Onuma Kaewkla

Nocardia callitridis sp. nov., an endophytic actinobacterium isolated from a surface-sterilized root of an Australian native pine tree.

A novel actinobacterium strain, CAP 290(T), was isolated from a surface-sterilized root of an Australian native pine tree, Callitris preissii. Comparative 16S rRNA gene sequence analysis showed that the strain belongs to the family Nocardiaceae. Strain CAP 290(T) was most closely related to Nocardia nova JCM 6044(T) (97.4 % 16S rRNA gene sequence similarity) and Nocardia terpenica IFM 0706(T) (96.7 %); similarity to other type strains of the genus Nocardia ranged from 95 to 97 %. Chemotaxonomic data [meso-diaminopimelic acid, major menaquinone MK-8(H(4omegacycl.)), major fatty acid C(16 : 0) and mycolate in the cell wall] confirmed the affiliation of strain CAP 290(T) to the genus Nocardia. The results of the phylogenetic analysis, together with the physiological and biochemical tests, allowed the differentiation of strain CAP 290(T) from strains of other Nocardia species. Therefore, strain CAP 290(T) represents a novel species, the first endophytic actinobacterium to be identified as belonging to the genus Nocardia, for which the name Nocardia callitridis sp. nov. is proposed. The type strain is strain CAP 290(T) (=DSM 45353(T) =ACM 5287(T)).

Pseudonocardia adelaidensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa).

An aerobic, actinobacterial strain with rod-shaped spores, EUM 221(T) [corrected], which was isolated from the surface-sterilized stem of a grey box tree (Eucalyptus microcarpa), is described. Phylogenetic evaluation based on 16S rRNA gene sequence similarity showed that this isolate belongs to the family Pseudonocardiaceae, with the closest neighbour being Pseudonocardia zijingensis 6330(T) (98.7 %). The level of 16S rRNA gene sequence similarity between the isolate and species of the genus Pseudonocardia with validly published names ranged from 95 to 98 %. Chemotaxonomic data (meso-diaminopimelic acid; major menaquinone MK-8(H(4)); major fatty acid iso-C(16 : 0)) confirmed the affiliation of strain EUM 221(T) [corrected] to the genus Pseudonocardia. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 221(T) [corrected] from the closest described species. Therefore, this strain represented a novel species and the name proposed is Pseudonocardia adelaidensis sp. nov. The type strain is EUM 221(T) [corrected] (=DSM 45352(T) =ACM 5286(T)).

Pseudonocardia eucalypti sp. nov., an endophytic actinobacterium with a unique knobby spore surface, isolated from roots of a native Australian eucalyptus tree

A novel strain, designated EUM 374(T), was isolated from the root of a native Australian eucalyptus tree, Eucalyptus microcarpa, and subjected to a range of morphological, phylogenetic and chemotaxonomic analyses. The strain was Gram-reaction-positive with well-developed aerial mycelia, which fragmented into rod-shaped spores that had unique knobby protrusions on the spore surface. Substrate mycelia were not present in the media used. Strain EUM 374(T) grew as a film on the surface of static liquid culture medium but did not grow under shaking conditions. Phylogenetic evaluation based on 16S rRNA gene sequences identified the new isolate as belonging to the family Pseudonocardiaceae with sequence similarities of 96.1 and 96.3 % to Pseudonocardia acaciae GMKU095(T) and Pseudonocardia spinosispora LM 141(T), respectively, and 93-96 % sequence similarity to other members of the genus Pseudonocardia. The results of comprehensive phylogenetic analyses, including physiological and biochemical tests, differentiated strain EUM 374(T) from related members of the genus Pseudonocardia. Based on the phenotypic, phylogenetic and chemotaxonomic evidence, strain EUM 374(T) represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia eucalypti sp. nov. is proposed. The type strain is EUM 374(T) ( = DSM 45351(T)  = ACM 5285(T)).

Kribbella endophytica sp. nov., an endophytic actinobacterium isolated from the surface-sterilized leaf of a native apricot tree

A new strain of the genus Kribbella, PIP 118(T), was isolated from the leaf of an Australian native apricot tree (Pittosporum angustifolium), or Gumbi Gumbi in the indigenous language. This strain is an aerobic actinobacterium consisting of hyphae that fragment into short to elongated rod-like elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate as a member of the family Nocardioidaceae and most closely related to Kribbella antibiotica YIM 31530(T) (98.6 %) and Kribbella koreensis LM 161(T) (98.4 %). Chemotaxonomic data including cell wall components, major menaquinone and major fatty acids confirmed the affiliation of strain PIP 118(T) to the genus Kribbella. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain PIP 118(T) and members of the most closely related species with validly published names. The name proposed for the new species is Kribbella endophytica sp. nov. The type strain is PIP 118(T) ( = DSM 23718(T) = NRRL B-24812(T)).

Promicromonospora endophytica sp. nov., an endophytic actinobacterium isolated from the root of an Australian native Grey Box tree.

A novel aerobic actinobacterium, strain EUM 273(T), was isolated from the root of a Grey Box tree (Eucalyptus microcarpa Maiden). Cells were Gram-staining-positive with well-developed substrate mycelia which were non-motile and rod-like, with coccoid elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed the isolate as a member of the family Promicromonosporaceae that was most closely related to Promicromonospora xylanilytica YIM 61515(T) (98.2%) and Promicromonospora vindobonensis V45(T) (98%). Chemotaxonomic data including cell wall components, major menaquinone and major fatty acids confirmed the affiliation of strain EUM 273(T) to the genus Promicromonospora. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 273(T) from the closest related species with validly published names. The name proposed for the novel species is Promicromonospora endophytica sp. nov. The type strain is EUM 273(T) (=DSM 23716(T)=NRRL B-24816(T)).

Flindersiella endophytica gen. nov., sp. nov., an endophytic actinobacterium isolated from the root of Grey Box, an endemic eucalyptus tree.

A novel endophytic actinobacterium, designated strain EUM 378(T), was isolated from the surface-sterilized root tissue of Eucalyptus microcarpa, a eucalyptus tree known as Grey Box. Phylogenetic evaluation based on 16S rRNA gene sequence analysis, including alignment with taxon-specific 16S rRNA gene signature nucleotides, placed this isolate as a member of the family Nocardioidaceae. Strain EUM 378(T) showed >5.5 % 16S rRNA gene sequence divergence from other members of this family and was related most closely to Actinopolymorpha alba YIM 48868(T) (94.2 %) and Actinopolymorpha singaporensis IM 7744(T) (94.4 %). This Gram-positive, aerobic actinobacterium has well-developed substrate mycelia that fragment into small rods. Chemotaxonomic data revealed that the cell wall contains LL-diaminopimelic acid, ribose, glucose and rhamnose. MK-10(H₆) is the predominant menaquinone. Chemotaxonomic and phylogenetic evidence confirmed that strain EUM 378(T) represents a novel species of a new genus, for which the name Flindersiella endophytica gen. nov., sp. nov. is proposed. The type strain is EUM 378(T) ( = DSM 45355(T) = ACM 5289(T)).

Streptomyces roietensis sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of jasmine rice, Oryza sativa KDML 105

An endophytic actinobacterium, strain WES2T, was isolated from the stem of a jasmine rice plant collected from a paddy field in Thung Gura Rong Hai, Roi Et province, Thailand. As a result of a polyphasic study, this strain was identified as representing a novel member of the genus Streptomyces. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia and forming chains of looped spores. The closest phylogenetic relations, which shared the highest 16S rRNA gene sequence similarity, were Streptomyces nogalater JCM 4799T and Streptomyces lavenduligriseus NRRL-ISP 5487T at 99.1 and 99.0 %, respectively. Chemotaxonomic data, including major fatty acids, cell wall components and major menaquinones, confirmed the affiliation of WES2T to the genus Streptomyces. The data from the phylogenetic analysis, including physiological and biochemical studies and DNA-DNA hybridization, revealed the genotypic and phenotypic differentiation of WES2T from the most closely related species with validly published names. The name proposed for the novel species is Streptomycesroietensis sp. nov. The type strain is WES2T (=DSM 101729=NRRL B-65344).

Actinopolymorpha pittospori sp. nov., an endophyte isolated from surface-sterilized leaves of an apricot tree (Pittosporum phylliraeoides)

A member of the genus Actinopolymorpha, designated PIP 143(T), was isolated from the leaves of an Australian native apricot tree (Pittosporum phylliraeoides). The isolate was a Gram-reaction-positive, aerobic actinobacterium, with a well-developed substrate mycelium that fragmented into small rods. Phylogenetic evaluation based on 16S rRNA gene sequences placed the isolate in the family Nocardioidaceae. Strain PIP 143(T) was most closely related to Actinopolymorpha cephalotaxi I06-2230(T) (98.7 %) and Actinopolymorpha rutila YIM 45725(T) (98.1 %). Chemotaxonomic data, including cell-wall components, menaquinones and fatty acids, confirmed the affiliation of strain PIP 143(T) to the genus Actinopolymorpha. Phylogenetic analysis and physiological and biochemical studies, in combination with DNA-DNA hybridization studies, allowed the differentiation of strain PIP 143(T) from its closest phylogenetic neighbours with validly published names. Therefore, a novel species is proposed, with the name Actinopolymorpha pittospori sp. nov. The type strain is PIP 143(T) ( = DSM 45354(T) = ACM 5288(T) = NRRL B-24810(T)).

Kribbella pittospori sp. nov., an endophytic actinobacterium isolated from the surface-sterilized stem of an Australian native apricot tree, Pittosporum angustifolium.

An endophytic actinobacterium, strain PIP 158T, was isolated from the stem of a native apricot tree (Pittosporum angustifolium) collected from the grounds of Flinders University, Adelaide, Australia. As a result of a polyphasic taxonomic study, this strain was identified as a member of the genus Kribbella. This strain was a Gram-stain-positive, aerobic actinobacterium with well-developed substrate mycelia which were non-motile and with hyphae fragmenting into short to elongated rod-like elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed this isolate in the family Nocardioidaceae, being most closely related to Kribbella sandramycini ATCC 39419T and Kribbella albertanoniae BC640T which share a similarity of 99. 26 and 99.18 % with Kribbella hippodromi S1.4T, respectively. Chemotaxonomic data including cell-wall components, major menaquinones and major fatty acids confirmed the affiliation of strain PIP 158T to the genus Kribbella. The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA-DNA hybridization, allowed the genotypic and phenotypic differentiation of strain PIP 158T from the closest related species with validly published names. The name proposed for the novel species is Kribbella pittospori sp. nov. The type strain is PIP 158T (=DSM 23717T=NRRL B-24813T).

Endophytic Actinobacteria: Beneficial Partners for Sustainable Agriculture

Endophytic actinobacteria have been proven to be effective partners that have beneficial functions with a number of crop plants. A large number of studies have been carried out, showing these positive effects in laboratories and glasshouses, but with fewer reports of their effectiveness in the field. This chapter highlights the results of field trials of actinobacterial endophytes conducted with cereals, vegetables such as tomato, cucumber, or cabbage, legumes such as chickpea or pea, fruits such as melon or grapes, peanuts, and woody plants.