Isolation and characterization of culturable endophytic actinobacteria associated with Artemisia annua L

Bioactive Compounds Produced by Endophytic Bacteria and Their Plant Hosts-An Insight into the World of Chosen Herbaceous Ruderal Plants in Central Europe

The natural environment has been significantly impacted by human activity, urbanization, and industrialization, leading to changes in living organisms and their adaptation to harsh conditions. Species, including plants, adapt to these changes by creating mechanisms and modifications that allow them to survive in harsh environments. Also, endophytes, microorganisms that live inside plants, can support plant growth and defense mechanisms in these conditions by synthesizing antimicrobial secondary metabolites. What is more, endophytes produce bioactive metabolites, including alkaloids, amines, and peptides, which play a crucial role in the relationship between endophytes and their host organisms. Endophytes themselves benefit from this by creating a stable environment for their survival and development. The aim of this review is to gain insight into endophytic bioactive metabolites from chosen synanthropic ruderal plants. Industrial activities release pollutants like heavy metals, by-products, and waste, which challenge living organisms and require adaptation. Synanthropic plants, where endophytes are abundant, are particularly valuable for their bioactive compounds, which are used in agriculture and medicine. This review presents, among others, endophytes of herbaceous ruderal plants from central Europe-Chelidonium majus L., Urtica dioica L., Plantago lanceolata L., Matricaria chamomilla L., Equisetum arvense L., Oenothera biennis L., Silybum marianum L., and Mentha piperita L.

Comparative seasonal analysis of Eri silkworm (Samia ricini Donovan) gut composition: implications for lignocellulose degradation

Conversion of biomass such as lignocelluloses to an alternative energy source can contribute to sustainable development. Recently, biomass-degrading enzymes are reported to be common resources in insect-microbe interacting systems. Northeast India harbors ample sericigenous insect resources which are exploited for their silk products. Samia ricini Donovan is an economically important poly-phytophagous silkmoth capable of digesting foliage from different plant species, suggesting the versatility of a robust gut system. Here, a gut bacterial profile was determined by 16S rRNA gene characterization across the holometabolous life cycle during the summer and winter seasons, revealing 3 phyla, 13 families, and 22 genera. Comparative analysis among the seasonal gut isolates revealed a high diversity in summer, predominated by the genus Bacillus due to its high occurrence in all developmental stages. Shannon's diversity index demonstrated the second and fourth instars of summer as well as the fifth instar of winter to be relatively better developmental stages for gut bacteria assembly. Bacterial community shifts in concert to host developmental changes were found to be apparent between early instars and late instars in summer, which differed from those of winter. Forty-three and twenty-nine gut bacterial isolates were found to be cellulolytic and xylanolytic enzyme producers, respectively. The present results illustrate the gut microbiota of S. ricini over the seasons and support the holometabolous life cycle effect as the most likely factor shaping the gut bacterial microbiota. These findings may provide leads for the development of new cleaner and environmentally friendly lignocellulose-degrading enzymes.

Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants

Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.

Endophytic Streptomyces sp. NEAU-ZSY13 from the leaf of Perilla frutescens, as a promising broad-spectrum biocontrol agent against soil-borne diseases

Soil-borne diseases cause significant economic losses in global agricultural production. These diseases are challenging to control due to the invasion of multiple pathogens into host plants, and traditional chemical control methods often yield unsatisfactory results. In this study, we isolated and identified an endophytic Streptomyces, designated as NEAU-ZSY13, from the leaf of Perilla frutescens. This isolate exhibited broad-spectrum antifungal activity against 17 soil-borne phytopathogenic fungi, with Bipolaris sorokiniana being the most prominent. Additionally, it displayed strong antibacterial activity against the soil-borne phytopathogenic bacterium Ralstonia solanacearum. To assess its biocontrol potential, the isolate was utilized to produce a biofertilizer through solid-state fermentation. The fermentation conditions were optimized using response surface methodology to maximize the spore production. The results revealed that more abundant spores were produced with a 1:2 ratio of vermicompost to wheat bran, 60% water content, 20% inoculation amount and 28°C. Subsequent pot experiments demonstrated that the application of the biofertilizer with a spore concentration of 108 CFU/g soil effectively suppressed the occurrence of tomato bacterial wilt caused by R. solanacearum and wheat root rot caused by B. sorokiniana, with biocontrol efficacies of 72.2 and 78.3%, respectively. Chemical analysis of NEAU-ZSY13 extracts, using nuclear magnetic resonance spectrometry and mass analysis, identified niphimycin C and niphimycin A as the primary active constituents. These compounds exhibited high activity against R. solanacearum (EC50 of 3.6 and 2.4 μg mL-1) and B. sorokiniana (EC50 of 3.9 and 3.4 μg mL-1). In conclusion, this study demonstrates the potential of Streptomyces sp. NEAU-ZSY13 as a biofertilizer for the control of soil-borne diseases.

Exploring the Potentiality of Native Actinobacteria to Combat the Chilli Fruit Rot Pathogens under Post-Harvest Pathosystem

Chilli is an universal spice cum solanaceous vegetable crop rich in vitamin A, vitamin C, capsaicin and capsanthin. Its cultivation is highly threatened by fruit rot disease which cause yield loss as high as 80-100% under congenial environment conditions. Currently actinobacteria are considered as eco-friendly alternatives to synthetic fungicides at pre and post-harvest pathosystems. Hence, this research work focuses on the exploitation of rhizospheric, phyllospheric and endophytic actinobacteria associated with chilli plants for their antagonistic activity against fruit rot pathogens viz., Colletotrichum scovillei, Colletotrichum truncatum and Fusarium oxysporum. In vitro bioassays revealed that the actinobacterial isolate AR26 was found to be the most potent antagonist with multifarious biocontrol mechanisms such as production of volatile, non-volatile, thermostable compounds, siderophores, extracellular lytic enzymes. 16S rRNA gene sequence confirmed that the isolate AR26 belongs to Streptomyces tuirus. The results of detached fruit assay revealed that application of liquid bio-formulation of Stretomyces tuirus @ 10 mL/L concentration completely inhibited the development of fruit rot symptoms in pepper fruits compared to methanol extracts. Hence, the present research work have a great scope for evaluating the biocontrol potential of native S. tuirus AR26 against chilli fruit rot disease under field condition as well against a broad spectrum of post-harvest plant pathogens.

Diversity and Bioactivity of Endophytic Actinobacteria Associated with Grapevines

Grapevine trunk diseases (GTDs) are a significant problem for New Zealand viticulture. Endophytic actinobacteria are of interest as potential biocontrol agents due to their ability to inhibit plant pathogens and improve plant growth. However, no studies have investigated the diversity of actinobacteria associated with grapevines in New Zealand vineyards and their bioactivity. Actinobacteria diversity in different ‘Sauvignon blanc’ vine tissues from three vineyards (conventional and organic management, and different vine ages) was assessed using different methods and media. Forty-six endophytic actinobacteria were isolated, with more isolates recovered from roots (n = 45) than leaves (n = 1) and shoot internodes (n = 0). More isolates were recovered from the organic (n = 21) than conventional (n = 8) vineyard, mature (25-year old; n = 21) than young (2-year old; n = 2) vines and using a tissue maceration technique (n = 40). Actinomycete Isolation Agar, International Streptomyces Project 2, and Starch Casein media were effective for actinobacteria isolation. Most of the isolates recovered belonged to Streptomyces, with one isolate identified as Mycolicibacterium. Forty isolates were assessed for antifungal activity and plant growth-promoting (PGP) characteristics. Of these, 13 isolates had antifungal activity against test GTD pathogens (Dactylonectria macrodidyma, Eutypa lata, Ilyonectria liriodendri, Neofusicoccum parvum, and N. luteum). Eighteen isolates exhibited more than one PGP trait; 25siderophore production (n = 25), phosphate solubilization (n = 6), and indole acetic acid production (n = 16). Two strains, Streptomyces sp. LUVPK-22 and Streptomyces sp. LUVPK-30, exhibited the best antifungal and PGP properties. This study revealed the diversity of culturable endophytic actinobacteria from grapevines in New Zealand vineyards and their biocontrol potential against GTD pathogens.

Uncovering the biodiversity and biosynthetic potentials of rare actinomycetes

Background

Antibiotic resistance is on the rise, and new antibiotic research has slowed in recent years, necessitating the discovery of possibly novel microbial resources capable of producing bioactive compounds. Microbial infections are gaining resistance to existing antibiotics, emphasizing the need for novel medicinal molecules to be discovered as soon as possible. Because the possibilities of isolating undiscovered actinomycetes strains have decreased, the quest for novel products has shifted to rare actinomycetes genera from regular environments or the identification of new species identified in unusual habitats.

Main body of the abstract

The non-streptomyces actinobacteria are known as rare actinomycetes that are extremely difficult to cultivate. Rare actinomycetes are known to produce a variety of secondary metabolites with varying medicinal value. In this review, we reported the diversity of rare actinomycetes in several habitat including soil, plants, aquatic environment, caves, insects and extreme environments. We also reported some isolation methods to easily recover rare Actinobacteria from various sources guided with some procedures to identify the rare Actinobacteria isolates. Finally, we reported the biosynthetic potential of rare actinomycetes and its role in the production of unique secondary metabolites that could be used in medicine, agriculture, and industry. These microbial resources will be of interest to humanity, as antibiotics, insecticides, anticancer, antioxidants, to mention but a few.

Short conclusion

Rare actinomycetes are increasingly being investigated for new medicinal compounds that could help to address existing human health challenges such as newly emerging infectious illnesses, antibiotic resistance, and metabolic disorders. The bioactive secondary metabolites from uncommon actinomycetes are the subject of this review, which focuses on their diversity in different habitats, isolation, identification and biosynthetic potentials.

Surface sterilization for isolation of endophytes: Ensuring what (not) to grow

Endophytic microbiota opens a magnificent arena of metabolites that served as a potential source of medicines for treating a variety of ailments and having prospective uses in agriculture, food, cosmetics, and many more. There are umpteen reports of endophytes improving the growth and tolerance of plants. In addition, endophytes from lifesaving drug-producing plants such as Taxus, Nothapodytes, Catharanthus, and so forth have the ability to produce host mimicking compounds. To harness these benefits, it is imperative to isolate the true endophytes, not the surface microflora. The foremost step in endophyte isolation is the removal of epiphytic microbes from plant tissues, called as surface sterilization. The success of surface sterilization decides "what to grow" (the endophytes) and "what not to grow" (the epiphytes). It is very crucial to use an appropriate sterilant solution, concentration, and exposure time to ensure thorough surface disinfection with minimal damage to the endophytic diversity. Commonly used surface sterilants include sodium hypochlorite (2%-10%), ethanol (70%-90%), mercuric chloride (0.1%), formaldehyde (40%), and so forth. In addition, the efficiency could further be improved by pretreatment with surfactants such as Triton X-100, Tween 80, and Tween 20. This review comprehensively deals with the various sterilants and sterilization methods for the isolation of endophytic microbes. In addition, the mechanisms and rationale behind using specific surface sterilants have also been elaborated at length.

Bioactivities of endophytic actinobacteria inhabiting Artemisia herba-alba emphasizing differences from free-living strains

The endophytic actinobacteria associated with Artemisia herba-alba (synonym: Seriphidium herba-alba) are highly diverse. This study aimed to illustrate the extent of their differences from the free-living actinobacteria in the surrounding environment. A selection of eighteen actinobacteria inhabiting A. herba-alba were compared with twenty and ten actinobatceria isolates from the surrounding desert and groundwater, respectively, representing six genera. Antagonistic and enzymatic activities, plant growth-promoting traits, and the occurrence of biosynthetic genes were compared among the isolates. Data were analyzed statistically using principal component analysis (PCA) and were visualized using heat map. Endophytic strains showed higher antimicrobial activity and production of plant growth promoters compared to desert and groundwater strains. Polyketide synthase and non-ribosomal peptide synthetase gene clusters were detected at higher frequencies in the endophytic strains (8 and 11 strains, respectively) than the desert strains (1 and 2 strains, respectively). In contrast, both gene clusters were not detected in the groundwater strains. The PCA revealed unique metabolic characteristics of the endophytes. The heatmap clustered the endophytic strains apart from the free-living strains, indicating distinctive qualitative and quantitative bioactivities. Analysis of 16S rRNA genes confirmed the chemotaxonomic identity of all but two strains, with > 94.5% similarity. Six endophytes displayed < 99.5% similarity with their closest type strains, which might indicate species novelty. This study provides an evidence of functional differences and possible species novelty of the endophytic actinobacteria inhabiting A. herba-alba, compared with the free-living species.

Impact of Olive Saplings and Organic Amendments on Soil Microbial Communities and Effects of Mineral Fertilization

Plant communities and fertilization may have an impact on soil microbiome. Most commercial olive trees are minerally fertilized, while this practice is being replaced by the use of organic amendments. Organic amendments can both fertilize and promote plant growth-promoting organisms. Our aims were (i) to describe the changes in soil bacterial and fungal communities induced by the presence of young olive trees and their interaction with organic amendments and (ii) to compare the effects of mineral and organic fertilization. We set up two parallel experiments in pots using a previously homogenized soil collected from a commercial olive orchard: in the first one, we grew olive saplings in unamended and organically amended soils with two distinct composts and compared these two soils incubated without a plant, while in the second experiment, we comparatively tested the effects of organic and mineral fertilization. OTUs and the relative abundances of bacterial and fungal genera and phyla were analyzed by 16S rRNA and ITS1 gene amplicon using high-throughput sequencing. Basal respiration and substrate-induced respiration were measured by MicroResp^TM. The effects of the different treatments were analyzed in all phyla and in the 100 most abundant genera. The presence of olive saplings increased substrate-induced respiration and bacterial and fungal richness and diversity. Organic amendments greatly affected both bacterial and fungal phyla and increased bacterial richness while not affecting fungal richness. Mineral fertilization increased the relative abundance of the less metabolically active bacterial phyla (Actinobacteria and Firmicutes), while it reduced the most metabolically active phylum, Bacteroidetes. Mineral fertilization increased the relative abundance of three N₂-fixing Actinobacteria genera, while organic fertilization only increased one genus of Proteobacteria. In organically and minerally fertilized soils, high basal respiration rates were associated with low fungal diversity. Basidiomycota and Chytridiomycota relative abundances positively correlated with basal respiration and substrate-induced respiration, while Ascomycota correlated negatively. Indeed, the Ascomycota phyla comprised most of the fungal genera decreased by organic amendments. The symbiotrophic phylum Glomeromycota did not correlate with any of the C sources. The relative abundance of this phylum was promoted by the presence of plants but decreased when amending soils with composts.

From ecophysiology to cultivation methodology: filling the knowledge gap between uncultured and cultured microbes

Earth is dominated by a myriad of microbial communities, but the majority fails to grow under in situ laboratory conditions. The basic cause of unculturability is that bacteria dominantly occur as biofilms in natural environments. Earlier improvements in the culture techniques are mostly done by optimizing media components. However, with technological advancement particularly in the field of genome sequencing and cell imagining techniques, new tools have become available to understand the ecophysiology of microbial communities. Hence, it becomes easier to mimic environmental conditions in the culture plate. Other methods include co-culturing, emendation of growth factors, and cultivation after physical cell sorting. Most recently, techniques have been proposed for bacterial cultivation by employing genomic data to understand either microbial interactions (network-directed targeted bacterial isolation) or ecosystem engineering (reverse genomics). Hopefully, these techniques may be applied to almost all environmental samples, and help fill the gaps between the cultured and uncultured microbial communities.

Culturable diversity of bacterial endophytes associated with medicinal plants of the Western Ghats, India

Bacterial endophytes are found in the internal tissues of plants and have intimate associations with their host. However, little is known about the diversity of medicinal plant endophytes (ME) or their capability to produce specialised metabolites that may contribute to therapeutic properties. We isolated 75 bacterial ME from 24 plant species of the Western Ghats, India. Molecular identification by 16S rRNA gene sequencing grouped MEs into 13 bacterial genera, with members of Gammaproteobacteria and Firmicutes being the most abundant. To improve taxonomic identification, 26 selected MEs were genome sequenced and average nucleotide identity (ANI) used to identify them to the species-level. This identified multiple species in the most common genus as Bacillus. Similarly, identity of the Enterobacterales was also distinguished within Enterobacter and Serratia by ANI and core-gene analysis. AntiSMASH identified non-ribosomal peptide synthase, lantipeptide and bacteriocin biosynthetic gene clusters (BGC) as the most common BGCs found in the ME genomes. A total of five of the ME isolates belonging to Bacillus, Serratia and Enterobacter showed antimicrobial activity against the plant pathogen Pectobacterium carotovorum. Using molecular and genomic approaches we have characterised a unique collection of endophytic bacteria from medicinal plants. Their genomes encode multiple specialised metabolite gene clusters and the collection can now be screened for novel bioactive and medicinal metabolites.

Medicinal Plants and Their Bacterial Microbiota: A Review on Antimicrobial Compounds Production for Plant and Human Health

Medicinal plants (MPs) have been used since antiquity in traditional and popular medicine, and they represent a very important source of bioactive molecules, including antibiotic, antiviral, and antifungal molecules. Such compounds are often of plant origin, but in some cases, an origin or a modification from plant microbiota has been shown. Actually, the research continues to report the production of bioactive molecules by plants, but the role of plant–endophytic interaction is emerging. Classic examples are mainly concerned with fungal endophytes; however, it has been recently shown that bacterial endophytes can also play an important role in influencing the plant metabolism related to the synthesis of bioactive compounds. In spite of this, a deep investigation on the power of MP bacterial endophytes is lacking. Here, an overview of the studies on MP bacterial microbiota and its role in the production of plant antimicrobial compounds contributing to prime host defense system and representing a huge resource for biotech and therapeutic applications is provided.

Exploring the potentialities of beneficial endophytes for improved plant growth

Pathogen affects plant growth, host health and productivity. Endophytes, presumed to live inside the plant tissues, might be helpful in sustaining the future of agriculture. Although recent studies have proven that endophytes can be pathogenic, commensal, non-pathogenic, and/or beneficial, this review will focus on the beneficial category only. Beneficial endophytes produce a number of compounds which are useful for protecting plants from environmental conditions, enhancing plant growth and sustainability, while living conveniently inside the hosts. The population of endophytes is majorly controlled by location, and climatic conditions where the host plant grows. Often the most frequently isolated endophytes from the tissues of the plant are fungi, but sometimes greater numbers of bacteria are isolated. Beneficial endophytes stand a chance to replace the synthetic chemicals currently being used for plant growth promotion if carefully explored by researchers and embraced by policymakers. However, the roles of endophytes in plant growth improvement and their behavior in the host plant have not been fully understood. This review presents the current development of research into beneficial endophytes and their effect in improving plant growth.

Community Composition, Antifungal Activity and Chemical Analyses of Ant-Derived Actinobacteria

Actinobacteria associated with insects represent one potentially rich source of novel natural products with antifungal activity. Here, we investigated the phylogenetic diversity and community composition of actinobacteria associated with ants using a combination of culture-dependent and -independent methods. Further, we assessed the antagonistic activity against phytopathogenic fungi and identified the secondary metabolites from isolates with bioactivity. A total of 416 actinobacterial isolates were obtained from three ant species (Camponotus japonicus, Lasius fuliginosus, and Lasius flavus) located in five nests. The largest amount of isolates were observed in the head samples. 16S rRNA gene sequencing showed that the isolates were diverse and belonged to ten genera within the phylum Actinobacteria, with Streptomyces and Micromonospora comprising the most abundant genera. High-throughput sequencing analyses revealed that the actinobacterial communities were more diverse and dominated by the families Nocardioidaceae, Nocardiaceae, Dermacoccaceae, Intrasporangiaceae, and Streptomycetaceae. In addition, 52.3% of the representative isolates had inhibitory properties against phytopathogenic fungi. Chemical analysis of one Streptomyces strain led to the discovery of two known compounds and one new compound. These results demonstrated that ant-derived actinobacteria represented an underexplored bioresource library of diverse and novel taxa that may be of potential interest in the discovery of new agroactive compounds.

Exploring Actinobacteria Associated With Rhizosphere and Endosphere of the Native Alpine Medicinal Plant Leontopodium nivale Subspecies alpinum

The rhizosphere of plants is enriched in nutrients facilitating growth of microorganisms, some of which are recruited as endophytes. Endophytes, especially Actinobacteria, are known to produce a plethora of bioactive compounds. We hypothesized that Leontopodium nivale subsp. alpinum (Edelweiss), a rare alpine medicinal plant, may serve as yet untapped source for uncommon Actinobacteria associated with this plant. Rhizosphere soil of native Alpine plants was used, after physical and chemical pre-treatments, for isolating Actinobacteria. Isolates were selected based on morphology and identified by 16S rRNA gene-based barcoding. Resulting 77 Actinobacteria isolates represented the genera Actinokineospora, Kitasatospora, Asanoa, Microbacterium, Micromonospora, Micrococcus, Mycobacterium, Nocardia, and Streptomyces. In parallel, Edelweiss plants from the same location were surface-sterilized, separated into leaves, roots, rhizomes, and inflorescence and pooled within tissues before genomic DNA extraction. Metagenomic 16S rRNA gene amplicons confirmed large numbers of actinobacterial operational taxonomic units (OTUs) descending in diversity from roots to rhizomes, leaves and inflorescences. These metagenomic data, when queried with isolate sequences, revealed an overlap between the two datasets, suggesting recruitment of soil bacteria by the plant. Moreover, this study uncovered a profound diversity of uncultured Actinobacteria from Rubrobacteridae, Thermoleophilales, Acidimicrobiales and unclassified Actinobacteria specifically in belowground tissues, which may be exploited by a targeted isolation approach in the future.

Molecular profiling of endophytic Streptomyces cavourensis MH16 inhabiting Millingtonia hortensis Linn. and influence of different culture media on biosynthesis of antimicrobial metabolites

Endophytic actinomycetes, a prolific source of natural products, are well known for their diverse metabolic versatility, and their association with medicinal plants and antimicrobial potential are well worth exploring. We isolated and identified the Streptomyces cavourensis strain MH16 inhabiting the tree Millingtonia hortensis Linn. using phylogenetic analysis based on a 16S rRNA molecular approach. We used the disc diffusion method to evaluate the impact of differences in the compositions of the media on the production of secondary metabolites from strain MH16. The production of antimicrobial metabolites was determined by the observation of inhibition zones on intensive bands when using a TLC-bioautography assay. Biosynthesis of secondary metabolites was optimal when the strain MH16 was cultured in ISP-2 medium as depicted by a zone of inhibition. Strain MH16 effectively inhibited methicillin-resistant Staphylococcus aureus, Escherichia coli, Candida albicans, and other multi drug-resistant pathogens. The minimum inhibitory concentration of the antimicrobial metabolites was 25-100 μg mL^-1. The study manifests the optimization and utilization of different fermentation media which best suits for increased production of the secondary metabolites from Streptomyces cavourensis. This research suggests that the antimicrobial metabolites of strain MH16 found in M. hortensis has great potential for the biodiscovery of new anti-infective drugs against a wide range of multidrug-resistant pathogens.

Community Structures and Antifungal Activity of Root-Associated Endophytic Actinobacteria of Healthy and Diseased Soybean

The present study was conducted to examine the influence of a pathogen Sclerotinia sclerotiorum (Lib.) de Bary on the actinobacterial community associated with the soybean roots. A total of 70 endophytic actinobacteria were isolated from the surface-sterilized roots of either healthy or diseased soybeans, and they were distributed under 14 genera. Some rare genera, including Rhodococcus, Kribbella, Glycomyces, Saccharothrix, Streptosporangium and Cellulosimicrobium, were endemic to the diseased samples, and the actinobacterial community was more diverse in the diseased samples compared with that in the heathy samples. Culture-independent analysis of root-associated actinobacterial community using the high-throughput sequencing approach also showed similar results. Four Streptomyces strains that were significantly abundant in the diseased samples exhibited strong antagonistic activity with the inhibition percentage of 54.1-87.6%. A bioactivity-guided approach was then employed to isolate and determine the chemical identity of antifungal constituents derived from the four strains. One new maremycin analogue, together with eight known compounds, were detected. All compounds showed significantly antifungal activity against S. sclerotiorum with the 50% inhibition (EC₅₀) values of 49.14-0.21 mg/L. The higher actinobacterial diversity and more antifungal strains associated with roots of diseased plants indicate a possible role of the root-associated actinobacteria in natural defense against phytopathogens. Furthermore, these results also suggest that the root of diseased plant may be a potential reservoir of actinobacteria producing new agroactive compounds.

Endophytic actinomycetes associated with Cinnamomum cassia Presl in Hoa Binh province, Vietnam: Distribution, antimicrobial activity and, genetic features

Endophytic microbes associated with medicinal plants are considered to be potential producers of various bioactive secondary metabolites. The present study investigated the distribution, antimicrobial activity and genetic features of endophytic actinomycetes isolated from the medicinal plant Cinnamomum cassia Presl collected in Hoa Binh province of northern Vietnam. Based on phenotypic characteristics, 111 actinomycetes were isolated from roots, stems and leaves of the host plants by using nine selective media. The isolated actinomycetes were mainly recovered from stems (n = 67; 60.4%), followed by roots (n = 29; 26.1%) and leaves (n = 15; 13.5%). The isolates were accordingly assigned into 5 color categories of aerial mycelium, of which gray is the most dominant (n = 42; 37.8%), followed by white (n = 33; 29.7%), yellow (n = 25; 22,5%), red (n = 8; 7.2%) and green (n = 3; 2.7%). Of the total endophytic actinomycetes tested, 38 strains (occupying 34.2%) showed antimicrobial activity against at least one of nine tested microbes and, among them, 26 actinomycetes (68.4%) revealed anthracycline-like antibiotics production. Analysis of 16S rRNA gene sequences deposited on GenBank (NCBI) of the antibiotic-producing actinomycetes identified 3 distinct genera, including Streptomyces, Microbacterium, and Nocardia, among which Streptomyces genus was the most dominant and represented 25 different species. Further genetic investigation of the antibiotic-producing actinomycetes found that 28 (73.7%) and 11 (28.9%) strains possessed genes encoding polyketide synthase (pks) and nonribosomal peptide synthetase (nrps), respectively. The findings in the present study highlighted endophytic actinomycetes from C. cassia Presl which possessed broad-spectrum bioactivities with the potential for applications in the agricultural and pharmaceutical sectors.

Community Composition and Metabolic Potential of Endophytic Actinobacteria From Coastal Salt Marsh Plants in Jiangsu, China

The diversity and functional roles of the plant associated endophytic actinobacteria in unique habitats remain poorly understood. In this paper, we examined the phylogenetic diversity and community composition of endophytic actinobacteria associated with native coastal salt marsh plants in Jiangsu, China using a combination of cultivation and 16S rRNA gene-based high-throughput sequencing (HTS) methods. Further, we evaluated the antifungal, fibrinolytic activities and the secondary metabolite biosynthesis potential of isolates via gene screening. A total of 278 actinobacterial isolates were isolated from 19 plant samples. 16S rRNA gene sequencing revealed that the isolates were highly diverse and belonged to 23 genera within the Actinomycetales order, with Streptomyces, Saccharopolyspora, and Pseudonocardia comprising the most abundant genera. In addition, more than 10 of the isolates were novel actinobacterial taxa distributed across eight genera. HTS analyses of seven representative plant root samples revealed that Actinobacteria phylum constituted 0.04–28.66% of root endophytic bacterial communities. A total of four actinobacterial classes, 14 orders, 35 families, and 63 known genera were detected via HTS, and these communities were found to be dominated by the members of the order Actinomycetales including the genera Streptomyces, Mycobacterium, Arthrobacter, Nocardioides, and Micromonospora. In addition, 30.4% of the representative isolates exhibited antifungal activities, 40.5% of them showed fibrinolytic activities, while 43.0% of the strains harbored secondary metabolite biosynthesis genes. These results demonstrated that coastal salt marsh plants in the Jiangsu Province represented an underexplored new reservoir of diverse and novel endophytic actinobacteria that may be of potential interest in the discovery of bioactive compounds with potential as biocontrol agents and for fibrinolytic enzyme production.

Developing tools for evaluating inoculation methods of biocontrol Streptomyces sp. strains into grapevine plants

The endophytic Streptomyces sp. VV/E1, and rhizosphere Streptomyces sp. VV/R4 strains, isolated from grapevine plants were shown in a previous work to reduce the infection rate of fungal pathogens involved in young grapevine decline. In this study we cloned fragments from randomly amplified polymorphic DNA (RAPD), and developed two stably diagnostic sequence-characterized amplified region (SCAR) markers of 182 and 160 bp for the VV/E1 and VV/R4 strains, respectively. The SCAR markers were not found in another 50 actinobacterial strains isolated from grapevine plants. Quantitative real-time PCR protocols based on the amplification of these SCAR markers were used for the detection and quantification of both strains in plant material. These strains were applied on young potted plants using two methods: perforation of the rootstock followed by injection of the microorganisms or soaking the root system in a bacterial suspension. Both methods were combined with a booster treatment by direct addition of a bacterial suspension to the soil near the root system. Analysis of uprooted plants showed that those inoculated by injection exhibited the highest rate of colonization. In contrast, direct addition of either strain to the soil did not lead to reliable colonization. This study has developed molecular tools for analyzing different methods for inoculating grapevine plants with selected Streptomyces sp. strains which protect them from fungal infections that enter through their root system. These tools are of great applied interest since they could easily be established in nurseries to produce grafted grapevine plants that are protected against fungal pathogens. Finally, this methodology might also be applied to other vascular plants for their colonization with beneficial biological control agents.

Effects of an Endophytic Fungus Umbelopsis dimorpha on the Secondary Metabolites of Host-Plant Kadsura angustifolia

Fungal endophytes live widely inside plant tissues and some have been revealed to provide benefits to their host and ecological environment. Considering the fact that endophytes are engaged in remarkably stable long-term interactions with the host for their whole life cycle, it's conceivable that both partners have substantial influence on each other's metabolic processes. Here, we investigated the fermented products of an endophytic fungus Umbelopsis dimorpha SWUKD3.1410 grown on host-plant Kadsura angustifolia and wheat bran, respectively, to assess the impact of SWUKD3.1410 on the secondary metabolites of K. angustifolia. Twenty compounds (1-20) were isolated and identified as 11 schitriterpenoids (1-9, 17-18), two lignans (10, 20), two sesquiterpenoids (11-12), one trinorsesquiterpenoid (13), one monoterpene (14), one sterol (19), and two simple aromatic compounds (15-16) by the extensive 1D-, 2D-NMR and HR-ESI-MS data analysis. Except for nigranoic acid (1), compounds 2-19 have been firstly found from K. angustifolia. Of them, metabolites 2, 11, and 14 were identified to be new. Obtained results indicated that U. dimorpha SWUKD3.1410 could not only produce the same/similar components as its host does, and modify the host-plant components, but also enhance the production of these highly oxygenated schitriterpenoids/schinortriterpenoids in plants. This study suggested an interesting prospective for setting up alternative processing techniques to improve the quality of crude drugs derived from K. angustifolia and increase their values.

Arthrobacter silvisoli sp. nov., isolated from forest soil

A novel Gram-stain-positive, strictly aerobic strain, NEAU-SA1^T, which showed a rod-coccus growth life cycle, was isolated from forest soil from Zhangjiajie, Hunan Province, China. The isolate grew at 10-40 °C (optimum 28 °C), at pH 5.0-10.0 (optimum pH 7.0) and in the presence of up to 5 % (w/v) NaCl, although NaCl was not required for growth. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NEAU-SA1^T belonged to the genus Arthrobacter and was closely related to Arthrobacter cupressi DSM 24664^T (98.1 % similarity). Average nucleotide identity values between NEAU-SA1^T and A. cupressi DSM 24664^T were 88.91 and 87.41 % by ANIm and ANIb analysis, respectively. The in silico DNA-DNA hybridization value between strain NEAU-SA1^T and A. cupressi DSM 24664^T was 34.20 %, again indicating they belong to different taxa. The genomic DNA G+C content was 66.74 mol%. The major cellular fatty acids (>10 %) were anteiso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified glycolipids. The predominant menaquinone was MK-9(H2). The peptidoglycan type was A3α with an interpeptide bridge comprising l-Lys and l-Ala. Glucose, ribose and galactose were the whole-cell sugars. On the basis of morphological, physiological, biochemical and chemotaxonomic analysis, strain NEAU-SA1^T was classified as representing a novel species in the genus Arthrobacter, for which the name Arthrobacter silvisoli sp. nov. is proposed. The type strain is NEAU-SA1^T (=DSM 106716^T=CCTCC AB 2017271^T).

Actinobacteria associated with Glycyrrhiza inflata Bat. are diverse and have plant growth promoting and antimicrobial activity

Many of the plant associated microbes may directly and indirectly contribute to plant growth and stress resistance. Our aim was to assess the plant growth-promoting and antimicrobial activities of actinobacteria isolated from Glycyrrhiza inflata Bat. plants to find strains that could be applied in agricultural industry, for example in reclaiming saline soils. We isolated 36 and 52 strains that showed morphological characteristics of actinobacteria from one year old and three year old G. inflata plants, respectively. Based on 16S rRNA gene sequence analysis, the strains represented ten actinobacterial genera. Most of the strains had plant growth promoting characteristics in vitro, tolerated 200 mM NaCl and inhibited the growth of at least one indicator organism. The eight selected Streptomyces strains increased the germination rate of G. inflata seeds under salt stress. In addition, the four best seed germination promoters promoted the growth of G. inflata in vivo. The best promoters of G. inflata growth, strains SCAU5283 and SCAU5215, inhibited a wide range of indicator organisms, and may thus be considered as promising candidates to be applied in inoculating G. inflata.

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.

Actinobacteria associated with Chinaberry tree are diverse and show antimicrobial activity

Many actinobacteria produce secondary metabolites that include antimicrobial compounds. Since most of the actinobacteria cannot be cultivated, their antimicrobial potential awaits to be revealed. We hypothesized that the actinobacterial endophyte communities inside Melia toosendan (Chinaberry) tree are diverse, include strains with antimicrobial activity, and that antimicrobial activity can be detected using a cultivation independent approach and co-occurrence analysis. We isolated and identified actinobacteria from Chinaberry, tested their antimicrobial activities, and characterized the communities using amplicon sequencing and denaturing gradient gel electrophoresis as cultivation independent methods. Most of the isolates were identified as Streptomyces spp., whereas based on amplicon sequencing the most abundant OTU was assigned to Rhodococcus, and Tomitella was the most diverse genus. Out of the 135 isolates, 113 inhibited the growth of at least one indicator organism. Six out of the 7577 operational taxonomic units (OTUs) matched 46 cultivated isolates. Only three OTUs, Streptomyces OTU4, OTU11, and OTU26, and their corresponding isolate groups were available for comparing co-occurrences and antimicrobial activity. Streptomyces OTU4 correlated negatively with a high number of OTUs, and the isolates corresponding to Streptomyces OTU4 had high antimicrobial activity. However, for the other two OTUs and their corresponding isolate groups there was no clear relation between the numbers of negative correlations and antimicrobial activity. Thus, the applicability of co-occurrence analysis in detecting antimicrobially active actinobacteria could not be proven.

Limoniibacter endophyticus gen. nov., sp. nov., an alphaproteobacterium isolated from the roots of Limonium otolepis

A Gram-negative bacterium, designated as strain YIM 690229^T, was isolated from the roots of Limonium otolepis. The strain was able to grow at 10-40 °C (optimum, 28-37 °C), pH 6.0-8.0 (optimum, 7.0) and in the presence of up to 7% NaCl (w/v) (optimum, up to 2.5%). Comparative 16S rRNA gene sequence analysis revealed that strain YIM 690229^T shared less than 93.9% sequence similarities with members within the order Rhizobiales, and was remotely related to members of the family Hyphomicrobiaceae. Strain YIM 690229^T was characterized by the presence of Q-10 as the predominant respiratory lipoquinone. The major fatty acids (> 10%) detected were C_18:1 ω7c, C_16:0, anteiso-C_15:0 and summed feature 4 (iso-C_17:1 I and/or anteiso-C_17:1 B). The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanoamine and two unidentified lipids. The genomic DNA G + C content was 57.2 mol%. Data from this polyphasic taxonomy study suggested that strain YIM 690229^T should be classified as a new species of a new genus within the family Hyphomicrobiaceae for which the name Limoniibacter endophyticus gen. nov., sp. nov., is proposed. The type species of the genus Limoniibacter gen. nov. is Limoniibacter endophyticus. The type strain of the species Limoniibacter endophyticus sp. nov. is YIM 690229^T (= KCTC 42097^T = JCM 30141^T = CCTCC AB 2014130^T = CGMCC 1.12906^T).

An insight into the ecology, diversity and adaptations of Gordonia species

The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.

Use of Endophytic and Rhizosphere Actinobacteria from Grapevine Plants To Reduce Nursery Fungal Graft Infections That Lead to Young Grapevine Decline

Endophytic and rhizosphere actinobacteria isolated from the root system of 1-year-old grafted Vitis vinifera plants were evaluated for their activities against fungi that cause grapevine trunk diseases. A total of 58 endophytic and 94 rhizosphere isolates were tested. Based on an in vitro bioassay, 15.5% of the endophytic isolates and 30.8% of the rhizosphere isolates exhibited antifungal activity against the fungal pathogen Diplodia seriata, whereas 13.8% of the endophytic isolates and 16.0% of the rhizosphere isolates showed antifungal activity against Dactylonectria macrodidyma (formerly Ilyonectria macrodidyma). The strains which showed the greatest in vitro efficacy against both pathogens were further analyzed for their ability to inhibit the growth of Phaeomoniella chlamydospora and Phaeoacremonium minimum (formerly Phaeoacremonium aleophilum). Based on their antifungal activity, three rhizosphere isolates and three endophytic isolates were applied on grafts in an open-root field nursery in a 3-year trial. The field trial led to the identification of one endophytic strain, Streptomyces sp. VV/E1, and two rhizosphere isolates, Streptomyces sp. VV/R1 and Streptomyces sp. VV/R4, which significantly reduced the infection rates produced by the fungal pathogens Dactylonectria sp., Ilyonectria sp., P. chlamydospora, and P. minimum, all of which cause young grapevine decline. The VV/R1 and VV/R4 isolates also significantly reduced the mortality level of grafted plants in the nursery. This study shows that certain actinobacteria could represent a promising new tool for controlling fungal trunk pathogens that infect grapevine plants through the root system in nurseries.IMPORTANCE Grapevine trunk diseases are a major threat to the wine and grape industry worldwide. They cause a significant reduction in yields as well as in grape quality, and they can even cause plant death. Trunk diseases are caused by fungal pathogens that enter through pruning wounds and/or the root system. Although different strategies have recently been developed to protect pruning wounds using antifungal compounds (natural or synthetic) or biocontrol agents, no tools are yet available for controlling soil pathogens that infect plants through their root system. This study shows that different actinobacterial isolates, when applied to grafts in a nursery, can significantly reduce the infection rate caused by fungal pathogens that enter through the root system. This is a new, promising, and green alternative for preventing the decline of young grapevines in nurseries and vineyards.

Diversity of antagonistic bacteria isolated from medicinal plant Peganum harmala L

The antimicrobial activity of plant extract of Peganum harmala, a medicinal plant has been studied already. However, knowledge about bacterial diversity associated with different parts of host plant antagonistic to different human pathogenic bacteria is limited. In this study, bacteria were isolated from root, leaf and fruit of plant. Among 188 bacterial isolates isolated from different parts of the plant only 24 were found to be active against different pathogenic bacteria i.e. Escherichia coli, Methicillin-resistant Staphylococcus aureus (MRSA), Enterococcus faecium, Enterococcus faecalis and Pseudomonas aeruginosa. These active bacterial isolates were identified on the basis of 16S rRNA gene analysis. Total population of bacteria isolated from plant was high in root, following leaf and fruit. Antagonistic bacteria were also more abundant in root as compared to leaf and fruit. Two isolates (EA5 and EA18) exhibited antagonistic activity against most of the targeted pathogenic bacteria mentioned above. Some isolates showed strong inhibition for one targeted pathogenic bacterium while weak or no inhibition for others. Most of the antagonistic isolates were active against MRSA, following E. faecium, P. aeruginosa, E. coli and E. faecalis. Taken together, our results show that medicinal plants are good source of antagonistic bacteria having inhibitory effect against clinical bacterial pathogens.

Endophytic Nocardiopsis sp. from Zingiber officinale with both antiphytopathogenic mechanisms and antibiofilm activity against clinical isolates

Novel and potential antimicrobial compounds are essential to tackle the frequently emerging multidrug-resistant pathogens and also to develop environment friendly agricultural practices. In the current study, endophytic actinomycetes from rhizome of Zingiber officinale were explored in terms of its diversity and bioactive properties. Fourteen different organisms were isolated, identified and screened for activity against Pythium myriotylum and human clinical pathogens. Among these, Nocardiopsis sp. ZoA1 was found to have highest inhibition with excellent antibacterial effects compared to standard antibiotics. Remarkable antibiofilm property was also shown by the extract of ZoA1. Its antifungal activity against Pythium and other common phytopathogens was also found to be promising as confirmed by scanning electron microscopic analysis. By PCR-based sequence analysis of phz E gene, the organism was confirmed for the genetic basis of phenazine biosynthesis. Further GC-MS analysis of Nocardiopsis sp. revealed the presence of various compounds including Phenol, 2,4-bis (1,1-dimethylethyl) and trans cinnamic acid which can have significant role in the observed result. The current study is the first report on endophytic Nocardiopsis sp. from ginger with promising applications. In vivo treatment of Nocardiopsis sp. on ginger rhizome has revealed its inhibition towards the colonization of P. myriotylum which makes the study to have promises to manage the severe diseases in ginger like rhizome rot.

Endophytic Actinobacteria Associated with Dracaena cochinchinensis Lour.: Isolation, Diversity, and Their Cytotoxic Activities

Dracaena cochinchinensis Lour. is an ethnomedicinally important plant used in traditional Chinese medicine known as dragon's blood. Excessive utilization of the plant for extraction of dragon's blood had resulted in the destruction of the important niche. During a study to provide a sustainable way of utilizing the resources, the endophytic Actinobacteria associated with the plant were explored for potential utilization of their medicinal properties. Three hundred and four endophytic Actinobacteria belonging to the genera Streptomyces, Nocardiopsis, Brevibacterium, Microbacterium, Tsukamurella, Arthrobacter, Brachybacterium, Nocardia, Rhodococcus, Kocuria, Nocardioides, and Pseudonocardia were isolated from different tissues of D. cochinchinensis Lour. Of these, 17 strains having antimicrobial and anthracyclines-producing activities were further selected for screening of antifungal and cytotoxic activities against two human cancer cell lines, MCF-7 and Hep G2. Ten of these selected endophytic Actinobacteria showed antifungal activities against at least one of the fungal pathogens, of which three strains exhibited cytotoxic activities with IC₅₀-values ranging between 3 and 33 μg·mL⁻¹. Frequencies for the presence of biosynthetic genes, polyketide synthase- (PKS-) I, PKS-II, and nonribosomal peptide synthetase (NRPS) among these 17 selected bioactive Actinobacteria were 29.4%, 70.6%, and 23.5%, respectively. The results indicated that the medicinal plant D. cochinchinensis Lour. is a good niche of biologically important metabolites-producing Actinobacteria.

Endophytic actinomycetes: promising source of novel bioactive compounds

Endophytic actinomycetes associated with plant roots are a relatively untapped source of potential new bioactive compounds. This is becoming increasingly important, as the returns from discovery research on soil-dwelling microbes, have been continuously diminishing. We have isolated more than 1000 strains of actinomycetes from plant roots in our search for novel bioactive compounds, identified and assayed their bioactive metabolites, as well as investigated their biosynthetic genes for generating secondary metabolites. This has resulted in the discovery of several interesting compounds. Creation of plant root clone libraries enabled us to confirm that we had, indeed, isolated endophytes. In this paper, we introduce our approach to this promising line of research, incorporating data from other publications, and illustrate the potential that endophytic actinomycetes offer as a new source of novel lead compounds.

Diversity of Culturable Thermophilic Actinobacteria in Hot Springs in Tengchong, China and Studies of their Biosynthetic Gene Profiles

The class Actinobacteria has been a goldmine for the discovery of antibiotics and has attracted interest from both academics and industries. However, an absence of novel approaches during the last few decades has limited the discovery of new microbial natural products useful for industries. Scientists are now focusing on the ecological aspects of diverse environments including unexplored or underexplored habitats and extreme environments in the search for new metabolites. This paper reports on the diversity of culturable actinobacteria associated with hot springs located in Tengchong County, Yunnan Province, southwestern China. A total of 58 thermophilic actinobacterial strains were isolated from the samples collected from ten hot springs distributed over three geothermal fields (e.g., Hehua, Rehai, and Ruidian). Phylogenetic positions and their biosynthetic profiles were analyzed by sequencing 16S rRNA gene and three biosynthetic gene clusters (KS domain of PKS-I, KSα domain of PKS-II and A domain of NRPS). On the basis of 16S rRNA gene phylogenetic analysis, the 58 strains were affiliated with 12 actinobacterial genera: Actinomadura Micromonospora, Microbispora, Micrococcus, Nocardiopsis, Nonomuraea, Promicromonospora, Pseudonocardia, Streptomyces, Thermoactinospora, Thermocatellispora, and Verrucosispora, of which the two novel genera Thermoactinospora and Thermocatellisopora were recently described from among these strains. Considering the biosynthetic potential of these actinobacterial strains, 22 were positive for PCR amplification of at least one of the three biosynthetic gene clusters (PKS-I, PKS-II, and NRPS). These actinobacteria were further subjected to antimicrobial assay against five opportunistic human pathogens (Acinetobacter baumannii, Escherichia coli, Micrococcus luteus, Staphylococcus aureus and Streptococcus faecalis). All of the 22 strains that were positive for PCR amplification of at least one of the biosynthetic gene domains exhibited antimicrobial activities against at least one of the five test organisms. Among the remaining 36 actinobacteria that are negative for PCR amplification of the domains for the biosynthetic genes, 33 strains showed antimicrobial activities against at least one of the five test pathogens. In summary, the findings presented in this study emphasized the importance of underexplored habitats such as Tengchong hot springs as potential sources for search of bioactive molecules.

Isolation and antimicrobial activities of actinobacteria closely associated with liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza inflate BAT. in Xinjiang, China

A total of 218 actinobacteria strains were isolated from wild perennial liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza. inflate BAT. Based on morphological characteristics, 45 and 32 strains from G. inflate and G. glabra, respectively, were selected for further analyses. According to 16S rRNA sequence analysis, most of the strains belonged to genus Streptomyces and a few strains represented the rare actinobacteria Micromonospora, Rhodococcus and Tsukamurella. A total of 39 strains from G. inflate and 27 strains from G. glabra showed antimicrobial activity against at least one indicator organism. The range of the antimicrobial activity of the strains isolated from G. glabra and G. inflate was similar. A total of 34 strains from G. inflate and 29 strains from G. glabra carried at least one of the genes encoding polyketide synthases, non-ribosomal peptide synthetase and FADH2-dependent halogenase. In the type II polyketide synthase KSα gene phylogenetic analysis, the strains were divided into two major clades: one included known spore pigment production-linked KSα sequences and other sequences were linked to the production of different types of aromatic polyketide antibiotics. Based on the antimicrobial range, the isolates that carried different KSα types were not separated from each other or from the isolates that did not carry KSα. The incongruent phylogenies of 16S rRNA and KSα genes indicated that the KSα genes were possibly horizontally transferred. In all, the liquorice plants were a rich source of biocontrol agents that may produce novel bioactive compounds.

Antioxidant and DNA Damage Protecting Activity of Exopolysaccharides from the Endophytic Bacterium Bacillus cereus SZ1

An endophytic bacterium was isolated from the Chinese medicinal plant Artemisia annua L. The phylogenetic and physiological characterization indicated that the isolate, strain SZ-1, was Bacillus cereus. The endophyte could produce an exopolysaccharide (EPS) at 46 mg/L. The 1,1-diphenyl-2-picrylhydracyl (DPPH) radical scavenging activity of the EPS reached more than 50% at 3-5 mg/mL. The EPS was also effective in scavenging superoxide radical in a concentration dependent fashion with an EC50 value of 2.6 mg/mL. The corresponding EC50 for scavenging hydroxyl radical was 3.1 mg/mL. Moreover, phenanthroline-copper complex-mediated chemiluminescent emission of DNA damage was both inhibited and delayed by EPS. The EPS at 0.7-1.7 mg/mL also protected supercoiled DNA strands in plasmid pBR322 against scission induced by Fenton-mediated hydroxyl radical. The preincubation of PC12 cells with the EPS prior to H₂O₂ exposure increased the cell survival and glutathione (GSH) level and catalase (CAT) activities, and decreased the level of malondialdehyde (MDA) and lactate dehydrogenase (LDH) activity in a dose-dependent manner, suggesting a pronounced protective effect against H₂O₂-induced cytotoxicity. Our study indicated that the EPS could be useful for preventing oxidative DNA damage and cellular oxidation in pharmaceutical and food industries.

Bacterial Endo-Symbiont Inhabiting Tridax procumbens L. and Their Antimicrobial Potential

Bacterial symbionts inhabiting Tridax procumbens L. were screened for antimicrobial potential with the aim to isolate potent bacteria bearing significant activity against test pathogens. The selected isolate was subjected to large scale fermentation to extract antimicrobial metabolite. The organic phase was reduced under vacuum pressure and crude ethyl acetate extract (10 mg/mL) was evaluated for antimicrobial activity against panel of test pathogens. The antibacterial activity was measured as a zone of inhibition and compared with standard antibiotics, gentamicin and tetracycline. Similarly, antifungal activity was compared with miconazole and bavistin. Significant activity was conferred against Shigella flexneri (MTCC 731) with 27±1.5 mm zone across the disc. Partially, purification of antimicrobial metabolite with TLC-bioautography and HPLC resulted in active fraction bearing activity at Rf 0.65 and eluting between 4 and 5 retention times. The obtained results are promising enough for future purification and characterization of antimicrobial metabolite. Thus, the study attributes to the growing knowledge on endophytes as one of the rich sources of antimicrobial potentials.

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.

Antimicrobial biosynthetic potential and genetic diversity of endophytic actinomycetes associated with medicinal plants

Endophytic actinomycetes are one of the primary groups that share symbiotic relationships with medicinal plants and are key reservoir of biologically active compounds. In this study, six selective medicinal plants were targeted for the first time for endophytic actinomycetes isolation from Gibbon Wild Life Sanctuary, Assam, India, during winter and summer and 76 isolates were obtained. The isolates were found to be prevalent in roots followed by stem and leaves. 16S rRNA gene sequence analysis revealed 16 genera, including rare genera, Verrucosispora, Isoptericola and Kytococcus, which have never been previously reported as endophytic. The genus Streptomyces (66%) was dominant in both seasons. Shannon's diversity index showed that Azadirachta indica (1.49), Rauwolfia serpentina (1.43) and Emblica officinalis (1.24) were relatively good habitat for endophytic actinomycetes. Antimicrobial strains showed prevalence of polyketide synthase (PKS) type-II (85%) followed by PKS type-I (14%) encoded in the genomes. Expression studies showed 12-fold upregulation of PKSII gene in seventh day of incubation for Streptomyces antibioticus (EAAG90). Our results emphasize that the actinomycetes assemblages within plant tissue exhibited biosynthetic systems encoding for important biologically active compounds.

Endophytes as producers of peptides: an overview about the recently discovered peptides from endophytic microbes

An endophyte is a fungus or bacterium that lives within a plant in a symbiotic relationship. Extensive colonization of the plant tissue by endophytes creates a barrier effect, where they outcompete and prevent pathogenic organisms from taking hold. This happens by producing secondary metabolites that inhibit the growth of the competitors or pathogens. In this way they play a very important role in the plant defence mechanisms. The metabolites produced by these endophytes fall within a wide range of classes of compounds that include peptides which are the focus of this review. Peptides are increasingly being selected for drug development because they are specific for their targets and have a higher degree of interactions. There have been quite a number of endophytic peptides reported in the recent past indicating that endophytes can be used for the production of peptide based drugs. Molecular screening for NRPS, which shows peptide producing capability, has also shown that endophytes are potential producers of peptides. The presence of NRPS also offers the possibility of genetic modifications which may generate peptides with high pharmacological activities. This review, therefore, aims to show the current status of peptides isolated from endophytic bacteria and fungi in the recent decade. Endophytes as potential sources of peptides according to NRPS studies will also be discussed.

Metabolic potential of endophytic bacteria

The bacterial endophytic microbiome promotes plant growth and health and beneficial effects are in many cases mediated and characterized by metabolic interactions. Recent advances have been made in regard to metabolite production by plant microsymbionts showing that they may produce a range of different types of metabolites. These substances play a role in defense and competition, but may also be needed for specific interaction and communication with the plant host. Furthermore, few examples of bilateral metabolite production are known and endophytes may modulate plant metabolite synthesis as well. We have just started to understand such metabolic interactions between plants and endophytes, however, further research is needed to more efficiently make use of beneficial plant-microbe interactions and to reduce pathogen infestation as well as to reveal novel bioactive substances of commercial interest.

Impact of endophytic microorganisms on plants, environment and humans

Endophytes are microorganisms (bacteria or fungi or actinomycetes) that dwell within robust plant tissues by having a symbiotic association. They are ubiquitously associated with almost all plants studied till date. Some commonly found endophytes are those belonging to the genera Enterobacter sp., Colletotrichum sp., Phomopsis sp., Phyllosticta sp., Cladosporium sp., and so forth. Endophytic population is greatly affected by climatic conditions and location where the host plant grows. They produce a wide range of compounds useful for plants for their growth, protection to environmental conditions, and sustainability, in favour of a good dwelling place within the hosts. They protect plants from herbivory by producing certain compounds which will prevent animals from further grazing on the same plant and sometimes act as biocontrol agents. A large amount of bioactive compounds produced by them not only are useful for plants but also are of economical importance to humans. They serve as antibiotics, drugs or medicines, or the compounds of high relevance in research or as compounds useful to food industry. They are also found to have some important role in nutrient cycling, biodegradation, and bioremediation. In this review, we have tried to comprehend different roles of endophytes in plants and their significance and impacts on man and environment.

Diversity of endophytic bacteria in medicinally important Nepenthes species

BACKGROUND

Nepenthes species are used in traditional medicines to treat various health ailments. However, we do not know which types of endophytic bacteria (EB) are associated with Nepenthes spp.

OBJECTIVE

The objective of this study was to isolate and to identify EB associated with Nepenthes spp.

MATERIALS AND METHODS

Surface-sterilized leaf and stem tissues from nine Nepenthes spp. collected from Peninsular Malaysia were used to isolate EB. Isolates were identified using the polymerase chain reaction-amplified 16S ribosomal DNA (rDNA) sequence similarity based method.

RESULTS

Cultivable, 96 isolates were analyzed; and the 16S rDNA sequences analysis suggest that diverse bacterial species are associated with Nepenthes spp. Majority (55.2%) of the isolates were from Bacillus genus, and Bacillus cereus was the most dominant (14.6%) among isolates.

CONCLUSION

Nepenthes spp. do harbor a wide array of cultivable endophytic bacteria.

Sponge-derived Kocuria and Micrococcus spp. as sources of the new thiazolyl peptide antibiotic kocurin

Forty four marine actinomycetes of the family Microccocaceae isolated from sponges collected primarily in Florida Keys (USA) were selected from our strain collection to be studied as new sources for the production of bioactive natural products. A 16S rRNA gene based phylogenetic analysis showed that the strains are members of the genera Kocuria and Micrococcus. To assess their biosynthetic potential, the strains were PCR screened for the presence of secondary metabolite genes encoding nonribosomal synthetase (NRPS) and polyketide synthases (PKS). A small extract collection of 528 crude extracts generated from nutritional microfermentation arrays was tested for the production of bioactive secondary metabolites against clinically relevant strains (Bacillus subtilis, methicillin-resistant Staphylococcus aureus (MRSA), Acinetobacter baumannii and Candida albicans). Three independent isolates were shown to produce a new anti-MRSA bioactive compound that was identified as kocurin, a new member of the thiazolyl peptide family of antibiotics emphasizing the role of this family as a prolific resource for novel drugs.

Identification of bacterial endophytes associated with traditional medicinal plant Tridax procumbens Linn

BACKGROUND

In traditional medicine, Tridax procumbens Linn. is used in the treatment of injuries and wounds. The bacterial endophytes (BEs) of medicinal plants could produce medicinally important metabolites found in their hosts; and hence, the involvement of BEs in conferring wound healing properties to T. Procumbens cannot be ruled out. But, we do not know which types of BEs are associated with T. Procumbens.

OBJECTIVE

The objective of this study was to investigate the fast growing and cultivable BEs associated with T. procumbens.

MATERIALS AND METHODS

Leaves and stems of healthy T. Procumbens plants were collected and cultivable BEs were isolated from surface-sterilized leaf and stem tissue samples using Luria-Bertani (LB) agar (medium) at standard conditions. A polymerase chain reaction was employed to amplify 16S rRNA coding gene fragments from the isolates. Cultivable endophytic bacterial isolates (EBIs) were identified using 16S rRNA gene nucleotide sequence similarity based method of bacterial identification.

RESULTS

Altogether, 50 culturable EBIs were isolated. 16S rRNA gene nucleotide sequences analysis using the Basic Local Alignment Search Tool (BLAST) revealed identities of the EBIs. Analysis reveals that cultivable Bacillus spp., Cronobacter sakazakii, Enterobacter spp., Lysinibacillus sphaericus, Pantoea spp., Pseudomonas spp. and Terribacillus saccharophilus are associated with T. Procumbens.

CONCLUSION

Based on the results, we conclude that 24 different types of culturable BEs are associated with traditionally used medicinal plant, T. Procumbens, and require further study.