Actinoallomurus oryzae sp. nov., an endophytic actinomycete isolated from roots of a Thai jasmine rice plant

Actinoallomurus soli sp. nov. and Actinoallomurus rhizosphaericola sp. nov., two novel actinobacteria isolated from rhizosphere soil of Oryza rufipogon Griff

The taxonomic position of two novel Actinoallomurus strains isolated from rhizosphere soil of wild rice (Oryza rufipogon Griff.) was established using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WRP6H-15T and WRP9H-5T were closely related to Actinoallomurus spadix JCM 3146T and Actinoallomurus purpureus TTN02-30T. Chemotaxonomic and morphological characteristics of both strains were consistent with members of the genus Actinoallomurus, while phenotypic properties, genome-based comparisons and phylogenomic analyses distinguished strains WRP6H-15T and WRP9H-5T from their closest phylogenetic relatives. The two strains showed nearly identical 16S rRNA gene sequences (99.9 %). Strain WRP6H-15T showed 68.7 % digital DNA-DNA hybridization, 95.9 % average nucleotide identity (ANI) based on blast and 96.4 % ANI based on MUMmer to strain WRP9H-5T. A phylogenomic tree based on draft genome sequences of the strains and representative of the genus Actinoallomurus confirmed the phylogenetic relationships. The genomes sizes of strains WRP6H-15T and WRP9H-5T were 9.42 Mb and 9.68 Mb, with DNA G+C contents of 71.5 and 71.3 mol%, respectively. In silico analysis predicted that the strains contain biosynthetic gene clusters encoding for specialized metabolites. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strains WRP6H-15T and WRP9H-5T represent two novel species of the genus Actinoallomurus, for which the names Actinoallomurus soli sp. nov. (type strain WRP6H-15T=TBRC 15726T=NBRC 115556T) and Actinoallomurus rhizosphaericola sp. nov. (type strain WRP9H-5T=TBRC 15727T=NBRC 115557T) are proposed.

Endophytic microbes: biodiversity, plant growth-promoting mechanisms and potential applications for agricultural sustainability

Endophytic microbes are known to live asymptomatically inside their host throughout different stages of their life cycle and play crucial roles in the growth, development, fitness, and diversification of plants. The plant-endophyte association ranges from mutualism to pathogenicity. These microbes help the host to combat a diverse array of biotic and abiotic stressful conditions. Endophytic microbes play a major role in the growth promotion of their host by solubilizing of macronutrients such as phosphorous, potassium, and zinc; fixing of atmospheric nitrogen, synthesizing of phytohormones, siderophores, hydrogen cyanide, ammonia, and act as a biocontrol agent against wide array of phytopathogens. Endophytic microbes are beneficial to plants by directly promoting their growth or indirectly by inhibiting the growth of phytopathogens. Over a long period of co-evolution, endophytic microbes have attained the mechanism of synthesis of various hydrolytic enzymes such as pectinase, xylanases, cellulase, and proteinase which help in the penetration of endophytic microbes into tissues of plants. The effective usage of endophytic microbes in the form of bioinoculants reduce the usage of chemical fertilizers. Endophytic microbes belong to different phyla such as Actinobacteria, Acidobacteria, Bacteroidetes, Deinococcus-thermus, Firmicutes, Proteobacteria, and Verrucomicrobia. The most predominant and studied endophytic bacteria belonged to Proteobacteria followed by Firmicutes and then by Actinobacteria. The most dominant among reported genera in most of the leguminous and non-leguminous plants are Bacillus, Pseudomonas, Fusarium, Burkholderia, Rhizobium, and Klebsiella. In future, endophytic microbes have a wide range of potential for maintaining health of plant as well as environmental conditions for agricultural sustainability. The present review is focused on endophytic microbes, their diversity in leguminous as well as non-leguminous crops, biotechnological applications, and ability to promote the growth of plant for agro-environmental sustainability.

Phyllospheric Microbiomes: Diversity, Ecological Significance, and Biotechnological Applications

The phyllosphere referred to the total aerial plant surfaces (above-ground portions), as habitat for microorganisms. Microorganisms establish compositionally complex communities on the leaf surface. The microbiome of phyllosphere is rich in diversity of bacteria, fungi, actinomycetes, cyanobacteria, and viruses. The diversity, dispersal, and community development on the leaf surface are based on the physiochemistry, environment, and also the immunity of the host plant. A colonization process is an important event where both the microbe and the host plant have been benefited. Microbes commonly established either epiphytic or endophytic mode of life cycle on phyllosphere environment, which helps the host plant and functional communication with the surrounding environment. To the scientific advancement, several molecular techniques like metagenomics and metaproteomics have been used to study and understand the physiology and functional relationship of microbes to the host and its environment. Based on the available information, this chapter describes the basic understanding of microbiome in leaf structure and physiology, microbial interactions, especially bacteria, fungi, and actinomycetes, and their adaptation in the phyllosphere environment. Further, the detailed information related to the importance of the microbiome in phyllosphere to the host plant and their environment has been analyzed. Besides, biopotentials of the phyllosphere microbiome have been reviewed.

Comparison of Actinomycete Community Composition on the Surface and Inside of Japanese Black Pine (Pinus thunbergii) Tree Roots Colonized by the Ectomycorrhizal Fungus Cenococcum geophilum

Various bacteria are associated with ectomycorrhizal roots, which are symbiotic complexes formed between plant roots and fungi. Among these associated bacteria, actinomycetes have received attention for their ubiquity and diverse roles in forest ecosystems. Here, to examine the association of actinomycetes with ectomycorrhizal root tips, we compared the bacterial and actinomycete communities on the surface and inside of root tips of coastal Japanese black pine (Pinus thunbergii) colonized by the fungus Cenococcum geophilum. Next-generation sequences of 16S rDNA of bacteria communities using the Ion Torrent Personal Genome Machine showed that the number of bacterial classes in the surface of C. geophilum ECM roots was significantly higher than that in non-ECM roots. The bacterial community structure of surface, inside, and non-ECM roots was significantly discriminated each other. For an isolation method, a total of 762 and 335 actinomycete isolates were obtained from the surface and inside of the roots, respectively. In addition, the isolation ratio of actinomycetes in these root tips varied depending on the age of the tree and the season. Identification of the isolates based on partial 16S rDNA sequencing revealed that the isolates belonged to nine genera of the order Actinomycetales. On the surface of the roots, most of the isolates belonged to genus Streptomyces (90.4%); inside of the roots, most of the isolates belonged to genus Actinoallomurus (40.0%), which is a relatively new taxon. Our results suggest that actinomycetes as well as bacteria are ubiquitously associated with C. geophilum ectomycorrhizal roots of P. thunbergii, although their communities can vary either surface or inside of individual root tips.

Diversity and Applications of Endophytic Actinobacteria of Plants in Special and Other Ecological Niches

Actinobacteria are wide spread in nature and represent the largest taxonomic group within the domain Bacteria. They are abundant in soil and have been extensively explored for their therapeutic applications. This versatile group of bacteria has adapted to diverse ecological habitats, which has drawn considerable attention of the scientific community in recent times as it has opened up new possibilities for novel metabolites that may help in solving some of the most challenging problems of the day, for example, novel drugs for drug-resistant human pathogens, affordable means to maintain ecological balance in various habitats, and alternative practices for sustainable agriculture. Traditionally, free dwelling soil actinobacteria have been the subject of intensive research. Of late, symbiotic actinobacteria residing as endophytes within the plant tissues have generated immense interest as potential source of novel compounds, which may find applications in medicine, agriculture, and environment. In the light of these possibilities, this review focuses on the diversity of endophytic actinobacteria isolated from the plants of extreme habitats and specific ecological niches. Furthermore, an attempt has been made to assign chemical class to the compounds obtained from endophytic actinobacteria. Potential therapeutic applications of these compounds and the utility of endophytic actinobacteria in agriculture and environment are discussed.

Novel Polyethers from Screening Actinoallomurus spp

In screening for novel antibiotics, an attractive element of novelty can be represented by screening previously underexplored groups of microorganisms. We report the results of screening 200 strains belonging to the actinobacterial genus Actinoallomurus for their production of antibacterial compounds. When grown under just one condition, about half of the strains produced an extract that was able to inhibit growth of Staphylococcus aureus. We report here on the metabolites produced by 37 strains. In addition to previously reported aminocoumarins, lantibiotics and aromatic polyketides, we described two novel and structurally unrelated polyethers, designated α-770 and α-823. While we identified only one producer strain of the former polyether, 10 independent Actinoallomurus isolates were found to produce α-823, with the same molecule as main congener. Remarkably, production of α-823 was associated with a common lineage within Actinoallomurus, which includes A. fulvus and A. amamiensis. All polyether producers were isolated from soil samples collected in tropical parts of the world.

Contrasting microbial biogeographical patterns between anthropogenic subalpine grasslands and natural alpine grasslands

The effect of plant species composition on soil microbial communities was studied at the multiregional level. We compared the soil microbial communities of alpine natural grasslands dominated by Carex curvula and anthropogenic subalpine pastures dominated by Nardus stricta. We conducted paired sampling across the Carpathians and the Alps and used Illumina sequencing to reveal the molecular diversity of soil microbes. We found that bacterial and fungal communities exhibited contrasting regional distributions and that the distribution in each grassland is well discriminated. Beta diversity of microbial communities was much higher in C. curvula grasslands due to a marked regional effect. The composition of grassland-type core microbiomes suggest that C. curvula, and N. stricta to a lesser extent, tend to select a cohort of microbes related to antibiosis/exclusion, pathogenesis and endophytism. We discuss these findings in light of the postglacial history of the studied grasslands, the habitat connectivity and the disturbance regimes. Human-induced disturbance in the subalpine belt of European mountains has led to homogeneous soil microbial communities at large biogeographical scales. Our results confirm the overarching role of the dominant grassland plant species in the distribution of microbial communities and highlight the relevance of biogeographical history.

Amycolatopsis stemonae sp. nov., isolated from a Thai medicinal plant

A novel actinomycete, strain ST1-08T, was isolated from the stem of Stemona sp. in Thailand. The taxonomic position of this isolate was determined by using a polyphasic approach. Strain ST1-08T contained meso-diaminopimelic acid in the cell-wall peptidoglycan, and arabinose and galactose as diagnostic sugars of the whole-cell hydrolysate, which are typical properties of members of the genus Amycolatopsis. Strain ST1-08T grew at 15-40 °C, pH 6-9 and on 5 % (w/v) NaCl. Gelatin liquefaction, starch hydrolysis and skimmed milk peptonization were positive. The strain utilized l-arabinose, d-glucose, glycerol, myo-inositol, d-mannitol and l-rhamnose. The predominant menaquinone was MK-9(H4) and the major cellular fatty acids were iso-C16 : 0 and iso-C15 : 0.The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, hydroxyl-phosphatidylethanolamine, phosphatidylinositol and phosphatidylglycerol. The 16S rRNA gene sequence analysis revealed that the strain was closely related to Amycolatopsis pretoriensis JCM 12673T (98.99 %) and Amycolatopsis lexingtonensis JCM 12672T (98.87 %). The DNA G+C content of strain ST1-08T was 71.2 mol%. The DNA-DNA relatedness values among strain ST1-08T, A. pretoriensis JCM 12673T and A. lexingtonensis JCM 12672T were lower than 70 %, the cut-off level for assigning strains to the same species. On the basis of phenotypic and genotypic characteristics, strain ST1-08T represents a novel species of the genus Amycolatopsis, for which the name Amycolatopsis stemonae is proposed. The type strain is ST1-08T( = JCM 30050T = PCU 339T = TISTR 2278T).

Continuing hunt for endophytic actinomycetes as a source of novel biologically active metabolites

Drug-resistant pathogens and persistent agrochemicals mount the detrimental threats against human health and welfare. Exploitation of beneficial microorganisms and their metabolic inventions is most promising way to tackle these two problems. Since the successive discoveries of penicillin and streptomycin in 1940s, numerous biologically active metabolites have been discovered from different microorganisms, especially actinomycetes. In recent years, actinomycetes that inhabit unexplored environments have received significant attention due to their broad diversity and distinctive metabolic potential with medical, agricultural and industrial importance. In this scenario, endophytic actinomycetes that inhabit living tissues of plants are emerging as a potential source of novel bioactive compounds for the discovery of drug leads. Also, endophytic actinomycetes are considered as bio-inoculants to improve crop performance through organic farming practices. Further efforts on exploring the endophytic actinomycetes associated with the plants warrant the likelihood of discovering new taxa and their metabolites with novel chemical structures and biotechnological importance. This mini-review highlights the recent achievements in isolation of endophytic actinomycetes and an assortment of bioactive compounds.

Actinoallomurus bryophytorum sp. nov., an endophytic actinomycete isolated from moss (Bryophyta)

A novel endophytic actinomycete, strain NEAU-TX1-15(T), was isolated from moss, collected from Wuchang, Heilongjiang province, north China. A polyphasic taxonomic study was carried out to establish the status of strain NEAU-TX1-15(T). Morphological and chemotaxonomic properties of strain NEAU-TX1-15(T) are consistent with the description of the genus Actinoallomurus. Strain NEAU-TX1-15(T) was observed to form short spiral or looped spore chains on aerial hyphae. The cell wall peptidoglycan was found to contain lysine and meso-diaminopimelic acid. The major menaquinones were identified as MK-9(H6) and MK-9(H8). The only phospholipid identified was phosphatidylglycerol. The major fatty acid was identified as iso-C16:0. Analysis of the 16S rRNA gene sequence supports the assignment of the novel strain to the genus Actinoallomurus, as it exhibits 99.2 % gene sequence similarity to that of Actinoallomurus yoronensis NBRC 103686(T). However, the low level of DNA-DNA relatedness allowed the strain to be differentiated from its close relative. Moreover, strain NEAU-TX1-15(T) could also be differentiated from A. yoronensis NBRC 103686(T) and other Actinoallomurus species showing high 16S rRNA gene sequence similarity (>98.0 %) by cultural and physiological characteristics. Therefore, the combination of phenotypic and chemotaxonomic data, and the DNA-DNA hybridization value, indicated that strain NEAU-TX1-15(T) represents a novel species of the genus Actinoallomurus for which the name Actinoallomurus bryophytorum sp. nov. is proposed. The type strain is NEAU-TX1-15(T) (=CGMCC 4.7200(T) = JCM 30340(T)).

Biotechnological application and taxonomical distribution of plant growth promoting actinobacteria

Plant growth promoting (PGP) bacteria are involved in various interactions known to affect plant fitness and soil quality, thereby increasing the productivity of agriculture and stability of soil. Although the potential of actinobacteria in antibiotic production is well-investigated, their capacity to enhance plant growth is not fully surveyed. Due to the following justifications, PGP actinobacteria (PGPA) can be considered as a more promising taxonomical group of PGP bacteria: (1) high numbers of actinobacteria per gram of soil and their filamentous nature, (2) genome dedicated to the secondary metabolite production (~5 to 10 %) is distinctively more than that of other bacteria and (3) number of plant growth promoter genera reported from actinobacteria is 1.3 times higher than that of other bacteria. Mechanisms by which PGPA contribute to the plant growth by association are: (a) enhancing nutrients availability, (b) regulation of plant metabolism, (c) decreasing environmental stress, (d) control of phytopathogens and (e) improvement of soil texture. Taxonomical and chemical diversity of PGPA and their biotechnological application along with their associated challenges are summarized in this paper.

Actinoallomurus acanthiterrae sp. nov., an actinomycete isolated from rhizosphere soil of the mangrove plant Acanthus ilicifolius

A novel actinobacterium strain, 2614A723(T), was isolated from rhizosphere soil of mangrove plant Acanthus ilicifolius collected at Touyuan, Wenchang, Hainan province, China. A phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 2614A723(T) formed a distinct phyletic line in the genus Actinoallomurus, the 16S rRNA gene tree sharing similarities of 98.35%, 98.07% and 97.86% with Actinoallomurus spadix NBRC 14099(T), Actinoallomurus purpureus TTN02-30(T) and Actinoallomurus luridus TT02-15(T), respectively. Strain 2614A723(T) contained lysine and meso-diaminopimelic acid in the cell wall peptidoglycan and madurose, galactose and xylose in the whole-cell sugars. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major polar phospholipids were phosphatidylglycerol and diphosphatidylglycerol. The predominant fatty acids were iso-C16 : 0 and anteiso-C17 : 0. These chemotaxonomic data confirmed the affiliation of strain 2614A723(T) to the genus Actinoallomurus. It is apparent from the combined phenotypic data, biochemical tests and DNA-DNA hybridization values that strain 2614A723(T) should be classified in the genus Actinoallomurus as a representative of a novel species. The name Actinoallomurus acanthiterrae sp. nov. is proposed with strain 2614A723(T) ( = CCTCC AA 2012001(T) = DSM 45727(T)) as the type strain.

Plant growth enhancing effects by a siderophore-producing endophytic streptomycete isolated from a Thai jasmine rice plant (Oryza sativa L. cv. KDML105)

An endophytic Streptomyces sp. GMKU 3100 isolated from roots of a Thai jasmine rice plant (Oryza sativa L. cv. KDML105) showed the highest siderophore production on CAS agar while phosphate solubilization and IAA production were not detected. A mutant of Streptomyces sp. GMKU 3100 deficient in just one of the plant growth promoting traits, siderophore production, was generated by inactivation of a desD-like gene encoding a key enzyme controlling the final step of siderophore biosynthesis. Pot culture experiments revealed that rice and mungbean plants inoculated with the wild type gave the best enhancement of plant growth and significantly increased root and shoot biomass and lengths compared with untreated controls and siderophore-deficient mutant treatments. Application of the wild type in the presence or absence of ferric citrate significantly promoted plant growth of both plants. The siderophore-deficient mutant clearly showed the effect of this important trait involved in plant-microbe interaction in enhancement of growth in rice and mungbean plants supplied with sequestered iron. Our results highlight the value of a substantial understanding of the relationship of the plant growth promoting properties of endophytic actinomycetes to the plants. Endophytic actinomycetes, therefore, can be applied as potentially safe and environmentally friendly biofertilizers in agriculture.

Isolation of actinomycetes from the root of the plant, Ophiopogon japonicus, and proposal of two new species, Actinoallomurus liliacearum sp. nov. and Actinoallomurus vinaceus sp. nov

Actinomycete strains K10-0485(T) and K10-0528(T) were isolated from the roots of Ophiopogon japonicus collected in Yokohama, Kanagawa Prefecture, Japan. The 16S ribosomal RNA (rRNA) gene sequences, morphological characteristics and chemotaxonomic data indicated that these strains belonged to the genus Actinoallomurus. Strain K10-0485(T) showed high similarity of the 16S rRNA gene sequence with A. luridus TT02-15(T) (99.1%), but the DNA-DNA hybridization relatedness values between strain K10-0485(T) and A. luridus TT02-15(T) were below 70%. Three species showed similarities of 16S rRNA gene sequences with K10-0528(T), namely A. spadix JCM 3146(T) (98.0%), A. purpureus TTN02-30(T) (98.0%) and A. luridus TT02-15(T) (97.9%), but all similarity values of the 16S rRNA gene sequences were lower than the boundary value (98.7%) for distinguishing as different species. Based on phylogenetic analyses, DNA-DNA hybridization relatedness and physiological characteristics, the two isolated strains should be classified as two new species in the genus Actinoallomurus, and we propose the names Actinoallomurus liliacearum sp. nov. and Actinoallomurus vinaceus sp. nov. The type strain of Actinoallomurus liliacearum is K10-0485(T) (=JCM 17938(T), BCC 49424(T), NBRC 108672(T)) and that of Actinoallomurus vinaceus is K10-0528(T) (=JCM 17939(T), BCC 49425(T), NBRC 108763(T)).

Actinoallomurus radicium sp. nov., isolated from the roots of two plant species

Three strains, K08-0182T, K08-0178 and K08-0195 were isolated from the paste of ground plant roots collected in Kanagawa Prefecture, Japan. These strains contained meso-diaminopimelic acid and lysine as the diamino acids in cell-wall peptidoglycan, and MK-9(H6) and MK-9(H8) as the predominant menaquinones. The G+C contents of the DNA were 72–73 mol%. Taken together, these characteristics combined with 16S rRNA gene sequence analyses revealed that the isolated strains belong to the genus Actinoallomurus. DNA–DNA hybridization values showed that the three strains belonged to a novel species of the genus Actinoallomurus. Therefore strains K08-0182T, K08-0178 and K08-0195 are proposed as representatives of a novel species, Actinoallomurus radicium sp. nov. The type strain is K08-0182T ( = DSM 45523T  = NBRC 107678T  = JCM 17294T).