Biodiscovery from rare actinomycetes: an eco-taxonomical perspective

An Overview on Nocardiopsis Species Originating From North African Biotopes as a Promising Source of Bioactive Compounds and In Silico Genome Mining Analysis of Three Sequenced Genomes

Actinobacteria are renowned for their prolific production of diverse bioactive secondary metabolites. In recent years, there has been an increasing focus on exploring "rare" genera within this phylum for biodiscovery purposes, notably the Nocardiopsis genus, which will be the subject of the present study. Recognizing the absence of articles describing the research process of finding bioactive molecules from the genus Nocardiopsis in North African environments. We, therefore, present a historical overview of the discoveries of bioactive molecules of the genus Nocardiopsis originating from the region, highlighting their biological activities and associated reported molecules, providing a snapshot of the current state of the field, and offering insights into future opportunities and challenges for drug discovery. Additionally, we present a genome mining analysis of three genomes deposited in public databases that have been reported to be bioactive. A total of 36 biosynthetic gene clusters (BGCs) were identified, including those known to encode bioactive molecules. Notably, a substantial portion of the BGCs showed little to no similarity to those previously described, suggesting the possibility that the analyzed strains could be potential producers of new compounds. Further research on these genomes is essential to fully uncovering their biotechnological potential. Moving forward, we discuss the experimental designs adopted in the reported studies, as well as new avenues to guide the exploration of the Nocardiopsis genus in North Africa.

In vitro biological control of Pyrrhoderma noxium using volatile compounds produced by termite gut-associated streptomycetes

Introduction

Pyrrhoderma noxium is a plant pathogen that causes economic losses in agricultural and forestry industries, including significant destruction to amenity trees within the city of Brisbane in Australia. Use of chemical control agents are restricted in public areas, there is therefore an urgent need to investigate biological control approaches. Members of the phylum Actinomycetota, commonly known as actinomycetes, are known for their industrially important secondary metabolites including antifungal agents. They have proven to be ideal candidates to produce environmentally friendly compounds including the volatile organic compounds (VOCs) which can be used as biofumigants.

Methods

Different Streptomyces species (n=15) previously isolated from the guts of termites and stored in the University of the Sunshine Coast'sMicrobial Library were tested for their antifungal VOCs against Pyrrhoderma noxium.

Results

Fourteen of them were found to display inhibition (39.39-100%) to the mycelial development of the pathogen. Strongest antifungal activity displaying isolates USC-592, USC-595, USC-6910 and USC-6928 against the pathogen were selected for further investigations. Their VOCs were also found to have plant growth promotional activity observed for Arabidopsis thaliana with an increase of root length (22-36%) and shoot length (26-57%). The chlorophyll content of the test plant had a slight increase of 11.8% as well. Identified VOCs included geosmin, 2-methylisoborneol, 2-methylbutyrate, methylene cyclopentane, β-pinene, dimethyl disulfide, ethyl isovalerate, methoxyphenyl-oxime and α-pinene. Additionally, all 15 Streptomyces isolates were found to produce siderophores and indole acetic acid as well as the enzyme chitinase which is known to break down the fungal cell wall.

Discussion

Findings indicate that termite gut-associated streptomycetes might be used to control Pyrrhoderma noxium by utilizing their wide range of inhibitory mechanisms.

Isolation and structure determination of allopteridic acids A-C and allokutzmicin from an unexplored actinomycete of the genus Allokutzneria

Two classes of new polyketides, allopteridic acids A-C (1-3) and allokutzmicin (4), were isolated from the culture extract of an actinomycete of the genus Allokutzneria. The structures of 1-4 were elucidated through the interpretation of NMR and MS analytical data. Compounds 1-3 possess the same carbon skeleton with pteridic acids but their monocyclic core structures are distinct from the spiro-bicyclic acetal structures of pteridic acids. Compound 4 is a linear polyketide of an unprecedented class, featured by a guanidino-terminus and an epoxide modification. Compounds 1-3 promoted the root elongation of germinated lettuce seeds by ca. 10-40% at 1~10 μM whereas 4 retarded the seed growth. Compound 4 exhibited weak antimicrobial activity against Candida albicans with MIC 25 μg mL^-1.

Micrococcus spp. as a promising source for drug discovery: A review

Historically, bacteria of the phylum, Actinobacteria have been a very prominent source of bioactive compounds for drug discovery. Among the actinobacterial genera, Micrococcus has not generally been prioritized in the search for novel drugs. The bacteria in this genus are known to have very small genomes (generally < 3 Mb). Actinobacteria with small genomes seldom contain the well-characterized biosynthetic gene clusters such as those encoding polyketide synthases and nonribosomal peptide synthetases that current genome mining algorithms are optimized to detect. Nevertheless, there are many reports of substantial pharmaceutically relevant bioactivity of Micrococcus extracts. On the other hand, there are remarkably few descriptions of fully characterized and structurally elucidated bioactive compounds from Micrococcus spp. This review provides a comprehensive summary of the bioactivity of Micrococcus spp. that encompasses antibacterial, antifungal, cytotoxic, antioxidant, and anti-inflammatory activities. This review uncovers the considerable biosynthetic potential of this genus and highlights the need for a re-examination of these bioactive strains, with a particular emphasis on marine isolates, because of their potent bioactivity and high potential for encoding unique molecular scaffolds.

Selective isolation of Arctic marine actinobacteria and a down-scaled fermentation and extraction strategy for identifying bioactive compounds

Actinobacteria are among the most prolific producers of bioactive secondary metabolites. In order to collect Arctic marine bacteria for the discovery of new bioactive metabolites, actinobacteria were selectively isolated during a research cruise in the Greenland Sea, Norwegian Sea and the Barents Sea. In the frame of the isolation campaign, it was investigated how different sample treatments, isolation media and sample-sources, such as animals and sediments, affected the yield of actinobacterial isolates to aid further isolation campaigns. Special attention was given to sediments, where we expected spores of spore forming bacteria to enrich. Beside actinobacteria a high share of bacilli was obtained which was not desired. An experimental protocol for down-scaled cultivation and extraction was tested and compared with an established low-throughput cultivation and extraction protocol. The heat-shock method proved suitable to enrich spore-, or endospore forming bacteria such as bacilli. Finally, a group bioactive compounds could be tentatively identified using UHPLC–MS/MS analysis of the active fractions.

DETECTION OF ANTIMICROBIAL COMPOUNDS FROM THERMOPHILIC ACTINOMYCETES USING ONE STRAIN MANY COMPOUNDS (OSMAC) APPROACH

Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.

Selective isolation, antimicrobial screening and phylogenetic diversity of marine actinomycetes derived from the Coast of Bejaia City (Algeria), a polluted and microbiologically unexplored environment

AIMS

The current study aimed to evaluate the occurrence of actinomycetes in the Coast of Bejaia City using selective isolation, as well as their bioactivity and phylogenitic diversity.

METHODS AND RESULTS

Different selective media and methods were used, leading to the isolation of 103 actinomycete strains. The number of strains was influenced by isolation procedures and their interactions based on a three-way ANOVA and a post hoc Tukey test, which revealed that using M2 medium, dilution of samples followed by moderate heat treatment, and sampling at 10-20 m yielded the highest numbers of actinomycetes. The isolates were screened for their antimicrobial activity against human pathogenic microorganisms using agar and well diffusion methods. Of all the isolates, ten displayed activity against at least one Gram-positive bacterium, of which P21 showed the highest activity against Staphylococcus aureus, Methicillin-resistant S. aureus and Bacillus subtilis, with a diameter of 32, 28 and 25 mm respectively. Subsequently, active isolates were assigned to Streptomyces spp. and Nocardiopsis spp. based on 16S rRNA gene sequencing, including a putative new Streptomyces species (S3). The phenotypic characteristics of the P21 strain were determined, and interesting enzymatic capacities were shown.

CONCLUSION

The recovery of actinomycetes along the Coast of Bejaia City was influenced by the isolation procedure. Ten strains displayed interesting antibacterial activity against Gram-positive bacteria, of which the P21 strain was selected as the most active strain.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work provides a new insight into the occurrence of actinobacteria in the Coast of Bejaia. It suggests also that polluted environments such as Bejaia Bay could provide access to interesting actinomycetes as sources of antibiotic leads.

Deep-Sea Actinobacteria Mitigate Salinity Stress in Tomato Seedlings and Their Biosafety Testing

Soil salinity is an enormous problem affecting global agricultural productivity. Deep-sea actinobacteria are interesting due to their salt tolerance mechanisms. In the present study, we aim to determine the ability of deep-sea Dermacoccus (D. barathri MT2.1^T and D. profundi MT2.2^T) to promote tomato seedlings under 150 mM NaCl compared with the terrestrial strain D. nishinomiyaensis DSM20448^T. All strains exhibit in vitro plant growth-promoting traits of indole-3-acetic acid production, phosphate solubilization, and siderophore production. Tomato seedlings inoculated with D. barathri MT2.1^T showed higher growth parameters (shoot and root length, dry weight, and chlorophyll content) than non-inoculated tomato and the terrestrial strain under 150 mM NaCl. In addition, hydrogen peroxide (H₂O₂) in leaves of tomatoes inoculated with deep-sea Dermacoccus was lower than the control seedlings. This observation suggested that deep-sea Dermacoccus mitigated salt stress by reducing oxidative stress caused by hydrogen peroxide. D. barathri MT2.1^T showed no harmful effects on Caenorhabditis elegans, Daphnia magna, Eisenia foetida, and Escherichia coli MC4100 in biosafety tests. This evidence suggests that D. barathri MT2.1^T would be safe for use in the environment. Our results highlight the potential of deep-sea Dermacoccus as a plant growth promoter for tomatoes under salinity stress.

Isolation and Characterization of Nocardiae Associated with Foaming Coastal Marine Waters

Nocardiosis is an infectious disease caused by Nocardia species that occurs worldwide, albeit more prevalently in tropical/subtropical regions. It can appear as either acute, subacute or as a chronic infection mostly with those with a compromised/weakened immune system. Inhalation of spores and or mycelium fragments is the main transmission route for developing pulmonary nocardiosis. In contrast, cutaneous nocardiosis usually occurs via direct contact. In the subtropical region of the Sunshine Coast in Australia foaming events with thick and persistent and orange-brown color foam have been observed during summer seasons in the near shore marine environments. This study reports the existence of nocardiae in these near shore marine environments by the use of a novel isolation method which used the gas requirements of nocardiae as a selective battery. A total of 32 nocardiae were isolated with the use of this novel method and subsequently conducted molecular identification methods confirmed that the isolates belonged to the genus Nocardia. Twenty-one isolates out of the 32 were closely related to N. nova strains MGA115 and one was related to CBU 09/875, in addition when compared with human pathogenic nocardiae twenty of the isolates were found to be related to N. nova strain JCM 6044. Isolates displayed varied resistance against some of the antibiotics tested when interpretation threshold recommended the Comite de L'Antibiogramme de la Societe Francaise de Microbiologie were used. The highest level of resistance against cefotaxime (n = 27) and ceftriaxone (n = 24). Some of the isolates (n = 6) that displayed resistance to selected antibiotics also possessed potential human pathogenic characteristics such as adherence and translocation through human long epithelial cells as well as displaying phage resistance (n = 26). They might thus present a potential public health risk if frequently encountered through exposure to aerosols generated by the foam as well as direct contact through a wound. Preventative measures to control the growth of nocardiae in such environments such as the control of pollutants, might prevent potential infections that might be caused by these bacteria in humans as well as in marine animals.

Bluemomycin, a new naphthoquinone derivative from Streptomyces sp. with antimicrobial and cytotoxic properties

Streptomyces is one of the most prolific producers of economically important bioactive compounds used against several illnesses; it has also been found to produce industrially useful enzymes. In this study, Streptomyces sp. (ERINLG-201) was isolated from the soil sample of Kodanad forest (Southern Western Ghats), The Nilgiris, Tamil Nadu, India. ERINLG-201 isolate showed promising antibacterial activity against tested Gram-positive and Gram-negative bacteria which was confirmed by perpendicular 'T' streak method. Secondary metabolites of ERINLG-201 isolate exhibited promising antibacterial activity against tested Gram-positive and Gram-negative bacteria which was confirmed by disc diffusion method using the ethylacetate extract. Further, the ethylacetate extract of ERINLG-201 (15 g) was packed in column chromatography over silica gel and eluted; it resulted in isolation of a new naphthoquinone derivative named bluemomycin from the active fraction. Bluemomycin showed promising antibacterial activity against Gram-negative bacteria and clinical isolates at least concentration (6.25 µg/mL). Cytotoxic studies of bluemomycin showed promising activity against A549, Skvo-3 and HepG2 cell lines with IC₅₀ values of 5.9, 24.2 and 11 µM, respectively.

Isolation and identification of two alkaloid structures with radical scavenging activity from Actinokineospora sp. UTMC 968, a new promising source of alkaloid compounds

For decades, natural products from Actinomycetes have been recognized as one of the inestimable sources of therapeutic compounds. Presently, due to some challenges in the identification of novel compounds including the validation of novel natural products and their compatibility with the high throughput screening bioassays, evaluating new activity from known commercial ones would be an important designation. On the other hand, finding new sources of bioactive compounds from Actinomycetes can be promising in attaining pharmaceutical compounds with fewer purification steps and cost-effective production of the bioproducts. Here we describe the isolation and identification of two alkaloid compounds from a soil actinobacterium Actinokineospora sp. UTMC 968 including N-acetyltyramine (1) and N-acetyltryptamine (2) with revealing a new bioactivity for these molecules. The producer is a rare actinobacterium belonging to family Pseudonocardiaceae as the first alkaloid compounds producer genus in its family. The structures of alkaloid 1 and 2 were assigned on the basis of 1D and 2D NMR spectroscopy and MS analyses. Compound 1 and 2 are used commercially for their pharmaceutical activity but their radical scavenging activity has not previously been reported. The results of 1,1-diphenyl-2-picrylhydrazyl radical scavenging assay represented a remarkable DPPH radical scavenging capability with an IC₅₀ value of 64.7 ± 0.5 and 131.3 ± 1.8 µg/mL for compound 1 and 2, respectively.

Actinobacteria Associated With Arbuscular Mycorrhizal Funneliformis mosseae Spores, Taxonomic Characterization and Their Beneficial Traits to Plants: Evidence Obtained From Mung Bean (Vigna radiata) and Thai Jasmine Rice (Oryza sativa)

In this study, we report on the isolation of actinobacteria obtained from spores of Funneliformis mosseae and provide evidence for their potential in agricultural uses as plant growth promoters in vitro and in vivo. Actinobacteria were isolated from spores of F. mosseae using the dilution plate technique and media designed for the selective isolation of members of specific actinobacterial taxa. Six strains namely 48, S1, S3, S4, S4-1 and SP, were isolated and identified based on16S rRNA gene sequences. Phylogenetic analysis showed that isolate SP belonged to the genus Pseudonocardia with P. nantongensis KLBMP 1282^T as its closest neighbor. The remaining isolates belonged to the genus Streptomyces. Two isolates, 48 and S3 were most closely related to S. thermocarboxydus DSM 44293^T. Isolates S4 and S4-1 shared the highest 16S RNA gene similarity with S. pilosus NBRC 127772^T. Isolate S1 showed its closest relationship with the type strain of S. spinoverrucosus NBRC14228^T. The ability of these isolates to produce indole-3-acetic acid (IAA), siderophores and the ability to solubilize phosphate in vitro were examined. All isolates produced siderophores, four isolates produced IAA and two isolates solubilized inorganic phosphate at varying levels. S. thermocarboxydus isolate S3 showed the highest IAA production with high activities of phosphate solubilization and siderophore production. The inoculation of mung beans (Vigna radiata) with this strain resulted in a significant increase in fresh weight, root length and total length as an effect of IAA production. In an experiment with rice (Oryza sativa), S. thermocarboxydus isolate S3 promoted the growth of rice plants grown in low nutritional soil under induced drought stress. This report supports the view that the inoculation of rice with plant growth promoting actinobacteria mitigates some adverse effects of low nutrient and drought stress on rice.

Biological Control of Mango Dieback Disease Caused by Lasiodiplodia theobromae Using Streptomycete and Non-streptomycete Actinobacteria in the United Arab Emirates

Dieback caused by the fungus Lasiodiplodia theobromae is an important disease on mango plantations in the United Arab Emirates (UAE). In this study, 53 actinobacterial isolates were obtained from mango rhizosphere soil in the UAE, of which 35 (66%) were classified as streptomycetes (SA) and 18 (34%) as non-streptomycetes (NSA). Among these isolates, 19 (12 SA and 7 NSA) showed antagonistic activities against L. theobromae associated with either the production of diffusible antifungal metabolites, extracellular cell-wall-degrading enzymes (CWDEs), or both. Using a "novel" mango fruit bioassay, all isolates were screened in vivo for their abilities to reduce lesion severity on fruits inoculated with L. theobromae. Three isolates, two belonging to Streptomyces and one to Micromonospora spp., showed the strongest inhibitory effect against this pathogen in vitro and were therefore selected for tests on mango seedlings. Our results revealed that the antifungal action of S. samsunensis UAE1 was related to antibiosis, and the production of CWDEs (i.e., chitinase) and siderophores; whilst S. cavourensis UAE1 and M. tulbaghiae UAE1 were considered to be associated with antibiotic- and CWDE-production, respectively. Pre-inoculation in greenhouse experiments with the most promising actinobacterial isolates resulted in very high levels of disease protection in mango seedlings subsequently inoculated with the pathogen. This was evident by the dramatic reduction in the estimated disease severity indices of the mango dieback of individual biocontrol agent (BCA) applications compared with the pathogen alone, confirming their potential in the management of mango dieback disease. L. theobromae-infected mango seedlings treated with S. samsunensis showed significantly reduced number of defoliated leaves and conidia counts of L. theobromae by 2- and 4-fold, respectively, in comparison to the other two BCA applications. This indicates that the synergistic antifungal effects of S. samsunensis using multiple modes of action retarded the in planta invasion of L. theobromae. This is the first report of BCA effects against L. theobromae on mango seedlings by microbial antagonists. It is also the first report of actinobacteria naturally existing in the soils of the UAE or elsewhere that show the ability to suppress the mango dieback disease.

Intertidal marine sediment harbours Actinobacteria with promising bioactive and biosynthetic potential

Actinobacteria are the major source of bioactive natural products that find their value in research and drug discovery programmes. Antimicrobial resistance and the resulting high demand for novel antibiotics underscore the need for exploring novel sources of these bacteria endowed with biosynthetic potential. Intertidal ecosystems endure regular periods of immersion and emersion, and represent an untapped source of Actinobacteria. In this study, we studied the diversity and biosynthetic potential of cultivable Actinobacteria from intertidal sediments of Diu Island in the Arabian Sea. A total of 148 Actinobacteria were selectively isolated using a stamping method with eight isolation media. Isolates were grouped into OTUs based on their 16S rRNA gene sequence, and categorized within actinobacterial families such as Glycomycetaceae, Micromonosporaceae, Nocardiaceae, Nocardiopsaceae, Pseudonocardiaceae, Streptomycetaceae, and Thermomonosporaceae. The biosynthetic potential of the Actinobacteria, necessary for secondary metabolite biosynthesis, was screened and confirmed by extensive fingerprinting approaches based on genes coding for polyketide synthases and nonribosomal peptide synthetases. The observed biosynthetic potential was correlated with the antibacterial activity exhibited by these isolates in laboratory conditions. Ultimately, the results demonstrate that intertidal sediment is a rich source of diverse cultivable Actinobacteria with high potential to synthesize novel bioactive compounds in their genomes.

Lipids of Dietzia sp. A14101. Part II: A study of the dynamics of the release of surface active compounds by Dietzia sp. A14101 into the medium

Dietzia sp. A14101 isolated from an oil reservoir model column was found to induce a strong decrease of the interfacial tension (IFT) in hydrocarbon-water mixtures in the presence of the intact bacterial cells (Kowalewski et al., 2005). The strain was shown to be able to degrade a wide range of hydrocarbon substrates (Bødtker et al., 2009). Further studies showed that the surface-active compounds tentatively identified as glycolipids were produced by Dietzia sp. A14101 on non- and water-immiscible -hydrocarbon substrates, Part I (Hvidsten et al., 2017). The results suggested that biosurfactant (BS) was a mixture of several isomers. The study presented here is aimed to investigate whether BS are secreted into the aqueous medium, and if so, then at which phase of the culture growth and in which amounts - the dynamics of the BS release in incubations on water-immiscible hydrocarbons. Two methods of BS extraction from the medium were attempted and compared: a liquid-liquid extraction (LLE) and precipitation by acid. For qualitative and semi-quantitative assessment, gas chromatography-mass spectrometry (GC/MS), thin-layer chromatography (TLC), liquid chromatography-mass spectrometry (LC-MS), surface tension measurements (SFT), emulsification (E₂₄) and oil-spreading tests were employed. The results indicated that BS only partially were secreted into the medium. Detectable amounts of glycolipids in media were first identified during the exponential growth phase. However, only a slight decrease of SFT was observed in the cell-free medium. The emulsification index values of the sampled material were lower than those reported for related strains. The results suggested that most of the BS produced by Dietzia sp. A14101 remains cell-bound during the culture development in a batch mode and only a narrow range of the BS isomers can be detected in small amounts in media.

Two new species of the genus Streptomyces: Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. isolated from the cuticle of Camponotus japonicus Mayr

Two novel actinomycetes, designated strains 2C-SSA16(2)^T and 1C-GS8^T, were isolated from the cuticle of Camponotus japonicus Mayr, collected from Northeast Agricultural University, Heilongjiang Province, north China. Both of them contained genes (involved in antibiotics biosynthesis) of the ketosynthase (KS) and methyl malonyl transferase domains (PKS-I) and the adenylation domain (NRPS). A polyphasic study was carried out to establish the taxonomic positions of these strains. The 16S rRNA gene sequence analysis showed that the two novel isolates 2C-SSA16(2)^T and 1C-GS8^T exhibited 98.8% similarity with each other and that they are most closely related to Streptomyces umbrinus JCM 4521^T (99.0, 98.6%), Streptomyces ederensis JCM 4958^T (98.9, 98.7%), Streptomyces aurantiacus JCM 4453^T (98.6, 98.2%), Streptomyces glomeroaurantiacus JCM 4677^T (98.6, 98.1%), Streptomyces tauricus JCM4837^T (98.2, 98.0%) and Streptomyces phaeochromogenes JCM 4070^T (98.2, 99.2%). The corresponding phylogenetic analysis based on partial gyrB gene sequences showed that strains 2C-SSA16(2)^T and 1C-GS8^T formed a cluster with the above-mentioned strains. The DNA-DNA hybridization data and phenotypic characteristics indicated that strains 2C-SSA16(2)^T and 1C-GS8^T could be readily distinguished from each other and their closest phylogenetic relatives. Therefore, these two strains are suggested to represent two novel species of the genus Streptomyces, for which the names Streptomyces camponoti sp. nov. and Streptomyces cuticulae sp. nov. are proposed. The type strains are 2C-SSA16(2)^T (=CGMCC 4.7276^T = DSM 100522^T) and 1C-GS8^T (=CGMCC 4.7348 = DSM 103127^T), respectively.

Evaluation of fermentation conditions triggering increased antibacterial activity from a near-shore marine intertidal environment-associated Streptomyces species

A near-shore marine intertidal environment-associated Streptomyces isolate (USC-633) from the Sunshine Coast Region of Queensland, Australia, cultivated under a range of chemically defined and complex media to determine optimal parameters resulting in the secretion of diverse array of secondary metabolites with antimicrobial properties against various antibiotic resistant bacteria. Following extraction, fractioning and re-testing of active metabolites resulted in persistent antibacterial activity against Escherichia coli (Migula) (ATCC 13706) and subsequent Nuclear Magnetic Resonance (NMR) analysis of the active fractions confirmed the induction of metabolites different than the ones in fractions which did not display activity against the same bacterial species. Overall findings again confirmed the value of One Strain–Many Compounds (OSMAC) approach that tests a wide range of growth parameters to trigger bioactive compound secretion increasing the likelihood of finding novel therapeutic agents. The isolate was found to be adaptable to both marine and terrestrial conditions corresponding to its original near-shore marine intertidal environment. Wide variations in its morphology, sporulation and diffusible pigment production were observed when different growth media were used.

Isolation and Structure Elucidation of Cytotoxic Saccharothriolides D to F from a Rare Actinomycete Saccharothrix sp. and Their Structure-Activity Relationship

Three new 10-membered macrolides, saccharothriolides D-F (1-3), were isolated from a rare actinomycete, Saccharothrix sp. A1506. The planar structures were determined from analysis of extensive NMR and HR-ESI-MS data, and the absolute configurations were established by ECD spectroscopy analysis. Saccharothriolides D (1) and E (2) were determined to be C-2 epimers of saccharothriolides A (4) and B (5), respectively. Saccharothriolide F (3) was identified to be a demethylated congener of saccharothriolides D (1) and A (4) at the C-2 position. The availability of compounds 1-6 enabled a structure-activity relationship study that revealed the importance of the phenolic hydroxy group at C-2″ and the stereochemistry of C-2 for the inhibition of human fibrosarcoma HT1080 cell growth.

New antimicrobial anthraquinone 6,61-bis (1,5,7-trihydroxy-3-hydroxymethylanthraquinone) isolated from Streptomyces sp. isolate ERI-26

The present report is about Streptomyces sp. isolate ERI-26 isolated from the soil sample of Nilgiri forest, Western Ghats. The methanol extract of ERI-26 showed good antimicrobial activity against tested microbes. The antimicrobial novel anthraquinones were purified by bioactivity-guided fractionation using a silica gel column and preparative HPLC. The compound was characterized and identified by UV, IR, NMR and MASS spectral data. The compound named as 6,6¹-bis (1,5,7-trihydroxy-3-hydroxymethylanthraquinone), showed significant antimicrobial activities against tested microbes. The isolated compound inhibited the tested bacterial growth, Staphylococcus aureus at 62.5 μg/ml, Staphylococcus epidermidis at 15.62 μg/m, Bacillus subtilis at 62.5 μg/ml, fungi; Trichophyton mentagrophytes at 15.62 μg/m Trichophyton simii at 15.62 μg/ml, Aspergillus niger at. 7.81 μg/ml, Aspergiller flavus at 3.90 μg/ml, Trichophyton rubrum 296 at 62.5 μg/ml, T. rubrum 57/01 at 7.81 μg/ml, Magnaporthe grisea at 15.62 μg/ml. and Botrytis cinerea at 3.90 μg/ml. Isolated anthraquinone compound and its antimicrobial activity were newly reported.

Rare actinomycetes Nocardia caishijiensis and Pseudonocardia carboxydivorans as endophytes, their bioactivity and metabolites evaluation

Two strains identified as Nocardia caishijiensis (SORS 64b) and Pseudonocardia carboxydivorans (AGLS 2) were isolated as endophytes from Sonchus oleraceus and Ageratum conyzoides respectively. The analysis of their extracts revealed them to be strongly bioactive. The N. caishijiensis extract gave an LC50 of 570 μg/ml(-1) in the brine shrimp cytotoxicity assay and an EC50 of 0.552 μg/ml(-1) in the DPPH antioxidant assay. Antimicrobial activity was observed against Methicillin resistant Staphlococcus aureus (MRSA) and Escherichia coli ATCC 25922 (14 mm), Klebsiella pneumoniae ATCC 706003 (13 mm), S. aureus ATCC 25923 (11 mm) and Candida tropicalis (20 mm). For the extract of P. carboxydivorans the EC50 was 0.670 μg/ml(-1) and it was observed to be more bioactive against Bacillus subtilis DSM 10 ATCC 6051 (21 mm), C. tropicalis (20 mm), S. aureus ATCC 25923 (17 mm), MRSA (17 mm), E. coli K12 (W1130) (16 mm) and Chlorella vulgaris (10 mm). The genotoxicity testing revealed a 20 mm zone of inhibition against the polA mutant strain E. coli K-12 AB 3027 suggesting damage to the DNA and polA genes. The TLC and bioautography screening revealed a diversity of active bands of medium polar and nonpolar compounds. Metabolite analysis by HPLC-DAD via UV/vis spectral screening suggested the possibility of stenothricin and bagremycin A in the mycelium extract of N. caishijiensis respectively. In the broth and mycelium extract of P. carboxydivorans borrelidin was suggested along with α-pyrone. The HPLC-MS revealed bioactive long chained amide derivatives such as 7-Octadecenamide, 9, 12 octadecandienamide. This study reports the rare actinomycetes N. caishijiensis and P. carboxydivorans as endophytes and evaluates their bioactive metabolites.

Streptomyces daqingensis sp. nov., isolated from saline-alkaline soil

A novel strain of actinobacteria, designated strain NEAU-ZJC8^T, was isolated from a saline-alkaline soil collected from Heilongjiang Province, north-east China and characterized using a polyphasic approach. Strain NEAU-ZJC8^T exhibited morphological, cultural and chemotaxonomic features consistent with its classification as representing a member of the genus Streptomyces. Growth occurred at 16-35 °C, pH 5.0-11.0 and in the presence of 0-11 % (w/v) NaCl. The cell-wall peptidoglycan contained ll-diaminopimelic acid and glycine. Whole-cell hydrolysates mainly contained glucose, galactose and ribose. Predominant menaquinones were MK-9(H₆), MK-9(H₄) and MK-9(H₈). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside and two unidentified phospholipids. The major cellular fatty acids (>10 %) were iso-C_16 : 0, iso-C_15 : 0, anteiso-C_17 : 0 and C_16 : 0. The G+C content of the DNA was 72.7 mol%. A phylogenetic tree based on 16S rRNA sequences showed that strain NEAU-ZJC8^T formed a distinct clade within the genus Streptomyces and was closely related to Streptomyces haliclonae DSM 41970^T (98.56 % similarity) and Streptomyces marinus NBRC 105047^T (97.96 % similarity). A combination of DNA-DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-ZJC8^T could be distinguished from its closest phylogenetic relatives. Therefore, strain NEAU-ZJC8^T represents a novel species of the genus Streptomyces, for which the name Streptomyces daqingensis sp. nov. is proposed. The type strain is NEAU-ZJC8^T ( = CGMCC 4.7178^T = JCM 30057^T).

Antioxidant activity of 1-hydroxy-1-norresistomycin derived from Streptomyces variabilis KP149559 and evaluation of its toxicity against zebra fish Danio rerio

Extraction of bioactive compounds from marine actinomycetes and its antimicrobial activity.

Littoral lichens as a novel source of potentially bioactive Actinobacteria

Cultivable Actinobacteria are the largest source of microbially derived bioactive molecules. The high demand for novel antibiotics highlights the need for exploring novel sources of these bacteria. Microbial symbioses with sessile macro-organisms, known to contain bioactive compounds likely of bacterial origin, represent an interesting and underexplored source of Actinobacteria. We studied the diversity and potential for bioactive-metabolite production of Actinobacteria associated with two marine lichens (Lichina confinis and L. pygmaea; from intertidal and subtidal zones) and one littoral lichen (Roccella fuciformis; from supratidal zone) from the Brittany coast (France), as well as the terrestrial lichen Collema auriforme (from a riparian zone, Austria). A total of 247 bacterial strains were isolated using two selective media. Isolates were identified and clustered into 101 OTUs (98% identity) including 51 actinobacterial OTUs. The actinobacterial families observed were: Brevibacteriaceae, Cellulomonadaceae, Gordoniaceae, Micrococcaceae, Mycobacteriaceae, Nocardioidaceae, Promicromonosporaceae, Pseudonocardiaceae, Sanguibacteraceae and Streptomycetaceae. Interestingly, the diversity was most influenced by the selective media rather than lichen species or the level of lichen thallus association. The potential for bioactive-metabolite biosynthesis of the isolates was confirmed by screening genes coding for polyketide synthases types I and II. These results show that littoral lichens are a source of diverse potentially bioactive Actinobacteria.

Marine Actinomycetes as potential source for histone deacetylase inhibitors and epigenetic modulation

In the light of important detrimental role of aberrant histone deacetylases (HDAC) production during various clinical complications, development of therapeutically effective and specific inhibitors of HDAC is critically important. This study deals with the screening for HDAC inhibitors from marine Actinomycetes. The isolation of Actinomycetes from 22 sediment samples along the Southern Coast of India yielded 186 strains including Streptomyces, Nocardipsis, evaluated for HDAC inhibition using HeLa cells. Among the 186 isolates, 10 strains have shown moderate to strong inhibition. The maximum inhibition (61%) was seen with strain VITKSM06 and least inhibition (31%) was seen with strain VITSJT03. The MTT cell proliferation assay using HeLa cell line showed significant cytotoxicity with an IC50 of 5·9 μg ml(-1) by VITKSM06-derived metabolite and 26·2 μg ml(-1) by VITSJT03. The compound treated HeLa cells displayed an altered morphology and condensed chromatin which may be due to HDAC inhibition. Based on the phylogenetic analysis, the potential strains were identified as Nocardiopsis sp VITKSM06, Streptomyces sp VITAKS1 and Streptomyces sp VITRSM02. This study reveals the importance of screening marine Actinomycetes for the discovery of potential novel HDAC inhibitors of therapeutic importance.

SIGNIFICANCE AND IMPACT OF THE STUDY

Histone deacetylases (HDAC) are epigenetic enzymes that regulate the deacetylation in lysine group on a histone, and thus regulate the gene expression. The HDAC inhibitors are reported to promote apoptosis on tumour cells, thus become clinically important drug target. Several studies have addressed the identification of putative HDAC inhibitors as therapeutic agents for cancer and until now those cleared phase III human trials are very limited. This study attempts to investigate the chemical diversity found in marine Actinomycetes towards negative HDAC modulation, which could be used individually or in combination as anti-cancerous and other therapeutic measure.

Antifungal and antibacterial activities of Streptomyces polymachus sp. nov. isolated from soil

Strain T258T was isolated from forest soil at Bongnae Falls, South Korea. The strain exhibited antimicrobial and antifungal activity against the following strains: Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, Paenibacillus larvae, Escherichia coli, Candida albicans and Aspergillus niger. Growth occurred on all ISP media tested (2, 3, 4, 5, 6 and 7), Czapek-Dox agar, potato dextrose agar, trypticase soy agar, Bennett's modified agar and nutrient agar at 28 °C. Aerial spores were produced solely on ISP Medium 4; the colour of the aerial mycelium was white and the substrate mycelium was ivory. Melanin production was negative on peptone-yeast extract iron agar (ISP Medium 6). The cell-wall peptidoglycan contained ll-diaminopimelic acid, glutamic acid, alanine and glycine. Whole-cell hydrolysates contained glucose, ribose and galactose. The predominant menaquinones were MK-9(H6) and MK-9(H8) while the minor menaquinone was MK-10(H2). The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The major fatty acids (>10%) were C16 : 0 (29.8%), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (15.1%), anteiso-C15 : 0 (13.5%) and iso-C15 : 0 (10.3%). DNA-DNA similarity with other strains ranged between 37.84 ± 1.15% and 50.25 ± 1.91 %. On the basis of these data, we suggest that strain T258T represents a novel species that belong to the genus Streptomyces, for which we propose a name Streptomyces polymachus sp. nov. The type strain is T258T ( = KACC 18247T = KEMB 9005-212T = NBRC 110905T).

Red soils harbor diverse culturable actinomycetes that are promising sources of novel secondary metabolites

Red soils, which are widely distributed in tropical and subtropical regions of southern China, are characterized by low organic carbon, high content of iron oxides, and acidity and, hence, are likely to be ideal habitats for acidophilic actinomycetes. However, the diversity and biosynthetic potential of actinomycetes in such habitats are underexplored. Here, a total of 600 actinomycete strains were isolated from red soils collected in Jiangxi Province in southeast China. 16S rRNA gene sequence analysis revealed a high diversity of the isolates, which were distributed into 26 genera, 10 families, and 7 orders within the class Actinobacteria; these taxa contained at least 49 phylotypes that are likely to represent new species within 15 genera. The isolates showed good physiological potentials for biosynthesis and biocontrol. Chemical screening of 107 semirandomly selected isolates spanning 20 genera revealed the presence of at least 193 secondary metabolites from 52 isolates, of which 125 compounds from 39 isolates of 12 genera were putatively novel. Macrolides, polyethers, diketopiperazines, and siderophores accounted for most of the known compounds. The structures of six novel compounds were elucidated, two of which had a unique skeleton and represented characteristic secondary metabolites of a putative novel Streptomyces phylotype. These results demonstrate that red soils are rich reservoirs for diverse culturable actinomycetes, notably members of the families Streptomycetaceae, Pseudonocardiaceae, and Streptosporangiaceae, with the capacity to synthesize novel bioactive compounds.

The re-emergence of natural products for drug discovery in the genomics era

Natural products have been a rich source of compounds for drug discovery. However, their use has diminished in the past two decades, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. Here, we review strategies for natural product screening that harness the recent technical advances that have reduced these barriers. We also assess the use of genomic and metabolomic approaches to augment traditional methods of studying natural products, and highlight recent examples of natural products in antimicrobial drug discovery and as inhibitors of protein-protein interactions. The growing appreciation of functional assays and phenotypic screens may further contribute to a revival of interest in natural products for drug discovery.

NMR fingerprints, an integrated approach to uncover the unique components of the drug-like natural product metabolome of termite gut-associated Streptomyces species

A new NMR-based method to access to the unique components of the drug-like natural product metabolome of termite-gut associatedStreptomyces strainshas been developed.

Water and temperature relations of soil Actinobacteria

Actinobacteria perform essential functions within soils, and are dependent on available water to do so. We determined the water-activity (aw ) limits for cell division of Streptomyces albidoflavus, Streptomyces rectiviolaceus, Micromonospora grisea and Micromonospora (JCM 3050) over a range of temperatures, using culture media supplemented with a biologically permissive solute (glycerol). Each species grew optimally at 0.998 aw (control; no added glycerol) and growth rates were near-optimal in the range 0.971-0.974 (1 M glycerol) at permissive temperatures. Each was capable of cell division at 0.916-0.924 aw (2 M glycerol), but only S. albidoflavus grew at 0.895 or 0.897 aw (3 M glycerol, at 30 and 37°C respectively). For S. albidoflavus, however, no growth occurred on media at ≤ 0.870 (4 M glycerol) during the 40-day assessment period, regardless of temperature, and a theoretical limit of 0.877 aw was derived by extrapolation of growth curves. This level of solute tolerance is high for non-halophilic bacteria, but is consistent with reported limits for the growth and metabolic activities of soil microbes. The limit, within the range 0.895-0.870 aw , is very much inferior to those for obligately halophilic bacteria and extremely halophilic or xerophilic fungi, and is inconsistent with earlier reports of cell division at 0.500 aw . These findings are discussed in relation to planetary protection policy for space exploration and the microbiology of arid soils.

Improved group-specific primers based on the full SILVA 16S rRNA gene reference database

Quantitative PCR (qPCR) and community fingerprinting methods, such as the Terminal Restriction Fragment Length Polymorphism (T-RFLP) analysis,are well-suited techniques for the examination of microbial community structures. The use of phylum and class-specific primers can provide enhanced sensitivity and phylogenetic resolution as compared with domain-specific primers. To date, several phylum- and class-specific primers targeting the 16S ribosomal RNA gene have been published. However, many of these primers exhibit low discriminatory power against non-target bacteria in PCR. In this study, we evaluated the precision of certain published primers in silico and via specific PCR. We designed new qPCR and T-RFLP primer pairs (for the classes Alphaproteobacteria and Betaproteobacteria, and the phyla Bacteroidetes, Firmicutes and Actinobacteria) by combining the sequence information from a public dataset (SILVA SSU Ref 102 NR) with manual primer design. We evaluated the primer pairs via PCR using isolates of the above-mentioned groups and via screening of clone libraries from environmental soil samples and human faecal samples. As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.

Prauserella shujinwangii sp. nov., from a desert environment

A Gram-positive, spore-forming, rod-shaped actinomycete, designated XJ46(T), was isolated from Xinjiang Uyghur Autonomous Region, China and subjected to a polyphasic taxonomic analysis. Morphological and chemotaxonomic characteristics of XJ46(T) were identified as being similar to those of members of the genus Prauserella. The phylogenetic tree based on 16S rRNA gene sequences showed that XJ46(T) shared the highest similarity (95.9%) with Prauserella marina MS498(T). Based on its phenotypic characteristics, chemotaxonomic analysis and 16S rRNA gene sequence analysis, strain XJ46(T) is proposed to represent a novel species of the genus Prauserella, named Prauserella shujinwangii sp. nov. The type strain is XJ46(T) ( =CGMCC 4.7125(T) =JCM 19736(T)).

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.

Eco-taxonomic insights into actinomycete symbionts of termites for discovery of novel bioactive compounds

Termites play a major role in foraging and degradation of plant biomass as well as cultivating bioactive microorganisms for their defense. Current advances in "omics" sciences are revealing insights into function-related presence of these symbionts, and their related biosynthetic activities and genes identified in gut symbiotic bacteria might offer a significant potential for biotechnology and biodiscovery. Actinomycetes have been the major producers of bioactive compounds with an extraordinary range of biological activities. These metabolites have been in use as anticancer agents, immune suppressants, and most notably, as antibiotics. Insect-associated actinomycetes have also been reported to produce a range of antibiotics such as dentigerumycin and mycangimycin. Advances in genomics targeting a single species of the unculturable microbial members are currently aiding an improved understanding of the symbiotic interrelationships among the gut microorganisms as well as revealing the taxonomical identity and functions of the complex multilayered symbiotic actinofloral layers. If combined with target-directed approaches, these molecular advances can provide guidance towards the design of highly selective culturing methods to generate further information related to the physiology and growth requirements of these bioactive actinomycetes associated with the termite guts. This chapter provides an overview on the termite gut symbiotic actinoflora in the light of current advances in the "omics" science, with examples of their detection and selective isolation from the guts of the Sunshine Coast regional termite Coptotermes lacteus in Queensland, Australia.

Real-time image processing for label-free enrichment of Actinobacteria cultivated in picolitre droplets

The majority of today's antimicrobial therapeutics is derived from secondary metabolites produced by Actinobacteria. While it is generally assumed that less than 1% of Actinobacteria species from soil habitats have been cultivated so far, classic screening approaches fail to supply new substances, often due to limited throughput and frequent rediscovery of already known strains. To overcome these restrictions, we implement high-throughput cultivation of soil-derived Actinobacteria in microfluidic pL-droplets by generating more than 600,000 pure cultures per hour from a spore suspension that can subsequently be incubated for days to weeks. Moreover, we introduce triggered imaging with real-time image-based droplet classification as a novel universal method for pL-droplet sorting. Growth-dependent droplet sorting at frequencies above 100 Hz is performed for label-free enrichment and extraction of microcultures. The combination of both cultivation of Actinobacteria in pL-droplets and real-time detection of growing Actinobacteria has great potential in screening for yet unknown species as well as their undiscovered natural products.

Isolation of new polyketide metabolites, linearolides A and B, from Streptomyces sp. RK95-74

Although all Streptomyces strains are now thought to have 20–30 gene clusters for secondary metabolite biosynthesis, we cannot actually identify so many kinds of metabolites from one strain by conventional methods. Using Streptomyces sp. RK95-74, previously found as a cytotrienin producer, we searched new metabolites other than cytotrienin derivatives. Following the cultivation with new media and the peak-guided fractionation, we have found new compounds with new polyketide scaffold, named linearolides A and B.

RETRACTED: Marine actinobacterial metabolites: current status and future perspectives

This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal). This article has been retracted at the request of the Editor. Authors and Editor agreed to retract this article because substantial parts of the text were copied from the following sources without proper attribution: Lam, K.S. (2006), Discovery of novel metabolites from marine actinomycetes. Current Opinion in Microbiology 9(3), pp. 245–251; Subramani, R., Aalbersberg, W. (2012), Marine actinomycetes: An ongoing source of novel bioactive metabolites. Microbiological Research 167(10), pp. 571–580; Dharmaraj, S. (2010), Marine Streptomyces as a novel source of bioactive substances. World Journal of Microbiology and Biotechnology 26(12), pp. 2123–2139. The authors apologize for this oversight and any inconvenience caused.

Diversity and isolation of rare actinomycetes: an overview

A renewed interest in the development of new antimicrobial agents is urgently needed to combat the increasing number of antibiotic-resistant strains of pathogenic microorganisms. Actinomycetes continue to be the mainstream supplier of antibiotics used in industry. The likelihood of discovering a new compound with novel chemical structure can be increased with intensive efforts in isolating and screening of rare genera of microorganisms to include in natural-product-screening collections. An unexpected variety of rare actinomycetes is now being isolated worldwide from previously uninvestigated diverse natural habitats, using different selective isolation methods. These isolation efforts include methods to enhance growth (enrichment) of rare actinomycetes, and eliminate unwanted microorganisms (pretreatment). To speed up the strain isolation process, knowledge about the distribution of such unexploited groups of microorganisms must also be augmented. This is a summary of using these microorganisms as new potential biological resources, and a review of almost all of the selective isolation methods, including pretreatment and enrichment techniques that have been developed to date for the isolation of rare actinomycetes.

Marine actinomycetes: an ongoing source of novel bioactive metabolites

Actinomycetes are virtually unlimited sources of novel compounds with many therapeutic applications and hold a prominent position due to their diversity and proven ability to produce novel bioactive compounds. There are more than 22,000 known microbial secondary metabolites, 70% of which are produced by actinomycetes, 20% from fungi, 7% from Bacillus spp. and 1-2% by other bacteria. Among the actinomycetes, streptomycetes group are considered economically important because out of the approximately more than 10,000 known antibiotics, 50-55% are produced by this genus. The ecological role of actinomycetes in the marine ecosystem is largely neglected and various assumptions meant there was little incentive to isolate marine strains for search and discovery of new drugs. The search for and discovery of rare and new actinomycetes is of significant interest to drug discovery due to a growing need for the development of new and potent therapeutic agents. Modern molecular technologies are adding strength to the target-directed search for detection and isolation of bioactive actinomycetes, and continued development of improved cultivation methods and molecular technologies for accessing the marine environment promises to provide access to this significant new source of chemical diversity with novel/rare actinomycetes including new species of previously reported actinomycetes.