296(T) = CECT 8235(T)).


Subject(s)
Lupinus/microbiology , Paenibacillus/classification , Phylogeny , Root Nodules, Plant/microbiology , Base Composition , DNA, Bacterial/genetics , Diaminopimelic Acid/chemistry , Fatty Acids/chemistry , Molecular Sequence Data , Nucleic Acid Hybridization , Paenibacillus/genetics , Paenibacillus/isolation & purification , Peptidoglycan/chemistry , Phospholipids/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spain , Vitamin K 2/analogs & derivatives , Vitamin K 2/chemistry
17.
Int J Syst Evol Microbiol ; 64(Pt 7): 2338-2345, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24744015

ABSTRACT

A bacterial strain, OHA11(T), was isolated during the course of a study of phosphate-solubilizing bacteria occurring in a forest soil from Salamanca, Spain. The 16S rRNA gene sequence of strain OHA11(T) shared 99.1% similarity with respect to Pseudomonas baetica a390(T), and 98.9% similarity with the type strains of Pseudomonas jessenii, Pseudomonas moorei, Pseudomonas umsongensis, Pseudomonas mohnii and Pseudomonas koreensis. The analysis of housekeeping genes rpoB, rpoD and gyrB confirmed its phylogenetic affiliation to the genus Pseudomonas and showed similarities lower than 95% in almost all cases with respect to the above species. Cells possessed two polar flagella. The respiratory quinone was Q9. The major fatty acids were C16 : 0, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c/iso-C15 : 0 2-OH). The strain was oxidase-, catalase- and urease-positive, positive for arginine dihydrolase but negative for nitrate reduction, ß-galactosidase production and aesculin hydrolysis. It was able to grow at 31 °C and at pH 11. The DNA G+C content was 58.1 mol%. DNA-DNA hybridization results showed values lower than 49% relatedness with respect to the type strains of the seven closest related species. Therefore, the combined genotypic, phenotypic and chemotaxonomic data support the classification of strain OHA11(T) to a novel species of the genus Pseudomonas, for which the name Pseudomonas helmanticensis sp. nov. is proposed. The type strain is OHA11(T) ( = LMG 28168(T) = CECT 8548(T)).


Subject(s)
Phylogeny , Pseudomonas/classification , Soil Microbiology , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/chemistry , Genes, Bacterial , Molecular Sequence Data , Nucleic Acid Hybridization , Pseudomonas/genetics , Pseudomonas/isolation & purification , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spain , Trees , Ubiquinone/chemistry
18.
Antonie Van Leeuwenhoek ; 105(1): 23-8, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24122118

ABSTRACT

A bacterial strain, designated BAPVE7BT, was isolated from root nodules of Phaseolus vulgaris in Spain. Phylogenetic analysis based on its 16S rRNA gene sequence placed the isolate into the genus Fontibacillus with Fontibacillus panacisegetis KCTC 13564T its closest relative with 97.1 % identity. The isolate was observed to be a Gram-positive, motile and sporulating rod. The catalase test was negative and oxidase was weak. The strain was found to reduce nitrate to nitrite and to produce ß-galactosidase but the production of gelatinase, caseinase, urease, arginine dehydrolase, ornithine or lysine decarboxylase was negative. Acetoin production and aesculin hydrolysis were found to be positive. Growth was observed to be supported by many carbohydrates and organic acids as carbon source. MK-7 was identified as the predominant menaquinone and the major fatty acid (43.7 %) as anteiso-C15:0, as occurs in the other species of the genus Fontibacillus. Strain BAPVE7BT displayed a complex lipid profile consisting of diphosphatidylglycerol, phosphatidylglycerol, four glycolipids, four phospholipids, two lipids, two aminolipids and an aminophospholipid. Mesodiaminopimelic acid was detected in the peptidoglycan. The G+C content was determined to be 45.6 mol% (Tm). Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain BAPVE7BT should be considered a new species of genus Fontibacillus, for which the name Fontibacillus phaseoli sp. nov. is proposed (type strain, LMG 27589T, CECT 8333T).


Subject(s)
Bacillales/isolation & purification , Phaseolus/microbiology , Root Nodules, Plant/microbiology , Bacillales/classification , Bacillales/genetics , Bacillales/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Bacterial Typing Techniques , Base Composition , Fatty Acids/chemistry , Fatty Acids/metabolism , Molecular Sequence Data , Phylogeny
19.
Microorganisms ; 12(1)2024 Jan 18.
Article in English | MEDLINE | ID: mdl-38258016

ABSTRACT

The study of bacterial communities associated with plants, particularly those of agronomic interest, has been investigated since the late 19th century, revealing the relationship between nodule formation in leguminous plants, nitrogen fixation, their contribution to the plant, and the imperative presence of rhizobia within these nodules [...].

20.
Syst Appl Microbiol ; 47(4): 126517, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38772266

ABSTRACT

The symbiovar mediterranense of Sinorhizobium meliloti was initially found in Phaseolus vulgaris nodules in Tunisia and in an eastern location of Lanzarote (Canary Islands). Here we show that the symbiovar mediterranense of S. meliloti also nodulates P. vulgaris in two western locations of this Island. The analyses of the symbiotic nodA and nodC genes reveal the complexity of the symbiovar mediterranense which encompasses strains belonging to several phylogenetic lineages and clusters. The comparison of the nodA and nodC phylogenies showed that the nodC was the most resolutive phylogenetic marker for the delineation of Sinorhizobium symbiovars. Considering that the similarity of this gene within several symbiovars, particularly mediterranense, is around 95 %, the cut-off value for their differentiation should be lower. Considering that a nodC gene cut-off similarity value of around 92 % is accepted for the genus Bradyrhizobium and that the symbiovar concept is identical in all rhizobial genera, we propose to apply this value for symbiovars delineation within all these genera. Therefore, using this cut-off value for the nodC gene analysis of Sinorhizobium symbiovars, we propose to merge the symbiovars aegeanense and fredii into the single symbiovar fredii and to define four novel symbiovars with the names asiaense, culleni, sudanense and tunisiaense.


Subject(s)
Bacterial Proteins , Phaseolus , Phylogeny , Sinorhizobium meliloti , Symbiosis , Phaseolus/microbiology , Sinorhizobium meliloti/genetics , Sinorhizobium meliloti/classification , Bacterial Proteins/genetics , Root Nodules, Plant/microbiology , Sequence Analysis, DNA , Tunisia , N-Acetylglucosaminyltransferases/genetics , DNA, Bacterial/genetics , Acyltransferases
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