RESUMEN
Phthalates (PAEs) accumulated in agricultural soils and rice have increased human exposure risks. Microbial degradation could efficiently reduce the residue of organic pollutants in soil and crop plants. Here, we hypothesized that endophytic bacteria from wild rice have the potential for degradation of PAEs and plant growth promoting. The endophytic bacterial community and functional diversity in wild rice (Oryza meridionalis) were analyzed for the first time, and the potential for PAE degradation and plant growth promoting by endophytes were investigated. The results of Illumina high-throughput sequencing revealed that abundant endophytes inhabited in wild rice with Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria being the dominant phyla. Endophytic bacterial diversity and complexity were confirmed by isolation and clustering of isolates. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that endophytes exerted diverse functions such as plant growth promoting, xenobiotics biodegradation, pollution remediation and bacterial chemotaxis. Pure culture experiment showed that 30 isolated endophytic strains exhibited in vitro plant growth promoting activities, and rice plants inoculated with these strains confirmed their growth promoting abilities. Some endophytic strains were capable of efficiently degrading PAEs, with the highest removal percentage of di-n-butyl phthalate (DBP) up to 96.1% by Bacillus amyloliquefaciens strain L381 within 5â¯days. Synthetic community F and strain L381 rapidly removed DBP from soil (removing 91.0%-99.2% within 10 d and from rice plant slurry (removing 93.4%-99.2% within 5 d). These results confirmed the hypothesis and demonstrated the diversity of endophytic bacteria in wild rice with diverse functions, especially for plant growth promoting and removing PAEs. These multifunctional endophytic bacteria provided good alternatives to reduce PAE accumulation in crops and increase yield.
Asunto(s)
Oryza , Bacterias/genética , Biodegradación Ambiental , Endófitos , Humanos , Desarrollo de la Planta , Raíces de PlantasRESUMEN
Three aniline-degrading bacteria, strains DN316(T), DN316-1 and DN365, were isolated from activated sludge. According to 16S rRNA gene sequence-based phylogenetic analysis, the isolates belonged to the genus Rhizobium, with Rhizobium (â=âAgrobacterium) radiobacter LMG 140(T) as the closest relative, with 96.5â% sequence similarity. Phylogenetic analysis of the representative strain DN316(T) using sequences of the glnA, thrC and recA genes and the 16S-23S intergenic spacer region confirmed the phylogenetic arrangement obtained from analysis of the 16S rRNA gene. DNA-DNA relatedness between DN316(T) and R. radiobacter LMG 140(T) was 43.7â%, clearly indicating that the representative strain DN316(T) represents a novel species. Phenotypic and biochemical characterization of the isolates and insertion sequence-PCR fingerprinting patterns showed several distinctive features that differentiated them from closely related species. The major components of the cellular fatty acids were C(18â:â1)ω7c (57.10â%), C(16â:â0) (11.31â%) and C(19â:â0) cyclo ω8c (10.13â%). Based on our taxonomic analysis, the three isolates from activated sludge represent a novel species of the genus Rhizobium, for which the name Rhizobium borbori sp. nov. is proposed. The type strain is DN316(T) (â=âCICC 10378(T) â=âLMG 23925(T)).
Asunto(s)
Compuestos de Anilina/metabolismo , Rhizobium/clasificación , Rhizobium/metabolismo , Aguas del Alcantarillado/microbiología , Técnicas de Tipificación Bacteriana , Análisis por Conglomerados , Dermatoglifia del ADN , Elementos Transponibles de ADN , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/química , ADN Ribosómico/genética , ADN Espaciador Ribosómico/química , ADN Espaciador Ribosómico/genética , Ácidos Grasos/análisis , Genotipo , Glutamato-Amoníaco Ligasa , Datos de Secuencia Molecular , Tipificación Molecular , Hibridación de Ácido Nucleico , Filogenia , ARN Ribosómico 16S/genética , Rec A Recombinasas , Rhizobium/genética , Rhizobium/aislamiento & purificación , Análisis de Secuencia de ADNRESUMEN
Twenty-three nitrogen-fixing bacteria were isolated from surface-sterilized stems and roots of wild rice Oryza rufipogon. Four clusters were defined among these bacteria by SDS-PAGE protein patterns and further confirmed by IS-PCR finger-printing analysis. Phylogenetic analysis of 16S rRNA gene sequences showed that the representative strains LS 8 and LS 18 of cluster II formed a monophyletic group sharing 94.0-97.3% similarities with defined enterobacterial species within the genera Salmonella, Citrobacter, Pantoea, Klebsiella, and Enterobacter. DNA-DNA hybridization, physiological, biochemical tests, and cell morphology also revealed that these strains could be differentiated from the related enterobacterial species. Based upon these results, we propose Phytobacter diazotrophicus gen. nov., sp. nov. to the bacterial group represented by strains LS 8 and LS 18. The type strain is LS 8(T) (=DSM 17806(T) = LMG 23328(T) = CGMCC 1.5339(T)). The DNA G+C content of strain LS 8(T) is 58.6 +/- 0.5 mol%.
Asunto(s)
Enterobacteriaceae/aislamiento & purificación , Fijación del Nitrógeno , Oryza/microbiología , Secuencia de Bases , Dermatoglifia del ADN , Electroforesis en Gel de Poliacrilamida , Enterobacteriaceae/clasificación , Enterobacteriaceae/ultraestructura , Datos de Secuencia Molecular , Oxidorreductasas/genética , Filogenia , Reacción en Cadena de la Polimerasa , ARN Bacteriano/genética , ARN Ribosómico 16S/genéticaRESUMEN
Conzattia multiflora is a leguminous tree present only in Mexico and Guatemala. There is no record about its symbiotic or pathogenic microbes. In this study, we found that numerous bacteria with 10(4)-10(6) individuals per gram of fresh epidermis were distributed in the tissue of this plant. All the bacteria isolated from the Conzattia epidermis were Gram-negative, facultative anaerobic rods and formed yellow or colorless colonies. They were identified as endophytes by inoculation tests. Some of the bacteria could significantly promote the growth of Conzattia seedlings. Nine different groups were defined by PCR-based RFLP, which were classified as Pantoea, Erwinia, Salmonella, Enterobacter, Citrobacter and Klebsiella by the phylogenetic analysis of 16S rRNA genes. The existence of plant-borne lineages of Salmonella indicates that the unexplored plants may harbor some unknown microbes.
Asunto(s)
Fabaceae/microbiología , Bacilos Gramnegativos Anaerobios Facultativos/clasificación , Bacilos Gramnegativos Anaerobios Facultativos/aislamiento & purificación , Árboles/microbiología , Acetileno/metabolismo , ADN Bacteriano/análisis , Fabaceae/crecimiento & desarrollo , Bacilos Gramnegativos Anaerobios Facultativos/genética , Bacilos Gramnegativos Anaerobios Facultativos/crecimiento & desarrollo , México , Datos de Secuencia Molecular , Oxidación-Reducción , Filogenia , Estructuras de las Plantas/microbiología , Reacción en Cadena de la Polimerasa , Polimorfismo de Longitud del Fragmento de Restricción , ARN Ribosómico 16S/genética , Simbiosis , Árboles/crecimiento & desarrolloRESUMEN
Ninety-five rhizobial strains isolated from Astragalus adsurgens growing in the northern regions of China were classified into three main groups, candidate species I, II and III, based on a polyphasic approach. Comparative analysis of full-length 16S rRNA gene sequences of representative strains showed that candidate species I and II were Mesorhizobium, while candidate species III, which consisted of non-nodulating strains, was closely related to Agrobacterium tumefaciens. The phylogenetic relationships of the three candidate species and some related strains were also confirmed by the sequencing of glnA genes, which were used as an alternative chromosomal marker. The DNA-DNA relatedness was between 11.3 and 47.1 % among representative strains of candidate species I and II and the type strains of defined Mesorhizobium species. Candidate III had DNA relatedness of between 4.3 and 25.2 % with type strains of Agrobacterium tumefaciens and Agrobacterium rubi. Two novel species are proposed to accommodate candidate species I and II, Mesorhizobium septentrionale sp. nov. (type strain, SDW014(T)=CCBAU 11014(T)=HAMBI 2582(T)) and Mesorhizobium temperatum sp. nov. (type strain, SDW018(T)=CCBAU 11018(T)=HAMBI 2583(T)), respectively. At least two distinct nodA sequences were identified among the strains. The numerically dominant nodA sequence type was most similar to that from the Mesorhizobium tianshanense type strain and was identified in strains belonging to the two novel species as well as other, as yet, undefined genome types. Host range studies indicate that the different nodA sequences correlate with different host ranges. Further comparative studies with the defined Agrobacterium species are needed to clarify the taxonomic identity of candidate species III.
Asunto(s)
Alphaproteobacteria/clasificación , Alphaproteobacteria/aislamiento & purificación , Planta del Astrágalo/microbiología , Aciltransferasas/genética , Proteínas Bacterianas/genética , Técnicas de Tipificación Bacteriana , China , ADN Bacteriano/química , ADN Bacteriano/aislamiento & purificación , ADN Ribosómico/química , ADN Ribosómico/aislamiento & purificación , Genes de ARNr , Genotipo , Glutamato-Amoníaco Ligasa/genética , Datos de Secuencia Molecular , Filogenia , ARN Bacteriano/genética , ARN Ribosómico 16S/genética , Rhizobium/genética , Análisis de Secuencia de ADNRESUMEN
Forty-six Mesorhizobium strains associated with the leguminous plants Leucaena leucocephala and Sesbania herbacea in an uncultivated Mexican field were characterized using a polyphasic approach. The strains were identified as Mesorhizobium plurifarium based upon the close relationships with the reference strains for this species in PCR-based restriction fragment length polymorphism analyses, sequencing of 16S rRNA genes, multilocus enzyme electrophoresis, and DNA-DNA hybridization. Although the strains isolated from both plants formed the same group in multilocus enzyme electrophoresis and cross-nodulations were observed in the laboratory, different electrophoretic types were obtained from the two plants grown in natural soils, indicating the existence of a preferable association between the plants and the rhizobia. The M. plurifarium strains from Mexico and the reference strains from Africa and Brazil formed different phenotypic clusters in a numerical taxonomy. The Mexican strains did not grow at 37 degrees C and were sensitive to salty-alkaline conditions, while the reference strains from Africa and Brazil grew at 42 degrees C and were more resistant to salty-alkaline conditions. These results demonstrate that both the plants and environmental factors affected the evolution of rhizobia and that the Mexican strains had adapted to the neutral soils and the cool climate where they were isolated.
Asunto(s)
Alphaproteobacteria/clasificación , Alphaproteobacteria/aislamiento & purificación , Biodiversidad , Fabaceae/microbiología , Microbiología del Suelo , Adaptación Biológica , Alphaproteobacteria/crecimiento & desarrollo , Proteínas Bacterianas/análisis , Proteínas Bacterianas/aislamiento & purificación , Evolución Biológica , ADN Ribosómico/química , ADN Ribosómico/aislamiento & purificación , Variación Genética , Concentración de Iones de Hidrógeno , México , Datos de Secuencia Molecular , Hibridación de Ácido Nucleico , Presión Osmótica , Filogenia , Polimorfismo de Longitud del Fragmento de Restricción , ARN Ribosómico 16S/genética , Análisis de Secuencia de ADN , Homología de Secuencia de Ácido Nucleico , Cloruro de Sodio , TemperaturaRESUMEN
Twenty-nine rhizobial isolates from root nodules of Astragalus and Lespedeza spp. growing in the Loess Plateau of China were characterized by numerical taxonomy, RFLP and sequencing of PCR-amplified 16S rRNA genes, measurement of DNA G+C content, DNA-DNA relatedness and cross-nodulation with selected legume species. Based on the results of numerical taxonomy, the isolates formed two clusters (1 and 2) with some single isolates at a similarity level of 82 %. Cluster 1 contained six isolates from Astragalus and Lespedeza spp. Cluster 2 consisted of nine isolates from Astragalus spp. DNA relatedness was greater than 80 % among isolates within cluster 2. Phylogenetic analysis based on 16S rRNA gene sequences showed that CCBAU 7190B(T), representing cluster 2, was closely related to Rhizobium galegae and Rhizobium huautlense. DNA-DNA relatedness between CCBAU 7190B(T) and reference strains of R. galegae, R. huautlense and other related species ranged from 0 to 48.6 %. The cluster 2 isolates could also be differentiated phenotypically from related species. Based on these data, a novel species, Rhizobium loessense sp. nov., is proposed for cluster 2, with the type strain CCBAU 7190B(T) (=AS1.3401(T)=LMG 21975(T)).
Asunto(s)
Planta del Astrágalo/microbiología , Lespedeza/microbiología , Rhizobium/clasificación , Rhizobium/aislamiento & purificación , Composición de Base , China , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/genética , Genes Bacterianos , Datos de Secuencia Molecular , Fenotipo , Filogenia , ARN Bacteriano/genética , ARN Ribosómico 16S/genética , Rhizobium/genética , Rhizobium/metabolismoRESUMEN
Sinorhizobium morelense sp. nov. is described to designate a group of bacteria isolated from root nodules of Leucaena leucocephala. S. morelense shows 98% 16S rRNA gene sequence similarity to some Sinorhizobium species and to Ensifer adhaerens. This novel species is distinguished from other Sinorhizobium species and from E. adhaerens by DNA-DNA hybridization, 165 rRNA gene restriction fragments and sequence and some distinctive phenotypic features. Strains of this species are highly resistant to some antibiotics, such as carbenicillin (1 mg ml(-1)), kanamycin (500 microg ml(-1)) and erythromycin (300 microg ml(-1)). They do not form nodules, but a nodulating strain, Lc57, is closely related to the novel species. Strain Lc04T (= LMG 21331T = CFN E1007T) is designated as the type strain of this novel species.
Asunto(s)
Sinorhizobium/clasificación , Composición de Base , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Ribosómico/genética , Farmacorresistencia Bacteriana Múltiple/genética , Fabaceae/microbiología , Datos de Secuencia Molecular , Fenotipo , Filogenia , Raíces de Plantas/microbiología , ARN Bacteriano/genética , ARN Ribosómico 16S/genética , Sinorhizobium/efectos de los fármacos , Sinorhizobium/genética , Sinorhizobium/aislamiento & purificación , Microbiología del SueloRESUMEN
Eight fast-growing rhizobial isolates from Xinjiang soils were identified as Sinorhizobium xinjiangense by analyses of 16S rRNA gene sequences, SDS-PAGE of proteins, intergenic spacer sequences and DNA-DNA hybridization. Based on all of the results, these isolates and the reference strains for S. xinjiangense were a distinct genomic species, although the 16S rRNA genes were closely related to that of Sinorhizobium fredii.
Asunto(s)
Glycine max/microbiología , Sinorhizobium/clasificación , Proteínas Bacterianas/análisis , Composición de Base , China , Análisis por Conglomerados , ADN Intergénico , Electroforesis en Gel de Poliacrilamida , Datos de Secuencia Molecular , Filogenia , ARN Bacteriano/química , ARN Ribosómico 16S/química , Homología de Secuencia de Ácido Nucleico , Sinorhizobium/genética , Especificidad de la EspecieRESUMEN
Forty-eight rhizobial isolates from root nodules of Indigofera and Kummerowia, two genera of annual or perennial wild legumes growing in the Loess Plateau in north-western China, were characterized by a polyphasic approach. Two main groups, cluster 1 and cluster 2, were defined based upon the results of numerical taxonomy, SDS-PAGE of whole-cell proteins and DNA relatedness. All the isolates within cluster 1 were isolated from Indigofera and they were identified as Rhizobium strains by 16S rRNA gene analysis. DNA relatedness of 29.5-48.9% was obtained among the cluster 1 isolates and the reference strains for defined Rhizobium species. Cluster 2 consisted of isolates from Kummerowia stipulacea and was identified as belonging to Sinorhizobium by 16S rRNA gene analyses. DNA relatedness varied from 5.2 to 41.7% among the isolates of cluster 2 and reference strains for Sinorhizobium species. Considering the existence of distinctive features among these two groups and related species within the genera Rhizobium and Sinorhizobium, we propose two novel species, Rhizobium indigoferae sp. nov. for cluster 1, with isolate CCBAU 71714(T) (= AS 1.3046(T)) as the type strain, and Sinorhizobium kummerowiae sp. nov. for cluster 2, with isolate CCBAU 71042(T) (= AS 1.3045(T)) as the type strain.